WorldWideScience

Sample records for evolutionary pattern search

  1. Protein structure database search and evolutionary classification.

    Science.gov (United States)

    Yang, Jinn-Moon; Tung, Chi-Hua

    2006-01-01

    As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the statistical significance (E-value) of an alignment to indicate the reliability of the prediction. Using this method, we first identified 23 states of the structural alphabet that represent pattern profiles of the backbone fragments and then used them to represent protein structure databases as structural alphabet sequence databases (SADB). Our method enhanced BLAST as a search method, using a new structural alphabet substitution matrix (SASM) to find the longest common substructures with high-scoring structured segment pairs from an SADB database. Using personal computers with Intel Pentium4 (2.8 GHz) processors, our method searched more than 10 000 protein structures in 1.3 s and achieved a good agreement with search results from detailed structure alignment methods. [3D-BLAST is available at http://3d-blast.life.nctu.edu.tw].

  2. Search Patterns

    CERN Document Server

    Morville, Peter

    2010-01-01

    What people are saying about Search Patterns "Search Patterns is a delight to read -- very thoughtful and thought provoking. It's the most comprehensive survey of designing effective search experiences I've seen." --Irene Au, Director of User Experience, Google "I love this book! Thanks to Peter and Jeffery, I now know that search (yes, boring old yucky who cares search) is one of the coolest ways around of looking at the world." --Dan Roam, author, The Back of the Napkin (Portfolio Hardcover) "Search Patterns is a playful guide to the practical concerns of search interface design. It cont

  3. Hybrid Projected Gradient-Evolutionary Search Algorithm for Mixed Integer Nonlinear Optimization Problems

    National Research Council Canada - National Science Library

    Homaifar, Abdollah; Esterline, Albert; Kimiaghalam, Bahram

    2005-01-01

    The Hybrid Projected Gradient-Evolutionary Search Algorithm (HPGES) algorithm uses a specially designed evolutionary-based global search strategy to efficiently create candidate solutions in the solution space...

  4. Hybridizing Evolutionary Algorithms with Opportunistic Local Search

    DEFF Research Database (Denmark)

    Gießen, Christian

    2013-01-01

    There is empirical evidence that memetic algorithms (MAs) can outperform plain evolutionary algorithms (EAs). Recently the first runtime analyses have been presented proving the aforementioned conjecture rigorously by investigating Variable-Depth Search, VDS for short (Sudholt, 2008). Sudholt...

  5. Face Alignment Using Boosting and Evolutionary Search

    NARCIS (Netherlands)

    Zhang, Hua; Liu, Duanduan; Poel, Mannes; Nijholt, Antinus; Zha, H.; Taniguchi, R.-I.; Maybank, S.

    2010-01-01

    In this paper, we present a face alignment approach using granular features, boosting, and an evolutionary search algorithm. Active Appearance Models (AAM) integrate a shape-texture-combined morphable face model into an efficient fitting strategy, then Boosting Appearance Models (BAM) consider the

  6. Applications of evolutionary computation in image processing and pattern recognition

    CERN Document Server

    Cuevas, Erik; Perez-Cisneros, Marco

    2016-01-01

    This book presents the use of efficient Evolutionary Computation (EC) algorithms for solving diverse real-world image processing and pattern recognition problems. It provides an overview of the different aspects of evolutionary methods in order to enable the reader in reaching a global understanding of the field and, in conducting studies on specific evolutionary techniques that are related to applications in image processing and pattern recognition. It explains the basic ideas of the proposed applications in a way that can also be understood by readers outside of the field. Image processing and pattern recognition practitioners who are not evolutionary computation researchers will appreciate the discussed techniques beyond simple theoretical tools since they have been adapted to solve significant problems that commonly arise on such areas. On the other hand, members of the evolutionary computation community can learn the way in which image processing and pattern recognition problems can be translated into an...

  7. Pattern Nulling of Linear Antenna Arrays Using Backtracking Search Optimization Algorithm

    Directory of Open Access Journals (Sweden)

    Kerim Guney

    2015-01-01

    Full Text Available An evolutionary method based on backtracking search optimization algorithm (BSA is proposed for linear antenna array pattern synthesis with prescribed nulls at interference directions. Pattern nulling is obtained by controlling only the amplitude, position, and phase of the antenna array elements. BSA is an innovative metaheuristic technique based on an iterative process. Various numerical examples of linear array patterns with the prescribed single, multiple, and wide nulls are given to illustrate the performance and flexibility of BSA. The results obtained by BSA are compared with the results of the following seventeen algorithms: particle swarm optimization (PSO, genetic algorithm (GA, modified touring ant colony algorithm (MTACO, quadratic programming method (QPM, bacterial foraging algorithm (BFA, bees algorithm (BA, clonal selection algorithm (CLONALG, plant growth simulation algorithm (PGSA, tabu search algorithm (TSA, memetic algorithm (MA, nondominated sorting GA-2 (NSGA-2, multiobjective differential evolution (MODE, decomposition with differential evolution (MOEA/D-DE, comprehensive learning PSO (CLPSO, harmony search algorithm (HSA, seeker optimization algorithm (SOA, and mean variance mapping optimization (MVMO. The simulation results show that the linear antenna array synthesis using BSA provides low side-lobe levels and deep null levels.

  8. Playing Multi-Action Adversarial Games: Online Evolutionary Planning versus Tree Search

    OpenAIRE

    Justesen, Niels; Mahlmann, Tobias; Risi, Sebastian; Togelius, Julian

    2017-01-01

    We address the problem of playing turn-based multi-action adversarial games, which include many strategy games with extremely high branching factors as players take multiple actions each turn. This leads to the breakdown of standard tree search methods, including Monte Carlo Tree Search (MCTS), as they become unable to reach a sufficient depth in the game tree. In this paper, we introduce Online Evolutionary Planning (OEP) to address this challenge, which searches for combinations of actions ...

  9. Evolutionary rate patterns of the Gibberellin pathway genes

    Directory of Open Access Journals (Sweden)

    Zhang Fu-min

    2009-08-01

    Full Text Available Abstract Background Analysis of molecular evolutionary patterns of different genes within metabolic pathways allows us to determine whether these genes are subject to equivalent evolutionary forces and how natural selection shapes the evolution of proteins in an interacting system. Although previous studies found that upstream genes in the pathway evolved more slowly than downstream genes, the correlation between evolutionary rate and position of the genes in metabolic pathways as well as its implications in molecular evolution are still less understood. Results We sequenced and characterized 7 core structural genes of the gibberellin biosynthetic pathway from 8 representative species of the rice tribe (Oryzeae to address alternative hypotheses regarding evolutionary rates and patterns of metabolic pathway genes. We have detected significant rate heterogeneity among 7 GA pathway genes for both synonymous and nonsynonymous sites. Such rate variation is mostly likely attributed to differences of selection intensity rather than differential mutation pressures on the genes. Unlike previous argument that downstream genes in metabolic pathways would evolve more slowly than upstream genes, the downstream genes in the GA pathway did not exhibited the elevated substitution rate and instead, the genes that encode either the enzyme at the branch point (GA20ox or enzymes catalyzing multiple steps (KO, KAO and GA3ox in the pathway had the lowest evolutionary rates due to strong purifying selection. Our branch and codon models failed to detect signature of positive selection for any lineage and codon of the GA pathway genes. Conclusion This study suggests that significant heterogeneity of evolutionary rate of the GA pathway genes is mainly ascribed to differential constraint relaxation rather than the positive selection and supports the pathway flux theory that predicts that natural selection primarily targets enzymes that have the greatest control on fluxes.

  10. δ-Similar Elimination to Enhance Search Performance of Multiobjective Evolutionary Algorithms

    Science.gov (United States)

    Aguirre, Hernán; Sato, Masahiko; Tanaka, Kiyoshi

    In this paper, we propose δ-similar elimination to improve the search performance of multiobjective evolutionary algorithms in combinatorial optimization problems. This method eliminates similar individuals in objective space to fairly distribute selection among the different regions of the instantaneous Pareto front. We investigate four eliminating methods analyzing their effects using NSGA-II. In addition, we compare the search performance of NSGA-II enhanced by our method and NSGA-II enhanced by controlled elitism.

  11. Evolutionary Policy Transfer and Search Methods for Boosting Behavior Quality: RoboCup Keep-Away Case Study

    Directory of Open Access Journals (Sweden)

    Geoff Nitschke

    2017-11-01

    Full Text Available This study evaluates various evolutionary search methods to direct neural controller evolution in company with policy (behavior transfer across increasingly complex collective robotic (RoboCup keep-away tasks. Robot behaviors are first evolved in a source task and then transferred for further evolution to more complex target tasks. Evolutionary search methods tested include objective-based search (fitness function, behavioral and genotypic diversity maintenance, and hybrids of such diversity maintenance and objective-based search. Evolved behavior quality is evaluated according to effectiveness and efficiency. Effectiveness is the average task performance of transferred and evolved behaviors, where task performance is the average time the ball is controlled by a keeper team. Efficiency is the average number of generations taken for the fittest evolved behaviors to reach a minimum task performance threshold given policy transfer. Results indicate that policy transfer coupled with hybridized evolution (behavioral diversity maintenance and objective-based search addresses the bootstrapping problem for increasingly complex keep-away tasks. That is, this hybrid method (coupled with policy transfer evolves behaviors that could not otherwise be evolved. Also, this hybrid evolutionary search was demonstrated as consistently evolving topologically simple neural controllers that elicited high-quality behaviors.

  12. Application of pattern search method to power system security constrained economic dispatch with non-smooth cost function

    International Nuclear Information System (INIS)

    Al-Othman, A.K.; El-Naggar, K.M.

    2008-01-01

    Direct search methods are evolutionary algorithms used to solve optimization problems. (DS) methods do not require any information about the gradient of the objective function at hand while searching for an optimum solution. One of such methods is Pattern Search (PS) algorithm. This paper presents a new approach based on a constrained pattern search algorithm to solve a security constrained power system economic dispatch problem (SCED) with non-smooth cost function. Operation of power systems demands a high degree of security to keep the system satisfactorily operating when subjected to disturbances, while and at the same time it is required to pay attention to the economic aspects. Pattern recognition technique is used first to assess dynamic security. Linear classifiers that determine the stability of electric power system are presented and added to other system stability and operational constraints. The problem is formulated as a constrained optimization problem in a way that insures a secure-economic system operation. Pattern search method is then applied to solve the constrained optimization formulation. In particular, the method is tested using three different test systems. Simulation results of the proposed approach are compared with those reported in literature. The outcome is very encouraging and proves that pattern search (PS) is very applicable for solving security constrained power system economic dispatch problem (SCED). In addition, valve-point effect loading and total system losses are considered to further investigate the potential of the PS technique. Based on the results, it can be concluded that the PS has demonstrated ability in handling highly nonlinear discontinuous non-smooth cost function of the SCED. (author)

  13. Playing Multi-Action Adversarial Games: Online Evolutionary Planning versus Tree Search

    DEFF Research Database (Denmark)

    Justesen, Niels; Mahlmann, Tobias; Risi, Sebastian

    2017-01-01

    We address the problem of playing turn-based multi-action adversarial games, which include many strategy games with extremely high branching factors as players take multiple actions each turn. This leads to the breakdown of standard tree search methods, including Monte Carlo Tree Search (MCTS......), as they become unable to reach a sufficient depth in the game tree. In this paper, we introduce Online Evolutionary Planning (OEP) to address this challenge, which searches for combinations of actions to perform during a single turn guided by a fitness function that evaluates the quality of a particular state....... We compare OEP to different MCTS variations that constrain the exploration to deal with the high branching factor in the turn-based multi-action game Hero Academy. While the constrained MCTS variations outperform the vanilla MCTS implementation by a large margin, OEP is able to search the space...

  14. On the Convergence of Asynchronous Parallel Pattern Search

    International Nuclear Information System (INIS)

    Tamara Gilbson Kolda

    2002-01-01

    In this paper the authors prove global convergence for asynchronous parallel pattern search. In standard pattern search, decisions regarding the update of the iterate and the step-length control parameter are synchronized implicitly across all search directions. They lose this feature in asynchronous parallel pattern search since the search along each direction proceeds semi-autonomously. By bounding the value of the step-length control parameter after any step that produces decrease along a single search direction, they can prove that all the processes share a common accumulation point and that such a point is a stationary point of the standard nonlinear unconstrained optimization problem

  15. A proposed heuristic methodology for searching reloading pattern

    International Nuclear Information System (INIS)

    Choi, K. Y.; Yoon, Y. K.

    1993-01-01

    A new heuristic method for loading pattern search has been developed to overcome shortcomings of the algorithmic approach. To reduce the size of vast solution space, general shuffling rules, a regionwise shuffling method, and a pattern grouping method were introduced. The entropy theory was applied to classify possible loading patterns into groups with similarity between them. The pattern search program was implemented with use of the PROLOG language. A two-group nodal code MEDIUM-2D was used for analysis of power distribution in the core. The above mentioned methodology has been tested to show effectiveness in reducing of solution space down to a few hundred pattern groups. Burnable poison rods were then arranged in each pattern group in accordance with burnable poison distribution rules, which led to further reduction of the solution space to several scores of acceptable pattern groups. The method of maximizing cycle length (MCL) and minimizing power-peaking factor (MPF) were applied to search for specific useful loading patterns from the acceptable pattern groups. Thus, several specific loading patterns that have low power-peaking factor and large cycle length were successfully searched from the selected pattern groups. (Author)

  16. Selective modes determine evolutionary rates, gene compactness and expression patterns in Brassica.

    Science.gov (United States)

    Guo, Yue; Liu, Jing; Zhang, Jiefu; Liu, Shengyi; Du, Jianchang

    2017-07-01

    It has been well documented that most nuclear protein-coding genes in organisms can be classified into two categories: positively selected genes (PSGs) and negatively selected genes (NSGs). The characteristics and evolutionary fates of different types of genes, however, have been poorly understood. In this study, the rates of nonsynonymous substitution (K a ) and the rates of synonymous substitution (K s ) were investigated by comparing the orthologs between the two sequenced Brassica species, Brassica rapa and Brassica oleracea, and the evolutionary rates, gene structures, expression patterns, and codon bias were compared between PSGs and NSGs. The resulting data show that PSGs have higher protein evolutionary rates, lower synonymous substitution rates, shorter gene length, fewer exons, higher functional specificity, lower expression level, higher tissue-specific expression and stronger codon bias than NSGs. Although the quantities and values are different, the relative features of PSGs and NSGs have been largely verified in the model species Arabidopsis. These data suggest that PSGs and NSGs differ not only under selective pressure (K a /K s ), but also in their evolutionary, structural and functional properties, indicating that selective modes may serve as a determinant factor for measuring evolutionary rates, gene compactness and expression patterns in Brassica. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  17. A hydronitrogen solid: high pressure ab initio evolutionary structure searches

    International Nuclear Information System (INIS)

    Hu Anguang; Zhang Fan

    2011-01-01

    High pressure ab initio evolutionary structure searches resulted in a hydronitrogen solid with a composition of (NH) 4 . The structure searches also provided two molecular isomers, ammonium azide (AA) and trans-tetrazene (TTZ) which were previously discovered experimentally and can be taken as molecular precursors for high pressure synthesis of the hydronitrogen solid. The computed pressure versus enthalpy diagram showed that the transformation pressure to the hydronitrogen solid is 36 GPa from AA and 75 GPa from TTZ. Its metastability was analyzed by the phonon dispersion spectrum and room-temperature vibrational density of state together with the transformation energy barrier back to molecular phases at 298 K. The predicted energy barrier of 0.21 eV/atom means that the proposed hydronitrogen solid should be very stable at ambient conditions. (fast track communication)

  18. Global patterns of evolutionary distinct and globally endangered amphibians and mammals.

    Science.gov (United States)

    Safi, Kamran; Armour-Marshall, Katrina; Baillie, Jonathan E M; Isaac, Nick J B

    2013-01-01

    Conservation of phylogenetic diversity allows maximising evolutionary information preserved within fauna and flora. The "EDGE of Existence" programme is the first institutional conservation initiative that prioritises species based on phylogenetic information. Species are ranked in two ways: one according to their evolutionary distinctiveness (ED) and second, by including IUCN extinction status, their evolutionary distinctiveness and global endangerment (EDGE). Here, we describe the global patterns in the spatial distribution of priority ED and EDGE species, in order to identify conservation areas for mammalian and amphibian communities. In addition, we investigate whether environmental conditions can predict the observed spatial pattern in ED and EDGE globally. Priority zones with high concentrations of ED and EDGE scores were defined using two different methods. The overlap between mammal and amphibian zones was very small, reflecting the different phylo-biogeographic histories. Mammal ED zones were predominantly found on the African continent and the neotropical forests, whereas in amphibians, ED zones were concentrated in North America. Mammal EDGE zones were mainly in South-East Asia, southern Africa and Madagascar; for amphibians they were in central and south America. The spatial pattern of ED and EDGE was poorly described by a suite of environmental variables. Mapping the spatial distribution of ED and EDGE provides an important step towards identifying priority areas for the conservation of mammalian and amphibian phylogenetic diversity in the EDGE of existence programme.

  19. PTree: pattern-based, stochastic search for maximum parsimony phylogenies

    Directory of Open Access Journals (Sweden)

    Ivan Gregor

    2013-06-01

    Full Text Available Phylogenetic reconstruction is vital to analyzing the evolutionary relationship of genes within and across populations of different species. Nowadays, with next generation sequencing technologies producing sets comprising thousands of sequences, robust identification of the tree topology, which is optimal according to standard criteria such as maximum parsimony, maximum likelihood or posterior probability, with phylogenetic inference methods is a computationally very demanding task. Here, we describe a stochastic search method for a maximum parsimony tree, implemented in a software package we named PTree. Our method is based on a new pattern-based technique that enables us to infer intermediate sequences efficiently where the incorporation of these sequences in the current tree topology yields a phylogenetic tree with a lower cost. Evaluation across multiple datasets showed that our method is comparable to the algorithms implemented in PAUP* or TNT, which are widely used by the bioinformatics community, in terms of topological accuracy and runtime. We show that our method can process large-scale datasets of 1,000–8,000 sequences. We believe that our novel pattern-based method enriches the current set of tools and methods for phylogenetic tree inference. The software is available under: http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/.

  20. PTree: pattern-based, stochastic search for maximum parsimony phylogenies.

    Science.gov (United States)

    Gregor, Ivan; Steinbrück, Lars; McHardy, Alice C

    2013-01-01

    Phylogenetic reconstruction is vital to analyzing the evolutionary relationship of genes within and across populations of different species. Nowadays, with next generation sequencing technologies producing sets comprising thousands of sequences, robust identification of the tree topology, which is optimal according to standard criteria such as maximum parsimony, maximum likelihood or posterior probability, with phylogenetic inference methods is a computationally very demanding task. Here, we describe a stochastic search method for a maximum parsimony tree, implemented in a software package we named PTree. Our method is based on a new pattern-based technique that enables us to infer intermediate sequences efficiently where the incorporation of these sequences in the current tree topology yields a phylogenetic tree with a lower cost. Evaluation across multiple datasets showed that our method is comparable to the algorithms implemented in PAUP* or TNT, which are widely used by the bioinformatics community, in terms of topological accuracy and runtime. We show that our method can process large-scale datasets of 1,000-8,000 sequences. We believe that our novel pattern-based method enriches the current set of tools and methods for phylogenetic tree inference. The software is available under: http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/.

  1. Global patterns of evolutionary distinct and globally endangered amphibians and mammals.

    Directory of Open Access Journals (Sweden)

    Kamran Safi

    Full Text Available BACKGROUND: Conservation of phylogenetic diversity allows maximising evolutionary information preserved within fauna and flora. The "EDGE of Existence" programme is the first institutional conservation initiative that prioritises species based on phylogenetic information. Species are ranked in two ways: one according to their evolutionary distinctiveness (ED and second, by including IUCN extinction status, their evolutionary distinctiveness and global endangerment (EDGE. Here, we describe the global patterns in the spatial distribution of priority ED and EDGE species, in order to identify conservation areas for mammalian and amphibian communities. In addition, we investigate whether environmental conditions can predict the observed spatial pattern in ED and EDGE globally. METHODS AND PRINCIPAL FINDINGS: Priority zones with high concentrations of ED and EDGE scores were defined using two different methods. The overlap between mammal and amphibian zones was very small, reflecting the different phylo-biogeographic histories. Mammal ED zones were predominantly found on the African continent and the neotropical forests, whereas in amphibians, ED zones were concentrated in North America. Mammal EDGE zones were mainly in South-East Asia, southern Africa and Madagascar; for amphibians they were in central and south America. The spatial pattern of ED and EDGE was poorly described by a suite of environmental variables. CONCLUSIONS: Mapping the spatial distribution of ED and EDGE provides an important step towards identifying priority areas for the conservation of mammalian and amphibian phylogenetic diversity in the EDGE of existence programme.

  2. Search pattern of databases by the undergraduate students of ...

    African Journals Online (AJOL)

    The main objective of this study is to assess the awareness and search pattern of databases in order to determine the extent to which user are aware and search for databases by examining the relationship between their Awareness and search patterns of Databases, and their information literacy skills. The methodology ...

  3. Genetic evolutionary taboo search for optimal marker placement in infrared patient setup

    International Nuclear Information System (INIS)

    Riboldi, M; Baroni, G; Spadea, M F; Tagaste, B; Garibaldi, C; Cambria, R; Orecchia, R; Pedotti, A

    2007-01-01

    In infrared patient setup adequate selection of the external fiducial configuration is required for compensating inner target displacements (target registration error, TRE). Genetic algorithms (GA) and taboo search (TS) were applied in a newly designed approach to optimal marker placement: the genetic evolutionary taboo search (GETS) algorithm. In the GETS paradigm, multiple solutions are simultaneously tested in a stochastic evolutionary scheme, where taboo-based decision making and adaptive memory guide the optimization process. The GETS algorithm was tested on a group of ten prostate patients, to be compared to standard optimization and to randomly selected configurations. The changes in the optimal marker configuration, when TRE is minimized for OARs, were specifically examined. Optimal GETS configurations ensured a 26.5% mean decrease in the TRE value, versus 19.4% for conventional quasi-Newton optimization. Common features in GETS marker configurations were highlighted in the dataset of ten patients, even when multiple runs of the stochastic algorithm were performed. Including OARs in TRE minimization did not considerably affect the spatial distribution of GETS marker configurations. In conclusion, the GETS algorithm proved to be highly effective in solving the optimal marker placement problem. Further work is needed to embed site-specific deformation models in the optimization process

  4. Large-Scale Evolutionary Patterns of Host Plant Associations in the Lepidoptera

    DEFF Research Database (Denmark)

    Menken, S.B.J.; Boomsma, J.J.; van Nieukerken, E.J.

    2010-01-01

    We characterized evolutionary patterns of host plant use across about 2500 species of British Lepidoptera, using character optimization and independent phylogenetic contrasts among 95 operational taxa, and evaluated the extent to which caterpillars are monophagous, use woody host plants, and feed...

  5. Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling

    Science.gov (United States)

    Pardo-Diaz, Carolina; Hanly, Joseph J.; Martin, Simon H.; Mallet, James; Dasmahapatra, Kanchon K.; Salazar, Camilo; Joron, Mathieu; Nadeau, Nicola; McMillan, W. Owen; Jiggins, Chris D.

    2016-01-01

    An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in turn controls red pattern variation across Heliconius. Phylogenetic analysis of the two elements demonstrated that they have distinct evolutionary histories and that novel adaptive morphological variation was created by shuffling these cis-regulatory modules through recombination between divergent lineages. In addition, recombination of modules into different combinations within species further contributes to diversity. Analysis of the timing of diversification in these two regions supports the hypothesis of introgression moving regulatory modules between species, rather than shared ancestral variation. The dennis phenotype introgressed into Heliconius melpomene at about the same time that ray originated in this group, while ray introgressed back into H. elevatus much more recently. We show that shuffling of existing enhancer elements both within and between species provides a mechanism for rapid diversification and generation of novel morphological combinations during adaptive radiation. PMID:26771987

  6. On the Runtime of Randomized Local Search and Simple Evolutionary Algorithms for Dynamic Makespan Scheduling

    DEFF Research Database (Denmark)

    Neumann, Frank; Witt, Carsten

    2015-01-01

    combinatorial optimization problem, namely makespan scheduling. We study the model of a strong adversary which is allowed to change one job at regular intervals. Furthermore, we investigate the setting of random changes. Our results show that randomized local search and a simple evolutionary algorithm are very...

  7. Evidence of an evolutionary hourglass pattern in herbivory-induced transcriptomic responses.

    Science.gov (United States)

    Durrant, Matthew; Boyer, Justin; Zhou, Wenwu; Baldwin, Ian T; Xu, Shuqing

    2017-08-01

    Herbivory-induced defenses are specific and activated in plants when elicitors, frequently found in the herbivores' oral secretions, are introduced into wounds during attack. While complex signaling cascades are known to be involved, it remains largely unclear how natural selection has shaped the evolution of these induced defenses. We analyzed herbivory-induced transcriptomic responses in wild tobacco, Nicotiana attenuata, using a phylotranscriptomic approach that measures the origin and sequence divergence of herbivory-induced genes. Highly conserved and evolutionarily ancient genes of primary metabolism were activated at intermediate time points (2-6 h) after elicitation, while less constrained and young genes associated with defense signaling and biosynthesis of specialized metabolites were activated at early (before 2 h) and late (after 6 h) stages of the induced response, respectively - a pattern resembling the evolutionary hourglass pattern observed during embryogenesis in animals and the developmental process in plants and fungi. The hourglass patterns found in herbivory-induced defense responses and developmental process are both likely to be a result of signaling modularization and differential evolutionary constraints on the modules involved in the signaling cascade. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  8. Synthesis of Steered Flat-top Beam Pattern Using Evolutionary Algorithm

    Directory of Open Access Journals (Sweden)

    D. Mandal

    2016-12-01

    Full Text Available In this paper a pattern synthesis method based on Evolutionary Algorithm is presented. A Flat-top beam pattern has been generated from a concentric ring array of isotropic elements by finding out the optimum set of elements amplitudes and phases using Differential Evolution algorithm. The said pattern is generated in three predefined azimuth planes instate of a single phi plane and also verified for a range of azimuth plane for the same optimum excitations. The main beam is steered to an elevation angle of 30 degree with lower peak SLL and ripple. Dynamic range ratio (DRR is also being improved by eliminating the weakly excited array elements, which simplify the design complexity of feed networks.

  9. Evolutionary patterns of RNA-based duplication in non-mammalian chordates.

    Directory of Open Access Journals (Sweden)

    Ming Chen

    Full Text Available The role of RNA-based duplication, or retroposition, in the evolution of new gene functions in mammals, plants, and Drosophila has been widely reported. However, little is known about RNA-based duplication in non-mammalian chordates. In this study, we screened ten non-mammalian chordate genomes for retrocopies and investigated their evolutionary patterns. We identified numerous retrocopies in these species. Examination of the age distribution of these retrocopies revealed no burst of young retrocopies in ancient chordate species. Upon comparing these non-mammalian chordate species to the mammalian species, we observed that a larger fraction of the non-mammalian retrocopies was under strong evolutionary constraints than mammalian retrocopies are, as evidenced by signals of purifying selection and expression profiles. For the Western clawed frog, Medaka, and Sea squirt, many retrogenes have evolved gonad and brain expression patterns, similar to what was observed in human. Testing of retrogene movement in the Medaka genome, where the nascent sex chrosomes have been well assembled, did not reveal any significant gene movement. Taken together, our analyses demonstrate that RNA-based duplication generates many functional genes and can make a significant contribution to the evolution of non-mammalian genomes.

  10. Evolutionary relevance facilitates visual information processing.

    Science.gov (United States)

    Jackson, Russell E; Calvillo, Dusti P

    2013-11-03

    Visual search of the environment is a fundamental human behavior that perceptual load affects powerfully. Previously investigated means for overcoming the inhibitions of high perceptual load, however, generalize poorly to real-world human behavior. We hypothesized that humans would process evolutionarily relevant stimuli more efficiently than evolutionarily novel stimuli, and evolutionary relevance would mitigate the repercussions of high perceptual load during visual search. Animacy is a significant component to evolutionary relevance of visual stimuli because perceiving animate entities is time-sensitive in ways that pose significant evolutionary consequences. Participants completing a visual search task located evolutionarily relevant and animate objects fastest and with the least impact of high perceptual load. Evolutionarily novel and inanimate objects were located slowest and with the highest impact of perceptual load. Evolutionary relevance may importantly affect everyday visual information processing.

  11. Is There a Weekly Pattern for Health Searches on Wikipedia and Is the Pattern Unique to Health Topics?

    Science.gov (United States)

    Gabarron, Elia; Lau, Annie Y S; Wynn, Rolf

    2015-12-22

    Online health information-seeking behaviors have been reported to be more common at the beginning of the workweek. This behavior pattern has been interpreted as a kind of "healthy new start" or "fresh start" due to regrets or attempts to compensate for unhealthy behavior or poor choices made during the weekend. However, the observations regarding the most common health information-seeking day were based only on the analyses of users' behaviors with websites on health or on online health-related searches. We wanted to confirm if this pattern could be found in searches of Wikipedia on health-related topics and also if this search pattern was unique to health-related topics or if it could represent a more general pattern of online information searching--which could be of relevance even beyond the health sector. The aim was to examine the degree to which the search pattern described previously was specific to health-related information seeking or whether similar patterns could be found in other types of information-seeking behavior. We extracted the number of searches performed on Wikipedia in the Norwegian language for 911 days for the most common sexually transmitted diseases (chlamydia, gonorrhea, herpes, human immunodeficiency virus [HIV], and acquired immune deficiency syndrome [AIDS]), other health-related topics (influenza, diabetes, and menopause), and 2 nonhealth-related topics (footballer Lionel Messi and pop singer Justin Bieber). The search dates were classified according to the day of the week and ANOVA tests were used to compare the average number of hits per day of the week. The ANOVA tests showed that the sexually transmitted disease queries had their highest peaks on Tuesdays (PJustin Bieber had the most hits on Tuesdays. Both these tracked search queries also showed significantly lower numbers on Saturdays (P<.001). Our study supports prior studies finding an increase in health information searching at the beginning of the workweek. However, we also

  12. Hill-Climbing search and diversification within an evolutionary approach to protein structure prediction.

    Science.gov (United States)

    Chira, Camelia; Horvath, Dragos; Dumitrescu, D

    2011-07-30

    Proteins are complex structures made of amino acids having a fundamental role in the correct functioning of living cells. The structure of a protein is the result of the protein folding process. However, the general principles that govern the folding of natural proteins into a native structure are unknown. The problem of predicting a protein structure with minimum-energy starting from the unfolded amino acid sequence is a highly complex and important task in molecular and computational biology. Protein structure prediction has important applications in fields such as drug design and disease prediction. The protein structure prediction problem is NP-hard even in simplified lattice protein models. An evolutionary model based on hill-climbing genetic operators is proposed for protein structure prediction in the hydrophobic - polar (HP) model. Problem-specific search operators are implemented and applied using a steepest-ascent hill-climbing approach. Furthermore, the proposed model enforces an explicit diversification stage during the evolution in order to avoid local optimum. The main features of the resulting evolutionary algorithm - hill-climbing mechanism and diversification strategy - are evaluated in a set of numerical experiments for the protein structure prediction problem to assess their impact to the efficiency of the search process. Furthermore, the emerging consolidated model is compared to relevant algorithms from the literature for a set of difficult bidimensional instances from lattice protein models. The results obtained by the proposed algorithm are promising and competitive with those of related methods.

  13. Hill-Climbing search and diversification within an evolutionary approach to protein structure prediction

    Directory of Open Access Journals (Sweden)

    Chira Camelia

    2011-07-01

    Full Text Available Abstract Proteins are complex structures made of amino acids having a fundamental role in the correct functioning of living cells. The structure of a protein is the result of the protein folding process. However, the general principles that govern the folding of natural proteins into a native structure are unknown. The problem of predicting a protein structure with minimum-energy starting from the unfolded amino acid sequence is a highly complex and important task in molecular and computational biology. Protein structure prediction has important applications in fields such as drug design and disease prediction. The protein structure prediction problem is NP-hard even in simplified lattice protein models. An evolutionary model based on hill-climbing genetic operators is proposed for protein structure prediction in the hydrophobic - polar (HP model. Problem-specific search operators are implemented and applied using a steepest-ascent hill-climbing approach. Furthermore, the proposed model enforces an explicit diversification stage during the evolution in order to avoid local optimum. The main features of the resulting evolutionary algorithm - hill-climbing mechanism and diversification strategy - are evaluated in a set of numerical experiments for the protein structure prediction problem to assess their impact to the efficiency of the search process. Furthermore, the emerging consolidated model is compared to relevant algorithms from the literature for a set of difficult bidimensional instances from lattice protein models. The results obtained by the proposed algorithm are promising and competitive with those of related methods.

  14. Evolutionary Relevance Facilitates Visual Information Processing

    Directory of Open Access Journals (Sweden)

    Russell E. Jackson

    2013-07-01

    Full Text Available Visual search of the environment is a fundamental human behavior that perceptual load affects powerfully. Previously investigated means for overcoming the inhibitions of high perceptual load, however, generalize poorly to real-world human behavior. We hypothesized that humans would process evolutionarily relevant stimuli more efficiently than evolutionarily novel stimuli, and evolutionary relevance would mitigate the repercussions of high perceptual load during visual search. Animacy is a significant component to evolutionary relevance of visual stimuli because perceiving animate entities is time-sensitive in ways that pose significant evolutionary consequences. Participants completing a visual search task located evolutionarily relevant and animate objects fastest and with the least impact of high perceptual load. Evolutionarily novel and inanimate objects were located slowest and with the highest impact of perceptual load. Evolutionary relevance may importantly affect everyday visual information processing.

  15. WWER core pattern enhancement using adaptive improved harmony search

    International Nuclear Information System (INIS)

    Nazari, T.; Aghaie, M.; Zolfaghari, A.; Minuchehr, A.; Norouzi, A.

    2013-01-01

    Highlights: ► The classical and improved harmony search algorithms are introduced. ► The advantage of IHS is demonstrated in Shekel's Foxholes. ► The CHS and IHS are compared with other Heuristic algorithms. ► The adaptive improved harmony search is applied for two cases. ► Two cases of WWER core are optimized in BOC FA pattern. - Abstract: The efficient operation and fuel management of PWRs are of utmost importance. Core performance analysis constitutes an essential phase in core fuel management optimization. Finding an optimum core arrangement for loading of fuel assemblies, FAs, in a nuclear core is a complex problem. In this paper, application of classical harmony search (HS) and adaptive improved harmony search (IHS) in loading pattern (LP) design, for pressurized water reactors, is described. In this analysis, finding the best core pattern, which attains maximum multiplication factor, k eff , by considering maximum allowable power picking factors (PPF) is the main objective. Therefore a HS based, LP optimization code is prepared and CITATION code which is a neutronic calculation code, applied to obtain effective multiplication factor, neutron fluxes and power density in desired cores. Using adaptive improved harmony search and neutronic code, generated LP optimization code, could be applicable for PWRs core with many numbers of FAs. In this work, at first step, HS and IHS efficiencies are compared with some other heuristic algorithms in Shekel's Foxholes problem and capability of the adaptive improved harmony search is demonstrated. Results show, efficient application of IHS. At second step, two WWER cases are studied and then IHS proffered improved core patterns with regard to mentioned objective functions.

  16. Optimization of boiling water reactor control rod patterns using linear search

    International Nuclear Information System (INIS)

    Kiguchi, T.; Doi, K.; Fikuzaki, T.; Frogner, B.; Lin, C.; Long, A.B.

    1984-01-01

    A computer program for searching the optimal control rod pattern has been developed. The program is able to find a control rod pattern where the resulting power distribution is optimal in the sense that it is the closest to the desired power distribution, and it satisfies all operational constraints. The search procedure consists of iterative uses of two steps: sensitivity analyses of local power and thermal margins using a three-dimensional reactor simulator for a simplified prediction model; linear search for the optimal control rod pattern with the simplified model. The optimal control rod pattern is found along the direction where the performance index gradient is the steepest. This program has been verified to find the optimal control rod pattern through simulations using operational data from the Oyster Creek Reactor

  17. WWER core pattern enhancement using adaptive improved harmony search

    Energy Technology Data Exchange (ETDEWEB)

    Nazari, T. [Nuclear Engineering Department, Shahid Beheshti University, G.C., P.O. Box 1983963113, Tehran (Iran, Islamic Republic of); Aghaie, M., E-mail: M_Aghaie@sbu.ac.ir [Nuclear Engineering Department, Shahid Beheshti University, G.C., P.O. Box 1983963113, Tehran (Iran, Islamic Republic of); Zolfaghari, A.; Minuchehr, A.; Norouzi, A. [Nuclear Engineering Department, Shahid Beheshti University, G.C., P.O. Box 1983963113, Tehran (Iran, Islamic Republic of)

    2013-01-15

    Highlights: Black-Right-Pointing-Pointer The classical and improved harmony search algorithms are introduced. Black-Right-Pointing-Pointer The advantage of IHS is demonstrated in Shekel's Foxholes. Black-Right-Pointing-Pointer The CHS and IHS are compared with other Heuristic algorithms. Black-Right-Pointing-Pointer The adaptive improved harmony search is applied for two cases. Black-Right-Pointing-Pointer Two cases of WWER core are optimized in BOC FA pattern. - Abstract: The efficient operation and fuel management of PWRs are of utmost importance. Core performance analysis constitutes an essential phase in core fuel management optimization. Finding an optimum core arrangement for loading of fuel assemblies, FAs, in a nuclear core is a complex problem. In this paper, application of classical harmony search (HS) and adaptive improved harmony search (IHS) in loading pattern (LP) design, for pressurized water reactors, is described. In this analysis, finding the best core pattern, which attains maximum multiplication factor, k{sub eff}, by considering maximum allowable power picking factors (PPF) is the main objective. Therefore a HS based, LP optimization code is prepared and CITATION code which is a neutronic calculation code, applied to obtain effective multiplication factor, neutron fluxes and power density in desired cores. Using adaptive improved harmony search and neutronic code, generated LP optimization code, could be applicable for PWRs core with many numbers of FAs. In this work, at first step, HS and IHS efficiencies are compared with some other heuristic algorithms in Shekel's Foxholes problem and capability of the adaptive improved harmony search is demonstrated. Results show, efficient application of IHS. At second step, two WWER cases are studied and then IHS proffered improved core patterns with regard to mentioned objective functions.

  18. SpolSimilaritySearch - A web tool to compare and search similarities between spoligotypes of Mycobacterium tuberculosis complex.

    Science.gov (United States)

    Couvin, David; Zozio, Thierry; Rastogi, Nalin

    2017-07-01

    Spoligotyping is one of the most commonly used polymerase chain reaction (PCR)-based methods for identification and study of genetic diversity of Mycobacterium tuberculosis complex (MTBC). Despite its known limitations if used alone, the methodology is particularly useful when used in combination with other methods such as mycobacterial interspersed repetitive units - variable number of tandem DNA repeats (MIRU-VNTRs). At a worldwide scale, spoligotyping has allowed identification of information on 103,856 MTBC isolates (corresponding to 98049 clustered strains plus 5807 unique isolates from 169 countries of patient origin) contained within the SITVIT2 proprietary database of the Institut Pasteur de la Guadeloupe. The SpolSimilaritySearch web-tool described herein (available at: http://www.pasteur-guadeloupe.fr:8081/SpolSimilaritySearch) incorporates a similarity search algorithm allowing users to get a complete overview of similar spoligotype patterns (with information on presence or absence of 43 spacers) in the aforementioned worldwide database. This tool allows one to analyze spread and evolutionary patterns of MTBC by comparing similar spoligotype patterns, to distinguish between widespread, specific and/or confined patterns, as well as to pinpoint patterns with large deleted blocks, which play an intriguing role in the genetic epidemiology of M. tuberculosis. Finally, the SpolSimilaritySearch tool also provides with the country distribution patterns for each queried spoligotype. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Physiologically induced color-pattern changes in butterfly wings: mechanistic and evolutionary implications.

    Science.gov (United States)

    Otaki, Joji M

    2008-07-01

    A mechanistic understanding of the butterfly wing color-pattern determination can be facilitated by experimental pattern changes. Here I review physiologically induced color-pattern changes in nymphalid butterflies and their mechanistic and evolutionary implications. A type of color-pattern change can be elicited by elemental changes in size and position throughout the wing, as suggested by the nymphalid groundplan. These changes of pattern elements are bi-directional and bi-sided dislocation toward or away from eyespot foci and in both proximal and distal sides of the foci. The peripheral elements are dislocated even in the eyespot-less compartments. Anterior spots are more severely modified, suggesting the existence of an anterior-posterior gradient. In one species, eyespots are transformed into white spots with remnant-like orange scales, and such patterns emerge even at the eyespot-less "imaginary" foci. A series of these color-pattern modifications probably reveal "snap-shots" of a dynamic morphogenic signal due to heterochronic uncoupling between the signaling and reception steps. The conventional gradient model can be revised to account for these observed color-pattern changes.

  20. Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm

    Directory of Open Access Journals (Sweden)

    Xiaoli Jin

    2017-06-01

    Full Text Available NAC (NAM/ATAF/CUC proteins constitute one of the biggest plant-specific transcription factor (TF families and have crucial roles in diverse developmental programs during plant growth. Phylogenetic analyses have revealed both conserved and lineage-specific NAC subfamilies, among which various origins and distinct features were observed. It is reasonable to hypothesize that there should be divergent evolutionary patterns of NAC TFs both between dicots and monocots, and among NAC subfamilies. In this study, we compared the gene duplication and loss, evolutionary rate, and selective pattern among non-lineage specific NAC subfamilies, as well as those between dicots and monocots, through genome-wide analyses of sequence and functional data in six dicot and five grass lineages. The number of genes gained in the dicot lineages was much larger than that in the grass lineages, while fewer gene losses were observed in the grass than that in the dicots. We revealed (1 uneven constitution of Clusters of Orthologous Groups (COGs and contrasting birth/death rates among subfamilies, and (2 two distinct evolutionary scenarios of NAC TFs between dicots and grasses. Our results demonstrated that relaxed selection, resulting from concerted gene duplications, may have permitted substitutions responsible for functional divergence of NAC genes into new lineages. The underlying mechanism of distinct evolutionary fates of NAC TFs shed lights on how evolutionary divergence contributes to differences in establishing NAC gene subfamilies and thus impacts the distinct features between dicots and grasses.

  1. Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom

    Science.gov (United States)

    Song, Xiaoming; Duan, Weike; Huang, Zhinan; Liu, Gaofeng; Wu, Peng; Liu, Tongkun; Li, Ying; Hou, Xilin

    2015-09-01

    In plants, flowering is the most important transition from vegetative to reproductive growth. The flowering patterns of monocots and eudicots are distinctly different, but few studies have described the evolutionary patterns of the flowering genes in them. In this study, we analysed the evolutionary pattern, duplication and expression level of these genes. The main results were as follows: (i) characterization of flowering genes in monocots and eudicots, including the identification of family-specific, orthologous and collinear genes; (ii) full characterization of CONSTANS-like genes in Brassica rapa (BraCOL genes), the key flowering genes; (iii) exploration of the evolution of COL genes in plant kingdom and construction of the evolutionary pattern of COL genes; (iv) comparative analysis of CO and FT genes between Brassicaceae and Grass, which identified several family-specific amino acids, and revealed that CO and FT protein structures were similar in B. rapa and Arabidopsis but different in rice; and (v) expression analysis of photoperiod pathway-related genes in B. rapa under different photoperiod treatments by RT-qPCR. This analysis will provide resources for understanding the flowering mechanisms and evolutionary pattern of COL genes. In addition, this genome-wide comparative study of COL genes may also provide clues for evolution of other flowering genes.

  2. Optimal search behavior and classic foraging theory

    International Nuclear Information System (INIS)

    Bartumeus, F; Catalan, J

    2009-01-01

    Random walk methods and diffusion theory pervaded ecological sciences as methods to analyze and describe animal movement. Consequently, statistical physics was mostly seen as a toolbox rather than as a conceptual framework that could contribute to theory on evolutionary biology and ecology. However, the existence of mechanistic relationships and feedbacks between behavioral processes and statistical patterns of movement suggests that, beyond movement quantification, statistical physics may prove to be an adequate framework to understand animal behavior across scales from an ecological and evolutionary perspective. Recently developed random search theory has served to critically re-evaluate classic ecological questions on animal foraging. For instance, during the last few years, there has been a growing debate on whether search behavior can include traits that improve success by optimizing random (stochastic) searches. Here, we stress the need to bring together the general encounter problem within foraging theory, as a mean for making progress in the biological understanding of random searching. By sketching the assumptions of optimal foraging theory (OFT) and by summarizing recent results on random search strategies, we pinpoint ways to extend classic OFT, and integrate the study of search strategies and its main results into the more general theory of optimal foraging.

  3. Automatic feature design for optical character recognition using an evolutionary search procedure.

    Science.gov (United States)

    Stentiford, F W

    1985-03-01

    An automatic evolutionary search is applied to the problem of feature extraction in an OCR application. A performance measure based on feature independence is used to generate features which do not appear to suffer from peaking effects [17]. Features are extracted from a training set of 30 600 machine printed 34 class alphanumeric characters derived from British mail. Classification results on the training set and a test set of 10 200 characters are reported for an increasing number of features. A 1.01 percent forced decision error rate is obtained on the test data using 316 features. The hardware implementation should be cheap and fast to operate. The performance compares favorably with current low cost OCR page readers.

  4. Patscanui: an intuitive web interface for searching patterns in DNA and protein data

    DEFF Research Database (Denmark)

    Blin, Kai; Wohlleben, Wolfgang; Weber, Tilmann

    2018-01-01

    Patterns in biological sequences frequently signify interesting features in the underlying molecule. Many tools exist to search for well-known patterns. Less support is available for exploratory analysis, where no well-defined patterns are known yet. PatScanUI (https://patscan.secondarymetabolite......Patterns in biological sequences frequently signify interesting features in the underlying molecule. Many tools exist to search for well-known patterns. Less support is available for exploratory analysis, where no well-defined patterns are known yet. PatScanUI (https......://patscan.secondarymetabolites.org/) provides a highly interactive web interface to the powerful generic pattern search tool PatScan. The complex PatScan-patterns are created in a drag-and-drop aware interface allowing researchers to do rapid prototyping of the often complicated patterns useful to identifying features of interest....

  5. Westinghouse loading pattern search methodology for complex core designs

    International Nuclear Information System (INIS)

    Chao, Y.A.; Alsop, B.H.; Johansen, B.J.; Morita, T.

    1991-01-01

    Pressurized water reactor core designs have become more complex and must meet a plethora of design constraints. Trends have been toward longer cycles with increased discharge burnup, increased burnable absorber (BA) number, mixed BA types, reduced radial leakage, axially blanketed fuel, and multiple-batch feed fuel regions. Obtaining economical reload core loading patterns (LPs) that meet design criteria is a difficult task to do manually. Automated LP search tools are needed. An LP search tool cannot possibly perform an exhaustive search because of the sheer size of the combinatorial problem. On the other hand, evolving complexity of the design features and constraints often invalidates expert rules based on past design experiences. Westinghouse has developed a sophisticated loading pattern search methodology. This methodology is embodied in the LPOP code, which Westinghouse nuclear designers use extensively. The LPOP code generates a variety of LPs meeting design constraints and performs a two-cycle economic evaluation of the generated LPs. The designer selects the most appropriate patterns for fine tuning and evaluation by the design codes. This paper describes the major features of the LPOP methodology that are relevant to fulfilling the aforementioned requirements. Data and examples are also provided to demonstrate the performance of LPOP in meeting the complex design needs

  6. Contemporary and historical evolutionary processes interact to shape patterns of within-lake phenotypic divergences in polyphenic pumpkinseed sunfish, Lepomis gibbosus.

    Science.gov (United States)

    Weese, Dylan J; Ferguson, Moira M; Robinson, Beren W

    2012-03-01

    Historical and contemporary evolutionary processes can both contribute to patterns of phenotypic variation among populations of a species. Recent studies are revealing how interactions between historical and contemporary processes better explain observed patterns of phenotypic divergence than either process alone. Here, we investigate the roles of evolutionary history and adaptation to current environmental conditions in structuring phenotypic variation among polyphenic populations of sunfish inhabiting 12 postglacial lakes in eastern North America. The pumpkinseed sunfish polyphenism includes sympatric ecomorphs specialized for littoral or pelagic lake habitats. First, we use population genetic methods to test the evolutionary independence of within-lake phenotypic divergences of ecomorphs and to describe patterns of genetic structure among lake populations that clustered into three geographical groupings. We then used multivariate analysis of covariance (MANCOVA) to partition body shape variation (quantified with geometric morphometrics) among the effects of evolutionary history (reflecting phenotypic variation among genetic clusters), the shared phenotypic response of all populations to alternate habitats within lakes (reflecting adaptation to contemporary conditions), and unique phenotypic responses to habitats within lakes nested within genetic clusters. All effects had a significant influence on body form, but the effects of history and the interaction between history and contemporary habitat were larger than contemporary processes in structuring phenotypic variation. This highlights how divergence can be better understood against a known backdrop of evolutionary history.

  7. Patterns of coordinated cortical remodeling during adolescence and their associations with functional specialization and evolutionary expansion.

    Science.gov (United States)

    Sotiras, Aristeidis; Toledo, Jon B; Gur, Raquel E; Gur, Ruben C; Satterthwaite, Theodore D; Davatzikos, Christos

    2017-03-28

    During adolescence, the human cortex undergoes substantial remodeling to support a rapid expansion of behavioral repertoire. Accurately quantifying these changes is a prerequisite for understanding normal brain development, as well as the neuropsychiatric disorders that emerge in this vulnerable period. Past accounts have demonstrated substantial regional heterogeneity in patterns of brain development, but frequently have been limited by small samples and analytics that do not evaluate complex multivariate imaging patterns. Capitalizing on recent advances in multivariate analysis methods, we used nonnegative matrix factorization (NMF) to uncover coordinated patterns of cortical development in a sample of 934 youths ages 8-20, who completed structural neuroimaging as part of the Philadelphia Neurodevelopmental Cohort. Patterns of structural covariance (PSCs) derived by NMF were highly reproducible over a range of resolutions, and differed markedly from common gyral-based structural atlases. Moreover, PSCs were largely symmetric and showed correspondence to specific large-scale functional networks. The level of correspondence was ordered according to their functional role and position in the evolutionary hierarchy, being high in lower-order visual and somatomotor networks and diminishing in higher-order association cortex. Furthermore, PSCs showed divergent developmental associations, with PSCs in higher-order association cortex networks showing greater changes with age than primary somatomotor and visual networks. Critically, such developmental changes within PSCs were significantly associated with the degree of evolutionary cortical expansion. Together, our findings delineate a set of structural brain networks that undergo coordinated cortical thinning during adolescence, which is in part governed by evolutionary novelty and functional specialization.

  8. Differential Infection Patterns and Recent Evolutionary Origins of Equine Hepaciviruses in Donkeys

    Science.gov (United States)

    Walter, Stephanie; Rasche, Andrea; Moreira-Soto, Andrés; Pfaender, Stephanie; Bletsa, Magda; Corman, Victor Max; Aguilar-Setien, Alvaro; García-Lacy, Fernando; Hans, Aymeric; Todt, Daniel; Schuler, Gerhard; Shnaiderman-Torban, Anat; Steinman, Amir; Roncoroni, Cristina; Veneziano, Vincenzo; Rusenova, Nikolina; Sandev, Nikolay; Rusenov, Anton; Zapryanova, Dimitrinka; García-Bocanegra, Ignacio; Jores, Joerg; Carluccio, Augusto; Veronesi, Maria Cristina; Cavalleri, Jessika M. V.; Drosten, Christian; Lemey, Philippe

    2016-01-01

    ABSTRACT The hepatitis C virus (HCV) is a major human pathogen. Genetically related viruses in animals suggest a zoonotic origin of HCV. The closest relative of HCV is found in horses (termed equine hepacivirus [EqHV]). However, low EqHV genetic diversity implies relatively recent acquisition of EqHV by horses, making a derivation of HCV from EqHV unlikely. To unravel the EqHV evolutionary history within equid sister species, we analyzed 829 donkeys and 53 mules sampled in nine European, Asian, African, and American countries by molecular and serologic tools for EqHV infection. Antibodies were found in 278 animals (31.5%), and viral RNA was found in 3 animals (0.3%), all of which were simultaneously seropositive. A low RNA prevalence in spite of high seroprevalence suggests a predominance of acute infection, a possible difference from the mostly chronic hepacivirus infection pattern seen in horses and humans. Limitation of transmission due to short courses of infection may explain the existence of entirely seronegative groups of animals. Donkey and horse EqHV strains were paraphyletic and 97.5 to 98.2% identical in their translated polyprotein sequences, making virus/host cospeciation unlikely. Evolutionary reconstructions supported host switches of EqHV between horses and donkeys without the involvement of adaptive evolution. Global admixture of donkey and horse hepaciviruses was compatible with anthropogenic alterations of EqHV ecology. In summary, our findings do not support EqHV as the origin of the significantly more diversified HCV. Identification of a host system with predominantly acute hepacivirus infection may enable new insights into the chronic infection pattern associated with HCV. IMPORTANCE The evolutionary origins of the human hepatitis C virus (HCV) are unclear. The closest animal-associated relative of HCV occurs in horses (equine hepacivirus [EqHV]). The low EqHV genetic diversity implies a relatively recent acquisition of EqHV by horses

  9. Differential Infection Patterns and Recent Evolutionary Origins of Equine Hepaciviruses in Donkeys.

    Science.gov (United States)

    Walter, Stephanie; Rasche, Andrea; Moreira-Soto, Andrés; Pfaender, Stephanie; Bletsa, Magda; Corman, Victor Max; Aguilar-Setien, Alvaro; García-Lacy, Fernando; Hans, Aymeric; Todt, Daniel; Schuler, Gerhard; Shnaiderman-Torban, Anat; Steinman, Amir; Roncoroni, Cristina; Veneziano, Vincenzo; Rusenova, Nikolina; Sandev, Nikolay; Rusenov, Anton; Zapryanova, Dimitrinka; García-Bocanegra, Ignacio; Jores, Joerg; Carluccio, Augusto; Veronesi, Maria Cristina; Cavalleri, Jessika M V; Drosten, Christian; Lemey, Philippe; Steinmann, Eike; Drexler, Jan Felix

    2017-01-01

    The hepatitis C virus (HCV) is a major human pathogen. Genetically related viruses in animals suggest a zoonotic origin of HCV. The closest relative of HCV is found in horses (termed equine hepacivirus [EqHV]). However, low EqHV genetic diversity implies relatively recent acquisition of EqHV by horses, making a derivation of HCV from EqHV unlikely. To unravel the EqHV evolutionary history within equid sister species, we analyzed 829 donkeys and 53 mules sampled in nine European, Asian, African, and American countries by molecular and serologic tools for EqHV infection. Antibodies were found in 278 animals (31.5%), and viral RNA was found in 3 animals (0.3%), all of which were simultaneously seropositive. A low RNA prevalence in spite of high seroprevalence suggests a predominance of acute infection, a possible difference from the mostly chronic hepacivirus infection pattern seen in horses and humans. Limitation of transmission due to short courses of infection may explain the existence of entirely seronegative groups of animals. Donkey and horse EqHV strains were paraphyletic and 97.5 to 98.2% identical in their translated polyprotein sequences, making virus/host cospeciation unlikely. Evolutionary reconstructions supported host switches of EqHV between horses and donkeys without the involvement of adaptive evolution. Global admixture of donkey and horse hepaciviruses was compatible with anthropogenic alterations of EqHV ecology. In summary, our findings do not support EqHV as the origin of the significantly more diversified HCV. Identification of a host system with predominantly acute hepacivirus infection may enable new insights into the chronic infection pattern associated with HCV. The evolutionary origins of the human hepatitis C virus (HCV) are unclear. The closest animal-associated relative of HCV occurs in horses (equine hepacivirus [EqHV]). The low EqHV genetic diversity implies a relatively recent acquisition of EqHV by horses, limiting the time span for

  10. Optimizing a reconfigurable material via evolutionary computation

    Science.gov (United States)

    Wilken, Sam; Miskin, Marc Z.; Jaeger, Heinrich M.

    2015-08-01

    Rapid prototyping by combining evolutionary computation with simulations is becoming a powerful tool for solving complex design problems in materials science. This method of optimization operates in a virtual design space that simulates potential material behaviors and after completion needs to be validated by experiment. However, in principle an evolutionary optimizer can also operate on an actual physical structure or laboratory experiment directly, provided the relevant material parameters can be accessed by the optimizer and information about the material's performance can be updated by direct measurements. Here we provide a proof of concept of such direct, physical optimization by showing how a reconfigurable, highly nonlinear material can be tuned to respond to impact. We report on an entirely computer controlled laboratory experiment in which a 6 ×6 grid of electromagnets creates a magnetic field pattern that tunes the local rigidity of a concentrated suspension of ferrofluid and iron filings. A genetic algorithm is implemented and tasked to find field patterns that minimize the force transmitted through the suspension. Searching within a space of roughly 1010 possible configurations, after testing only 1500 independent trials the algorithm identifies an optimized configuration of layered rigid and compliant regions.

  11. The Roles and Evolutionary Patterns of Intronless Genes in Deuterostomes

    Directory of Open Access Journals (Sweden)

    Ming Zou

    2011-01-01

    Full Text Available Genes without introns are a characteristic feature of prokaryotes, but there are still a number of intronless genes in eukaryotes. To study these eukaryotic genes that have prokaryotic architecture could help to understand the evolutionary patterns of related genes and genomes. Our analyses revealed a number of intronless genes that reside in 6 deuterostomes (sea urchin, sea squirt, zebrafish, chicken, platypus, and human. We also determined the conservation for each intronless gene in archaea, bacteria, fungi, plants, metazoans, and other eukaryotes. Proportions of intronless genes that are inherited from the common ancestor of archaea, bacteria, and eukaryotes in these species were consistent with their phylogenetic positions, with more proportions of ancient intronless genes residing in more primitive species. In these species, intronless genes belong to different cellular roles and gene ontology (GO categories, and some of these functions are very basic. Part of intronless genes is derived from other intronless genes or multiexon genes in each species. In conclusion, we showed that a varying number and proportion of intronless genes reside in these 6 deuterostomes, and some of them function importantly. These genes are good candidates for subsequent functional and evolutionary analyses specifically.

  12. Effects of Individual Health Topic Familiarity on Activity Patterns During Health Information Searches

    Science.gov (United States)

    Moriyama, Koichi; Fukui, Ken–ichi; Numao, Masayuki

    2015-01-01

    Background Non-medical professionals (consumers) are increasingly using the Internet to support their health information needs. However, the cognitive effort required to perform health information searches is affected by the consumer’s familiarity with health topics. Consumers may have different levels of familiarity with individual health topics. This variation in familiarity may cause misunderstandings because the information presented by search engines may not be understood correctly by the consumers. Objective As a first step toward the improvement of the health information search process, we aimed to examine the effects of health topic familiarity on health information search behaviors by identifying the common search activity patterns exhibited by groups of consumers with different levels of familiarity. Methods Each participant completed a health terminology familiarity questionnaire and health information search tasks. The responses to the familiarity questionnaire were used to grade the familiarity of participants with predefined health topics. The search task data were transcribed into a sequence of search activities using a coding scheme. A computational model was constructed from the sequence data using a Markov chain model to identify the common search patterns in each familiarity group. Results Forty participants were classified into L1 (not familiar), L2 (somewhat familiar), and L3 (familiar) groups based on their questionnaire responses. They had different levels of familiarity with four health topics. The video data obtained from all of the participants were transcribed into 4595 search activities (mean 28.7, SD 23.27 per session). The most frequent search activities and transitions in all the familiarity groups were related to evaluations of the relevancy of selected web pages in the retrieval results. However, the next most frequent transitions differed in each group and a chi-squared test confirmed this finding (Pinformation search patterns

  13. Connecting proximate mechanisms and evolutionary patterns: pituitary gland size and mammalian life history.

    Science.gov (United States)

    Kamilar, J M; Tecot, S R

    2015-11-01

    At the proximate level, hormones are known to play a critical role in influencing the life history of mammals, including humans. The pituitary gland is directly responsible for producing several hormones, including those related to growth and reproduction. Although we have a basic understanding of how hormones affect life history characteristics, we still have little knowledge of this relationship in an evolutionary context. We used data from 129 mammal species representing 14 orders to investigate the relationship between pituitary gland size and life history variation. Because pituitary gland size should be related to hormone production and action, we predicted that species with relatively large pituitaries should be associated with fast life histories, especially increased foetal and post-natal growth rates. Phylogenetic analyses revealed that total pituitary size and the size of the anterior lobe of the pituitary significantly predicted a life history axis that was correlated with several traits including body mass, and foetal and post-natal growth rates. Additional models directly examining the association between relative pituitary size and growth rates produced concordant results. We also found that relative pituitary size variation across mammals was best explained by an Ornstein-Uhlenbeck model of evolution, suggesting an important role of stabilizing selection. Our results support the idea that the size of the pituitary is linked to life history variation through evolutionary time. This pattern is likely due to mediating hormone levels but additional work is needed. We suggest that future investigations incorporating endocrine gland size may be critical for understanding life history evolution. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

  14. HIV-1 Evolutionary Patterns Associated with Metastatic Kaposi’s Sarcoma during AIDS

    Directory of Open Access Journals (Sweden)

    Susanna L. Lamers

    2016-01-01

    Full Text Available Kaposi’s sarcoma (KS in HIV-infected individuals can have a wide range of clinical outcomes, from indolent skin tumors to a life-threatening visceral cancer. KS tumors contain endothelial-related cells and inflammatory cells that may be HIV-infected. In this study we tested if HIV evolutionary patterns distinguish KS tumor relatedness and progression. Multisite autopsies from participants who died from HIV-AIDS with KS prior to the availability of antiretroviral therapy were identified at the AIDS and Cancer Specimen Resource (ACSR. Two patients (KS1 and KS2 died predominantly from non-KS-associated disease and KS3 died due to aggressive and metastatic KS within one month of diagnosis. Skin and visceral tumor and nontumor autopsy tissues were obtained (n=12. Single genome sequencing was used to amplify HIV RNA and DNA, which was present in all tumors. Independent HIV tumor clades in phylogenies differentiated KS1 and KS2 from KS3, whose sequences were interrelated by both phylogeny and selection. HIV compartmentalization was confirmed in KS1 and KS2 tumors; however, in KS3, no compartmentalization was observed among sampled tissues. While the sample size is small, the HIV evolutionary patterns observed in all patients suggest an interplay between tumor cells and HIV-infected cells which provides a selective advantage and could promote KS progression.

  15. Practical advantages of evolutionary computation

    Science.gov (United States)

    Fogel, David B.

    1997-10-01

    Evolutionary computation is becoming a common technique for solving difficult, real-world problems in industry, medicine, and defense. This paper reviews some of the practical advantages to using evolutionary algorithms as compared with classic methods of optimization or artificial intelligence. Specific advantages include the flexibility of the procedures, as well as their ability to self-adapt the search for optimum solutions on the fly. As desktop computers increase in speed, the application of evolutionary algorithms will become routine.

  16. Mate choice and the evolutionary stability of a fixed threshold in a sequential search strategy

    Directory of Open Access Journals (Sweden)

    Raymond Cheng

    2014-06-01

    Full Text Available The sequential search strategy is a prominent model of searcher behavior, derived as a rule by which females might sample and choose a mate from a distribution of prospective partners. The strategy involves a threshold criterion against which prospective mates are evaluated. The optimal threshold depends on the attributes of prospective mates, which are likely to vary across generations or within the lifetime of searchers due to stochastic environmental events. The extent of this variability and the cost to acquire information on the distribution of the quality of prospective mates determine whether a learned or environmentally canalized threshold is likely to be favored. In this paper, we determine conditions on cross-generational perturbations of the distribution of male phenotypes that allow for the evolutionary stability of an environmentally canalized threshold. In particular, we derive conditions under which there is a genetically determined threshold that is optimal over an evolutionary time scale in comparison to any other unlearned threshold. These considerations also reveal a simple algorithm by which the threshold could be learned.

  17. Molecular evolutionary patterns of NAD+/Sirtuin aging signaling pathway across taxa.

    Directory of Open Access Journals (Sweden)

    Uma Gaur

    Full Text Available A deeper understanding of the conserved molecular mechanisms in different taxa have been made possible only because of the evolutionary conservation of crucial signaling pathways. In the present study, we explored the molecular evolutionary pattern of selection signatures in 51 species for 10 genes which are important components of NAD+/Sirtuin pathway and have already been directly linked to lifespan extension in worms and mice. Selection pressure analysis using PAML program revealed that MRPS5 and PPARGC1A were under significant constraints because of their functional significance. FOXO3a also displayed strong purifying selection. All three sirtuins, which were SIRT1, SIRT2 and SIRT6, displayed a great degree of conservation between taxa, which is consistent with the previous report. A significant evolutionary constraint is seen on the anti-oxidant gene, SOD3. As expected, TP53 gene was under significant selection pressure in mammals, owing to its major role in tumor progression. Poly-ADP-ribose polymerase (PARP genes displayed the most sites under positive selection. Further 3D structural analysis of PARP1 and PARP2 protein revealed that some of these positively selected sites caused a change in the electrostatic potential of the protein structure, which may allow a change in its interaction with other proteins and molecules ultimately leading to difference in the function. Although the functional significance of the positively selected sites could not be established in the variants databases, yet it will be interesting to see if these sites actually affect the function of PARP1 and PARP2.

  18. The evolutionary history of vertebrate cranial placodes II. Evolution of ectodermal patterning.

    Science.gov (United States)

    Schlosser, Gerhard; Patthey, Cedric; Shimeld, Sebastian M

    2014-05-01

    Cranial placodes are evolutionary innovations of vertebrates. However, they most likely evolved by redeployment, rewiring and diversification of preexisting cell types and patterning mechanisms. In the second part of this review we compare vertebrates with other animal groups to elucidate the evolutionary history of ectodermal patterning. We show that several transcription factors have ancient bilaterian roles in dorsoventral and anteroposterior regionalisation of the ectoderm. Evidence from amphioxus suggests that ancestral chordates then concentrated neurosecretory cells in the anteriormost non-neural ectoderm. This anterior proto-placodal domain subsequently gave rise to the oral siphon primordia in tunicates (with neurosecretory cells being lost) and anterior (adenohypophyseal, olfactory, and lens) placodes of vertebrates. Likewise, tunicate atrial siphon primordia and posterior (otic, lateral line, and epibranchial) placodes of vertebrates probably evolved from a posterior proto-placodal region in the tunicate-vertebrate ancestor. Since both siphon primordia in tunicates give rise to sparse populations of sensory cells, both proto-placodal domains probably also gave rise to some sensory receptors in the tunicate-vertebrate ancestor. However, proper cranial placodes, which give rise to high density arrays of specialised sensory receptors and neurons, evolved from these domains only in the vertebrate lineage. We propose that this may have involved rewiring of the regulatory network upstream and downstream of Six1/2 and Six4/5 transcription factors and their Eya family cofactors. These proteins, which play ancient roles in neuronal differentiation were first recruited to the dorsal non-neural ectoderm in the tunicate-vertebrate ancestor but subsequently probably acquired new target genes in the vertebrate lineage, allowing them to adopt new functions in regulating proliferation and patterning of neuronal progenitors. Copyright © 2014 Elsevier Inc. All rights

  19. Age differences in visual search for compound patterns: long- versus short-range grouping.

    Science.gov (United States)

    Burack, J A; Enns, J T; Iarocci, G; Randolph, B

    2000-11-01

    Visual search for compound patterns was examined in observers aged 6, 8, 10, and 22 years. The main question was whether age-related improvement in search rate (response time slope over number of items) was different for patterns defined by short- versus long-range spatial relations. Perceptual access to each type of relation was varied by using elements of same contrast (easy to access) or mixed contrast (hard to access). The results showed large improvements with age in search rate for long-range targets; search rate for short-range targets was fairly constant across age. This pattern held regardless of whether perceptual access to a target was easy or hard, supporting the hypothesis that different processes are involved in perceptual grouping at these two levels. The results also point to important links between ontogenic and microgenic change in perception (H. Werner, 1948, 1957).

  20. Risk attitudes in a changing environment: An evolutionary model of the fourfold pattern of risk preferences.

    Science.gov (United States)

    Mallpress, Dave E W; Fawcett, Tim W; Houston, Alasdair I; McNamara, John M

    2015-04-01

    A striking feature of human decision making is the fourfold pattern of risk attitudes, involving risk-averse behavior in situations of unlikely losses and likely gains, but risk-seeking behavior in response to likely losses and unlikely gains. Current theories to explain this pattern assume particular psychological processes to reproduce empirical observations, but do not address whether it is adaptive for the decision maker to respond to risk in this way. Here, drawing on insights from behavioral ecology, we build an evolutionary model of risk-sensitive behavior, to investigate whether particular types of environmental conditions could favor a fourfold pattern of risk attitudes. We consider an individual foraging in a changing environment, where energy is needed to prevent starvation and build up reserves for reproduction. The outcome, in terms of reproductive value (a rigorous measure of evolutionary success), of a one-off choice between a risky and a safe gain, or between a risky and a safe loss, determines the risk-sensitive behavior we should expect to see in this environment. Our results show that the fourfold pattern of risk attitudes may be adaptive in an environment in which conditions vary stochastically but are autocorrelated in time. In such an environment the current options provide information about the likely environmental conditions in the future, which affect the optimal pattern of risk sensitivity. Our model predicts that risk preferences should be both path dependent and affected by the decision maker's current state. (c) 2015 APA, all rights reserved).

  1. Optimal Point-to-Point Trajectory Tracking of Redundant Manipulators using Generalized Pattern Search

    Directory of Open Access Journals (Sweden)

    Thi Rein Myo

    2008-11-01

    Full Text Available Optimal point-to-point trajectory planning for planar redundant manipulator is considered in this study. The main objective is to minimize the sum of the position error of the end-effector at each intermediate point along the trajectory so that the end-effector can track the prescribed trajectory accurately. An algorithm combining Genetic Algorithm and Pattern Search as a Generalized Pattern Search GPS is introduced to design the optimal trajectory. To verify the proposed algorithm, simulations for a 3-D-O-F planar manipulator with different end-effector trajectories have been carried out. A comparison between the Genetic Algorithm and the Generalized Pattern Search shows that The GPS gives excellent tracking performance.

  2. A feasibility study of low-order harmonics expansion applied to loading pattern search

    Energy Technology Data Exchange (ETDEWEB)

    Shaohong, Z.; Dong, L.; Tao, W. [Shanghai Jiao Tong Univ., 1954 Hua Shan Road, Shanghai, 200030 (China); Chao, Y. A. [Westinghouse Electric Company, P. O. Box 355, Pittsburgh, PA 15230-0355 (United States)

    2006-07-01

    Despite significant progress in core loading pattern search methods over years, there still remains the issue of large computing workload and the need for improving the speed of evaluating loading pattern candidates during the search process. This paper focuses on improving the computing speed for loading pattern evaluation, rather than the method of searching for the patterns. A low order harmonics expansion method for flux distribution representation is proposed for fast LP evaluation application. The novel feature of the method is the separation of the short range local perturbation effect from the long range global tilt effect. The latter effect can be captured by low order harmonics expansion. Demonstration examples are presented to show that even for extremely large perturbations induced by fuel shuffling the proposed method can accurately calculate the flux distribution for the LP with very minimal computation. (authors)

  3. Complex evolutionary patterns revealed by mitochondrial genomes of the domestic horse.

    Science.gov (United States)

    Ning, T; Li, J; Lin, K; Xiao, H; Wylie, S; Hua, S; Li, H; Zhang, Y-P

    2014-01-01

    The domestic horse is the most widely used and important stock and recreational animal, valued for its strength and endurance. The energy required by the domestic horse is mainly supplied by mitochondria via oxidative phosphorylation. Thus, selection may have played an essential role in the evolution of the horse mitochondria. Besides, demographic events also affect the DNA polymorphic pattern on mitochondria. To understand the evolutionary patterns of the mitochondria of the domestic horse, we used a deep sequencing approach to obtain the complete sequences of 15 mitochondrial genomes, and four mitochondrial gene sequences, ND6, ATP8, ATP6 and CYTB, collected from 509, 363, 363 and 409 domestic horses, respectively. Evidence of strong substitution rate heterogeneity was found at nonsynonymous sites across the genomes. Signatures of recent positive selection on mtDNA of domestic horse were detected. Specifically, five amino acids in the four mitochondrial genes were identified as the targets of positive selection. Coalescentbased simulations imply that recent population expansion is the most probable explanation for the matrilineal population history for domestic horse. Our findings reveal a complex pattern of non-neutral evolution of the mitochondrial genome in the domestic horses.

  4. Searching for truth: internet search patterns as a method of investigating online responses to a Russian illicit drug policy debate.

    Science.gov (United States)

    Zheluk, Andrey; Gillespie, James A; Quinn, Casey

    2012-12-13

    This is a methodological study investigating the online responses to a national debate over an important health and social problem in Russia. Russia is the largest Internet market in Europe, exceeding Germany in the absolute number of users. However, Russia is unusual in that the main search provider is not Google, but Yandex. This study had two main objectives. First, to validate Yandex search patterns against those provided by Google, and second, to test this method's adequacy for investigating online interest in a 2010 national debate over Russian illicit drug policy. We hoped to learn what search patterns and specific search terms could reveal about the relative importance and geographic distribution of interest in this debate. A national drug debate, centering on the anti-drug campaigner Egor Bychkov, was one of the main Russian domestic news events of 2010. Public interest in this episode was accompanied by increased Internet search. First, we measured the search patterns for 13 search terms related to the Bychkov episode and concurrent domestic events by extracting data from Google Insights for Search (GIFS) and Yandex WordStat (YaW). We conducted Spearman Rank Correlation of GIFS and YaW search data series. Second, we coded all 420 primary posts from Bychkov's personal blog between March 2010 and March 2012 to identify the main themes. Third, we compared GIFS and Yandex policies concerning the public release of search volume data. Finally, we established the relationship between salient drug issues and the Bychkov episode. We found a consistent pattern of strong to moderate positive correlations between Google and Yandex for the terms "Egor Bychkov" (r(s) = 0.88, P < .001), "Bychkov" (r(s) = .78, P < .001) and "Khimki"(r(s) = 0.92, P < .001). Peak search volumes for the Bychkov episode were comparable to other prominent domestic political events during 2010. Monthly search counts were 146,689 for "Bychkov" and 48,084 for "Egor Bychkov", compared to 53

  5. Filter Pattern Search Algorithms for Mixed Variable Constrained Optimization Problems

    National Research Council Canada - National Science Library

    Abramson, Mark A; Audet, Charles; Dennis, Jr, J. E

    2004-01-01

    .... This class combines and extends the Audet-Dennis Generalized Pattern Search (GPS) algorithms for bound constrained mixed variable optimization, and their GPS-filter algorithms for general nonlinear constraints...

  6. Beam angle optimization for intensity-modulated radiation therapy using a guided pattern search method

    International Nuclear Information System (INIS)

    Rocha, Humberto; Dias, Joana M; Ferreira, Brígida C; Lopes, Maria C

    2013-01-01

    Generally, the inverse planning of radiation therapy consists mainly of the fluence optimization. The beam angle optimization (BAO) in intensity-modulated radiation therapy (IMRT) consists of selecting appropriate radiation incidence directions and may influence the quality of the IMRT plans, both to enhance better organ sparing and to improve tumor coverage. However, in clinical practice, most of the time, beam directions continue to be manually selected by the treatment planner without objective and rigorous criteria. The goal of this paper is to introduce a novel approach that uses beam’s-eye-view dose ray tracing metrics within a pattern search method framework in the optimization of the highly non-convex BAO problem. Pattern search methods are derivative-free optimization methods that require a few function evaluations to progress and converge and have the ability to better avoid local entrapment. The pattern search method framework is composed of a search step and a poll step at each iteration. The poll step performs a local search in a mesh neighborhood and ensures the convergence to a local minimizer or stationary point. The search step provides the flexibility for a global search since it allows searches away from the neighborhood of the current iterate. Beam’s-eye-view dose metrics assign a score to each radiation beam direction and can be used within the pattern search framework furnishing a priori knowledge of the problem so that directions with larger dosimetric scores are tested first. A set of clinical cases of head-and-neck tumors treated at the Portuguese Institute of Oncology of Coimbra is used to discuss the potential of this approach in the optimization of the BAO problem. (paper)

  7. Obtention control bars patterns for a BWR using Tabo search

    International Nuclear Information System (INIS)

    Castillo, A.; Ortiz, J.J.; Alonso, G.; Morales, L.B.; Valle, E. del

    2004-01-01

    The obtained results when implementing the technique of tabu search, for to optimize patterns of control bars in a BWR type reactor, using the CM-PRESTO code are presented. The patterns of control bars were obtained for the designs of fuel reloads obtained in a previous work, using the same technique. The obtained results correspond to a cycle of 18 months using 112 fresh fuels enriched at the 3.53 of U-235. The used technique of tabu search, prohibits recently visited movements, in the position that correspond to the axial positions of the control bars, additionally the tiempo t abu matrix is used for to manage a size of variable tabu list and the objective function is punished with the frequency of the forbidden movements. The obtained patterns of control bars improve the longitude of the cycle with regard to the reference values and they complete the restrictions of safety. (Author)

  8. A Novel Handwritten Letter Recognizer Using Enhanced Evolutionary Neural Network

    Science.gov (United States)

    Mahmoudi, Fariborz; Mirzashaeri, Mohsen; Shahamatnia, Ehsan; Faridnia, Saed

    This paper introduces a novel design for handwritten letter recognition by employing a hybrid back-propagation neural network with an enhanced evolutionary algorithm. Feeding the neural network consists of a new approach which is invariant to translation, rotation, and scaling of input letters. Evolutionary algorithm is used for the global search of the search space and the back-propagation algorithm is used for the local search. The results have been computed by implementing this approach for recognizing 26 English capital letters in the handwritings of different people. The computational results show that the neural network reaches very satisfying results with relatively scarce input data and a promising performance improvement in convergence of the hybrid evolutionary back-propagation algorithms is exhibited.

  9. Searching for Truth: Internet Search Patterns as a Method of Investigating Online Responses to a Russian Illicit Drug Policy Debate

    Science.gov (United States)

    Gillespie, James A; Quinn, Casey

    2012-01-01

    Background This is a methodological study investigating the online responses to a national debate over an important health and social problem in Russia. Russia is the largest Internet market in Europe, exceeding Germany in the absolute number of users. However, Russia is unusual in that the main search provider is not Google, but Yandex. Objective This study had two main objectives. First, to validate Yandex search patterns against those provided by Google, and second, to test this method's adequacy for investigating online interest in a 2010 national debate over Russian illicit drug policy. We hoped to learn what search patterns and specific search terms could reveal about the relative importance and geographic distribution of interest in this debate. Methods A national drug debate, centering on the anti-drug campaigner Egor Bychkov, was one of the main Russian domestic news events of 2010. Public interest in this episode was accompanied by increased Internet search. First, we measured the search patterns for 13 search terms related to the Bychkov episode and concurrent domestic events by extracting data from Google Insights for Search (GIFS) and Yandex WordStat (YaW). We conducted Spearman Rank Correlation of GIFS and YaW search data series. Second, we coded all 420 primary posts from Bychkov's personal blog between March 2010 and March 2012 to identify the main themes. Third, we compared GIFS and Yandex policies concerning the public release of search volume data. Finally, we established the relationship between salient drug issues and the Bychkov episode. Results We found a consistent pattern of strong to moderate positive correlations between Google and Yandex for the terms "Egor Bychkov" (r s = 0.88, P < .001), “Bychkov” (r s = .78, P < .001) and “Khimki”(r s = 0.92, P < .001). Peak search volumes for the Bychkov episode were comparable to other prominent domestic political events during 2010. Monthly search counts were 146,689 for “Bychkov” and

  10. Diversity-Guided Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    2002-01-01

    Population diversity is undoubtably a key issue in the performance of evolutionary algorithms. A common hypothesis is that high diversity is important to avoid premature convergence and to escape local optima. Various diversity measures have been used to analyze algorithms, but so far few...... algorithms have used a measure to guide the search. The diversity-guided evolutionary algorithm (DGEA) uses the wellknown distance-to-average-point measure to alternate between phases of exploration (mutation) and phases of exploitation (recombination and selection). The DGEA showed remarkable results...

  11. Patterns and processes in the evolutionary history of parrotfishes (Family Labridae)

    KAUST Repository

    Choat, John. H.; klanten, Oya. S.; Van Herwerden, Lynne; Robertson, D. Ross; Clements, Kendall D.

    2012-01-01

    Phylogenetic reconstruction of the evolutionary relationships among 61 of the 70 species of the parrotfish genera Chlorurus and Scarus (Family Labridae) based on mitochondrial and nuclear gene sequences retrieved 15 well-supported clades with mid Pliocene/Pleistocene diversification. Twenty-two reciprocally monophyletic sister-species pairs were identified: 64% were allopatric, and the remainder were sympatric. Age of divergence was similar for allopatric and sympatric species pairs. Sympatric sister pairs displayed greater divergence in morphology, ecology, and sexually dimorphic colour patterns than did allopatric pairs, suggesting that both genetic drift in allopatric species pairs and ecologically adaptive divergence between members of sympatric pairs have played a role in diversification. Basal species typically have small geographical ranges and are restricted to geographically and ecologically peripheral reef habitats. We found little evidence that a single dominant process has driven diversification, nor did we detect a pattern of discrete, sequential stages of diversification in relation to habitat, ecology, and reproductive biology. The evolution of Chlorurus and Scarus has been complex, involving a number of speciation processes. © 2012 The Linnean Society of London.

  12. Patterns and processes in the evolutionary history of parrotfishes (Family Labridae)

    KAUST Repository

    Choat, John. H.

    2012-09-05

    Phylogenetic reconstruction of the evolutionary relationships among 61 of the 70 species of the parrotfish genera Chlorurus and Scarus (Family Labridae) based on mitochondrial and nuclear gene sequences retrieved 15 well-supported clades with mid Pliocene/Pleistocene diversification. Twenty-two reciprocally monophyletic sister-species pairs were identified: 64% were allopatric, and the remainder were sympatric. Age of divergence was similar for allopatric and sympatric species pairs. Sympatric sister pairs displayed greater divergence in morphology, ecology, and sexually dimorphic colour patterns than did allopatric pairs, suggesting that both genetic drift in allopatric species pairs and ecologically adaptive divergence between members of sympatric pairs have played a role in diversification. Basal species typically have small geographical ranges and are restricted to geographically and ecologically peripheral reef habitats. We found little evidence that a single dominant process has driven diversification, nor did we detect a pattern of discrete, sequential stages of diversification in relation to habitat, ecology, and reproductive biology. The evolution of Chlorurus and Scarus has been complex, involving a number of speciation processes. © 2012 The Linnean Society of London.

  13. Part E: Evolutionary Computation

    DEFF Research Database (Denmark)

    2015-01-01

    of Computational Intelligence. First, comprehensive surveys of genetic algorithms, genetic programming, evolution strategies, parallel evolutionary algorithms are presented, which are readable and constructive so that a large audience might find them useful and – to some extent – ready to use. Some more general...... kinds of evolutionary algorithms, have been prudently analyzed. This analysis was followed by a thorough analysis of various issues involved in stochastic local search algorithms. An interesting survey of various technological and industrial applications in mechanical engineering and design has been...... topics like the estimation of distribution algorithms, indicator-based selection, etc., are also discussed. An important problem, from a theoretical and practical point of view, of learning classifier systems is presented in depth. Multiobjective evolutionary algorithms, which constitute one of the most...

  14. Selectionist and evolutionary approaches to brain function: a critical appraisal

    Directory of Open Access Journals (Sweden)

    Chrisantha Thomas Fernando

    2012-04-01

    Full Text Available We consider approaches to brain dynamics and function that have been claimed to be Darwinian. These include Edelman’s theory of neuronal group selection, Changeux’s theory of synaptic selection and selective stabilization of pre-representations, Seung’s Darwinian synapse, Loewenstein’s synaptic melioration, Adam’s selfish synapse and Calvin’s replicating activity patterns. Except for the last two, the proposed mechanisms are selectionist but not truly Darwinian, because no replicators with information transfer to copies and hereditary variation can be identified in them. All of them fit, however, a generalized selectionist framework conforming to the picture of Price’s covariance formulation, which deliberately was not specific even to selection in biology, and therefore does not imply an algorithmic picture of biological evolution. Bayesian models and reinforcement learning are formally in agreement with selection dynamics. A classification of search algorithms is shown to include Darwinian replicators (evolutionary units with multiplication, heredity and variability as the most powerful mechanism in a sparsely occupied search space. Examples of why parallel competitive search with information transfer among the units is efficient are given. Finally, we review our recent attempts to construct and analyze simple models of true Darwinian evolutionary units in the brain in terms of connectivity and activity copying of neuronal groups. Although none of the proposed neuronal replicators include miraculous mechanisms, their identification remains a challenge but also a great promise.

  15. Solution of Fractional Order System of Bagley-Torvik Equation Using Evolutionary Computational Intelligence

    Directory of Open Access Journals (Sweden)

    Muhammad Asif Zahoor Raja

    2011-01-01

    Full Text Available A stochastic technique has been developed for the solution of fractional order system represented by Bagley-Torvik equation. The mathematical model of the equation was developed with the help of feed-forward artificial neural networks. The training of the networks was made with evolutionary computational intelligence based on genetic algorithm hybrid with pattern search technique. Designed scheme was successfully applied to different forms of the equation. Results are compared with standard approximate analytic, stochastic numerical solvers and exact solutions.

  16. Investigation on the improvement of genetic algorithm for PWR loading pattern search and its benchmark verification

    International Nuclear Information System (INIS)

    Li Qianqian; Jiang Xiaofeng; Zhang Shaohong

    2009-01-01

    In this study, the age technique, the concepts of relativeness degree and worth function are exploited to improve the performance of genetic algorithm (GA) for PWR loading pattern search. Among them, the age technique endows the algorithm be capable of learning from previous search 'experience' and guides it to do a better search in the vicinity ora local optimal; the introduction of the relativeness degree checks the relativeness of two loading patterns before performing crossover between them, which can significantly reduce the possibility of prematurity of the algorithm; while the application of the worth function makes the algorithm be capable of generating new loading patterns based on the statistics of common features of evaluated good loading patterns. Numerical verification against a loading pattern search benchmark problem ora two-loop reactor demonstrates that the adoption of these techniques is able to significantly enhance the efficiency of the genetic algorithm while improves the quality of the final solution as well. (authors)

  17. Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and viruses.

    Directory of Open Access Journals (Sweden)

    Feng-Jie Sun

    2008-03-01

    Full Text Available Transfer RNAs (tRNAs are ancient molecules that are central to translation. Since they probably carry evolutionary signatures that were left behind when the living world diversified, we reconstructed phylogenies directly from the sequence and structure of tRNA using well-established phylogenetic methods. The trees placed tRNAs with long variable arms charging Sec, Tyr, Ser, and Leu consistently at the base of the rooted phylogenies, but failed to reveal groupings that would indicate clear evolutionary links to organismal origin or molecular functions. In order to uncover evolutionary patterns in the trees, we forced tRNAs into monophyletic groups using constraint analyses to generate timelines of organismal diversification and test competing evolutionary hypotheses. Remarkably, organismal timelines showed Archaea was the most ancestral superkingdom, followed by viruses, then superkingdoms Eukarya and Bacteria, in that order, supporting conclusions from recent phylogenomic studies of protein architecture. Strikingly, constraint analyses showed that the origin of viruses was not only ancient, but was linked to Archaea. Our findings have important implications. They support the notion that the archaeal lineage was very ancient, resulted in the first organismal divide, and predated diversification of tRNA function and specificity. Results are also consistent with the concept that viruses contributed to the development of the DNA replication machinery during the early diversification of the living world.

  18. Internet search patterns of human immunodeficiency virus and the digital divide in the Russian Federation: infoveillance study.

    Science.gov (United States)

    Zheluk, Andrey; Quinn, Casey; Hercz, Daniel; Gillespie, James A

    2013-11-12

    Human immunodeficiency virus (HIV) is a serious health problem in the Russian Federation. However, the true scale of HIV in Russia has long been the subject of considerable debate. Using digital surveillance to monitor diseases has become increasingly popular in high income countries. But Internet users may not be representative of overall populations, and the characteristics of the Internet-using population cannot be directly ascertained from search pattern data. This exploratory infoveillance study examined if Internet search patterns can be used for disease surveillance in a large middle-income country with a dispersed population. This study had two main objectives: (1) to validate Internet search patterns against national HIV prevalence data, and (2) to investigate the relationship between search patterns and the determinants of Internet access. We first assessed whether online surveillance is a valid and reliable method for monitoring HIV in the Russian Federation. Yandex and Google both provided tools to study search patterns in the Russian Federation. We evaluated the relationship between both Yandex and Google aggregated search patterns and HIV prevalence in 2011 at national and regional tiers. Second, we analyzed the determinants of Internet access to determine the extent to which they explained regional variations in searches for the Russian terms for "HIV" and "AIDS". We sought to extend understanding of the characteristics of Internet searching populations by data matching the determinants of Internet access (age, education, income, broadband access price, and urbanization ratios) and searches for the term "HIV" using principal component analysis (PCA). We found generally strong correlations between HIV prevalence and searches for the terms "HIV" and "AIDS". National correlations for Yandex searches for "HIV" were very strongly correlated with HIV prevalence (Spearman rank-order coefficient [rs]=.881, P ≤ .001) and strongly correlated for "AIDS" (rs

  19. Differential harmony search algorithm to optimize PWRs loading pattern

    Energy Technology Data Exchange (ETDEWEB)

    Poursalehi, N., E-mail: npsalehi@yahoo.com [Engineering Department, Shahid Beheshti University, G.C, P.O.Box: 1983963113, Tehran (Iran, Islamic Republic of); Zolfaghari, A.; Minuchehr, A. [Engineering Department, Shahid Beheshti University, G.C, P.O.Box: 1983963113, Tehran (Iran, Islamic Republic of)

    2013-04-15

    Highlights: ► Exploit of DHS algorithm in LP optimization reveals its flexibility, robustness and reliability. ► Upshot of our experiments with DHS shows that the search approach to optimal LP is quickly. ► On the average, the final band width of DHS fitness values is narrow relative to HS and GHS. -- Abstract: The objective of this work is to develop a core loading optimization technique using differential harmony search algorithm in the context of obtaining an optimal configuration of fuel assemblies in pressurized water reactors. To implement and evaluate the proposed technique, differential harmony search nodal expansion package for 2-D geometry, DHSNEP-2D, is developed. The package includes two modules; in the first modules differential harmony search (DHS) is implemented and nodal expansion code which solves two dimensional-multi group neutron diffusion equations using fourth degree flux expansion with one node per a fuel assembly is in the second module. For evaluation of DHS algorithm, classical harmony search (HS) and global-best harmony search (GHS) algorithms are also included in DHSNEP-2D in order to compare the outcome of techniques together. For this purpose, two PWR test cases have been investigated to demonstrate the DHS algorithm capability in obtaining near optimal loading pattern. Results show that the convergence rate of DHS and execution times are quite promising and also is reliable for the fuel management operation. Moreover, numerical results show the good performance of DHS relative to other competitive algorithms such as genetic algorithm (GA), classical harmony search (HS) and global-best harmony search (GHS) algorithms.

  20. Differential harmony search algorithm to optimize PWRs loading pattern

    International Nuclear Information System (INIS)

    Poursalehi, N.; Zolfaghari, A.; Minuchehr, A.

    2013-01-01

    Highlights: ► Exploit of DHS algorithm in LP optimization reveals its flexibility, robustness and reliability. ► Upshot of our experiments with DHS shows that the search approach to optimal LP is quickly. ► On the average, the final band width of DHS fitness values is narrow relative to HS and GHS. -- Abstract: The objective of this work is to develop a core loading optimization technique using differential harmony search algorithm in the context of obtaining an optimal configuration of fuel assemblies in pressurized water reactors. To implement and evaluate the proposed technique, differential harmony search nodal expansion package for 2-D geometry, DHSNEP-2D, is developed. The package includes two modules; in the first modules differential harmony search (DHS) is implemented and nodal expansion code which solves two dimensional-multi group neutron diffusion equations using fourth degree flux expansion with one node per a fuel assembly is in the second module. For evaluation of DHS algorithm, classical harmony search (HS) and global-best harmony search (GHS) algorithms are also included in DHSNEP-2D in order to compare the outcome of techniques together. For this purpose, two PWR test cases have been investigated to demonstrate the DHS algorithm capability in obtaining near optimal loading pattern. Results show that the convergence rate of DHS and execution times are quite promising and also is reliable for the fuel management operation. Moreover, numerical results show the good performance of DHS relative to other competitive algorithms such as genetic algorithm (GA), classical harmony search (HS) and global-best harmony search (GHS) algorithms

  1. PWR loading pattern optimization using Harmony Search algorithm

    International Nuclear Information System (INIS)

    Poursalehi, N.; Zolfaghari, A.; Minuchehr, A.

    2013-01-01

    Highlights: ► Numerical results reveal that the HS method is reliable. ► The great advantage of HS is significant gain in computational cost. ► On the average, the final band width of search fitness values is narrow. ► Our experiments show that the search approaches the optimal value fast. - Abstract: In this paper a core reloading technique using Harmony Search, HS, is presented in the context of finding an optimal configuration of fuel assemblies, FA, in pressurized water reactors. To implement and evaluate the proposed technique a Harmony Search along Nodal Expansion Code for 2-D geometry, HSNEC2D, is developed to obtain nearly optimal arrangement of fuel assemblies in PWR cores. This code consists of two sections including Harmony Search algorithm and Nodal Expansion modules using fourth degree flux expansion which solves two dimensional-multi group diffusion equations with one node per fuel assembly. Two optimization test problems are investigated to demonstrate the HS algorithm capability in converging to near optimal loading pattern in the fuel management field and other subjects. Results, convergence rate and reliability of the method are quite promising and show the HS algorithm performs very well and is comparable to other competitive algorithms such as Genetic Algorithm and Particle Swarm Intelligence. Furthermore, implementation of nodal expansion technique along HS causes considerable reduction of computational time to process and analysis optimization in the core fuel management problems

  2. Combining evolutionary game theory and network theory to analyze human cooperation patterns

    International Nuclear Information System (INIS)

    Scatà, Marialisa; Di Stefano, Alessandro; La Corte, Aurelio; Liò, Pietro; Catania, Emanuele; Guardo, Ermanno; Pagano, Salvatore

    2016-01-01

    Highlights: • We investigate the evolutionary dynamics of human cooperation in a social network. • We introduce the concepts of “Critical Mass”, centrality measure and homophily. • The emergence of cooperation is affected by the spatial choice of the “Critical Mass”. • Our findings show that homophily speeds up the convergence towards cooperation. • Centrality and “Critical Mass” spatial choice partially offset the impact of homophily. - Abstract: As natural systems continuously evolve, the human cooperation dilemma represents an increasingly more challenging question. Humans cooperate in natural and social systems, but how it happens and what are the mechanisms which rule the emergence of cooperation, represent an open and fascinating issue. In this work, we investigate the evolution of cooperation through the analysis of the evolutionary dynamics of behaviours within the social network, where nodes can choose to cooperate or defect following the classical social dilemmas represented by Prisoner’s Dilemma and Snowdrift games. To this aim, we introduce a sociological concept and statistical estimator, “Critical Mass”, to detect the minimum initial seed of cooperators able to trigger the diffusion process, and the centrality measure to select within the social network. Selecting different spatial configurations of the Critical Mass nodes, we highlight how the emergence of cooperation can be influenced by this spatial choice of the initial core in the network. Moreover, we target to shed light how the concept of homophily, a social shaping factor for which “birds of a feather flock together”, can affect the evolutionary process. Our findings show that homophily allows speeding up the diffusion process and make quicker the convergence towards human cooperation, while centrality measure and thus the Critical Mass selection, play a key role in the evolution showing how the spatial configurations can create some hidden patterns, partially

  3. PROSPECT improves cis-acting regulatory element prediction by integrating expression profile data with consensus pattern searches

    Science.gov (United States)

    Fujibuchi, Wataru; Anderson, John S. J.; Landsman, David

    2001-01-01

    Consensus pattern and matrix-based searches designed to predict cis-acting transcriptional regulatory sequences have historically been subject to large numbers of false positives. We sought to decrease false positives by incorporating expression profile data into a consensus pattern-based search method. We have systematically analyzed the expression phenotypes of over 6000 yeast genes, across 121 expression profile experiments, and correlated them with the distribution of 14 known regulatory elements over sequences upstream of the genes. Our method is based on a metric we term probabilistic element assessment (PEA), which is a ranking of potential sites based on sequence similarity in the upstream regions of genes with similar expression phenotypes. For eight of the 14 known elements that we examined, our method had a much higher selectivity than a naïve consensus pattern search. Based on our analysis, we have developed a web-based tool called PROSPECT, which allows consensus pattern-based searching of gene clusters obtained from microarray data. PMID:11574681

  4. Mitochondrial DNA haplotype distribution patterns in Pinus ponderosa (Pinaceae): range-wide evolutionary history and implications for conservation.

    Science.gov (United States)

    Potter, Kevin M; Hipkins, Valerie D; Mahalovich, Mary F; Means, Robert E

    2013-08-01

    Ponderosa pine (Pinus ponderosa Douglas ex P. Lawson & C. Lawson) exhibits complicated patterns of morphological and genetic variation across its range in western North America. This study aims to clarify P. ponderosa evolutionary history and phylogeography using a highly polymorphic mitochondrial DNA marker, with results offering insights into how geographical and climatological processes drove the modern evolutionary structure of tree species in the region. We amplified the mtDNA nad1 second intron minisatellite region for 3,100 trees representing 104 populations, and sequenced all length variants. We estimated population-level haplotypic diversity and determined diversity partitioning among varieties, races and populations. After aligning sequences of minisatellite repeat motifs, we evaluated evolutionary relationships among haplotypes. The geographical structuring of the 10 haplotypes corresponded with division between Pacific and Rocky Mountain varieties. Pacific haplotypes clustered with high bootstrap support, and appear to have descended from Rocky Mountain haplotypes. A greater proportion of diversity was partitioned between Rocky Mountain races than between Pacific races. Areas of highest haplotypic diversity were the southern Sierra Nevada mountain range in California, northwestern California, and southern Nevada. Pinus ponderosa haplotype distribution patterns suggest a complex phylogeographic history not revealed by other genetic and morphological data, or by the sparse paleoecological record. The results appear consistent with long-term divergence between the Pacific and Rocky Mountain varieties, along with more recent divergences not well-associated with race. Pleistocene refugia may have existed in areas of high haplotypic diversity, as well as the Great Basin, Southwestern United States/northern Mexico, and the High Plains.

  5. Evolutionary Pattern and Regulation Analysis to Support Why Diversity Functions Existed within PPAR Gene Family Members

    Directory of Open Access Journals (Sweden)

    Tianyu Zhou

    2015-01-01

    Full Text Available Peroxisome proliferators-activated receptor (PPAR gene family members exhibit distinct patterns of distribution in tissues and differ in functions. The purpose of this study is to investigate the evolutionary impacts on diversity functions of PPAR members and the regulatory differences on gene expression patterns. 63 homology sequences of PPAR genes from 31 species were collected and analyzed. The results showed that three isolated types of PPAR gene family may emerge from twice times of gene duplication events. The conserved domains of HOLI (ligand binding domain of hormone receptors domain and ZnF_C4 (C4 zinc finger in nuclear in hormone receptors are essential for keeping basic roles of PPAR gene family, and the variant domains of LCRs may be responsible for their divergence in functions. The positive selection sites in HOLI domain are benefit for PPARs to evolve towards diversity functions. The evolutionary variants in the promoter regions and 3′ UTR regions of PPARs result into differential transcription factors and miRNAs involved in regulating PPAR members, which may eventually affect their expressions and tissues distributions. These results indicate that gene duplication event, selection pressure on HOLI domain, and the variants on promoter and 3′ UTR are essential for PPARs evolution and diversity functions acquired.

  6. Evolutionary Pattern and Regulation Analysis to Support Why Diversity Functions Existed within PPAR Gene Family Members.

    Science.gov (United States)

    Zhou, Tianyu; Yan, Xiping; Wang, Guosong; Liu, Hehe; Gan, Xiang; Zhang, Tao; Wang, Jiwen; Li, Liang

    2015-01-01

    Peroxisome proliferators-activated receptor (PPAR) gene family members exhibit distinct patterns of distribution in tissues and differ in functions. The purpose of this study is to investigate the evolutionary impacts on diversity functions of PPAR members and the regulatory differences on gene expression patterns. 63 homology sequences of PPAR genes from 31 species were collected and analyzed. The results showed that three isolated types of PPAR gene family may emerge from twice times of gene duplication events. The conserved domains of HOLI (ligand binding domain of hormone receptors) domain and ZnF_C4 (C4 zinc finger in nuclear in hormone receptors) are essential for keeping basic roles of PPAR gene family, and the variant domains of LCRs may be responsible for their divergence in functions. The positive selection sites in HOLI domain are benefit for PPARs to evolve towards diversity functions. The evolutionary variants in the promoter regions and 3' UTR regions of PPARs result into differential transcription factors and miRNAs involved in regulating PPAR members, which may eventually affect their expressions and tissues distributions. These results indicate that gene duplication event, selection pressure on HOLI domain, and the variants on promoter and 3' UTR are essential for PPARs evolution and diversity functions acquired.

  7. HIERARCHICAL ADAPTIVE ROOD PATTERN SEARCH FOR MOTION ESTIMATION AT VIDEO SEQUENCE ANALYSIS

    Directory of Open Access Journals (Sweden)

    V. T. Nguyen

    2016-05-01

    Full Text Available Subject of Research.The paper deals with the motion estimation algorithms for the analysis of video sequences in compression standards MPEG-4 Visual and H.264. Anew algorithm has been offered based on the analysis of the advantages and disadvantages of existing algorithms. Method. Thealgorithm is called hierarchical adaptive rood pattern search (Hierarchical ARPS, HARPS. This new algorithm includes the classic adaptive rood pattern search ARPS and hierarchical search MP (Hierarchical search or Mean pyramid. All motion estimation algorithms have been implemented using MATLAB package and tested with several video sequences. Main Results. The criteria for evaluating the algorithms were: speed, peak signal to noise ratio, mean square error and mean absolute deviation. The proposed method showed a much better performance at a comparable error and deviation. The peak signal to noise ratio in different video sequences shows better and worse results than characteristics of known algorithms so it requires further investigation. Practical Relevance. Application of this algorithm in MPEG-4 and H.264 codecs instead of the standard can significantly reduce compression time. This feature enables to recommend it in telecommunication systems for multimedia data storing, transmission and processing.

  8. [Charles Darwin and the problem of evolutionary progress].

    Science.gov (United States)

    Iordanskiĭ, N N

    2010-01-01

    According to Ch. Darwin's evolutionary theory, evolutionary progress (interpreted as morpho-physiological progress or arogenesis in recent terminology) is one of logical results of natural selection. At the same time, natural selection does not hold any factors especially promoting evolutionary progress. Darwin emphasized that the pattern of evolutionary changes depends on organism nature more than on the pattern of environment changes. Arogenesis specificity is determined by organization of rigorous biological systems - integral organisms. Onward progressive development is determined by fundamental features of living organisms: metabolism and homeostasis. The concept of social Darwinism differs fundamentally from Darwin's ideas about the most important role of social instincts in progress of mankind. Competition and selection play secondary role in socio-cultural progress of human society.

  9. Evolutionary Theory's Increasing Role in Personality and Social Psychology

    Directory of Open Access Journals (Sweden)

    Gregory D. Webster

    2007-01-01

    Full Text Available Has the emergence of evolutionary psychology had an increasing impact on personality and social psychological research published over the past two decades? If so, is its growing influence substantially different from that of other emerging psychological areas? These questions were addressed in the present study by conducting a content analysis of the Journal of Personality and Social Psychology (JPSP from 1985 to 2004 using the PsycINFO online abstract database. Specifically, keyword searches for “evol*” or “Darwin*” revealed that the percentage of JPSP articles drawing on evolutionary theory was modest, but increased significantly between 1985 and 2004. To compare the growing impact of evolutionary psychology with other psychological areas, similar keywords searches were performed in JPSP for emotion and motivation, judgment and decision making, neuroscience and psychophysiology, stereotyping and prejudice, and terror management theory. The increase in evolutionary theory in JPSP over time was practically equal to the mean increase over time for the other five areas. Thus, evolutionary psychology has played an increasing role in shaping personality and social psychological research over the past 20 years, and is growing at a rate consistent with other emerging psychological areas.

  10. Algorithmic Mechanism Design of Evolutionary Computation.

    Science.gov (United States)

    Pei, Yan

    2015-01-01

    We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm.

  11. Generating high-speed dynamic running gaits in a quadruped robot using an evolutionary search.

    Science.gov (United States)

    Krasny, Darren P; Orin, David E

    2004-08-01

    Over the past several decades, there has been a considerable interest in investigating high-speed dynamic gaits for legged robots. While much research has been published, both in the biomechanics and engineering fields regarding the analysis of these gaits, no single study has adequately characterized the dynamics of high-speed running as can be achieved in a realistic, yet simple, robotic system. The goal of this paper is to find the most energy-efficient, natural, and unconstrained gallop that can be achieved using a simulated quadrupedal robot with articulated legs, asymmetric mass distribution, and compliant legs. For comparison purposes, we also implement the bound and canter. The model used here is planar, although we will show that it captures much of the predominant dynamic characteristics observed in animals. While it is not our goal to prove anything about biological locomotion, the dynamic similarities between the gaits we produce and those found in animals does indicate a similar underlying dynamic mechanism. Thus, we will show that achieving natural, efficient high-speed locomotion is possible even with a fairly simple robotic system. To generate the high-speed gaits, we use an efficient evolutionary algorithm called set-based stochastic optimization. This algorithm finds open-loop control parameters to generate periodic trajectories for the body. Several alternative methods are tested to generate periodic trajectories for the legs. The combined solutions found by the evolutionary search and the periodic-leg methods, over a range of speeds up to 10.0 m/s, reveal "biological" characteristics that are emergent properties of the underlying gaits.

  12. Improvements in seismic event locations in a deep western U.S. coal mine using tomographic velocity models and an evolutionary search algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Adam Lurka; Peter Swanson [Central Mining Institute, Katowice (Poland)

    2009-09-15

    Methods of improving seismic event locations were investigated as part of a research study aimed at reducing ground control safety hazards. Seismic event waveforms collected with a 23-station three-dimensional sensor array during longwall coal mining provide the data set used in the analyses. A spatially variable seismic velocity model is constructed using seismic event sources in a passive tomographic method. The resulting three-dimensional velocity model is used to relocate seismic event positions. An evolutionary optimization algorithm is implemented and used in both the velocity model development and in seeking improved event location solutions. Results obtained using the different velocity models are compared. The combination of the tomographic velocity model development and evolutionary search algorithm provides improvement to the event locations. 13 refs., 5 figs., 4 tabs.

  13. Autonomous change of behavior for environmental context: An intermittent search model with misunderstanding search pattern

    Science.gov (United States)

    Murakami, Hisashi; Gunji, Yukio-Pegio

    2017-07-01

    Although foraging patterns have long been predicted to optimally adapt to environmental conditions, empirical evidence has been found in recent years. This evidence suggests that the search strategy of animals is open to change so that animals can flexibly respond to their environment. In this study, we began with a simple computational model that possesses the principal features of an intermittent strategy, i.e., careful local searches separated by longer steps, as a mechanism for relocation, where an agent in the model follows a rule to switch between two phases, but it could misunderstand this rule, i.e., the agent follows an ambiguous switching rule. Thanks to this ambiguity, the agent's foraging strategy can continuously change. First, we demonstrate that our model can exhibit an optimal change of strategy from Brownian-type to Lévy-type depending on the prey density, and we investigate the distribution of time intervals for switching between the phases. Moreover, we show that the model can display higher search efficiency than a correlated random walk.

  14. Group of Hexagonal Search Patterns for Motion Estimation and Object Tracking

    International Nuclear Information System (INIS)

    Elazm, A.A.; Mahmoud, I.I; Hashima, S.M.

    2010-01-01

    This paper presents a group of fast block matching algorithms based on the hexagon pattern search .A new predicted one point hexagon (POPHEX) algorithm is proposed and compared with other well known algorithms. The comparison of these algorithms and our proposed one is performed for both motion estimation and object tracking. Test video sequences are used to demonstrate the behavior of studied algorithms. All algorithms are implemented in MATLAB environment .Experimental results showed that the proposed algorithm posses less number of search points however its computational overhead is little increased due to prediction procedure.

  15. Plans, Patterns, and Move Categories Guiding a Highly Selective Search

    Science.gov (United States)

    Trippen, Gerhard

    In this paper we present our ideas for an Arimaa-playing program (also called a bot) that uses plans and pattern matching to guide a highly selective search. We restrict move generation to moves in certain move categories to reduce the number of moves considered by the bot significantly. Arimaa is a modern board game that can be played with a standard Chess set. However, the rules of the game are not at all like those of Chess. Furthermore, Arimaa was designed to be as simple and intuitive as possible for humans, yet challenging for computers. While all established Arimaa bots use alpha-beta search with a variety of pruning techniques and other heuristics ending in an extensive positional leaf node evaluation, our new bot, Rat, starts with a positional evaluation of the current position. Based on features found in the current position - supported by pattern matching using a directed position graph - our bot Rat decides which of a given set of plans to follow. The plan then dictates what types of moves can be chosen. This is another major difference from bots that generate "all" possible moves for a particular position. Rat is only allowed to generate moves that belong to certain categories. Leaf nodes are evaluated only by a straightforward material evaluation to help avoid moves that lose material. This highly selective search looks, on average, at only 5 moves out of 5,000 to over 40,000 possible moves in a middle game position.

  16. Optimal Refueling Pattern Search for a CANDU Reactor Using a Genetic Algorithm

    International Nuclear Information System (INIS)

    Quang Binh, DO; Gyuhong, ROH; Hangbok, CHOI

    2006-01-01

    This paper presents the results from the application of genetic algorithms to a refueling optimization of a Canada deuterium uranium (CANDU) reactor. This work aims at making a mathematical model of the refueling optimization problem including the objective function and constraints and developing a method based on genetic algorithms to solve the problem. The model of the optimization problem and the proposed method comply with the key features of the refueling strategy of the CANDU reactor which adopts an on-power refueling operation. In this study, a genetic algorithm combined with an elitism strategy was used to automatically search for the refueling patterns. The objective of the optimization was to maximize the discharge burn-up of the refueling bundles, minimize the maximum channel power, or minimize the maximum change in the zone controller unit (ZCU) water levels. A combination of these objectives was also investigated. The constraints include the discharge burn-up, maximum channel power, maximum bundle power, channel power peaking factor and the ZCU water level. A refueling pattern that represents the refueling rate and channels was coded by a one-dimensional binary chromosome, which is a string of binary numbers 0 and 1. A computer program was developed in FORTRAN 90 running on an HP 9000 workstation to conduct the search for the optimal refueling patterns for a CANDU reactor at the equilibrium state. The results showed that it was possible to apply genetic algorithms to automatically search for the refueling channels of the CANDU reactor. The optimal refueling patterns were compared with the solutions obtained from the AUTOREFUEL program and the results were consistent with each other. (authors)

  17. Lévy flight and Brownian search patterns of a free-ranging predator reflect different prey field characteristics.

    Science.gov (United States)

    Sims, David W; Humphries, Nicolas E; Bradford, Russell W; Bruce, Barry D

    2012-03-01

    1. Search processes play an important role in physical, chemical and biological systems. In animal foraging, the search strategy predators should use to search optimally for prey is an enduring question. Some models demonstrate that when prey is sparsely distributed, an optimal search pattern is a specialised random walk known as a Lévy flight, whereas when prey is abundant, simple Brownian motion is sufficiently efficient. These predictions form part of what has been termed the Lévy flight foraging hypothesis (LFF) which states that as Lévy flights optimise random searches, movements approximated by optimal Lévy flights may have naturally evolved in organisms to enhance encounters with targets (e.g. prey) when knowledge of their locations is incomplete. 2. Whether free-ranging predators exhibit the movement patterns predicted in the LFF hypothesis in response to known prey types and distributions, however, has not been determined. We tested this using vertical and horizontal movement data from electronic tagging of an apex predator, the great white shark Carcharodon carcharias, across widely differing habitats reflecting different prey types. 3. Individual white sharks exhibited movement patterns that predicted well the prey types expected under the LFF hypothesis. Shark movements were best approximated by Brownian motion when hunting near abundant, predictable sources of prey (e.g. seal colonies, fish aggregations), whereas movements approximating truncated Lévy flights were present when searching for sparsely distributed or potentially difficult-to-detect prey in oceanic or shelf environments, respectively. 4. That movement patterns approximated by truncated Lévy flights and Brownian behaviour were present in the predicted prey fields indicates search strategies adopted by white sharks appear to be the most efficient ones for encountering prey in the habitats where such patterns are observed. This suggests that C. carcharias appears capable of exhibiting

  18. A Novel Self-Adaptive Harmony Search Algorithm

    Directory of Open Access Journals (Sweden)

    Kaiping Luo

    2013-01-01

    Full Text Available The harmony search algorithm is a music-inspired optimization technology and has been successfully applied to diverse scientific and engineering problems. However, like other metaheuristic algorithms, it still faces two difficulties: parameter setting and finding the optimal balance between diversity and intensity in searching. This paper proposes a novel, self-adaptive search mechanism for optimization problems with continuous variables. This new variant can automatically configure the evolutionary parameters in accordance with problem characteristics, such as the scale and the boundaries, and dynamically select evolutionary strategies in accordance with its search performance. The new variant simplifies the parameter setting and efficiently solves all types of optimization problems with continuous variables. Statistical test results show that this variant is considerably robust and outperforms the original harmony search (HS, improved harmony search (IHS, and other self-adaptive variants for large-scale optimization problems and constrained problems.

  19. Scale-free animal movement patterns: Levy walks outperform fractional Brownian motions and fractional Levy motions in random search scenarios

    International Nuclear Information System (INIS)

    Reynolds, A M

    2009-01-01

    The movement patterns of a diverse range of animals have scale-free characteristics. These characteristics provide necessary but not sufficient conditions for the presence of movement patterns that can be approximated by Levy walks. Nevertheless, it has been widely assumed that the occurrence of scale-free animal movements can indeed be attributed to the presence of Levy walks. This is, in part, because it is known that the super-diffusive properties of Levy walks can be advantageous in random search scenarios when searchers have little or no prior knowledge of target locations. However, fractional Brownian motions (fBms) and fractional Levy motions (fLms) are both scale-free and super-diffusive, and so it is possible that these motions rather than Levy walks underlie some or all occurrences of scale-free animal movement patterns. Here this possibility is examined in numerical simulations through a determination of the searching efficiencies of fBm and fLm searches. It is shown that these searches are less efficient than Levy walk searches. This finding does not rule out the possibility that some animals with scale-free movement patterns are executing fBm and fLm searches, but it does make Levy walk searches the more likely possibility.

  20. Searching for Truth: Internet Search Patterns as a Method of Investigating Online Responses to a Russian Illicit Drug Policy Debate

    OpenAIRE

    Zheluk, Andrey; Gillespie, James A; Quinn, Casey

    2012-01-01

    Background This is a methodological study investigating the online responses to a national debate over an important health and social problem in Russia. Russia is the largest Internet market in Europe, exceeding Germany in the absolute number of users. However, Russia is unusual in that the main search provider is not Google, but Yandex. Objective This study had two main objectives. First, to validate Yandex search patterns against those provided by Google, and second, to test this method's a...

  1. Applied evolutionary economics and economic geography

    OpenAIRE

    Peter Sunley

    2008-01-01

    Applied Evolutionary Economics and Economic Geography aims to further advance empirical methodologies in evolutionary economics, with a special emphasis on geography and firm location. It does so by bringing together a select group of leading scholars including economists, geographers and sociologists, all of whom share an interest in explaining the uneven distribution of economic activities in space and the historical processes that have produced these patterns.

  2. Evolutionary and Ecological Consequences of Interspecific Hybridization in Cladocerans

    NARCIS (Netherlands)

    Schwenk, K.; Spaak, P.

    1995-01-01

    The evolutionary process of interspecific hybridization in cladocerans is reviewed based on ecological and population genetic data. The evolutionary consequences of hybridization, biogeographic patterns and fitness comparisons are analyzed within the conceptual framework of theories on

  3. Can Evolutionary Principles Explain Patterns of Family Violence?

    Science.gov (United States)

    Archer, John

    2013-01-01

    The article's aim is to evaluate the application of the evolutionary principles of kin selection, reproductive value, and resource holding power to the understanding of family violence. The principles are described in relation to specific predictions and the mechanisms underlying these. Predictions are evaluated for physical violence perpetrated…

  4. Evolutionary dynamics of mammalian karyotypes

    Directory of Open Access Journals (Sweden)

    Carlo Alberto Redi

    2012-12-01

    Full Text Available This special volume of Cytogenetic and Genome Research (edited by Roscoe Stanyon, University of Florence and Alexander Graphodatsky, Siberian division of the Russian Academy of Sciences is dedicated to the fascinating long search of the forces behind the evolutionary dynamics of mammalian karyotypes, revealed after the hypotonic miracle of the 1950s....

  5. On the expected duration of a search for a fixed pattern in random data

    DEFF Research Database (Denmark)

    Nielsen, Peter Tolstrup

    1973-01-01

    An expression is obtained for the expected duration of a search to find a givenL-ary sequence in a semi-infinite stream of randomL-ary data. The search time is found to be an increasing function of the lengths of the "bifices" of the pattern, where the term bifix denotes a sequence which is both...

  6. A brief introduction to continuous evolutionary optimization

    CERN Document Server

    Kramer, Oliver

    2014-01-01

    Practical optimization problems are often hard to solve, in particular when they are black boxes and no further information about the problem is available except via function evaluations. This work introduces a collection of heuristics and algorithms for black box optimization with evolutionary algorithms in continuous solution spaces. The book gives an introduction to evolution strategies and parameter control. Heuristic extensions are presented that allow optimization in constrained, multimodal, and multi-objective solution spaces. An adaptive penalty function is introduced for constrained optimization. Meta-models reduce the number of fitness and constraint function calls in expensive optimization problems. The hybridization of evolution strategies with local search allows fast optimization in solution spaces with many local optima. A selection operator based on reference lines in objective space is introduced to optimize multiple conflictive objectives. Evolutionary search is employed for learning kernel ...

  7. An efficient and accurate solution methodology for bilevel multi-objective programming problems using a hybrid evolutionary-local-search algorithm.

    Science.gov (United States)

    Deb, Kalyanmoy; Sinha, Ankur

    2010-01-01

    Bilevel optimization problems involve two optimization tasks (upper and lower level), in which every feasible upper level solution must correspond to an optimal solution to a lower level optimization problem. These problems commonly appear in many practical problem solving tasks including optimal control, process optimization, game-playing strategy developments, transportation problems, and others. However, they are commonly converted into a single level optimization problem by using an approximate solution procedure to replace the lower level optimization task. Although there exist a number of theoretical, numerical, and evolutionary optimization studies involving single-objective bilevel programming problems, not many studies look at the context of multiple conflicting objectives in each level of a bilevel programming problem. In this paper, we address certain intricate issues related to solving multi-objective bilevel programming problems, present challenging test problems, and propose a viable and hybrid evolutionary-cum-local-search based algorithm as a solution methodology. The hybrid approach performs better than a number of existing methodologies and scales well up to 40-variable difficult test problems used in this study. The population sizing and termination criteria are made self-adaptive, so that no additional parameters need to be supplied by the user. The study indicates a clear niche of evolutionary algorithms in solving such difficult problems of practical importance compared to their usual solution by a computationally expensive nested procedure. The study opens up many issues related to multi-objective bilevel programming and hopefully this study will motivate EMO and other researchers to pay more attention to this important and difficult problem solving activity.

  8. Selective Search, Sectoral Patterns, and the Impact on Product Innovation Performance

    DEFF Research Database (Denmark)

    Köhler, Christian; Sofka, Wolfgang; Grimpe, Christoph

    2012-01-01

    The shift toward more open and interconnected innovation activities has been a major topic in recent academic and practitioner discussions. Firms must connect their in-house R&D activities with external partners, such as leading customers or universities, to increase the effectiveness of their in......The shift toward more open and interconnected innovation activities has been a major topic in recent academic and practitioner discussions. Firms must connect their in-house R&D activities with external partners, such as leading customers or universities, to increase the effectiveness...... of their innovation activities. Hence, management needs to define where to search for valuable knowledge in its environment. In this paper we argue that knowledge search has to reflect the heterogeneity of various knowledge sources with regard to the knowledge they can provide and how these sources can be activated....... We hypothesize that search strategies driven by science, suppliers and the product market will contribute differently to innovation success with new-to-market versus imitated products. Moreover, we explore the effect of these types of knowledge search within different sectoral patterns of innovation...

  9. A theoty of fast search for feul loading pattern in lWRs

    International Nuclear Information System (INIS)

    Suo Changan

    1990-01-01

    In order to fast search for fuel loading pattern without trial and error, a theory for predicting in-core reactivity distribution, according to power necessity and available assemblies, has been developed on basis of the fast computing nodal method and two group diffusion theory. In that, the fast group flux distribution can be predicted from power necessity and the approximation of fast group constants to be independent of nodes. Then, the thermal group fluxes are expressed by both known powers and predicted fast fluxes. After replacing thermal flux, the thermal diffusion equations turn into some equations that have only unknown group constants. The unknown constants are expressed approximately by making use of some expansions of infinite multiplication factors of available assemblies. In such a way, the non-linear reactivity equations are developed and then solved, where node reactivities are the only unknown physical quantities, Finally, the loading pattern is obtained by setting some of available assemblies at each node location where corresponds to a closest reactivity of between laid assembly and node. A computer code LOADMP based on the theory has been made. The theory has been tested numerically on IAEA benchmark problem, and gives an accurate prediction of reactivity distribution and loading pattern. The CPU-time for making a loading pattern search is saved very much, about one second on the CYPER-825/170 machine

  10. Are hotspots of evolutionary potential adequately protected in southern California?

    Science.gov (United States)

    Vandergast, A.G.; Bohonak, A.J.; Hathaway, S.A.; Boys, J.; Fisher, R.N.

    2008-01-01

    Reserves are often designed to protect rare habitats, or "typical" exemplars of ecoregions and geomorphic provinces. This approach focuses on current patterns of organismal and ecosystem-level biodiversity, but typically ignores the evolutionary processes that control the gain and loss of biodiversity at these and other levels (e.g., genetic, ecological). In order to include evolutionary processes in conservation planning efforts, their spatial components must first be identified and mapped. We describe a GIS-based approach for explicitly mapping patterns of genetic divergence and diversity for multiple species (a "multi-species genetic landscape"). Using this approach, we analyzed mitochondrial DNA datasets from 21 vertebrate and invertebrate species in southern California to identify areas with common phylogeographic breaks and high intrapopulation diversity. The result is an evolutionary framework for southern California within which patterns of genetic diversity can be analyzed in the context of historical processes, future evolutionary potential and current reserve design. Our multi-species genetic landscapes pinpoint six hotspots where interpopulation genetic divergence is consistently high, five evolutionary hotspots within which genetic connectivity is high, and three hotspots where intrapopulation genetic diversity is high. These 14 hotspots can be grouped into eight geographic areas, of which five largely are unprotected at this time. The multi-species genetic landscape approach may provide an avenue to readily incorporate measures of evolutionary process into GIS-based systematic conservation assessment and land-use planning.

  11. AN EVOLUTIONARY ALGORITHM FOR FAST INTENSITY BASED IMAGE MATCHING BETWEEN OPTICAL AND SAR SATELLITE IMAGERY

    Directory of Open Access Journals (Sweden)

    P. Fischer

    2018-04-01

    Full Text Available This paper presents a hybrid evolutionary algorithm for fast intensity based matching between satellite imagery from SAR and very high-resolution (VHR optical sensor systems. The precise and accurate co-registration of image time series and images of different sensors is a key task in multi-sensor image processing scenarios. The necessary preprocessing step of image matching and tie-point detection is divided into a search problem and a similarity measurement. Within this paper we evaluate the use of an evolutionary search strategy for establishing the spatial correspondence between satellite imagery of optical and radar sensors. The aim of the proposed algorithm is to decrease the computational costs during the search process by formulating the search as an optimization problem. Based upon the canonical evolutionary algorithm, the proposed algorithm is adapted for SAR/optical imagery intensity based matching. Extensions are drawn using techniques like hybridization (e.g. local search and others to lower the number of objective function calls and refine the result. The algorithm significantely decreases the computational costs whilst finding the optimal solution in a reliable way.

  12. Evolutionary engineering for industrial microbiology.

    Science.gov (United States)

    Vanee, Niti; Fisher, Adam B; Fong, Stephen S

    2012-01-01

    Superficially, evolutionary engineering is a paradoxical field that balances competing interests. In natural settings, evolution iteratively selects and enriches subpopulations that are best adapted to a particular ecological niche using random processes such as genetic mutation. In engineering desired approaches utilize rational prospective design to address targeted problems. When considering details of evolutionary and engineering processes, more commonality can be found. Engineering relies on detailed knowledge of the problem parameters and design properties in order to predict design outcomes that would be an optimized solution. When detailed knowledge of a system is lacking, engineers often employ algorithmic search strategies to identify empirical solutions. Evolution epitomizes this iterative optimization by continuously diversifying design options from a parental design, and then selecting the progeny designs that represent satisfactory solutions. In this chapter, the technique of applying the natural principles of evolution to engineer microbes for industrial applications is discussed to highlight the challenges and principles of evolutionary engineering.

  13. Enhancing Divergent Search through Extinction Events

    DEFF Research Database (Denmark)

    Lehman, Joel; Miikkulainen, Risto

    2015-01-01

    for the capacity to evolve. This hypothesis is tested through experiments in two evolutionary robotics domains. The results show that combining extinction events with divergent search increases evolvability, while combining them with convergent search offers no similar benefit. The conclusion is that extinction...

  14. Scavengers on the move: behavioural changes in foraging search patterns during the annual cycle.

    Directory of Open Access Journals (Sweden)

    Pascual López-López

    Full Text Available BACKGROUND: Optimal foraging theory predicts that animals will tend to maximize foraging success by optimizing search strategies. However, how organisms detect sparsely distributed food resources remains an open question. When targets are sparse and unpredictably distributed, a Lévy strategy should maximize foraging success. By contrast, when resources are abundant and regularly distributed, simple brownian random movement should be sufficient. Although very different groups of organisms exhibit Lévy motion, the shift from a Lévy to a brownian search strategy has been suggested to depend on internal and external factors such as sex, prey density, or environmental context. However, animal response at the individual level has received little attention. METHODOLOGY/PRINCIPAL FINDINGS: We used GPS satellite-telemetry data of Egyptian vultures Neophron percnopterus to examine movement patterns at the individual level during consecutive years, with particular interest in the variations in foraging search patterns during the different periods of the annual cycle (i.e. breeding vs. non-breeding. Our results show that vultures followed a brownian search strategy in their wintering sojourn in Africa, whereas they exhibited a more complex foraging search pattern at breeding grounds in Europe, including Lévy motion. Interestingly, our results showed that individuals shifted between search strategies within the same period of the annual cycle in successive years. CONCLUSIONS/SIGNIFICANCE: Results could be primarily explained by the different environmental conditions in which foraging activities occur. However, the high degree of behavioural flexibility exhibited during the breeding period in contrast to the non-breeding period is challenging, suggesting that not only environmental conditions explain individuals' behaviour but also individuals' cognitive abilities (e.g., memory effects could play an important role. Our results support the growing

  15. Derivation of Optimal Cropping Pattern in Part of Hirakud Command using Cuckoo Search

    Science.gov (United States)

    Rath, Ashutosh; Biswal, Sudarsan; Samantaray, Sandeep; Swain, Prakash Chandra, PROF.

    2017-08-01

    The economicgrowth of a Nation depends on agriculture which relies on the obtainable water resources, available land and crops. The contribution of water in an appropriate quantity at appropriate time plays avitalrole to increase the agricultural production. Optimal utilization of available resources can be achieved by proper planning and management of water resources projects and adoption of appropriate technology. In the present work, the command area of Sambalpur distribrutary System is taken up for investigation. Further, adoption of a fixed cropping pattern causes the reduction of yield. The present study aims at developing different crop planning strategies to increase the net benefit from the command area with minimum investment. Optimization models are developed for Kharif season using LINDO and Cuckoo Search (CS) algorithm for maximization of the net benefits. In process of development of Optimization model the factors such as cultivable land, seeds, fertilizers, man power, water cost, etc. are taken as constraints. The irrigation water needs of major crops and the total available water through canals in the command of Sambalpur Distributary are estimated. LINDO and Cuckoo Search models are formulated and used to derive the optimal cropping pattern yielding maximum net benefits. The net benefits of Rs.585.0 lakhs in Kharif Season are obtained by adopting LINGO and 596.07 lakhs from Cuckoo Search, respectively, whereas the net benefits of 447.0 lakhs is received by the farmers of the locality with the adopting present cropping pattern.

  16. Archaeogenetics in evolutionary medicine.

    Science.gov (United States)

    Bouwman, Abigail; Rühli, Frank

    2016-09-01

    Archaeogenetics is the study of exploration of ancient DNA (aDNA) of more than 70 years old. It is an important part of the wider studies of many different areas of our past, including animal, plant and pathogen evolution and domestication events. Hereby, we address specifically the impact of research in archaeogenetics in the broader field of evolutionary medicine. Studies on ancient hominid genomes help to understand even modern health patterns. Human genetic microevolution, e.g. related to abilities of post-weaning milk consumption, and specifically genetic adaptation in disease susceptibility, e.g. towards malaria and other infectious diseases, are of the upmost importance in contributions of archeogenetics on the evolutionary understanding of human health and disease. With the increase in both the understanding of modern medical genetics and the ability to deep sequence ancient genetic information, the field of archaeogenetic evolutionary medicine is blossoming.

  17. Performance comparison of some evolutionary algorithms on job shop scheduling problems

    Science.gov (United States)

    Mishra, S. K.; Rao, C. S. P.

    2016-09-01

    Job Shop Scheduling as a state space search problem belonging to NP-hard category due to its complexity and combinational explosion of states. Several naturally inspire evolutionary methods have been developed to solve Job Shop Scheduling Problems. In this paper the evolutionary methods namely Particles Swarm Optimization, Artificial Intelligence, Invasive Weed Optimization, Bacterial Foraging Optimization, Music Based Harmony Search Algorithms are applied and find tuned to model and solve Job Shop Scheduling Problems. To compare about 250 Bench Mark instances have been used to evaluate the performance of these algorithms. The capabilities of each these algorithms in solving Job Shop Scheduling Problems are outlined.

  18. Research reactor loading pattern optimization using estimation of distribution algorithms

    International Nuclear Information System (INIS)

    Jiang, S.; Ziver, K.; Carter, J. N.; Pain, C. C.; Eaton, M. D.; Goddard, A. J. H.; Franklin, S. J.; Phillips, H. J.

    2006-01-01

    A new evolutionary search based approach for solving the nuclear reactor loading pattern optimization problems is presented based on the Estimation of Distribution Algorithms. The optimization technique developed is then applied to the maximization of the effective multiplication factor (K eff ) of the Imperial College CONSORT research reactor (the last remaining civilian research reactor in the United Kingdom). A new elitism-guided searching strategy has been developed and applied to improve the local convergence together with some problem-dependent information based on the 'stand-alone K eff with fuel coupling calculations. A comparison study between the EDAs and a Genetic Algorithm with Heuristic Tie Breaking Crossover operator has shown that the new algorithm is efficient and robust. (authors)

  19. Evolutionary search for new high-k dielectric materials: methodology and applications to hafnia-based oxides.

    Science.gov (United States)

    Zeng, Qingfeng; Oganov, Artem R; Lyakhov, Andriy O; Xie, Congwei; Zhang, Xiaodong; Zhang, Jin; Zhu, Qiang; Wei, Bingqing; Grigorenko, Ilya; Zhang, Litong; Cheng, Laifei

    2014-02-01

    High-k dielectric materials are important as gate oxides in microelectronics and as potential dielectrics for capacitors. In order to enable computational discovery of novel high-k dielectric materials, we propose a fitness model (energy storage density) that includes the dielectric constant, bandgap, and intrinsic breakdown field. This model, used as a fitness function in conjunction with first-principles calculations and the global optimization evolutionary algorithm USPEX, efficiently leads to practically important results. We found a number of high-fitness structures of SiO2 and HfO2, some of which correspond to known phases and some of which are new. The results allow us to propose characteristics (genes) common to high-fitness structures--these are the coordination polyhedra and their degree of distortion. Our variable-composition searches in the HfO2-SiO2 system uncovered several high-fitness states. This hybrid algorithm opens up a new avenue for discovering novel high-k dielectrics with both fixed and variable compositions, and will speed up the process of materials discovery.

  20. Sounds unheard of evolutionary algorithms as creative tools for the contemporary composer

    DEFF Research Database (Denmark)

    Dahlstedt, Palle

    2004-01-01

    Evolutionary algorithms are studied as tools for generating novel musical material in the form of musical scores and synthesized sounds. The choice of genetic representation defines a space of potential music. This space is explored using evolutionary algorithms, in search of useful musical mater...... composed with the tools described in the thesis are presented....

  1. Evolutionary games on graphs

    Science.gov (United States)

    Szabó, György; Fáth, Gábor

    2007-07-01

    Game theory is one of the key paradigms behind many scientific disciplines from biology to behavioral sciences to economics. In its evolutionary form and especially when the interacting agents are linked in a specific social network the underlying solution concepts and methods are very similar to those applied in non-equilibrium statistical physics. This review gives a tutorial-type overview of the field for physicists. The first four sections introduce the necessary background in classical and evolutionary game theory from the basic definitions to the most important results. The fifth section surveys the topological complications implied by non-mean-field-type social network structures in general. The next three sections discuss in detail the dynamic behavior of three prominent classes of models: the Prisoner's Dilemma, the Rock-Scissors-Paper game, and Competing Associations. The major theme of the review is in what sense and how the graph structure of interactions can modify and enrich the picture of long term behavioral patterns emerging in evolutionary games.

  2. Evolutionary Patterns of Renewable Energy Technology Development in East Asia (1990–2010

    Directory of Open Access Journals (Sweden)

    Yoonhwan Oh

    2016-07-01

    Full Text Available This study investigates the evolutionary patterns of renewable energy technology in East Asian countries—Japan, Korea, and China—as an emerging technology where the catch-up strategy is actively taking place. To reflect the quality of technology development activities, we assess each country’s research and development (R&D activities using patent citation analysis. The goal of this study is to overcome the limitations of prior research that uses quantitative information, such as R&D expenditures and number of patents. This study observes the process of technological catch-up and leapfrogging in the East Asian renewable energy sector. Furthermore, we find that each nation’s technology development portfolio differs depending on the composition share of technologies. Policymakers in emerging economies can use the findings to shape R&D strategies to develop the renewable energy sector and provide an alternative method of evaluating the qualitative development of technology.

  3. A Game of Hide and Seek: Expectations of Clumpy Resources Influence Hiding and Searching Patterns.

    Directory of Open Access Journals (Sweden)

    Andreas Wilke

    Full Text Available Resources are often distributed in clumps or patches in space, unless an agent is trying to protect them from discovery and theft using a dispersed distribution. We uncover human expectations of such spatial resource patterns in collaborative and competitive settings via a sequential multi-person game in which participants hid resources for the next participant to seek. When collaborating, resources were mostly hidden in clumpy distributions, but when competing, resources were hidden in more dispersed (random or hyperdispersed patterns to increase the searching difficulty for the other player. More dispersed resource distributions came at the cost of higher overall hiding (as well as searching times, decreased payoffs, and an increased difficulty when the hider had to recall earlier hiding locations at the end of the experiment. Participants' search strategies were also affected by their underlying expectations, using a win-stay lose-shift strategy appropriate for clumpy resources when searching for collaboratively-hidden items, but moving equally far after finding or not finding an item in competitive settings, as appropriate for dispersed resources. Thus participants showed expectations for clumpy versus dispersed spatial resources that matched the distributions commonly found in collaborative versus competitive foraging settings.

  4. Search for Anti-EA(D Antibodies in Subjects with an “Isolated VCA IgG” Pattern

    Directory of Open Access Journals (Sweden)

    Massimo De Paschale

    2010-01-01

    Full Text Available The presence of an “isolated viral capsid antigen (VCA IgG” pattern in serum is not easy to interpret without the aid of further tests, such as specific immunoblotting or a virus genome search, that often give rise to organisational and economic problems. However, one alternative is to use an enzyme-linked immunosorbent assay (ELISA to detect anti-early antigen (EA antibodies, which can be found in about 85% of subjects with acute Epstein-Barr virus (EBV infections. The purpose of this work was to search for anti-EA(D antibodies in 130 samples with an isolated VCA IgG pattern at ELISA screening and classified as being indicative of past (102 cases or acute (28 cases infection on the basis of the immunoblotting results. Thirty-seven samples (28.5% were positive for anti-EA(D, of which 25 (89.3% had been classified by immunoblotting as indicating acute and 12 (11.8% past EBV infection. This difference was statistically significant (<.01. The results of our search for anti-EA(D antibodies correctly identified nearly 90% of acute (presence or past EBV infections (absence. When other tests are not available, the search for anti-EA antibodies may therefore be helpful in diagnosing patients with an isolated VCA IgG pattern at screening tests.

  5. Search for patterns by combining cosmic-ray energy and arrival directions at the Pierre Auger Observatory

    International Nuclear Information System (INIS)

    Aab, A.; Buchholz, P.; Erfani, M.; Froehlich, U.; Heimann, P.; Niechciol, M.; Ochilo, L.; Risse, M.; Tepe, A.; Yushkov, A.; Ziolkowski, M.; Abreu, P.; Andringa, S.; Assis, P.; Brogueira, P.; Cazon, L.; Conceicao, R.; Diogo, F.; Espadanal, J.; Goncalves, P.; Oliveira, M.; Pimenta, M.; Santo, C.E.; Sarmento, R.; Tome, B.; Aglietta, M.; Bertaina, M.E.; Bonino, R.; Castellina, A.; Chiavassa, A.; Gorgi, A.; Latronico, L.; Maldera, S.; Morello, C.; Navarra, G.; Ahn, E.J.; Fazzini, N.; Glass, H.; Hojvat, C.; Kasper, P.; Lebrun, P.; Mantsch, P.; Mazur, P.O.; Al Samarai, I.; Deligny, O.; Lhenry-Yvon, I.; Martraire, D.; Salamida, F.; Suomijaervi, T.; Albuquerque, I.F.M.; Gouffon, P.; Santos, E.M.; Allekotte, I.; Asorey, H.; Bertou, X.; Berisso, M.G.; Harari, D.; Mollerach, S.; Purrello, V.; Roulet, E.; Sidelnik, I.; Taborda, O.A.; Allen, J.; Awal, N.; Farrar, G.; Zaw, I.; Allison, P.; Beatty, J.J.; Gordon, J.; Griffith, N.; Stapleton, J.; Sutherland, M.S.; Almela, A.; Etchegoyen, A.; Wainberg, O.; Castillo, J.A.; D'Olivo, J.C.; Medina-Tanco, G.; Nellen, L.; Galicia, J.F.V.; Vargas Cardenas, B.; Alvarez-Muniz, J.; Ave, M.; Roca, S.T.G.; Agueera, A.L.; Parente, G.; Parra, A.; Carvalho, W.R. de; Cabo, I.R.; Elipe, G.T.; Tueros, M.; Valino, I.; Vazquez, R.A.; Zas, E.; Batista, R.A.; Schiffer, P.; Sigl, G.; Vliet, A. van; Ambrosio, M.; Aramo, C.; Buscemi, M.; Cilmo, M.; Colalillo, R.; Guarino, F.; Valore, L.; Aminaei, A.; Buitink, S.; Schulz, J.; Aar, G. van; Velzen, S. van; Wykes, S.; Anchordoqui, L.; Aranda, V.M.; Arqueros, F.; Garcia-Pinto, D.; Minaya, I.A.; Rosado, J.; Vazquez, J.R.; Aublin, J.; Billoir, P.; Blanco, M.; Caccianiga, L.; Gaior, R.; Ghia, P.L.; Letessier-Selvon, A.; Muenchmeyer, M.; Settimo, M.; Avenier, M.; Berat, C.; Le Coz, S.; Lebrun, D.; Louedec, K.; Montanet, F.; Stutz, A.; Tartare, M.; Avila, G.; Vitale, P.F.G.; Badescu, A.M.; Fratu, O.; Barber, K.B.; Bellido, J.A.; Blaess, S.; Clay, R.W.; Cooper, M.J.; Dawson, B.R.; Grubb, T.D.; Harrison, T.A.; Hill, G.C.; Malacari, M.; Nguyen, P.; Saffi, S.J.; Sorokin, J.; Bodegom, P. van; Baeuml, J.; Baus, C.; Fuchs, B.; Gonzalez, J.G.; Huber, D.; Kambeitz, O.; Katkov, I.; Link, K.; Ludwig, M.; Maurel, D.; Melissas, M.; Palmieri, N.; Werner, F.; Becker, K.H.; Homola, P.; Jandt, I.; Kaeaepae, A.; Kampert, K.H.; Krohm, N.; Kruppke-Hansen, D.; Mathys, S.; Neuser, J.; Niemietz, L.; Papenbreer, P.; Querchfeld, S.; Rautenberg, J.; Sarkar, B.; Winchen, T.; Wittkowski, D.; Biermann, P.L.; Caramete, L.; Curutiu, A.; Bleve, C.; Cataldi, G.; Cocciolo, G.; Coluccia, M.R.; De Mitri, I.; Marsella, G.; Martello, D.; Perrone, L.; Scherini, V.

    2015-01-01

    Energy-dependent patterns in the arrival directions of cosmic rays are searched for using data of the Pierre Auger Observatory. We investigate local regions around the highest-energy cosmic rays with E ≥ 6 x 10 19 eV by analyzing cosmic rays with energies above E ≥ 5 x 10 18 eVarriving within an angular separation of approximately 15 circle . We characterize the energy distributions inside these regions by two independent methods, one searching for angular dependence of energy-energy correlations and one searching for collimation of energy along the local system of principal axes of the energy distribution. No significant patterns are found with this analysis. The comparison of these measurements with astrophysical scenarios can therefore be used to obtain constraints on related model parameters such as strength of cosmic-ray deflection and density of point sources. (orig.)

  6. Analysis for Performance of Symbiosis Co-evolutionary Algorithm

    OpenAIRE

    根路銘, もえ子; 遠藤, 聡志; 山田, 孝治; 宮城, 隼夫; Nerome, Moeko; Endo, Satoshi; Yamada, Koji; Miyagi, Hayao

    2000-01-01

    In this paper, we analyze the behavior of symbiotic evolution algorithm for the N-Queens problem as benchmark problem for search methods in the field of aritificial intelligence. It is shown that this algorithm improves the ability of evolutionary search method. When the problem is solved by Genetic Algorithms (GAs), an ordinal representation is often used as one of gene conversion methods which convert from phenotype to genotype and reconvert. The representation can hinder occurrence of leth...

  7. Early Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas.

    Directory of Open Access Journals (Sweden)

    Diane I Schroeder

    2015-08-01

    Full Text Available Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs and highly methylated domains (HMDs with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane. We found that, similar to human placenta, mammalian placentas and opossum extraembryonic membrane have globally lower levels of methylation compared to somatic tissues. Higher relative gene body methylation was the conserved feature across all mammalian placentas, despite differences in PMD/HMDs and absolute methylation levels. Specifically, higher methylation over the bodies of genes involved in mitosis, vesicle-mediated transport, protein phosphorylation, and chromatin modification was observed compared with the rest of the genome. As in human placenta, higher methylation is associated with higher gene expression and is predictive of genic location across species. Analysis of DNA methylation in oocytes and preimplantation embryos shows a conserved pattern of gene body methylation similar to the placenta. Intriguingly, mouse and cow oocytes and mouse early embryos have PMD/HMDs but their placentas do not, suggesting that PMD/HMDs are a feature of early preimplantation methylation patterns that become lost during placental development in some species and following implantation of the embryo.

  8. Multilevel Thresholding Segmentation Based on Harmony Search Optimization

    Directory of Open Access Journals (Sweden)

    Diego Oliva

    2013-01-01

    Full Text Available In this paper, a multilevel thresholding (MT algorithm based on the harmony search algorithm (HSA is introduced. HSA is an evolutionary method which is inspired in musicians improvising new harmonies while playing. Different to other evolutionary algorithms, HSA exhibits interesting search capabilities still keeping a low computational overhead. The proposed algorithm encodes random samples from a feasible search space inside the image histogram as candidate solutions, whereas their quality is evaluated considering the objective functions that are employed by the Otsu’s or Kapur’s methods. Guided by these objective values, the set of candidate solutions are evolved through the HSA operators until an optimal solution is found. Experimental results demonstrate the high performance of the proposed method for the segmentation of digital images.

  9. The max–min ant system and tabu search for pressurized water reactor loading pattern design

    International Nuclear Information System (INIS)

    Lin, Chaung; Chen, Ying-Hsiu

    2014-01-01

    Highlights: • An automatic loading pattern design tool for a pressurized water reactor is developed. • The design method consists of max–min ant system and tabu search. • The heuristic rules are developed to generate the candidates for tabu search. • The initial solution of tabu search is provided by max–min ant system. • The new algorithm shows very satisfactory results compared to the old one. - Abstract: An automatic loading pattern (LP) design tool for a pressurized water reactor is developed. The design procedure consists of two steps: first, a LP is generated using max–min ant system (MMAS) and then tabu search (TS) is adopted to search the satisfactory LP. The MMAS is previously developed and the TS process is newly-developed. The heuristic rules are implemented to generate the candidate LP in TS process. The heuristic rules are comprised of two kinds of action, i.e., a single swap in the location of two fuel assemblies and rotation of fuel assembly. Since developed TS process is a local search algorithm, it is efficient for the minor change of LP. It means that a proper initial LP should be provided by the first step, i.e., by MMAS. The design requirements such as hot channel factor, the hot zero power moderator temperature coefficient, and cycle length are formulated in the objective function. The results show that the developed tool can obtain the satisfactory LP and dramatically reduce the computation time compared with previous tool using ant system alone

  10. Search for patterns by combining cosmic-ray energy and arrival directions at the Pierre Auger Observatory

    Energy Technology Data Exchange (ETDEWEB)

    Aab, A.; Buchholz, P.; Erfani, M.; Froehlich, U.; Heimann, P.; Niechciol, M.; Ochilo, L.; Risse, M.; Tepe, A.; Yushkov, A.; Ziolkowski, M. [Universitaet Siegen, Siegen (Germany); Abreu, P.; Andringa, S.; Assis, P.; Brogueira, P.; Cazon, L.; Conceicao, R.; Diogo, F.; Espadanal, J.; Goncalves, P.; Oliveira, M.; Pimenta, M.; Santo, C.E.; Sarmento, R.; Tome, B. [Universidade de Lisboa - UL, Laboratorio de Instrumentacao e Fisica Experimental de Particulas - LIP and Instituto Superior Tecnico - IST, Lisbon (Portugal); Aglietta, M.; Bertaina, M.E.; Bonino, R.; Castellina, A.; Chiavassa, A.; Gorgi, A.; Latronico, L.; Maldera, S.; Morello, C.; Navarra, G. [Universita di Torino, Osservatorio Astrofisico di Torino (INAF), Torino (Italy); INFN, Torino (Italy); Ahn, E.J.; Fazzini, N.; Glass, H.; Hojvat, C.; Kasper, P.; Lebrun, P.; Mantsch, P.; Mazur, P.O. [Fermilab, Batavia, IL (United States); Al Samarai, I.; Deligny, O.; Lhenry-Yvon, I.; Martraire, D.; Salamida, F.; Suomijaervi, T. [Universite Paris 11, CNRS-IN2P3, Institut de Physique Nucleaire d' Orsay (IPNO), Orsay (France); Albuquerque, I.F.M.; Gouffon, P.; Santos, E.M. [Universidade de Sao Paulo, Instituto de Fisica, Sao Paulo, SP (Brazil); Allekotte, I.; Asorey, H.; Bertou, X.; Berisso, M.G.; Harari, D.; Mollerach, S.; Purrello, V.; Roulet, E.; Sidelnik, I.; Taborda, O.A. [Centro Atomico Bariloche and Instituto Balseiro (CNEA-UNCuyo-CONICET), San Carlos de Bariloche (Argentina); Allen, J.; Awal, N.; Farrar, G.; Zaw, I. [New York University, New York, NY (United States); Allison, P.; Beatty, J.J.; Gordon, J.; Griffith, N.; Stapleton, J.; Sutherland, M.S. [Ohio State University, Columbus, OH (United States); Almela, A.; Etchegoyen, A.; Wainberg, O. [Instituto de Tecnologias en Deteccion y Astroparticulas (CNEA, CONICET, UNSAM), Buenos Aires (Argentina); Universidad Tecnologica Nacional - Facultad Regional Buenos Aires, Buenos Aires (Argentina); Castillo, J.A.; D' Olivo, J.C.; Medina-Tanco, G.; Nellen, L.; Galicia, J.F.V.; Vargas Cardenas, B. [Universidad Nacional Autonoma de Mexico, Mexico, D.F. (Mexico); Alvarez-Muniz, J.; Ave, M.; Roca, S.T.G.; Agueera, A.L.; Parente, G.; Parra, A.; Carvalho, W.R. de; Cabo, I.R.; Elipe, G.T.; Tueros, M.; Valino, I.; Vazquez, R.A.; Zas, E. [Universidad de Santiago de Compostela, Santiago de Compostela (Spain); Batista, R.A.; Schiffer, P.; Sigl, G.; Vliet, A. van [Universitaet Hamburg, Hamburg (Germany); Ambrosio, M.; Aramo, C.; Buscemi, M.; Cilmo, M.; Colalillo, R.; Guarino, F.; Valore, L. [Universita di Napoli ' ' Federico II' ' , Napoli (Italy); INFN, Napoli (Italy); Aminaei, A.; Buitink, S.; Schulz, J.; Aar, G. van; Velzen, S. van; Wykes, S. [IMAPP, Radboud University Nijmegen, Nijmegen (Netherlands); Anchordoqui, L. [City University of New York, Department of Physics and Astronomy, New York (United States); Aranda, V.M.; Arqueros, F.; Garcia-Pinto, D.; Minaya, I.A.; Rosado, J.; Vazquez, J.R. [Universidad Complutense de Madrid, Madrid (Spain); Aublin, J.; Billoir, P.; Blanco, M.; Caccianiga, L.; Gaior, R.; Ghia, P.L.; Letessier-Selvon, A.; Muenchmeyer, M.; Settimo, M. [Universites Paris 6 et Paris 7, CNRS-IN2P3, Laboratoire de Physique Nucleaire et de Hautes Energies (LPNHE), Paris (France); Avenier, M.; Berat, C.; Le Coz, S.; Lebrun, D.; Louedec, K.; Montanet, F.; Stutz, A.; Tartare, M. [Universite Grenoble-Alpes, CNRS/IN2P3, Laboratoire de Physique Subatomique et de Cosmologie (LPSC), Grenoble (France); Avila, G.; Vitale, P.F.G. [Observatorio Pierre Auger and Comision Nacional de Energia Atomica, Malarguee (Argentina); Badescu, A.M.; Fratu, O. [University Politehnica of Bucharest, Bucharest (Romania); Barber, K.B.; Bellido, J.A.; Blaess, S.; Clay, R.W.; Cooper, M.J.; Dawson, B.R.; Grubb, T.D.; Harrison, T.A.; Hill, G.C.; Malacari, M.; Nguyen, P.; Saffi, S.J.; Sorokin, J.; Bodegom, P. van [University of Adelaide, Adelaide, SA (Australia); Baeuml, J.; Baus, C.; Fuchs, B.; Gonzalez, J.G.; Huber, D.; Kambeitz, O.; Katkov, I.; Link, K.; Ludwig, M.; Maurel, D.; Melissas, M.; Palmieri, N.; Werner, F. [Karlsruhe Institute of Technology - Campus South - Institut fuer Experimentelle, Kernphysik (IEKP), Karlsruhe (Germany); Becker, K.H.; Homola, P.; Jandt, I.; Kaeaepae, A.; Kampert, K.H.; Krohm, N.; Kruppke-Hansen, D.; Mathys, S.; Neuser, J.; Niemietz, L.; Papenbreer, P.; Querchfeld, S.; Rautenberg, J.; Sarkar, B.; Winchen, T.; Wittkowski, D. [Bergische Universitaet Wuppertal, Wuppertal (Germany); Biermann, P.L.; Caramete, L.; Curutiu, A. [Max-Planck-Institut fuer Radioastronomie, Bonn (Germany); Bleve, C.; Cataldi, G.; Cocciolo, G.; Coluccia, M.R.; De Mitri, I.; Marsella, G.; Martello, D.; Perrone, L.; Scherini, V. [Dipartimento di Matematica e Fisica ' ' E. De Giorgi' ' , Universita del Salento, Lecce (Italy); INFN, Lecce (Italy); and others

    2015-06-15

    Energy-dependent patterns in the arrival directions of cosmic rays are searched for using data of the Pierre Auger Observatory. We investigate local regions around the highest-energy cosmic rays with E ≥ 6 x 10{sup 19} eV by analyzing cosmic rays with energies above E ≥ 5 x 10{sup 18} eVarriving within an angular separation of approximately 15 {sup circle}. We characterize the energy distributions inside these regions by two independent methods, one searching for angular dependence of energy-energy correlations and one searching for collimation of energy along the local system of principal axes of the energy distribution. No significant patterns are found with this analysis. The comparison of these measurements with astrophysical scenarios can therefore be used to obtain constraints on related model parameters such as strength of cosmic-ray deflection and density of point sources. (orig.)

  11. Evolutionary Pattern of N-Glycosylation Sequon Numbers  in Eukaryotic ABC Protein Superfamilies

    Directory of Open Access Journals (Sweden)

    R. Shyama Prasad Rao

    2010-02-01

    Full Text Available Many proteins contain a large number of NXS/T sequences (where X is any amino acid except proline which are the potential sites of asparagine (N linked glycosylation. However, the patterns of occurrence of these N-glycosylation sequons in related proteins or groups of proteins and their underlying causes have largely been unexplored. We computed the actual and probabilistic occurrence of NXS/T sequons in ABC protein superfamilies from eight diverse eukaryotic organisms. The ABC proteins contained significantly higher NXS/T sequon numbers compared to respective genome-wide average, but the sequon density was significantly lower owing to the increase in protein size and decrease in sequon specific amino acids. However, mammalian ABC proteins have significantly higher sequon density, and both serine and threonine containing sequons (NXS and NXT have been positively selected—against the recent findings of only threonine specific Darwinian selection of sequons in proteins. The occurrence of sequons was positively correlated with the frequency of sequon specific amino acids and negatively correlated with proline and the NPS/T sequences. Further, the NPS/T sequences were significantly higher than expected in plant ABC proteins which have the lowest number of NXS/T sequons. Accord- ingly, compared to overall proteins, N-glycosylation sequons in ABC protein superfamilies have a distinct pattern of occurrence, and the results are discussed in an evolutionary perspective.

  12. Research reactor loading pattern optimization using estimation of distribution algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, S. [Dept. of Earth Science and Engineering, Applied Modeling and Computation Group AMCG, Imperial College, London, SW7 2AZ (United Kingdom); Ziver, K. [Dept. of Earth Science and Engineering, Applied Modeling and Computation Group AMCG, Imperial College, London, SW7 2AZ (United Kingdom); AMCG Group, RM Consultants, Abingdon (United Kingdom); Carter, J. N.; Pain, C. C.; Eaton, M. D.; Goddard, A. J. H. [Dept. of Earth Science and Engineering, Applied Modeling and Computation Group AMCG, Imperial College, London, SW7 2AZ (United Kingdom); Franklin, S. J.; Phillips, H. J. [Imperial College, Reactor Centre, Silwood Park, Buckhurst Road, Ascot, Berkshire, SL5 7TE (United Kingdom)

    2006-07-01

    A new evolutionary search based approach for solving the nuclear reactor loading pattern optimization problems is presented based on the Estimation of Distribution Algorithms. The optimization technique developed is then applied to the maximization of the effective multiplication factor (K{sub eff}) of the Imperial College CONSORT research reactor (the last remaining civilian research reactor in the United Kingdom). A new elitism-guided searching strategy has been developed and applied to improve the local convergence together with some problem-dependent information based on the 'stand-alone K{sub eff} with fuel coupling calculations. A comparison study between the EDAs and a Genetic Algorithm with Heuristic Tie Breaking Crossover operator has shown that the new algorithm is efficient and robust. (authors)

  13. Corrigendum: Information Search in Decisions From Experience: Do Our Patterns of Sampling Foreshadow Our Decisions?

    Science.gov (United States)

    2017-09-01

    Original article: Hills, T. T., & Hertwig, R. (2010). Information search in decisions from experience: Do our patterns of sampling foreshadow our decisions? Psychological Science, 21, 1787-1792. doi:10.1177/0956797610387443.

  14. Sex Differences in Social Behavior: Are the Social Role and Evolutionary Explanations Compatible?

    Science.gov (United States)

    Archer, John

    1996-01-01

    Examines competing claims of two explanations of sex differences in social behavior, social role theory, and evolutionary psychology. Findings associated with social role theory are weighed against evolutionary explanations. It is suggested that evolutionary theory better accounts for the overall pattern of sex differences and for their origins.…

  15. The role of pattern recognition in creative problem solving: a case study in search of new mathematics for biology.

    Science.gov (United States)

    Hong, Felix T

    2013-09-01

    is in line with Campbell's evolutionary epistemology. Instead of treating science as immutable Natural Laws, which already existed and which were just waiting to be discovered, scientific theories are regarded as humans' mental constructs, which must be invented to reconcile with observed natural phenomena. In this way, the pursuit of science is shifted from diligent and systematic (or random) searching for existing Natural Laws to firing up humans' imagination to comprehend Nature's behavioral pattern. The insights gained in understanding human creativity indicated that new mathematics that is capable of handling effectively parallel processing and human subjectivity is sorely needed. The past classification of formalizability vs. non-formalizability was made in reference to contemporary mathematics. Rosen's conclusion did not preclude future inventions of new biology-friendly mathematics. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Testing evolutionary convergence on Europa

    Energy Technology Data Exchange (ETDEWEB)

    Chela-Flores, Julian [Instituto de Estudios Avanzados, Caracas (Venezuela); [Abdus Salam International Centre for Theoretical Physics, Trieste (Italy)

    2002-11-01

    A major objective in solar system exploration is the insertion of appropriate biology-oriented experiments in future missions. We discuss various reasons for suggesting that this type of research be considered a high priority for feasibility studies and, subsequently, for technological development of appropriate melters and submersibles. Based on numerous examples, we argue in favour of the assumption that Darwin's theory is valid for the evolution of life anywhere in the universe. We have suggested how to obtain preliminary insights into the question of the distribution of life in the universe. Universal evolution of intelligent behaviour is at the end of an evolutionary pathway, in which evolution of ion channels in the membrane of microorganisms occurs in its early stages. Further, we have argued that a preliminary test of this conjecture is feasible with experiments on the Europan surface or ocean, involving evolutionary biosignatures (ion channels). This aspect of the exploration for life in the solar system should be viewed as a complement to the astronomical approach for the search of evidence of the later stages of the evolutionary pathways towards intelligent behaviour. (author)

  17. Phylogeny and evolutionary patterns in the Dwarf crayfish subfamily (Decapoda: Cambarellinae.

    Directory of Open Access Journals (Sweden)

    Carlos Pedraza-Lara

    Full Text Available The Dwarf crayfish or Cambarellinae, is a morphologically singular subfamily of decapod crustaceans that contains only one genus, Cambarellus. Its intriguing distribution, along the river basins of the Gulf Coast of United States (Gulf Group and into Central México (Mexican Group, has until now lacked of satisfactory explanation. This study provides a comprehensive sampling of most of the extant species of Cambarellus and sheds light on its evolutionary history, systematics and biogeography. We tested the impact of Gulf Group versus Mexican Group geography on rates of cladogenesis using a maximum likelihood framework, testing different models of birth/extinction of lineages. We propose a comprehensive phylogenetic hypothesis for the subfamily based on mitochondrial and nuclear loci (3,833 bp using Bayesian and Maximum Likelihood methods. The phylogenetic structure found two phylogenetic groups associated to the two main geographic components (Gulf Group and Mexican Group and is partially consistent with the historical structure of river basins. The previous hypothesis, which divided the genus into three subgenera based on genitalia morphology was only partially supported (P = 0.047, resulting in a paraphyletic subgenus Pandicambarus. We found at least two cases in which phylogenetic structure failed to recover monophyly of recognized species while detecting several cases of cryptic diversity, corresponding to lineages not assigned to any described species. Cladogenetic patterns in the entire subfamily are better explained by an allopatric model of speciation. Diversification analyses showed similar cladogenesis patterns between both groups and did not significantly differ from the constant rate models. While cladogenesis in the Gulf Group is coincident in time with changes in the sea levels, in the Mexican Group, cladogenesis is congruent with the formation of the Trans-Mexican Volcanic Belt. Our results show how similar allopatric

  18. Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses

    Science.gov (United States)

    Bidon, Tobias; Schreck, Nancy; Hailer, Frank; Nilsson, Maria A.; Janke, Axel

    2015-01-01

    The male-inherited Y chromosome is the major haploid fraction of the mammalian genome, rendering Y-linked sequences an indispensable resource for evolutionary research. However, despite recent large-scale genome sequencing approaches, only a handful of Y chromosome sequences have been characterized to date, mainly in model organisms. Using polar bear (Ursus maritimus) genomes, we compare two different in silico approaches to identify Y-linked sequences: 1) Similarity to known Y-linked genes and 2) difference in the average read depth of autosomal versus sex chromosomal scaffolds. Specifically, we mapped available genomic sequencing short reads from a male and a female polar bear against the reference genome and identify 112 Y-chromosomal scaffolds with a combined length of 1.9 Mb. We verified the in silico findings for the longer polar bear scaffolds by male-specific in vitro amplification, demonstrating the reliability of the average read depth approach. The obtained Y chromosome sequences contain protein-coding sequences, single nucleotide polymorphisms, microsatellites, and transposable elements that are useful for evolutionary studies. A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes. Moreover, we find evidence of gene conversion among ZFX and ZFY sequences in the giant panda lineage and in the ancestor of ursine and tremarctine bears. Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears. PMID:26019166

  19. How Do Severe Constraints Affect the Search Ability of Multiobjective Evolutionary Algorithms in Water Resources?

    Science.gov (United States)

    Clarkin, T. J.; Kasprzyk, J. R.; Raseman, W. J.; Herman, J. D.

    2015-12-01

    This study contributes a diagnostic assessment of multiobjective evolutionary algorithm (MOEA) search on a set of water resources problem formulations with different configurations of constraints. Unlike constraints in classical optimization modeling, constraints within MOEA simulation-optimization represent limits on acceptable performance that delineate whether solutions within the search problem are feasible. Constraints are relevant because of the emergent pressures on water resources systems: increasing public awareness of their sustainability, coupled with regulatory pressures on water management agencies. In this study, we test several state-of-the-art MOEAs that utilize restricted tournament selection for constraint handling on varying configurations of water resources planning problems. For example, a problem that has no constraints on performance levels will be compared with a problem with several severe constraints, and a problem with constraints that have less severe values on the constraint thresholds. One such problem, Lower Rio Grande Valley (LRGV) portfolio planning, has been solved with a suite of constraints that ensure high reliability, low cost variability, and acceptable performance in a single year severe drought. But to date, it is unclear whether or not the constraints are negatively affecting MOEAs' ability to solve the problem effectively. Two categories of results are explored. The first category uses control maps of algorithm performance to determine if the algorithm's performance is sensitive to user-defined parameters. The second category uses run-time performance metrics to determine the time required for the algorithm to reach sufficient levels of convergence and diversity on the solution sets. Our work exploring the effect of constraints will better enable practitioners to define MOEA problem formulations for real-world systems, especially when stakeholders are concerned with achieving fixed levels of performance according to one or

  20. Physical Mapping Using Simulated Annealing and Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Vesterstrøm, Jacob Svaneborg

    2003-01-01

    optimization method when searching for an ordering of the fragments in PM. In this paper, we applied an evolutionary algorithm to the problem, and compared its performance to that of SA and local search on simulated PM data, in order to determine the important factors in finding a good ordering of the segments....... The analysis highlights the importance of a good PM model, a well-correlated fitness function, and high quality hybridization data. We suggest that future work in PM should focus on design of more reliable fitness functions and on developing error-screening algorithms....

  1. Evolutionary speed limited by water in arid Australia.

    Science.gov (United States)

    Goldie, Xavier; Gillman, Len; Crisp, Mike; Wright, Shane

    2010-09-07

    The covariation of biodiversity with climate is a fundamental pattern in nature. However, despite the ubiquity of this relationship, a consensus on the ultimate cause remains elusive. The evolutionary speed hypothesis posits direct mechanistic links between ambient temperature, the tempo of micro-evolution and, ultimately, species richness. Previous research has demonstrated faster rates of molecular evolution in warmer climates for a broad range of poikilothermic and homeothermic organisms, in both terrestrial and aquatic environments. In terrestrial systems, species richness increases with both temperature and water availability and the interaction of those terms: productivity. However, the influence of water availability as an independent variable on micro-evolutionary processes has not been examined previously. Here, using methodology that limits the potentially confounding role of cladogenetic and demographic processes, we report, to our knowledge, the first evidence that woody plants living in the arid Australian Outback are evolving more slowly than related species growing at similar latitudes in moist habitats on the mesic continental margins. These results support a modified evolutionary speed explanation for the relationship between the water-energy balance and plant diversity patterns.

  2. Evolutionary Aesthetics and Print Advertising

    Directory of Open Access Journals (Sweden)

    Kamil Luczaj

    2015-06-01

    Full Text Available The article analyzes the extent to which predictions based on the theory of evolutionary aesthetics are utilized by the advertising industry. The purpose of a comprehensive content analysis of print advertising is to determine whether the items indicated by evolutionists such as animals, flowers, certain types of landscapes, beautiful humans, and some colors are part of real advertising strategies. This article has shown that many evolutionary hypotheses (although not all of them are supported by empirical data. Along with these hypotheses, some inferences from Bourdieu’s cultural capital theory were tested. It turned out that advertising uses both biological schemata and cultural patterns to make an image more likable.

  3. Evolutionary cell biology: two origins, one objective.

    Science.gov (United States)

    Lynch, Michael; Field, Mark C; Goodson, Holly V; Malik, Harmit S; Pereira-Leal, José B; Roos, David S; Turkewitz, Aaron P; Sazer, Shelley

    2014-12-02

    All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology.

  4. Evolutionary Models for Simple Biosystems

    Science.gov (United States)

    Bagnoli, Franco

    The concept of evolutionary development of structures constituted a real revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of such systems has shown that indeed, systems under a flux of energy or matter can self-organize into complex patterns, think for instance to Rayleigh-Bernard convection, Liesegang rings, patterns formed by granular systems under shear. Following this line, one could characterize life as a state of matter, characterized by the slow, continuous process that we call evolution. In this paper we try to identify the organizational level of life, that spans several orders of magnitude from the elementary constituents to whole ecosystems. Although similar structures can be found in other contexts like ideas (memes) in neural systems and self-replicating elements (computer viruses, worms, etc.) in computer systems, we shall concentrate on biological evolutionary structure, and try to put into evidence the role and the emergence of network structure in such systems.

  5. Evolutionary medicine: update on the relevance to family practice.

    Science.gov (United States)

    Naugler, Christopher T

    2008-09-01

    To review the relevance of evolutionary medicine to family practice and family physician training. Articles were located through a MEDLINE search, using the key words evolution, Darwin, and adaptation. Most references presented level III evidence (expert opinion), while a minority provided level II evidence (epidemiologic studies). Evolutionary medicine deals with the interplay of biology and the environment in the understanding of human disease. Yet medical schools have virtually ignored the need for family physicians to have more than a cursory knowledge of this topic. A review of the main trends in this field most relevant to family practice revealed that a basic knowledge of evolutionary medicine might help in explaining the causation of diseases to patients. Evolutionary medicine has also proven key to explaining the reasons for the development of antibiotic resistance and has the potential to explain cancer pathogenesis. As an organizing principle, this field also has potential in the teaching of family medicine. Evolutionary medicine should be studied further and incorporated into medical training and practice. Its practical utility will be proven through the generation of testable hypotheses and their application in relation to disease causation and possible prevention.

  6. Evolutionary convergence and biologically embodied cognition

    NARCIS (Netherlands)

    Keijzer, Franciscus

    2017-01-01

    The study of evolutionary patterns of cognitive convergence would be greatly helped by a clear demarcation of cognition. Cognition is often used as an equivalent of mind, making it difficult to pin down empirically or to apply it confidently beyond the human condition. Recent developments in

  7. Searching for patterns in caldera unrest

    Science.gov (United States)

    Sandri, Laura; Acocella, Valerio; Newhall, Chris

    2017-07-01

    The ultimate goal of volcanology is forecasting eruptions. This task is particularly challenging at calderas, where unrest is frequent, affects wider areas and its evidence is often masked by the activity of hydrothermal systems. A recent study has compiled a database on caldera unrest, derived from seismicity, geodetic, gravity, and geochemical monitoring data at calderas worldwide, from 1988 to 2014. Here we exploit this database, searching for the most recurring features of unrest and, in turn, its possible dynamics. In particular, we focus on (a) the duration of unrest at calderas; (b) recurring patterns in unrest; (c) unrest episodes culminating in eruptions, including time-predictability or size-predictability and a multivariate regression analysis. Our analysis indicates that preeruptive unrest is shorter than noneruptive unrest, particularly with open or semiplugged calderas, calderas with mafic or mixed composition of past eruptive products, or unrest driven by mafic magma; conversely, lack of data on preeruptive unrest driven by felsic magma and/or at felsic or plugged calderas prevents an analysis of these specific subsets. In addition, 72% of preeruptive unrest lasts reliable to characterize preeruptive unrest. Our analysis suggests that magma may withstand only a limited period of "eruptability," before becoming stored in the upper crust.

  8. The ecology of parasites of freshwater fishes: the search for patterns.

    Science.gov (United States)

    Kennedy, C R

    2009-10-01

    Developments in the study of the ecology of helminth parasites of freshwater fishes over the last half century are reviewed. Most research has of necessity been field based and has involved the search for patterns in population and community dynamics that are repeatable in space and time. Mathematical models predict that under certain conditions host and parasite populations can attain equilibrial levels through operation of regulatory factors. Such factors have been identified in several host-parasite systems and some parasite populations have been shown to persist over long time-periods. However, there is no convincing evidence that fish parasite populations are stable and regulated since in all cases alternative explanations are equally acceptable and it appears that they are non-equilibrial systems. It has proved particularly difficult to detect replicable patterns in parasite communities. Inter-specific competition, evidenced by functional and numerical responses, has been detected in several communities but its occurrence is erratic and its significance unclear. Some studies have failed to find any nested patterns in parasite community structure and richness, whereas others have identified such patterns although they are seldom constant over space and time. Departures from randomness appear to be the exception and then only temporary. It appears that parasite communities are non-equilibrial, stochastic assemblages rather than structured and organized.

  9. Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses.

    Science.gov (United States)

    Bidon, Tobias; Schreck, Nancy; Hailer, Frank; Nilsson, Maria A; Janke, Axel

    2015-05-27

    The male-inherited Y chromosome is the major haploid fraction of the mammalian genome, rendering Y-linked sequences an indispensable resource for evolutionary research. However, despite recent large-scale genome sequencing approaches, only a handful of Y chromosome sequences have been characterized to date, mainly in model organisms. Using polar bear (Ursus maritimus) genomes, we compare two different in silico approaches to identify Y-linked sequences: 1) Similarity to known Y-linked genes and 2) difference in the average read depth of autosomal versus sex chromosomal scaffolds. Specifically, we mapped available genomic sequencing short reads from a male and a female polar bear against the reference genome and identify 112 Y-chromosomal scaffolds with a combined length of 1.9 Mb. We verified the in silico findings for the longer polar bear scaffolds by male-specific in vitro amplification, demonstrating the reliability of the average read depth approach. The obtained Y chromosome sequences contain protein-coding sequences, single nucleotide polymorphisms, microsatellites, and transposable elements that are useful for evolutionary studies. A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes. Moreover, we find evidence of gene conversion among ZFX and ZFY sequences in the giant panda lineage and in the ancestor of ursine and tremarctine bears. Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  10. Evolutionary ecology of virus emergence.

    Science.gov (United States)

    Dennehy, John J

    2017-02-01

    The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between-host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead-end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment. © 2016 New York Academy of Sciences.

  11. Evolutionary genomics and HIV restriction factors.

    Science.gov (United States)

    Pyndiah, Nitisha; Telenti, Amalio; Rausell, Antonio

    2015-03-01

    To provide updated insights into innate antiviral immunity and highlight prototypical evolutionary features of well characterized HIV restriction factors. Recently, a new HIV restriction factor, Myxovirus resistance 2, has been discovered and the region/residue responsible for its activity identified using an evolutionary approach. Furthermore, IFI16, an innate immunity protein known to sense several viruses, has been shown to contribute to the defense to HIV-1 by causing cell death upon sensing HIV-1 DNA. Restriction factors against HIV show characteristic signatures of positive selection. Different patterns of accelerated sequence evolution can distinguish antiviral strategies--offense or defence--as well as the level of specificity of the antiviral properties. Sequence analysis of primate orthologs of restriction factors serves to localize functional domains and sites responsible for antiviral action. We use recent discoveries to illustrate how evolutionary genomic analyses help identify new antiviral genes and their mechanisms of action.

  12. Advances of evolutionary computation methods and operators

    CERN Document Server

    Cuevas, Erik; Oliva Navarro, Diego Alberto

    2016-01-01

    The goal of this book is to present advances that discuss alternative Evolutionary Computation (EC) developments and non-conventional operators which have proved to be effective in the solution of several complex problems. The book has been structured so that each chapter can be read independently from the others. The book contains nine chapters with the following themes: 1) Introduction, 2) the Social Spider Optimization (SSO), 3) the States of Matter Search (SMS), 4) the collective animal behavior (CAB) algorithm, 5) the Allostatic Optimization (AO) method, 6) the Locust Search (LS) algorithm, 7) the Adaptive Population with Reduced Evaluations (APRE) method, 8) the multimodal CAB, 9) the constrained SSO method.

  13. Patterns of evolutionary conservation of essential genes correlate with their compensability.

    Directory of Open Access Journals (Sweden)

    Tobias Bergmiller

    2012-06-01

    Full Text Available Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes.

  14. Multiscale structure in eco-evolutionary dynamics

    Science.gov (United States)

    Stacey, Blake C.

    In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of interdependency lead to structure at multiple scales of organization. Evolution excels at producing such complex structures. In turn, the existence of these complex interrelationships within a biological system affects the evolutionary dynamics of that system. I present a mathematical formalism for multiscale structure, grounded in information theory, which makes these intuitions quantitative, and I show how dynamics defined in terms of population genetics or evolutionary game theory can lead to multiscale organization. For complex systems, "more is different," and I address this from several perspectives. Spatial host--consumer models demonstrate the importance of the structures which can arise due to dynamical pattern formation. Evolutionary game theory reveals the novel effects which can result from multiplayer games, nonlinear payoffs and ecological stochasticity. Replicator dynamics in an environment with mesoscale structure relates to generalized conditionalization rules in probability theory. The idea of natural selection "acting at multiple levels" has been mathematized in a variety of ways, not all of which are equivalent. We will face down the confusion, using the experience developed over the course of this thesis to clarify the situation.

  15. The concept of ageing in evolutionary algorithms: Discussion and inspirations for human ageing.

    Science.gov (United States)

    Dimopoulos, Christos; Papageorgis, Panagiotis; Boustras, George; Efstathiades, Christodoulos

    2017-04-01

    This paper discusses the concept of ageing as this applies to the operation of Evolutionary Algorithms, and examines its relationship to the concept of ageing as this is understood for human beings. Evolutionary Algorithms constitute a family of search algorithms which base their operation on an analogy from the evolution of species in nature. The paper initially provides the necessary knowledge on the operation of Evolutionary Algorithms, focusing on the use of ageing strategies during the implementation of the evolutionary process. Background knowledge on the concept of ageing, as this is defined scientifically for biological systems, is subsequently presented. Based on this information, the paper provides a comparison between the two ageing concepts, and discusses the philosophical inspirations which can be drawn for human ageing based on the operation of Evolutionary Algorithms. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Evolvability Search: Directly Selecting for Evolvability in order to Study and Produce It

    DEFF Research Database (Denmark)

    Mengistu, Henok; Lehman, Joel Anthony; Clune, Jeff

    2016-01-01

    of evolvable digital phenotypes. Although some types of selection in evolutionary computation indirectly encourage evolvability, one unexplored possibility is to directly select for evolvability. To do so, we estimate an individual's future potential for diversity by calculating the behavioral diversity of its...... immediate offspring, and select organisms with increased offspring variation. While the technique is computationally expensive, we hypothesized that direct selection would better encourage evolvability than indirect methods. Experiments in two evolutionary robotics domains confirm this hypothesis: in both...... domains, such Evolvability Search produces solutions with higher evolvability than those produced with Novelty Search or traditional objective-based search algorithms. Further experiments demonstrate that the higher evolvability produced by Evolvability Search in a training environment also generalizes...

  17. Evolutionary perspectives on ageing.

    Science.gov (United States)

    Reichard, Martin

    2017-10-01

    From an evolutionary perspective, ageing is a decrease in fitness with chronological age - expressed by an increase in mortality risk and/or decline in reproductive success and mediated by deterioration of functional performance. While this makes ageing intuitively paradoxical - detrimental to individual fitness - evolutionary theory offers answers as to why ageing has evolved. In this review, I first briefly examine the classic evolutionary theories of ageing and their empirical tests, and highlight recent findings that have advanced our understanding of the evolution of ageing (condition-dependent survival, positive pleiotropy). I then provide an overview of recent theoretical extensions and modifications that accommodate those new discoveries. I discuss the role of indeterminate (asymptotic) growth for lifetime increases in fecundity and ageing trajectories. I outline alternative views that challenge a universal existence of senescence - namely the lack of a germ-soma distinction and the ability of tissue replacement and retrogression to younger developmental stages in modular organisms. I argue that rejuvenation at the organismal level is plausible, but includes a return to a simple developmental stage. This may exempt a particular genotype from somatic defects but, correspondingly, removes any information acquired during development. A resolution of the question of whether a rejuvenated individual is the same entity is central to the recognition of whether current evolutionary theories of ageing, with their extensions and modifications, can explain the patterns of ageing across the Tree of Life. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Evolutionary computation techniques a comparative perspective

    CERN Document Server

    Cuevas, Erik; Oliva, Diego

    2017-01-01

    This book compares the performance of various evolutionary computation (EC) techniques when they are faced with complex optimization problems extracted from different engineering domains. Particularly focusing on recently developed algorithms, it is designed so that each chapter can be read independently. Several comparisons among EC techniques have been reported in the literature, however, they all suffer from one limitation: their conclusions are based on the performance of popular evolutionary approaches over a set of synthetic functions with exact solutions and well-known behaviors, without considering the application context or including recent developments. In each chapter, a complex engineering optimization problem is posed, and then a particular EC technique is presented as the best choice, according to its search characteristics. Lastly, a set of experiments is conducted in order to compare its performance to other popular EC methods.

  19. Application of a sensitive collection heuristic for very large protein families: Evolutionary relationship between adipose triglyceride lipase (ATGL and classic mammalian lipases

    Directory of Open Access Journals (Sweden)

    Berezovsky Igor

    2006-03-01

    Full Text Available Abstract Background Manually finding subtle yet statistically significant links to distantly related homologues becomes practically impossible for very populated protein families due to the sheer number of similarity searches to be invoked and analyzed. The unclear evolutionary relationship between classical mammalian lipases and the recently discovered human adipose triglyceride lipase (ATGL; a patatin family member is an exemplary case for such a problem. Results We describe an unsupervised, sensitive sequence segment collection heuristic suitable for assembling very large protein families. It is based on fan-like expanding, iterative database searches. To prevent inclusion of unrelated hits, additional criteria are introduced: minimal alignment length and overlap with starting sequence segments, finding starting sequences in reciprocal searches, automated filtering for compositional bias and repetitive patterns. This heuristic was implemented as FAMILYSEARCHER in the ANNIE sequence analysis environment and applied to search for protein links between the classical lipase family and the patatin-like group. Conclusion The FAMILYSEARCHER is an efficient tool for tracing distant evolutionary relationships involving large protein families. Although classical lipases and ATGL have no obvious sequence similarity and differ with regard to fold and catalytic mechanism, homology links detected with FAMILYSEARCHER show that they are evolutionarily related. The conserved sequence parts can be narrowed down to an ancestral core module consisting of three β-strands, one α-helix and a turn containing the typical nucleophilic serine. Moreover, this ancestral module also appears in numerous enzymes with various substrate specificities, but that critically rely on nucleophilic attack mechanisms.

  20. Electronic Book Usage Patterns as Observed at an Academic Library: Searches and Viewings

    Directory of Open Access Journals (Sweden)

    Alain R. Lamothe

    2010-06-01

    Full Text Available In 2009, e-book usage statistics were evaluated at Laurentian University, Canada, to provide a better understanding in how the e-book collection has been utilized as well as to give direction for further collection development. The number of e-books, the number of viewings and the number of searches were examined. The size of the collection grew from a single book in 2002 to more than 60,000 in 2008. The pattern of purchase varied from that of bulk purchasing of large e-book collections to a more selective purchase from 2005 to 2007 and then back to that of bulk purchasing in 2008. Both viewings and searches have increased from year to year at a greater pace than the size e-book collection. The number of searches also appeared to provide a viable means to measure the use of an e-book collection rather than relying entirely on viewings or downloads. Ratios were calculated when comparing viewings and searches to the size of the collection. The largest viewings per e-book and searches per e-book ratios were observed in those years when purchasing was done more selectively. It is also clear that the electronic reference collection has seen far greater use then the electronic monographs. Furthermore, usage of electronic monographs also appeared to be directly proportional to the size of the collection.

  1. A Novel Pattern of Yolk Processing in Developing Snake Eggs (Colubridae: Lampropeltini) and its Functional and Evolutionary Implications.

    Science.gov (United States)

    Powers, Kathryn G; Blackburn, Daniel G

    2017-07-01

    Early amniotic vertebrates evolved large-yolked eggs that permitted production of well-developed, terrestrial hatchlings. This reproductive pattern required new mechanisms for cellularizing the yolk and mobilizing it for embryonic use. In birds, cells that line the yolk sac cavity phagocytose and digest the yolk material, a pattern that is commonly assumed to be universal among oviparous amniotes. However, recent evidence challenges the assumption that all squamate reptiles conform to the avian developmental pattern. In this paper, scanning electron microscopy and histology were used to study mechanisms of yolk processing in two colubrid snakes, the kingsnake Lampropeltis getula and the milksnake L. triangulum. Endodermal cells from the yolk sac splanchnopleure proliferate massively as they invade the yolk sac cavity, forming elaborate chains of interlinked cells. These cells grow in size as they phagocytose yolk material. Subsequently, vitelline capillaries invade the masses of yolk-laden cells and become coated with the endodermal cells, forming an elaborate meshwork of cell-coated strands. The close association of cells, yolk, and blood vessels allows yolk material to be cellularized, digested, and transported for embryonic use. The overall pattern is like that of the corn snake Pantherophis guttatus, but contrasts markedly with that of birds. Given recent evidence that this developmental pattern may also occur in certain lizards, we postulate that it is ancestral for squamates. Studies of lizards, crocodilians, and turtles are needed to clarify the evolutionary history of this pattern and its implications for the evolution of the amniotic (terrestrial) vertebrate egg. © 2017 Wiley Periodicals, Inc.

  2. Evolutionary signals of symbiotic persistence in the legume-rhizobia mutualism.

    Science.gov (United States)

    Werner, Gijsbert D A; Cornwell, William K; Cornelissen, Johannes H C; Kiers, E Toby

    2015-08-18

    Understanding the origins and evolutionary trajectories of symbiotic partnerships remains a major challenge. Why are some symbioses lost over evolutionary time whereas others become crucial for survival? Here, we use a quantitative trait reconstruction method to characterize different evolutionary stages in the ancient symbiosis between legumes (Fabaceae) and nitrogen-fixing bacteria, asking how labile is symbiosis across different host clades. We find that more than half of the 1,195 extant nodulating legumes analyzed have a high likelihood (>95%) of being in a state of high symbiotic persistence, meaning that they show a continued capacity to form the symbiosis over evolutionary time, even though the partnership has remained facultative and is not obligate. To explore patterns associated with the likelihood of loss and retention of the N2-fixing symbiosis, we tested for correlations between symbiotic persistence and legume distribution, climate, soil and trait data. We found a strong latitudinal effect and demonstrated that low mean annual temperatures are associated with high symbiotic persistence in legumes. Although no significant correlations between soil variables and symbiotic persistence were found, nitrogen and phosphorus leaf contents were positively correlated with legumes in a state of high symbiotic persistence. This pattern suggests that highly demanding nutrient lifestyles are associated with more stable partnerships, potentially because they "lock" the hosts into symbiotic dependency. Quantitative reconstruction methods are emerging as a powerful comparative tool to study broad patterns of symbiont loss and retention across diverse partnerships.

  3. Evolutionary signals of symbiotic persistence in the legume–rhizobia mutualism

    Science.gov (United States)

    Werner, Gijsbert D. A.; Cornwell, William K.; Cornelissen, Johannes H. C.; Kiers, E. Toby

    2015-01-01

    Understanding the origins and evolutionary trajectories of symbiotic partnerships remains a major challenge. Why are some symbioses lost over evolutionary time whereas others become crucial for survival? Here, we use a quantitative trait reconstruction method to characterize different evolutionary stages in the ancient symbiosis between legumes (Fabaceae) and nitrogen-fixing bacteria, asking how labile is symbiosis across different host clades. We find that more than half of the 1,195 extant nodulating legumes analyzed have a high likelihood (>95%) of being in a state of high symbiotic persistence, meaning that they show a continued capacity to form the symbiosis over evolutionary time, even though the partnership has remained facultative and is not obligate. To explore patterns associated with the likelihood of loss and retention of the N2-fixing symbiosis, we tested for correlations between symbiotic persistence and legume distribution, climate, soil and trait data. We found a strong latitudinal effect and demonstrated that low mean annual temperatures are associated with high symbiotic persistence in legumes. Although no significant correlations between soil variables and symbiotic persistence were found, nitrogen and phosphorus leaf contents were positively correlated with legumes in a state of high symbiotic persistence. This pattern suggests that highly demanding nutrient lifestyles are associated with more stable partnerships, potentially because they “lock” the hosts into symbiotic dependency. Quantitative reconstruction methods are emerging as a powerful comparative tool to study broad patterns of symbiont loss and retention across diverse partnerships. PMID:26041807

  4. Contrasting patterns of evolutionary constraint and novelty revealed by comparative sperm proteomic analysis in Lepidoptera.

    Science.gov (United States)

    Whittington, Emma; Forsythe, Desiree; Borziak, Kirill; Karr, Timothy L; Walters, James R; Dorus, Steve

    2017-12-02

    Rapid evolution is a hallmark of reproductive genetic systems and arises through the combined processes of sequence divergence, gene gain and loss, and changes in gene and protein expression. While studies aiming to disentangle the molecular ramifications of these processes are progressing, we still know little about the genetic basis of evolutionary transitions in reproductive systems. Here we conduct the first comparative analysis of sperm proteomes in Lepidoptera, a group that exhibits dichotomous spermatogenesis, in which males produce a functional fertilization-competent sperm (eupyrene) and an incompetent sperm morph lacking nuclear DNA (apyrene). Through the integrated application of evolutionary proteomics and genomics, we characterize the genomic patterns potentially associated with the origination and evolution of this unique spermatogenic process and assess the importance of genetic novelty in Lepidopteran sperm biology. Comparison of the newly characterized Monarch butterfly (Danaus plexippus) sperm proteome to those of the Carolina sphinx moth (Manduca sexta) and the fruit fly (Drosophila melanogaster) demonstrated conservation at the level of protein abundance and post-translational modification within Lepidoptera. In contrast, comparative genomic analyses across insects reveals significant divergence at two levels that differentiate the genetic architecture of sperm in Lepidoptera from other insects. First, a significant reduction in orthology among Monarch sperm genes relative to the remainder of the genome in non-Lepidopteran insect species was observed. Second, a substantial number of sperm proteins were found to be specific to Lepidoptera, in that they lack detectable homology to the genomes of more distantly related insects. Lastly, the functional importance of Lepidoptera specific sperm proteins is broadly supported by their increased abundance relative to proteins conserved across insects. Our results identify a burst of genetic novelty

  5. Googling in anatomy education: Can google trends inform educators of national online search patterns of anatomical syllabi?

    Science.gov (United States)

    Phelan, Nigel; Davy, Shane; O'Keeffe, Gerard W; Barry, Denis S

    2017-03-01

    The role of e-learning platforms in anatomy education continues to expand as self-directed learning is promoted in higher education. Although a wide range of e-learning resources are available, determining student use of non-academic internet resources requires novel approaches. One such approach that may be useful is the Google Trends © web application. To determine the feasibility of Google Trends to gain insights into anatomy-related online searches, Google Trends data from the United States from January 2010 to December 2015 were analyzed. Data collected were based on the recurrence of keywords related to head and neck anatomy generated from the American Association of Clinical Anatomists and the Anatomical Society suggested anatomy syllabi. Relative search volume (RSV) data were analyzed for seasonal periodicity and their overall temporal trends. Following exclusions due to insufficient search volume data, 29 out of 36 search terms were analyzed. Significant seasonal patterns occurred in 23 search terms. Thirty-nine seasonal peaks were identified, mainly in October and April, coinciding with teaching periods in anatomy curricula. A positive correlation of RSV with time over the 6-year study period occurred in 25 out of 29 search terms. These data demonstrate how Google Trends may offer insights into the nature and timing of online search patterns of anatomical syllabi and may potentially inform the development and timing of targeted online supports to ensure that students of anatomy have the opportunity to engage with online content that is both accurate and fit for purpose. Anat Sci Educ 10: 152-159. © 2016 American Association of Anatomists. © 2016 American Association of Anatomists.

  6. Evolutionary analyses of non-genealogical bonds produced by introgressive descent.

    Science.gov (United States)

    Bapteste, Eric; Lopez, Philippe; Bouchard, Frédéric; Baquero, Fernando; McInerney, James O; Burian, Richard M

    2012-11-06

    All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.

  7. Random searching

    International Nuclear Information System (INIS)

    Shlesinger, Michael F

    2009-01-01

    There are a wide variety of searching problems from molecules seeking receptor sites to predators seeking prey. The optimal search strategy can depend on constraints on time, energy, supplies or other variables. We discuss a number of cases and especially remark on the usefulness of Levy walk search patterns when the targets of the search are scarce.

  8. Human genomic disease variants: a neutral evolutionary explanation.

    Science.gov (United States)

    Dudley, Joel T; Kim, Yuseob; Liu, Li; Markov, Glenn J; Gerold, Kristyn; Chen, Rong; Butte, Atul J; Kumar, Sudhir

    2012-08-01

    Many perspectives on the role of evolution in human health include nonempirical assumptions concerning the adaptive evolutionary origins of human diseases. Evolutionary analyses of the increasing wealth of clinical and population genomic data have begun to challenge these presumptions. In order to systematically evaluate such claims, the time has come to build a common framework for an empirical and intellectual unification of evolution and modern medicine. We review the emerging evidence and provide a supporting conceptual framework that establishes the classical neutral theory of molecular evolution (NTME) as the basis for evaluating disease- associated genomic variations in health and medicine. For over a decade, the NTME has already explained the origins and distribution of variants implicated in diseases and has illuminated the power of evolutionary thinking in genomic medicine. We suggest that a majority of disease variants in modern populations will have neutral evolutionary origins (previously neutral), with a relatively smaller fraction exhibiting adaptive evolutionary origins (previously adaptive). This pattern is expected to hold true for common as well as rare disease variants. Ultimately, a neutral evolutionary perspective will provide medicine with an informative and actionable framework that enables objective clinical assessment beyond convenient tendencies to invoke past adaptive events in human history as a root cause of human disease.

  9. Searching for pulsars using image pattern recognition

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, W. W.; Berndsen, A.; Madsen, E. C.; Tan, M.; Stairs, I. H. [Department of Physics and Astronomy, 6224 Agricultural Road, University of British Columbia, Vancouver, BC, V6T 1Z1 (Canada); Brazier, A. [Astronomy Department, Cornell University, Ithaca, NY 14853 (United States); Lazarus, P. [Max-Planck-Institut für Radioastronomie, Auf dem Hügel 69, D-53121 Bonn (Germany); Lynch, R.; Scholz, P. [Department of Physics, McGill University, Montreal, QC H3A 2T8 (Canada); Stovall, K.; Cohen, S.; Dartez, L. P.; Lunsford, G.; Martinez, J. G.; Mata, A. [Center for Advanced Radio Astronomy, University of Texas at Brownsville, Brownsville, TX 78520 (United States); Ransom, S. M. [NRAO, Charlottesville, VA 22903 (United States); Banaszak, S.; Biwer, C. M.; Flanigan, J.; Rohr, M., E-mail: zhuww@phas.ubc.ca, E-mail: berndsen@phas.ubc.ca [Center for Gravitation, Cosmology and Astrophysics. University of Wisconsin Milwaukee, Milwaukee, WI 53211 (United States); and others

    2014-02-01

    In the modern era of big data, many fields of astronomy are generating huge volumes of data, the analysis of which can sometimes be the limiting factor in research. Fortunately, computer scientists have developed powerful data-mining techniques that can be applied to various fields. In this paper, we present a novel artificial intelligence (AI) program that identifies pulsars from recent surveys by using image pattern recognition with deep neural nets—the PICS (Pulsar Image-based Classification System) AI. The AI mimics human experts and distinguishes pulsars from noise and interference by looking for patterns from candidate plots. Different from other pulsar selection programs that search for expected patterns, the PICS AI is taught the salient features of different pulsars from a set of human-labeled candidates through machine learning. The training candidates are collected from the Pulsar Arecibo L-band Feed Array (PALFA) survey. The information from each pulsar candidate is synthesized in four diagnostic plots, which consist of image data with up to thousands of pixels. The AI takes these data from each candidate as its input and uses thousands of such candidates to train its ∼9000 neurons. The deep neural networks in this AI system grant it superior ability to recognize various types of pulsars as well as their harmonic signals. The trained AI's performance has been validated with a large set of candidates from a different pulsar survey, the Green Bank North Celestial Cap survey. In this completely independent test, the PICS ranked 264 out of 277 pulsar-related candidates, including all 56 previously known pulsars and 208 of their harmonics, in the top 961 (1%) of 90,008 test candidates, missing only 13 harmonics. The first non-pulsar candidate appears at rank 187, following 45 pulsars and 141 harmonics. In other words, 100% of the pulsars were ranked in the top 1% of all candidates, while 80% were ranked higher than any noise or interference. The

  10. Searching for pulsars using image pattern recognition

    International Nuclear Information System (INIS)

    Zhu, W. W.; Berndsen, A.; Madsen, E. C.; Tan, M.; Stairs, I. H.; Brazier, A.; Lazarus, P.; Lynch, R.; Scholz, P.; Stovall, K.; Cohen, S.; Dartez, L. P.; Lunsford, G.; Martinez, J. G.; Mata, A.; Ransom, S. M.; Banaszak, S.; Biwer, C. M.; Flanigan, J.; Rohr, M.

    2014-01-01

    In the modern era of big data, many fields of astronomy are generating huge volumes of data, the analysis of which can sometimes be the limiting factor in research. Fortunately, computer scientists have developed powerful data-mining techniques that can be applied to various fields. In this paper, we present a novel artificial intelligence (AI) program that identifies pulsars from recent surveys by using image pattern recognition with deep neural nets—the PICS (Pulsar Image-based Classification System) AI. The AI mimics human experts and distinguishes pulsars from noise and interference by looking for patterns from candidate plots. Different from other pulsar selection programs that search for expected patterns, the PICS AI is taught the salient features of different pulsars from a set of human-labeled candidates through machine learning. The training candidates are collected from the Pulsar Arecibo L-band Feed Array (PALFA) survey. The information from each pulsar candidate is synthesized in four diagnostic plots, which consist of image data with up to thousands of pixels. The AI takes these data from each candidate as its input and uses thousands of such candidates to train its ∼9000 neurons. The deep neural networks in this AI system grant it superior ability to recognize various types of pulsars as well as their harmonic signals. The trained AI's performance has been validated with a large set of candidates from a different pulsar survey, the Green Bank North Celestial Cap survey. In this completely independent test, the PICS ranked 264 out of 277 pulsar-related candidates, including all 56 previously known pulsars and 208 of their harmonics, in the top 961 (1%) of 90,008 test candidates, missing only 13 harmonics. The first non-pulsar candidate appears at rank 187, following 45 pulsars and 141 harmonics. In other words, 100% of the pulsars were ranked in the top 1% of all candidates, while 80% were ranked higher than any noise or interference. The

  11. Searching for Pulsars Using Image Pattern Recognition

    Science.gov (United States)

    Zhu, W. W.; Berndsen, A.; Madsen, E. C.; Tan, M.; Stairs, I. H.; Brazier, A.; Lazarus, P.; Lynch, R.; Scholz, P.; Stovall, K.; Ransom, S. M.; Banaszak, S.; Biwer, C. M.; Cohen, S.; Dartez, L. P.; Flanigan, J.; Lunsford, G.; Martinez, J. G.; Mata, A.; Rohr, M.; Walker, A.; Allen, B.; Bhat, N. D. R.; Bogdanov, S.; Camilo, F.; Chatterjee, S.; Cordes, J. M.; Crawford, F.; Deneva, J. S.; Desvignes, G.; Ferdman, R. D.; Freire, P. C. C.; Hessels, J. W. T.; Jenet, F. A.; Kaplan, D. L.; Kaspi, V. M.; Knispel, B.; Lee, K. J.; van Leeuwen, J.; Lyne, A. G.; McLaughlin, M. A.; Siemens, X.; Spitler, L. G.; Venkataraman, A.

    2014-02-01

    In the modern era of big data, many fields of astronomy are generating huge volumes of data, the analysis of which can sometimes be the limiting factor in research. Fortunately, computer scientists have developed powerful data-mining techniques that can be applied to various fields. In this paper, we present a novel artificial intelligence (AI) program that identifies pulsars from recent surveys by using image pattern recognition with deep neural nets—the PICS (Pulsar Image-based Classification System) AI. The AI mimics human experts and distinguishes pulsars from noise and interference by looking for patterns from candidate plots. Different from other pulsar selection programs that search for expected patterns, the PICS AI is taught the salient features of different pulsars from a set of human-labeled candidates through machine learning. The training candidates are collected from the Pulsar Arecibo L-band Feed Array (PALFA) survey. The information from each pulsar candidate is synthesized in four diagnostic plots, which consist of image data with up to thousands of pixels. The AI takes these data from each candidate as its input and uses thousands of such candidates to train its ~9000 neurons. The deep neural networks in this AI system grant it superior ability to recognize various types of pulsars as well as their harmonic signals. The trained AI's performance has been validated with a large set of candidates from a different pulsar survey, the Green Bank North Celestial Cap survey. In this completely independent test, the PICS ranked 264 out of 277 pulsar-related candidates, including all 56 previously known pulsars and 208 of their harmonics, in the top 961 (1%) of 90,008 test candidates, missing only 13 harmonics. The first non-pulsar candidate appears at rank 187, following 45 pulsars and 141 harmonics. In other words, 100% of the pulsars were ranked in the top 1% of all candidates, while 80% were ranked higher than any noise or interference. The

  12. An Evolutionary Psychology Approach to Consumer Choice

    Directory of Open Access Journals (Sweden)

    ZURINA BT MOHAIDIN

    2013-07-01

    Full Text Available Human behaviour can be explained not only through experience and environments but also by incorporating evolutionary explanation. Consumer behaviour could not be understood accurately without infusing Darwinian evolutionary theory which has contributed in the knowledge of human nature. Evolutionary psychology revolves around the human’s evolved mental and the impact on human’s traits and behaviour where the influence of the environment to our genes would determine our individual behaviour and traits, resulting in variation among us. Foraging which is a part of behavioural ecology involves many sequences or repetitions of animals’ activities and decision making which is useful to relate these patterns of activities to the decisions made in human consumption. The aim of this research is to investigate the similarities of human consumption and ecological behaviour by employing interpretative and comparative approach. It is hoped that by applying the evolutionary theory in explaining consumer choice, this study is able to contribute to the development of behavioural ecology in human consumption. The analysis of the data is done aggregately for 200 consumers and individually for 20 consumers, who have purchased four product categories over a year. This study concludes that the theories of evolutionary psychology can fit to the consumers’ buying behaviour implicating its usefulness in explaining the consumers’ choice.

  13. Three dimensional pattern recognition using feature-based indexing and rule-based search

    Science.gov (United States)

    Lee, Jae-Kyu

    In flexible automated manufacturing, robots can perform routine operations as well as recover from atypical events, provided that process-relevant information is available to the robot controller. Real time vision is among the most versatile sensing tools, yet the reliability of machine-based scene interpretation can be questionable. The effort described here is focused on the development of machine-based vision methods to support autonomous nuclear fuel manufacturing operations in hot cells. This thesis presents a method to efficiently recognize 3D objects from 2D images based on feature-based indexing. Object recognition is the identification of correspondences between parts of a current scene and stored views of known objects, using chains of segments or indexing vectors. To create indexed object models, characteristic model image features are extracted during preprocessing. Feature vectors representing model object contours are acquired from several points of view around each object and stored. Recognition is the process of matching stored views with features or patterns detected in a test scene. Two sets of algorithms were developed, one for preprocessing and indexed database creation, and one for pattern searching and matching during recognition. At recognition time, those indexing vectors with the highest match probability are retrieved from the model image database, using a nearest neighbor search algorithm. The nearest neighbor search predicts the best possible match candidates. Extended searches are guided by a search strategy that employs knowledge-base (KB) selection criteria. The knowledge-based system simplifies the recognition process and minimizes the number of iterations and memory usage. Novel contributions include the use of a feature-based indexing data structure together with a knowledge base. Both components improve the efficiency of the recognition process by improved structuring of the database of object features and reducing data base size

  14. Phylogenetic Pattern, Evolutionary Processes and Species Delimitation in the Genus Echinococcus.

    Science.gov (United States)

    Lymbery, A J

    2017-01-01

    An accurate and stable alpha taxonomy requires a clear conception of what constitutes a species and agreed criteria for delimiting different species. An evolutionary or general lineage concept defines a species as a single lineage of organisms with a common evolutionary trajectory, distinguishable from other such lineages. Delimiting evolutionary species is a two-step process. In the first step, phylogenetic reconstruction identifies putative species as groups of organisms that are monophyletic (share a common ancestor) and exclusive (more closely related to each other than to organisms outside the group). The second step is to assess whether members of the group possess genetic exchangeability (where cohesion is maintained by gene flow among populations) or ecological exchangeability (where cohesion is maintained because populations occupy the same ecological niche). Recent taxonomic reviews have recognized nine species within the genus Echinococcus. Phylogenetic reconstructions of the relationships between these putative species using mtDNA and nuclear gene sequences show that for the most part these nine species are monophyletic, although there are important incongruences that need to be resolved. Applying the criteria of genetic and ecological exchangeability suggests that seven of the currently recognized species represent evolutionarily distinct lineages. The species status of Echinococcus canadensis and Echinococcus ortleppi could not be confirmed. Coalescent-based analyses represent a promising approach to species delimitation in these closely related taxa. It seems likely, from a comparison of sister species groups, that speciation in the genus has been driven by geographic isolation, but biogeographic scenarios are largely speculative and require further testing. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Do arms races punctuate evolutionary stasis? Unified insights from phylogeny, phylogeography and microevolutionary processes.

    Science.gov (United States)

    Toju, Hirokazu; Sota, Teiji

    2009-09-01

    One of the major controversies in evolutionary biology concerns the processes underlying macroevolutionary patterns in which prolonged stasis is disrupted by rapid, short-term evolution that leads species to new adaptive zones. Recent advances in the understanding of contemporary evolution have suggested that such rapid evolution can occur in the wild as a result of environmental changes. Here, we examined a novel hypothesis that evolutionary stasis is punctuated by co-evolutionary arms races, which continuously alter adaptive peaks and landscapes. Based on the phylogeny of long-mouthed weevils in the genus Curculio, likelihood ratio tests showed that the macroevolutionary pattern of the weevils coincides with the punctuational evolution model. A coalescent analysis of a species, Curculio camelliae, the mouthpart of which has diverged considerably among populations because of an arms race with its host plant, further suggested that major evolutionary shifts had occurred within 7000 generations. Through a microevolutionary analysis of the species, we also found that natural selection acting through co-evolutionary interactions is potentially strong enough to drive rapid evolutionary shifts between adaptive zones. Overall, we posit that co-evolution is an important factor driving the history of organismal evolution.

  16. Geography and major host evolutionary transitions shape the resource use of plant parasites.

    Science.gov (United States)

    Calatayud, Joaquín; Hórreo, José Luis; Madrigal-González, Jaime; Migeon, Alain; Rodríguez, Miguel Á; Magalhães, Sara; Hortal, Joaquín

    2016-08-30

    The evolution of resource use in herbivores has been conceptualized as an analog of the theory of island biogeography, assuming that plant species are islands separated by phylogenetic distances. Despite its usefulness, this analogy has paradoxically led to neglecting real biogeographical processes in the study of macroevolutionary patterns of herbivore-plant interactions. Here we show that host use is mostly determined by the geographical cooccurrence of hosts and parasites in spider mites (Tetranychidae), a globally distributed group of plant parasites. Strikingly, geography accounts for most of the phylogenetic signal in host use by these parasites. Beyond geography, only evolutionary transitions among major plant lineages (i.e., gymnosperms, commelinids, and eudicots) shape resource use patterns in these herbivores. Still, even these barriers have been repeatedly overcome in evolutionary time, resulting in phylogenetically diverse parasite communities feeding on similar hosts. Therefore, our results imply that patterns of apparent evolutionary conservatism may largely be a byproduct of the geographic cooccurrence of hosts and parasites.

  17. Threat-detection in child development: an evolutionary perspective.

    Science.gov (United States)

    Boyer, Pascal; Bergstrom, Brian

    2011-03-01

    Evidence for developmental aspects of fear-targets and anxiety suggests a complex but stable pattern whereby specific kinds of fears emerge at different periods of development. This developmental schedule seems appropriate to dangers encountered repeatedly during human evolution. Also consistent with evolutionary perspective, the threat-detection systems are domain-specific, comprising different kinds of cues to do with predation, intraspecific violence, contamination-contagion and status loss. Proper evolutionary models may also be relevant to outstanding issues in the domain, notably the connections between typical development and pathology. Copyright © 2010 Elsevier Ltd. All rights reserved.

  18. Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal

    DEFF Research Database (Denmark)

    Turajlic, Samra; Xu, Hang; Litchfield, Kevin

    2018-01-01

    The evolutionary features of clear-cell renal cell carcinoma (ccRCC) have not been systematically studied to date. We analyzed 1,206 primary tumor regions from 101 patients recruited into the multi-center prospective study, TRACERx Renal. We observe up to 30 driver events per tumor and show...... that subclonal diversification is associated with known prognostic parameters. By resolving the patterns of driver event ordering, co-occurrence, and mutual exclusivity at clone level, we show the deterministic nature of clonal evolution. ccRCC can be grouped into seven evolutionary subtypes, ranging from tumors...... outcome. Our insights reconcile the variable clinical behavior of ccRCC and suggest evolutionary potential as a biomarker for both intervention and surveillance....

  19. Evolutionary patterns and processes in the radiation of phyllostomid bats

    Directory of Open Access Journals (Sweden)

    Monteiro Leandro R

    2011-05-01

    Full Text Available Abstract Background The phyllostomid bats present the most extensive ecological and phenotypic radiation known among mammal families. This group is an important model system for studies of cranial ecomorphology and functional optimisation because of the constraints imposed by the requirements of flight. A number of studies supporting phyllostomid adaptation have focused on qualitative descriptions or correlating functional variables and diet, but explicit tests of possible evolutionary mechanisms and scenarios for phenotypic diversification have not been performed. We used a combination of morphometric and comparative methods to test hypotheses regarding the evolutionary processes behind the diversification of phenotype (mandible shape and size and diet during the phyllostomid radiation. Results The different phyllostomid lineages radiate in mandible shape space, with each feeding specialisation evolving towards different axes. Size and shape evolve quite independently, as the main directions of shape variation are associated with mandible elongation (nectarivores or the relative size of tooth rows and mandibular processes (sanguivores and frugivores, which are not associated with size changes in the mandible. The early period of phyllostomid diversification is marked by a burst of shape, size, and diet disparity (before 20 Mya, larger than expected by neutral evolution models, settling later to a period of relative phenotypic and ecological stasis. The best fitting evolutionary model for both mandible shape and size divergence was an Ornstein-Uhlenbeck process with five adaptive peaks (insectivory, carnivory, sanguivory, nectarivory and frugivory. Conclusions The radiation of phyllostomid bats presented adaptive and non-adaptive components nested together through the time frame of the family's evolution. The first 10 My of the radiation were marked by strong phenotypic and ecological divergence among ancestors of modern lineages, whereas the

  20. Evolutionary patterns and processes in the radiation of phyllostomid bats

    Science.gov (United States)

    2011-01-01

    Background The phyllostomid bats present the most extensive ecological and phenotypic radiation known among mammal families. This group is an important model system for studies of cranial ecomorphology and functional optimisation because of the constraints imposed by the requirements of flight. A number of studies supporting phyllostomid adaptation have focused on qualitative descriptions or correlating functional variables and diet, but explicit tests of possible evolutionary mechanisms and scenarios for phenotypic diversification have not been performed. We used a combination of morphometric and comparative methods to test hypotheses regarding the evolutionary processes behind the diversification of phenotype (mandible shape and size) and diet during the phyllostomid radiation. Results The different phyllostomid lineages radiate in mandible shape space, with each feeding specialisation evolving towards different axes. Size and shape evolve quite independently, as the main directions of shape variation are associated with mandible elongation (nectarivores) or the relative size of tooth rows and mandibular processes (sanguivores and frugivores), which are not associated with size changes in the mandible. The early period of phyllostomid diversification is marked by a burst of shape, size, and diet disparity (before 20 Mya), larger than expected by neutral evolution models, settling later to a period of relative phenotypic and ecological stasis. The best fitting evolutionary model for both mandible shape and size divergence was an Ornstein-Uhlenbeck process with five adaptive peaks (insectivory, carnivory, sanguivory, nectarivory and frugivory). Conclusions The radiation of phyllostomid bats presented adaptive and non-adaptive components nested together through the time frame of the family's evolution. The first 10 My of the radiation were marked by strong phenotypic and ecological divergence among ancestors of modern lineages, whereas the remaining 20 My were

  1. An Improved SPEA2 Algorithm with Adaptive Selection of Evolutionary Operators Scheme for Multiobjective Optimization Problems

    Directory of Open Access Journals (Sweden)

    Fuqing Zhao

    2016-01-01

    Full Text Available A fixed evolutionary mechanism is usually adopted in the multiobjective evolutionary algorithms and their operators are static during the evolutionary process, which causes the algorithm not to fully exploit the search space and is easy to trap in local optima. In this paper, a SPEA2 algorithm which is based on adaptive selection evolution operators (AOSPEA is proposed. The proposed algorithm can adaptively select simulated binary crossover, polynomial mutation, and differential evolution operator during the evolutionary process according to their contribution to the external archive. Meanwhile, the convergence performance of the proposed algorithm is analyzed with Markov chain. Simulation results on the standard benchmark functions reveal that the performance of the proposed algorithm outperforms the other classical multiobjective evolutionary algorithms.

  2. A study on PubMed search tag usage pattern: association rule mining of a full-day PubMed query log.

    Science.gov (United States)

    Mosa, Abu Saleh Mohammad; Yoo, Illhoi

    2013-01-09

    The practice of evidence-based medicine requires efficient biomedical literature search such as PubMed/MEDLINE. Retrieval performance relies highly on the efficient use of search field tags. The purpose of this study was to analyze PubMed log data in order to understand the usage pattern of search tags by the end user in PubMed/MEDLINE search. A PubMed query log file was obtained from the National Library of Medicine containing anonymous user identification, timestamp, and query text. Inconsistent records were removed from the dataset and the search tags were extracted from the query texts. A total of 2,917,159 queries were selected for this study issued by a total of 613,061 users. The analysis of frequent co-occurrences and usage patterns of the search tags was conducted using an association mining algorithm. The percentage of search tag usage was low (11.38% of the total queries) and only 2.95% of queries contained two or more tags. Three out of four users used no search tag and about two-third of them issued less than four queries. Among the queries containing at least one tagged search term, the average number of search tags was almost half of the number of total search terms. Navigational search tags are more frequently used than informational search tags. While no strong association was observed between informational and navigational tags, six (out of 19) informational tags and six (out of 29) navigational tags showed strong associations in PubMed searches. The low percentage of search tag usage implies that PubMed/MEDLINE users do not utilize the features of PubMed/MEDLINE widely or they are not aware of such features or solely depend on the high recall focused query translation by the PubMed's Automatic Term Mapping. The users need further education and interactive search application for effective use of the search tags in order to fulfill their biomedical information needs from PubMed/MEDLINE.

  3. Breeding novel solutions in the brain: a model of Darwinian neurodynamics [version 1; referees: 1 approved, 2 approved with reservations

    Directory of Open Access Journals (Sweden)

    András Szilágyi

    2016-09-01

    Full Text Available Background: The fact that surplus connections and neurons are pruned during development is well established. We complement this selectionist picture by a proof-of-principle model of evolutionary search in the brain, that accounts for new variations in theory space. We present a model for Darwinian evolutionary search for candidate solutions in the brain. Methods: We combine known components of the brain – recurrent neural networks (acting as attractors, the action selection loop and implicit working memory – to provide the appropriate Darwinian architecture. We employ a population of attractor networks with palimpsest memory. The action selection loop is employed with winners-share-all dynamics to select for candidate solutions that are transiently stored in implicit working memory. Results: We document two processes: selection of stored solutions and evolutionary search for novel solutions. During the replication of candidate solutions attractor networks occasionally produce recombinant patterns, increasing variation on which selection can act. Combinatorial search acts on multiplying units (activity patterns with hereditary variation and novel variants appear due to (i noisy recall of patterns from the attractor networks, (ii noise during transmission of candidate solutions as messages between networks, and, (iii spontaneously generated, untrained patterns in spurious attractors. Conclusions: Attractor dynamics of recurrent neural networks can be used to model Darwinian search. The proposed architecture can be used for fast search among stored solutions (by selection and for evolutionary search when novel candidate solutions are generated in successive iterations. Since all the suggested components are present in advanced nervous systems, we hypothesize that the brain could implement a truly evolutionary combinatorial search system, capable of generating novel variants.

  4. Breeding novel solutions in the brain: a model of Darwinian neurodynamics.

    Science.gov (United States)

    Szilágyi, András; Zachar, István; Fedor, Anna; de Vladar, Harold P; Szathmáry, Eörs

    2016-01-01

    Background : The fact that surplus connections and neurons are pruned during development is well established. We complement this selectionist picture by a proof-of-principle model of evolutionary search in the brain, that accounts for new variations in theory space. We present a model for Darwinian evolutionary search for candidate solutions in the brain. Methods : We combine known components of the brain - recurrent neural networks (acting as attractors), the action selection loop and implicit working memory - to provide the appropriate Darwinian architecture. We employ a population of attractor networks with palimpsest memory. The action selection loop is employed with winners-share-all dynamics to select for candidate solutions that are transiently stored in implicit working memory. Results : We document two processes: selection of stored solutions and evolutionary search for novel solutions. During the replication of candidate solutions attractor networks occasionally produce recombinant patterns, increasing variation on which selection can act. Combinatorial search acts on multiplying units (activity patterns) with hereditary variation and novel variants appear due to (i) noisy recall of patterns from the attractor networks, (ii) noise during transmission of candidate solutions as messages between networks, and, (iii) spontaneously generated, untrained patterns in spurious attractors. Conclusions : Attractor dynamics of recurrent neural networks can be used to model Darwinian search. The proposed architecture can be used for fast search among stored solutions (by selection) and for evolutionary search when novel candidate solutions are generated in successive iterations. Since all the suggested components are present in advanced nervous systems, we hypothesize that the brain could implement a truly evolutionary combinatorial search system, capable of generating novel variants.

  5. Breeding novel solutions in the brain: a model of Darwinian neurodynamics [version 2; referees: 1 approved, 2 approved with reservations

    Directory of Open Access Journals (Sweden)

    András Szilágyi

    2017-06-01

    Full Text Available Background: The fact that surplus connections and neurons are pruned during development is well established. We complement this selectionist picture by a proof-of-principle model of evolutionary search in the brain, that accounts for new variations in theory space. We present a model for Darwinian evolutionary search for candidate solutions in the brain. Methods: We combine known components of the brain – recurrent neural networks (acting as attractors, the action selection loop and implicit working memory – to provide the appropriate Darwinian architecture. We employ a population of attractor networks with palimpsest memory. The action selection loop is employed with winners-share-all dynamics to select for candidate solutions that are transiently stored in implicit working memory. Results: We document two processes: selection of stored solutions and evolutionary search for novel solutions. During the replication of candidate solutions attractor networks occasionally produce recombinant patterns, increasing variation on which selection can act. Combinatorial search acts on multiplying units (activity patterns with hereditary variation and novel variants appear due to (i noisy recall of patterns from the attractor networks, (ii noise during transmission of candidate solutions as messages between networks, and, (iii spontaneously generated, untrained patterns in spurious attractors. Conclusions: Attractor dynamics of recurrent neural networks can be used to model Darwinian search. The proposed architecture can be used for fast search among stored solutions (by selection and for evolutionary search when novel candidate solutions are generated in successive iterations. Since all the suggested components are present in advanced nervous systems, we hypothesize that the brain could implement a truly evolutionary combinatorial search system, capable of generating novel variants.

  6. Evolutionary aspects of life forms in angiosperm families

    NARCIS (Netherlands)

    Kremer, P; van Andel, J

    1995-01-01

    The distribution patterns of life forms among extant families, subclasses and classes are described with the aim of detecting evolutionary trends. The explosive diversification of angiosperms constrains the possibilities for detecting such trends. Moreover, the extant groups of seed plants are only

  7. Testing evolutionary hypotheses for phenotypic divergence using landscape genetics.

    Science.gov (United States)

    Funk, W Chris; Murphy, Melanie A

    2010-02-01

    Understanding the evolutionary causes of phenotypic variation among populations has long been a central theme in evolutionary biology. Several factors can influence phenotypic divergence, including geographic isolation, genetic drift, divergent natural or sexual selection, and phenotypic plasticity. But the relative importance of these factors in generating phenotypic divergence in nature is still a tantalizing and unresolved problem in evolutionary biology. The origin and maintenance of phenotypic divergence is also at the root of many ongoing debates in evolutionary biology, such as the extent to which gene flow constrains adaptive divergence (Garant et al. 2007) and the relative importance of genetic drift, natural selection, and sexual selection in initiating reproductive isolation and speciation (Coyne & Orr 2004). In this issue, Wang & Summers (2010) test the causes of one of the most fantastic examples of phenotypic divergence in nature: colour pattern divergence among populations of the strawberry poison frog (Dendrobates pumilio) in Panama and Costa Rica (Fig. 1). This study provides a beautiful example of the use of the emerging field of landscape genetics to differentiate among hypotheses for phenotypic divergence. Using landscape genetic analyses, Wang & Summers were able to reject the hypotheses that colour pattern divergence is due to isolation-by-distance (IBD) or landscape resistance. Instead, the hypothesis left standing is that colour divergence is due to divergent selection, in turn driving reproductive isolation among populations with different colour morphs. More generally, this study provides a wonderful example of how the emerging field of landscape genetics, which has primarily been applied to questions in conservation and ecology, now plays an essential role in evolutionary research.

  8. Testing the cranial evolutionary allometric 'rule' in Galliformes.

    Science.gov (United States)

    Linde-Medina, M

    2016-09-01

    Recent comparative studies have indicated the existence of a common cranial evolutionary allometric (CREA) pattern in mammals and birds, in which smaller species have relatively smaller faces and bigger braincases than larger species. In these studies, cranial allometry was tested using a multivariate regression between shape (described using landmarks coordinates) and size (i.e. centroid size), after accounting for phylogenetic relatedness. Alternatively, cranial allometry can be determined by comparing the sizes of two anatomical parts using a bivariate regression analysis. In this analysis, a slope higher or lower than one indicates the existence of positive or negative allometry, respectively. Thus, in those species that support the CREA 'rule', positive allometry is expected for the association between face size and braincase size, which would indicate that larger species have disproportionally larger faces. In this study, I applied these two approaches to explore cranial allometry in 83 Galliformes (Aves, Galloanserae), ranging in mean body weight from 30 g to 2.5 kg. The multivariate regression between shape and centroid size revealed the existence of a significant allometric pattern resembling CREA, whereas the second analysis revealed a negative allometry for beak size and braincase size (i.e. contrary to the CREA 'rule', larger galliform species have disproportionally shorter beaks than smaller galliform species). This study suggests that the presence of CREA may be overestimated when using cranium size as the standard measurement. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

  9. Fuel loading and control rod patterns optimization in a BWR using tabu search

    International Nuclear Information System (INIS)

    Castillo, Alejandro; Ortiz, Juan Jose; Montes, Jose Luis; Perusquia, Raul

    2007-01-01

    This paper presents the QuinalliBT system, a new approach to solve fuel loading and control rod patterns optimization problem in a coupled way. This system involves three different optimization stages; in the first one, a seed fuel loading using the Haling principle is designed. In the second stage, the corresponding control rod pattern for the previous fuel loading is obtained. Finally, in the last stage, a new fuel loading is created, starting from the previous fuel loading and using the corresponding set of optimized control rod patterns. For each stage, a different objective function is considered. In order to obtain the decision parameters used in those functions, the CM-PRESTO 3D steady-state reactor core simulator was used. Second and third stages are repeated until an appropriate fuel loading and its control rod pattern are obtained, or a stop criterion is achieved. In all stages, the tabu search optimization technique was used. The QuinalliBT system was tested and applied to a real BWR operation cycle. It was found that the value for k eff obtained by QuinalliBT was 0.0024 Δk/k greater than that of the reference cycle

  10. A Dynamic Neighborhood Learning-Based Gravitational Search Algorithm.

    Science.gov (United States)

    Zhang, Aizhu; Sun, Genyun; Ren, Jinchang; Li, Xiaodong; Wang, Zhenjie; Jia, Xiuping

    2018-01-01

    Balancing exploration and exploitation according to evolutionary states is crucial to meta-heuristic search (M-HS) algorithms. Owing to its simplicity in theory and effectiveness in global optimization, gravitational search algorithm (GSA) has attracted increasing attention in recent years. However, the tradeoff between exploration and exploitation in GSA is achieved mainly by adjusting the size of an archive, named , which stores those superior agents after fitness sorting in each iteration. Since the global property of remains unchanged in the whole evolutionary process, GSA emphasizes exploitation over exploration and suffers from rapid loss of diversity and premature convergence. To address these problems, in this paper, we propose a dynamic neighborhood learning (DNL) strategy to replace the model and thereby present a DNL-based GSA (DNLGSA). The method incorporates the local and global neighborhood topologies for enhancing the exploration and obtaining adaptive balance between exploration and exploitation. The local neighborhoods are dynamically formed based on evolutionary states. To delineate the evolutionary states, two convergence criteria named limit value and population diversity, are introduced. Moreover, a mutation operator is designed for escaping from the local optima on the basis of evolutionary states. The proposed algorithm was evaluated on 27 benchmark problems with different characteristic and various difficulties. The results reveal that DNLGSA exhibits competitive performances when compared with a variety of state-of-the-art M-HS algorithms. Moreover, the incorporation of local neighborhood topology reduces the numbers of calculations of gravitational force and thus alleviates the high computational cost of GSA.

  11. MultiSeq: unifying sequence and structure data for evolutionary analysis

    Directory of Open Access Journals (Sweden)

    Wright Dan

    2006-08-01

    Full Text Available Abstract Background Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate statistical inferences; and biology to analyze chemical and physical properties in terms of sequence and structure changes. Results Here we present MultiSeq, a unified bioinformatics analysis environment that allows one to organize, display, align and analyze both sequence and structure data for proteins and nucleic acids. While special emphasis is placed on analyzing the data within the framework of evolutionary biology, the environment is also flexible enough to accommodate other usage patterns. The evolutionary approach is supported by the use of predefined metadata, adherence to standard ontological mappings, and the ability for the user to adjust these classifications using an electronic notebook. MultiSeq contains a new algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of a homologous group of distantly related proteins. The method, based on the multidimensional QR factorization of multiple sequence and structure alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. Conclusion MultiSeq is a major extension of the Multiple Alignment tool that is provided as part of VMD, a structural

  12. Evolution of optimal Lévy-flight strategies in human mental searches

    Science.gov (United States)

    Radicchi, Filippo; Baronchelli, Andrea

    2012-06-01

    Recent analysis of empirical data [Radicchi, Baronchelli, and Amaral, PloS ONE1932-620310.1371/journal.pone.0029910 7, e029910 (2012)] showed that humans adopt Lévy-flight strategies when exploring the bid space in online auctions. A game theoretical model proved that the observed Lévy exponents are nearly optimal, being close to the exponent value that guarantees the maximal economical return to players. Here, we rationalize these findings by adopting an evolutionary perspective. We show that a simple evolutionary process is able to account for the empirical measurements with the only assumption that the reproductive fitness of the players is proportional to their search ability. Contrary to previous modeling, our approach describes the emergence of the observed exponent without resorting to any strong assumptions on the initial searching strategies. Our results generalize earlier research, and open novel questions in cognitive, behavioral, and evolutionary sciences.

  13. The four cornerstones of Evolutionary Toxicology.

    Science.gov (United States)

    Bickham, John W

    2011-05-01

    Evolutionary Toxicology is the study of the effects of chemical pollutants on the genetics of natural populations. Research in Evolutionary Toxicology uses experimental designs familiar to the ecotoxicologist with matched reference and contaminated sites and the selection of sentinel species. It uses the methods of molecular genetics and population genetics, and is based on the theories and concepts of evolutionary biology and conservation genetics. Although it is a relatively young field, interest is rapidly growing among ecotoxicologists and more and more field studies and even controlled laboratory experiments are appearing in the literature. A number of population genetic impacts have been observed in organisms exposed to pollutants which I refer to here as the four cornerstones of Evolutionary Toxicology. These include (1) genome-wide changes in genetic diversity, (2) changes in allelic or genotypic frequencies caused by contaminant-induced selection acting at survivorship loci, (3) changes in dispersal patterns or gene flow which alter the genetic relationships among populations, and (4) changes in allelic or genotypic frequencies caused by increased mutation rates. It is concluded that population genetic impacts of pollution exposure are emergent effects that are not necessarily predictable from the mode of toxicity of the pollutant. Thus, to attribute an effect to a particular contaminant requires a careful experimental design which includes selection of appropriate reference sites, detailed chemistry analyses of environmental samples and tissues, and the use of appropriate biomarkers to establish exposure and effect. This paper describes the field of Evolutionary Toxicology and discusses relevant field studies and their findings. © Springer Science+Business Media, LLC 2011

  14. Intrinsic Lévy behaviour in organisms - searching for a mechanism. Comment on "Liberating Lévy walk research from the shackles of optimal foraging" by A.M. Reynolds

    Science.gov (United States)

    Sims, David W.

    2015-09-01

    The seminal papers by Viswanathan and colleagues in the late 1990s [1,2] proposed not only that scale-free, superdiffusive Lévy walks can describe the free-ranging movement patterns observed in animals such as the albatross [1], but that the Lévy walk was optimal for searching for sparsely and randomly distributed resource targets [2]. This distinct advantage, now shown to be present over a much broader set of conditions than originally theorised [3], implied that the Lévy walk is a search strategy that should be found very widely in organisms [4]. In the years since there have been several influential empirical studies showing that Lévy walks can indeed be detected in the movement patterns of a very broad range of taxa, from jellyfish, insects, fish, reptiles, seabirds, humans [5-10], and even in the fossilised trails of extinct invertebrates [11]. The broad optimality and apparent deep evolutionary origin of movement (search) patterns that are well approximated by Lévy walks led to the development of the Lévy flight foraging (LFF) hypothesis [12], which states that "since Lévy flights and walks can optimize search efficiencies, therefore natural selection should have led to adaptations for Lévy flight foraging".

  15. Evolutionary modelling of transitions to sustainable development

    International Nuclear Information System (INIS)

    Safarzynska, K.

    2010-01-01

    This thesis has examined how evolutionary economics can contribute to modelling the micromechanisms that underlie transitions towards sustainable development. In general, transitions are fundamental or structural system changes. They involve, or even require, escaping lock-in of dominant, environmentally unsustainable technologies, introducing major technical or social innovations, and changing prevailing social practices and structures. Due to the complexity of socioeconomic interactions, it is not always possible to identify, and thus target with appropriate policy instruments, causes of specific unsustainable patterns of behaviour. Formal modelling exercises can help improve our understanding of the interaction of various transition mechanisms which are otherwise difficult to grasp intuitively. They allow exploring effects of policy interventions in complex systems. However, existing models of transitions focus on social phenomena and seldom address economic problems. As opposed, mainstream (neoclassical) economic models of technological change do not account for social interactions, and changing heterogeneity of users and their perspectives - even though all of these can influence the direction of innovations and patterns of socio-technological development. Evolutionary economics offers an approach that goes beyond neoclassical economics - in the sense of employing more realistic assumptions regarding the behaviour and heterogeneity of consumers, firms and investors. It can complement current transition models by providing them with a better understanding of associated economic dynamics. In this thesis, formal models were proposed to illustrate the usefulness of a range of evolutionary-economic techniques for modelling transitions. Modelling exercises aimed to explain the core properties of socio-economic systems, such as lock-in, path-dependence, coevolution, group selection and recombinant innovation. The studies collected in this dissertation illustrate that

  16. Single-unit pattern generators for quadruped locomotion

    DEFF Research Database (Denmark)

    Morse, Gregory; Risi, Sebastian; Snyder, Charles R

    2013-01-01

    Legged robots can potentially venture beyond the limits of wheeled vehicles. While creating controllers for such robots by hand is possible, evolutionary algorithms are an alternative that can reduce the burden of hand-crafting robotic controllers. Although major evolutionary approaches to legged...... on a new type of neuron called a single-unit pattern generator (SUPG). The SUPG, which is indirectly encoded by a compositional pattern producing network (CPPN) evolved by HyperNEAT, produces a flexible temporal activation pattern that can be reset and repeated at any time through an explicit trigger input...

  17. Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-viral Infection Patterns.

    Science.gov (United States)

    Smoly, Ilan; Carmel, Amir; Shemer-Avni, Yonat; Yeger-Lotem, Esti; Ziv-Ukelson, Michal

    2016-03-01

    Network querying is a powerful approach to mine molecular interaction networks. Most state-of-the-art network querying tools either confine the search to a prespecified topology in the form of some template subnetwork, or do not specify any topological constraints at all. Another approach is grammar-based queries, which are more flexible and expressive as they allow for expressing the topology of the sought pattern according to some grammar-based logic. Previous grammar-based network querying tools were confined to the identification of paths. In this article, we extend the patterns identified by grammar-based query approaches from paths to trees. For this, we adopt a higher order query descriptor in the form of a regular tree grammar (RTG). We introduce a novel problem and propose an algorithm to search a given graph for the k highest scoring subgraphs matching a tree accepted by an RTG. Our algorithm is based on the combination of dynamic programming with color coding, and includes an extension of previous k-best parsing optimization approaches to avoid isomorphic trees in the output. We implement the new algorithm and exemplify its application to mining viral infection patterns within molecular interaction networks. Our code is available online.

  18. Evolutionary history of the somatostatin and somatostatin receptors

    Indian Academy of Sciences (India)

    Somatostatin and its receptors have a critical role in mammalian growth through their control pattern of secretion of growth hormone, but the evolutionary history of somatostatin and somatostatin receptors are ill defined. We used comparative whole genome analysis of Danio rerio, Carassius auratus, Xenopus tropicalis, ...

  19. Blind Channel Equalization Using Constrained Generalized Pattern Search Optimization and Reinitialization Strategy

    Directory of Open Access Journals (Sweden)

    Charles Tatkeu

    2008-12-01

    Full Text Available We propose a global convergence baud-spaced blind equalization method in this paper. This method is based on the application of both generalized pattern optimization and channel surfing reinitialization. The potentially used unimodal cost function relies on higher- order statistics, and its optimization is achieved using a pattern search algorithm. Since the convergence to the global minimum is not unconditionally warranted, we make use of channel surfing reinitialization (CSR strategy to find the right global minimum. The proposed algorithm is analyzed, and simulation results using a severe frequency selective propagation channel are given. Detailed comparisons with constant modulus algorithm (CMA are highlighted. The proposed algorithm performances are evaluated in terms of intersymbol interference, normalized received signal constellations, and root mean square error vector magnitude. In case of nonconstant modulus input signals, our algorithm outperforms significantly CMA algorithm with full channel surfing reinitialization strategy. However, comparable performances are obtained for constant modulus signals.

  20. Blind Channel Equalization Using Constrained Generalized Pattern Search Optimization and Reinitialization Strategy

    Science.gov (United States)

    Zaouche, Abdelouahib; Dayoub, Iyad; Rouvaen, Jean Michel; Tatkeu, Charles

    2008-12-01

    We propose a global convergence baud-spaced blind equalization method in this paper. This method is based on the application of both generalized pattern optimization and channel surfing reinitialization. The potentially used unimodal cost function relies on higher- order statistics, and its optimization is achieved using a pattern search algorithm. Since the convergence to the global minimum is not unconditionally warranted, we make use of channel surfing reinitialization (CSR) strategy to find the right global minimum. The proposed algorithm is analyzed, and simulation results using a severe frequency selective propagation channel are given. Detailed comparisons with constant modulus algorithm (CMA) are highlighted. The proposed algorithm performances are evaluated in terms of intersymbol interference, normalized received signal constellations, and root mean square error vector magnitude. In case of nonconstant modulus input signals, our algorithm outperforms significantly CMA algorithm with full channel surfing reinitialization strategy. However, comparable performances are obtained for constant modulus signals.

  1. ADAPTIVE SELECTION OF AUXILIARY OBJECTIVES IN MULTIOBJECTIVE EVOLUTIONARY ALGORITHMS

    Directory of Open Access Journals (Sweden)

    I. A. Petrova

    2016-05-01

    Full Text Available Subject of Research.We propose to modify the EA+RL method, which increases efficiency of evolutionary algorithms by means of auxiliary objectives. The proposed modification is compared to the existing objective selection methods on the example of travelling salesman problem. Method. In the EA+RL method a reinforcement learning algorithm is used to select an objective – the target objective or one of the auxiliary objectives – at each iteration of the single-objective evolutionary algorithm.The proposed modification of the EA+RL method adopts this approach for the usage with a multiobjective evolutionary algorithm. As opposed to theEA+RL method, in this modification one of the auxiliary objectives is selected by reinforcement learning and optimized together with the target objective at each step of the multiobjective evolutionary algorithm. Main Results.The proposed modification of the EA+RL method was compared to the existing objective selection methods on the example of travelling salesman problem. In the EA+RL method and its proposed modification reinforcement learning algorithms for stationary and non-stationary environment were used. The proposed modification of the EA+RL method applied with reinforcement learning for non-stationary environment outperformed the considered objective selection algorithms on the most problem instances. Practical Significance. The proposed approach increases efficiency of evolutionary algorithms, which may be used for solving discrete NP-hard optimization problems. They are, in particular, combinatorial path search problems and scheduling problems.

  2. Evolutionary Nephrology.

    Science.gov (United States)

    Chevalier, Robert L

    2017-05-01

    Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as "maladaptive." In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic) adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ~40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons), evolutionary selection for APOL1 mutations (that provide resistance to trypanosome infection, a tradeoff), and modern life experience (Western diet mismatch leading to diabetes and hypertension). Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo), developmental programming and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.

  3. Evolutionary Nephrology

    Directory of Open Access Journals (Sweden)

    Robert L. Chevalier

    2017-05-01

    Full Text Available Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as “maladaptive.” In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or from evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ∼40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons, evolutionary selection for APOL1 mutations (which provide resistance to trypanosome infection, a tradeoff, and modern life experience (Western diet mismatch leading to diabetes and hypertension. Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout the life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo, developmental programming, and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.

  4. Towards a Population Dynamics Theory for Evolutionary Computing: Learning from Biological Population Dynamics in Nature

    Science.gov (United States)

    Ma, Zhanshan (Sam)

    In evolutionary computing (EC), population size is one of the critical parameters that a researcher has to deal with. Hence, it was no surprise that the pioneers of EC, such as De Jong (1975) and Holland (1975), had already studied the population sizing from the very beginning of EC. What is perhaps surprising is that more than three decades later, we still largely depend on the experience or ad-hoc trial-and-error approach to set the population size. For example, in a recent monograph, Eiben and Smith (2003) indicated: "In almost all EC applications, the population size is constant and does not change during the evolutionary search." Despite enormous research on this issue in recent years, we still lack a well accepted theory for population sizing. In this paper, I propose to develop a population dynamics theory forEC with the inspiration from the population dynamics theory of biological populations in nature. Essentially, the EC population is considered as a dynamic system over time (generations) and space (search space or fitness landscape), similar to the spatial and temporal dynamics of biological populations in nature. With this conceptual mapping, I propose to 'transplant' the biological population dynamics theory to EC via three steps: (i) experimentally test the feasibility—whether or not emulating natural population dynamics improves the EC performance; (ii) comparatively study the underlying mechanisms—why there are improvements, primarily via statistical modeling analysis; (iii) conduct theoretical analysis with theoretical models such as percolation theory and extended evolutionary game theory that are generally applicable to both EC and natural populations. This article is a summary of a series of studies we have performed to achieve the general goal [27][30]-[32]. In the following, I start with an extremely brief introduction on the theory and models of natural population dynamics (Sections 1 & 2). In Sections 4 to 6, I briefly discuss three

  5. A new ARMAX model based on evolutionary algorithm and particle swarm optimization for short-term load forecasting

    International Nuclear Information System (INIS)

    Wang, Bo; Tai, Neng-ling; Zhai, Hai-qing; Ye, Jian; Zhu, Jia-dong; Qi, Liang-bo

    2008-01-01

    In this paper, a new ARMAX model based on evolutionary algorithm and particle swarm optimization for short-term load forecasting is proposed. Auto-regressive (AR) and moving average (MA) with exogenous variables (ARMAX) has been widely applied in the load forecasting area. Because of the nonlinear characteristics of the power system loads, the forecasting function has many local optimal points. The traditional method based on gradient searching may be trapped in local optimal points and lead to high error. While, the hybrid method based on evolutionary algorithm and particle swarm optimization can solve this problem more efficiently than the traditional ways. It takes advantage of evolutionary strategy to speed up the convergence of particle swarm optimization (PSO), and applies the crossover operation of genetic algorithm to enhance the global search ability. The new ARMAX model for short-term load forecasting has been tested based on the load data of Eastern China location market, and the results indicate that the proposed approach has achieved good accuracy. (author)

  6. An Adaptive Evolutionary Algorithm for Traveling Salesman Problem with Precedence Constraints

    Directory of Open Access Journals (Sweden)

    Jinmo Sung

    2014-01-01

    Full Text Available Traveling sales man problem with precedence constraints is one of the most notorious problems in terms of the efficiency of its solution approach, even though it has very wide range of industrial applications. We propose a new evolutionary algorithm to efficiently obtain good solutions by improving the search process. Our genetic operators guarantee the feasibility of solutions over the generations of population, which significantly improves the computational efficiency even when it is combined with our flexible adaptive searching strategy. The efficiency of the algorithm is investigated by computational experiments.

  7. Evolutionary patterns in the dentition of duplicidentata (mammalia) and a novel trend in the molarization of premolars.

    Science.gov (United States)

    Kraatz, Brian P; Meng, Jin; Weksler, Marcelo; Li, Chuankui

    2010-09-20

    The cusp homology of Lagomorpha has long been problematic largely because their teeth are highly derived relative to their more typically tribosphenic ancestors. Within this context, the lagomorph central cusp has been particularly difficult to homologize with other tribosphenic cusps; authors have previously considered it the paracone, protocone, metacone, amphicone, or an entirely new cusp. Here we present newly described fossil duplicidentates (Lagomorpha and Mimotonidae) in the context of a well-constrained phylogeny to establish a nomenclatural system for cusps based on the tribosphenic pattern. We show that the central cusp of lagomorphs is homologous with the metaconule of other mammals. We also show that the buccal acquisition of a second cusp on the premolars (molarization) within duplicidentates is atypical with respect to other mammalian lineages; within the earliest lagomorphs, a second buccal cusp is added mesially to an isolated buccal cusp. The distal shift of the 'ancestral' paracone within early duplicidentates amounts to the changing of a paracone into a metacone in these lineages. For this reason, we support a strictly topological approach to cusp names, and suggest a discontinuity in nomenclature to capture the complexity of the interplay between evolutionary history and the developmental process that have produced cusp patterns in duplicidentates.

  8. Evolutionary patterns in the dentition of duplicidentata (mammalia and a novel trend in the molarization of premolars.

    Directory of Open Access Journals (Sweden)

    Brian P Kraatz

    Full Text Available BACKGROUND: The cusp homology of Lagomorpha has long been problematic largely because their teeth are highly derived relative to their more typically tribosphenic ancestors. Within this context, the lagomorph central cusp has been particularly difficult to homologize with other tribosphenic cusps; authors have previously considered it the paracone, protocone, metacone, amphicone, or an entirely new cusp. METHODOLOGY/PRINCIPAL FINDINGS: Here we present newly described fossil duplicidentates (Lagomorpha and Mimotonidae in the context of a well-constrained phylogeny to establish a nomenclatural system for cusps based on the tribosphenic pattern. We show that the central cusp of lagomorphs is homologous with the metaconule of other mammals. We also show that the buccal acquisition of a second cusp on the premolars (molarization within duplicidentates is atypical with respect to other mammalian lineages; within the earliest lagomorphs, a second buccal cusp is added mesially to an isolated buccal cusp. CONCLUSIONS/SIGNIFICANCE: The distal shift of the 'ancestral' paracone within early duplicidentates amounts to the changing of a paracone into a metacone in these lineages. For this reason, we support a strictly topological approach to cusp names, and suggest a discontinuity in nomenclature to capture the complexity of the interplay between evolutionary history and the developmental process that have produced cusp patterns in duplicidentates.

  9. The pachytene checkpoint and its relationship to evolutionary patterns of polyploidization and hybrid sterility.

    Science.gov (United States)

    Li, X C; Barringer, B C; Barbash, D A

    2009-01-01

    Sterility is a commonly observed phenotype in interspecific hybrids. Sterility may result from chromosomal or genic incompatibilities, and much progress has been made toward understanding the genetic basis of hybrid sterility in various taxa. The underlying mechanisms causing hybrid sterility, however, are less well known. The pachytene checkpoint is a meiotic surveillance system that many organisms use to detect aberrant meiotic products, in order to prevent the production of defective gametes. We suggest that activation of the pachytene checkpoint may be an important mechanism contributing to two types of hybrid sterility. First, the pachytene checkpoint may form the mechanistic basis of some gene-based hybrid sterility phenotypes. Second, the pachytene checkpoint may be an important mechanism that mediates chromosomal-based hybrid sterility phenotypes involving gametes with non-haploid (either non-reduced or aneuploid) chromosome sets. Studies in several species suggest that the strength of the pachytene checkpoint is sexually dimorphic, observations that warrant future investigation into whether such variation may contribute to differences in patterns of sterility between male and female interspecific hybrids. In addition, plants seem to lack the pachytene checkpoint, which correlates with increased production of unreduced gametes and a higher incidence of polyploid species in plants versus animals. Although the pachytene checkpoint occurs in many animals and in fungi, at least some of the genes that execute the pachytene checkpoint are different among organisms. This finding suggests that the penetrance of the pachytene checkpoint, and even its presence or absence can evolve rapidly. The surprising degree of evolutionary flexibility in this meiotic surveillance system may contribute to the observed variation in patterns of hybrid sterility and in rates of polyploidization.

  10. Cultural evolutionary theory: How culture evolves and why it matters.

    Science.gov (United States)

    Creanza, Nicole; Kolodny, Oren; Feldman, Marcus W

    2017-07-24

    Human cultural traits-behaviors, ideas, and technologies that can be learned from other individuals-can exhibit complex patterns of transmission and evolution, and researchers have developed theoretical models, both verbal and mathematical, to facilitate our understanding of these patterns. Many of the first quantitative models of cultural evolution were modified from existing concepts in theoretical population genetics because cultural evolution has many parallels with, as well as clear differences from, genetic evolution. Furthermore, cultural and genetic evolution can interact with one another and influence both transmission and selection. This interaction requires theoretical treatments of gene-culture coevolution and dual inheritance, in addition to purely cultural evolution. In addition, cultural evolutionary theory is a natural component of studies in demography, human ecology, and many other disciplines. Here, we review the core concepts in cultural evolutionary theory as they pertain to the extension of biology through culture, focusing on cultural evolutionary applications in population genetics, ecology, and demography. For each of these disciplines, we review the theoretical literature and highlight relevant empirical studies. We also discuss the societal implications of the study of cultural evolution and of the interactions of humans with one another and with their environment.

  11. Recovery after mass extinction: evolutionary assembly in large-scale biosphere dynamics.

    Science.gov (United States)

    Solé, Ricard V; Montoya, José M; Erwin, Douglas H

    2002-01-01

    Biotic recoveries following mass extinctions are characterized by a process in which whole ecologies are reconstructed from low-diversity systems, often characterized by opportunistic groups. The recovery process provides an unexpected window to ecosystem dynamics. In many aspects, recovery is very similar to ecological succession, but important differences are also apparently linked to the innovative patterns of niche construction observed in the fossil record. In this paper, we analyse the similarities and differences between ecological succession and evolutionary recovery to provide a preliminary ecological theory of recoveries. A simple evolutionary model with three trophic levels is presented, and its properties (closely resembling those observed in the fossil record) are compared with characteristic patterns of ecological response to disturbances in continuous models of three-level ecosystems. PMID:12079530

  12. Evolutionary molecular medicine.

    Science.gov (United States)

    Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S

    2012-05-01

    Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

  13. Diabetes and Obesity—An Evolutionary Perspective

    Directory of Open Access Journals (Sweden)

    Sylvia Kirchengast

    2017-01-01

    Full Text Available Obesity and type II diabetes belong to the most serious public health challenges of the 21st century. Initially both diseases were typical of affluent societies. Currently both conditions however are increasingly found in low and middle income countries. In future obesity and diabetes are expected to reach epidemic proportions and affect developing countries to a greater extent than developed ones. A globalization of obesity and diabetes is observable. Recently prevalence rates increased, especially in Asia, the Near and Middle East, the Western Pacific region and even in Sub-Saharan Africa. Evolutionary Anthropology tries to understand the evolutionary mechanisms promoting rising obesity and diabetes type II rates. Homo sapiens evolved in an environment quite different from our recent one. Profound changes in physical activity patterns and nutritional habits during the last 10,000 years and increasingly during the last 200 years increased the risk of obesity and diabetes type II. Consequently our recent environment is called “obesogenic”. This mismatch has been recently observable among societies experiencing rapid cultural changes characterized by Westernization and modernization. This review focuses on obesity and type II diabetes from the viewpoint of evolutionary anthropology.

  14. Spatial evolutionary epidemiology of spreading epidemics.

    Science.gov (United States)

    Lion, S; Gandon, S

    2016-10-26

    Most spatial models of host-parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. © 2016 The Author(s).

  15. eHealth Search Patterns: A Comparison of Private and Public Health Care Markets Using Online Panel Data.

    Science.gov (United States)

    Schneider, Janina Anne; Holland, Christopher Patrick

    2017-04-13

    Patient and consumer access to eHealth information is of crucial importance because of its role in patient-centered medicine and to improve knowledge about general aspects of health and medical topics. The objectives were to analyze and compare eHealth search patterns in a private (United States) and a public (United Kingdom) health care market. A new taxonomy of eHealth websites is proposed to organize the largest eHealth websites. An online measurement framework is developed that provides a precise and detailed measurement system. Online panel data are used to accurately track and analyze detailed search behavior across 100 of the largest eHealth websites in the US and UK health care markets. The health, medical, and lifestyle categories account for approximately 90% of online activity, and e-pharmacies, social media, and professional categories account for the remaining 10% of online activity. Overall search penetration of eHealth websites is significantly higher in the private (United States) than the public market (United Kingdom). Almost twice the number of eHealth users in the private market have adopted online search in the health and lifestyle categories and also spend more time per website than those in the public market. The use of medical websites for specific conditions is almost identical in both markets. The allocation of search effort across categories is similar in both the markets. For all categories, the vast majority of eHealth users only access one website within each category. Those that conduct a search of two or more websites display very narrow search patterns. All users spend relatively little time on eHealth, that is, 3-7 minutes per website. The proposed online measurement framework exploits online panel data to provide a powerful and objective method of analyzing and exploring eHealth behavior. The private health care system does appear to have an influence on eHealth search behavior in terms of search penetration and time spent per

  16. Phase boundary estimation in electrical impedance tomography using the Hooke and Jeeves pattern search method

    International Nuclear Information System (INIS)

    Khambampati, Anil Kumar; Kim, Kyung Youn; Ijaz, Umer Zeeshan; Lee, Jeong Seong; Kim, Sin

    2010-01-01

    In industrial processes, monitoring of heterogeneous phases is crucial to the safety and operation of the engineering structures. Particularly, the visualization of voids and air bubbles is advantageous. As a result many studies have appeared in the literature that offer varying degrees of functionality. Electrical impedance tomography (EIT) has already been proved to be a hallmark for process monitoring and offers not only the visualization of the resistivity profile for a given flow mixture but is also used for detection of phase boundaries. Iterative image reconstruction algorithms, such as the modified Newton–Raphson (mNR) method, are commonly used as inverse solvers. However, their utility is problematic in a sense that they require the initial solution in close proximity of the ground truth. Furthermore, they also rely on the gradient information of the objective function to be minimized. Therefore, in this paper, we address all these issues by employing a direct search algorithm, namely the Hooke and Jeeves pattern search method, to estimate the phase boundaries that directly minimizes the cost function and does not require the gradient information. It is assumed that the resistivity profile is known a priori and therefore the unknown information will be the size and location of the object. The boundary coefficients are parameterized using truncated Fourier series and are estimated using the relationship between the measured voltages and injected currents. Through extensive simulation and experimental result and by comparison with mNR, we show that the Hooke and Jeeves pattern search method offers a promising prospect for process monitoring

  17. Analysis of the uniform augmentation of the flow through the nucleus in the searching process of the patterns of objective control bars in a BWR

    International Nuclear Information System (INIS)

    Montes, J.L.; Ortiz, J.J.; Perusquia, R.

    2004-01-01

    The search of the patterns of control bars (PBCs) in a power reactor of boiling water, requires to investigate a very wide space of solutions, in principle they are had of the order of 3 x 10 152 possible configurations to establish the PBC in a point given before reaching the end of the cycle. This situation suggests to define those restrictions and conditions initial appropriately so that the search converges toward the desirable results. Presently work the results of the search of patterns of bars based on different flow scenarios through the nucleus are presented. The Cycle 10 is analysed (C10) of the Unit One of the Nuclear Power station Laguna Verde (CNLV), which presents an interesting mixture of diverse designs of control bars used in operation to power. The search of the patterns of bars of objective control is carried out applying the GACRP program which is based on the calculation technique known as genetic algorithms. (Author)

  18. Evolution-development congruence in pattern formation dynamics: Bifurcations in gene expression and regulation of networks structures.

    Science.gov (United States)

    Kohsokabe, Takahiro; Kaneko, Kunihiko

    2016-01-01

    Search for possible relationships between phylogeny and ontogeny is important in evolutionary-developmental biology. Here we uncover such relationships by numerical evolution and unveil their origin in terms of dynamical systems theory. By representing developmental dynamics of spatially located cells with gene expression dynamics with cell-to-cell interaction under external morphogen gradient, gene regulation networks are evolved under mutation and selection with the fitness to approach a prescribed spatial pattern of expressed genes. For most numerical evolution experiments, evolution of pattern over generations and development of pattern by an evolved network exhibit remarkable congruence. Both in the evolution and development pattern changes consist of several epochs where stripes are formed in a short time, while for other temporal regimes, pattern hardly changes. In evolution, these quasi-stationary regimes are generations needed to hit relevant mutations, while in development, they are due to some gene expression that varies slowly and controls the pattern change. The morphogenesis is regulated by combinations of feedback or feedforward regulations, where the upstream feedforward network reads the external morphogen gradient, and generates a pattern used as a boundary condition for the later patterns. The ordering from up to downstream is common in evolution and development, while the successive epochal changes in development and evolution are represented as common bifurcations in dynamical-systems theory, which lead to the evolution-development congruence. Mechanism of exceptional violation of the congruence is also unveiled. Our results provide a new look on developmental stages, punctuated equilibrium, developmental bottlenecks, and evolutionary acquisition of novelty in morphogenesis. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution Published by Wiley Periodicals, Inc.

  19. Electronic Book Usage Patterns as Observed at an Academic Library: Searches and Viewings

    OpenAIRE

    Alain R. Lamothe

    2010-01-01

    In 2009, e-book usage statistics were evaluated at Laurentian University, Canada, to provide a better understanding in how the e-book collection has been utilized as well as to give direction for further collection development. The number of e-books, the number of viewings and the number of searches were examined. The size of the collection grew from a single book in 2002 to more than 60,000 in 2008. The pattern of purchase varied from that of bulk purchasing of large e-book collections to a ...

  20. Kernel Method Based Human Model for Enhancing Interactive Evolutionary Optimization

    Science.gov (United States)

    Zhao, Qiangfu; Liu, Yong

    2015-01-01

    A fitness landscape presents the relationship between individual and its reproductive success in evolutionary computation (EC). However, discrete and approximate landscape in an original search space may not support enough and accurate information for EC search, especially in interactive EC (IEC). The fitness landscape of human subjective evaluation in IEC is very difficult and impossible to model, even with a hypothesis of what its definition might be. In this paper, we propose a method to establish a human model in projected high dimensional search space by kernel classification for enhancing IEC search. Because bivalent logic is a simplest perceptual paradigm, the human model is established by considering this paradigm principle. In feature space, we design a linear classifier as a human model to obtain user preference knowledge, which cannot be supported linearly in original discrete search space. The human model is established by this method for predicting potential perceptual knowledge of human. With the human model, we design an evolution control method to enhance IEC search. From experimental evaluation results with a pseudo-IEC user, our proposed model and method can enhance IEC search significantly. PMID:25879050

  1. Comparing search patterns in digital breast tomosynthesis and full-field digital mammography: an eye tracking study.

    Science.gov (United States)

    Aizenman, Avi; Drew, Trafton; Ehinger, Krista A; Georgian-Smith, Dianne; Wolfe, Jeremy M

    2017-10-01

    As a promising imaging modality, digital breast tomosynthesis (DBT) leads to better diagnostic performance than traditional full-field digital mammograms (FFDM) alone. DBT allows different planes of the breast to be visualized, reducing occlusion from overlapping tissue. Although DBT is gaining popularity, best practices for search strategies in this medium are unclear. Eye tracking allowed us to describe search patterns adopted by radiologists searching DBT and FFDM images. Eleven radiologists examined eight DBT and FFDM cases. Observers marked suspicious masses with mouse clicks. Eye position was recorded at 1000 Hz and was coregistered with slice/depth plane as the radiologist scrolled through the DBT images, allowing a 3-D representation of eye position. Hit rate for masses was higher for tomography cases than 2-D cases and DBT led to lower false positive rates. However, search duration was much longer for DBT cases than FFDM. DBT was associated with longer fixations but similar saccadic amplitude compared with FFDM. When comparing radiologists' eye movements to a previous study, which tracked eye movements as radiologists read chest CT, we found DBT viewers did not align with previously identified "driller" or "scanner" strategies, although their search strategy most closely aligns with a type of vigorous drilling strategy.

  2. BLAST and FASTA similarity searching for multiple sequence alignment.

    Science.gov (United States)

    Pearson, William R

    2014-01-01

    BLAST, FASTA, and other similarity searching programs seek to identify homologous proteins and DNA sequences based on excess sequence similarity. If two sequences share much more similarity than expected by chance, the simplest explanation for the excess similarity is common ancestry-homology. The most effective similarity searches compare protein sequences, rather than DNA sequences, for sequences that encode proteins, and use expectation values, rather than percent identity, to infer homology. The BLAST and FASTA packages of sequence comparison programs provide programs for comparing protein and DNA sequences to protein databases (the most sensitive searches). Protein and translated-DNA comparisons to protein databases routinely allow evolutionary look back times from 1 to 2 billion years; DNA:DNA searches are 5-10-fold less sensitive. BLAST and FASTA can be run on popular web sites, but can also be downloaded and installed on local computers. With local installation, target databases can be customized for the sequence data being characterized. With today's very large protein databases, search sensitivity can also be improved by searching smaller comprehensive databases, for example, a complete protein set from an evolutionarily neighboring model organism. By default, BLAST and FASTA use scoring strategies target for distant evolutionary relationships; for comparisons involving short domains or queries, or searches that seek relatively close homologs (e.g. mouse-human), shallower scoring matrices will be more effective. Both BLAST and FASTA provide very accurate statistical estimates, which can be used to reliably identify protein sequences that diverged more than 2 billion years ago.

  3. Patterns and Processes of Vertebrate Evolution

    Science.gov (United States)

    Carroll, Robert Lynn

    1997-04-01

    This new text provides an integrated view of the forces that influence the patterns and rates of vertebrate evolution from the level of living populations and species to those that resulted in the origin of the major vertebrate groups. The evolutionary roles of behavior, development, continental drift, and mass extinctions are compared with the importance of variation and natural selection that were emphasized by Darwin. It is extensively illustrated, showing major transitions between fish and amphibians, dinosaurs and birds, and land mammals to whales. No book since Simpson's Major Features of Evolution has attempted such a broad study of the patterns and forces of evolutionary change. Undergraduate students taking a general or advanced course on evolution, and graduate students and professionals in evolutionary biology and paleontology will find the book of great interest.

  4. Woodpeckers and Diamonds: Some Aspects of Evolutionary Convergence in Astrobiology.

    Science.gov (United States)

    Ćirković, Milan M

    2018-05-01

    Jared Diamond's argument against extraterrestrial intelligence from evolutionary contingency is subjected to critical scrutiny. As with the earlier arguments of George Gaylord Simpson, it contains critical loopholes that lead to its unraveling. From the point of view of the contemporary debates about biological evolution, perhaps the most contentious aspect of such arguments is their atemporal and gradualist usage of the space of all possible biological forms (morphospace). Such usage enables the translation of the adaptive value of a trait into the probability of its evolving. This procedure, it is argued, is dangerously misleading. Contra Diamond, there are reasons to believe that convergence not only plays an important role in the history of life, but also profoundly improves the prospects for search for extraterrestrial intelligence success. Some further considerations about the role of observation selection effects and our scaling of complexity in the great debate about contingency and convergence are given. Taken together, these considerations militate against the pessimism of Diamond's conclusion, and suggest that the search for traces and manifestations of extraterrestrial intelligences is far from forlorn. Key Words: Astrobiology-Evolution-Contingency-Convergence-Complex life-SETI-Major evolutionary transitions-Selection effects-Jared Diamond. Astrobiology 18, 491-502.

  5. On the evolution of misunderstandings about evolutionary psychology.

    Science.gov (United States)

    Young, J; Persell, R

    2000-04-01

    Some of the controversy surrounding evolutionary explanations of human behavior may be due to cognitive information-processing patterns that are themselves the result of evolutionary processes. Two such patterns are (1) the tendency to oversimplify information so as to reduce demand on cognitive resources and (2) our strong desire to generate predictability and stability from perceptions of the external world. For example, research on social stereotyping has found that people tend to focus automatically on simplified social-categorical information, to use such information when deciding how to behave, and to rely on such information even in the face of contradictory evidence. Similarly, an undying debate over nature vs. nurture is shaped by various data-reduction strategies that frequently oversimplify, and thus distort, the intent of the supporting arguments. This debate is also often marked by an assumption that either the nature or the nurture domain may be justifiably excluded at an explanatory level because one domain appears to operate in a sufficiently stable and predictable way for a particular argument. As a result, critiques in-veighed against evolutionary explanations of behavior often incorporate simplified--and erroneous--assumptions about either the mechanics of how evolution operates or the inevitable implications of evolution for understanding human behavior. The influences of these tendencies are applied to a discussion of the heritability of behavioral characteristics. It is suggested that the common view that Mendelian genetics can explain the heritability of complex behaviors, with a one-gene-one-trait process, is misguided. Complex behaviors are undoubtedly a product of a more complex interaction between genes and environment, ensuring that both nature and nurture must be accommodated in a yet-to-be-developed post-Mendelian model of genetic influence. As a result, current public perceptions of evolutionary explanations of behavior are

  6. Origin of the fittest: link between emergent variation and evolutionary change as a critical question in evolutionary biology.

    Science.gov (United States)

    Badyaev, Alexander V

    2011-07-07

    In complex organisms, neutral evolution of genomic architecture, associated compensatory interactions in protein networks and emergent developmental processes can delineate the directions of evolutionary change, including the opportunity for natural selection. These effects are reflected in the evolution of developmental programmes that link genomic architecture with a corresponding functioning phenotype. Two recent findings call for closer examination of the rules by which these links are constructed. First is the realization that high dimensionality of genotypes and emergent properties of autonomous developmental processes (such as capacity for self-organization) result in the vast areas of fitness neutrality at both the phenotypic and genetic levels. Second is the ubiquity of context- and taxa-specific regulation of deeply conserved gene networks, such that exceptional phenotypic diversification coexists with remarkably conserved generative processes. Establishing the causal reciprocal links between ongoing neutral expansion of genomic architecture, emergent features of organisms' functionality, and often precisely adaptive phenotypic diversification therefore becomes an important goal of evolutionary biology and is the latest reincarnation of the search for a framework that links development, functioning and evolution of phenotypes. Here I examine, in the light of recent empirical advances, two evolutionary concepts that are central to this framework-natural selection and inheritance-the general rules by which they become associated with emergent developmental and homeostatic processes and the role that they play in descent with modification.

  7. How cultural evolutionary theory can inform social psychology and vice versa.

    Science.gov (United States)

    Mesoudi, Alex

    2009-10-01

    Cultural evolutionary theory is an interdisciplinary field in which human culture is viewed as a Darwinian process of variation, competition, and inheritance, and the tools, methods, and theories developed by evolutionary biologists to study genetic evolution are adapted to study cultural change. It is argued here that an integration of the theories and findings of mainstream social psychology and of cultural evolutionary theory can be mutually beneficial. Social psychology provides cultural evolution with a set of empirically verified microevolutionary cultural processes, such as conformity, model-based biases, and content biases, that are responsible for specific patterns of cultural change. Cultural evolutionary theory provides social psychology with ultimate explanations for, and an understanding of the population-level consequences of, many social psychological phenomena, such as social learning, conformity, social comparison, and intergroup processes, as well as linking social psychology with other social science disciplines such as cultural anthropology, archaeology, and sociology.

  8. Variants of Evolutionary Algorithms for Real-World Applications

    CERN Document Server

    Weise, Thomas; Michalewicz, Zbigniew

    2012-01-01

    Evolutionary Algorithms (EAs) are population-based, stochastic search algorithms that mimic natural evolution. Due to their ability to find excellent solutions for conventionally hard and dynamic problems within acceptable time, EAs have attracted interest from many researchers and practitioners in recent years. This book “Variants of Evolutionary Algorithms for Real-World Applications” aims to promote the practitioner’s view on EAs by providing a comprehensive discussion of how EAs can be adapted to the requirements of various applications in the real-world domains. It comprises 14 chapters, including an introductory chapter re-visiting the fundamental question of what an EA is and other chapters addressing a range of real-world problems such as production process planning, inventory system and supply chain network optimisation, task-based jobs assignment, planning for CNC-based work piece construction, mechanical/ship design tasks that involve runtime-intense simulations, data mining for the predictio...

  9. Evolutionary origin of the Asteraceae capitulum: Insights from Calyceraceae.

    Science.gov (United States)

    Pozner, Raúl; Zanotti, Christian; Johnson, Leigh A

    2012-01-01

    Phylogenies based on molecular data are revealing that generalizations about complex morphological structures often obscure variation and developmental patterns important for understanding the evolution of forms, as is the case for inflorescence morphology within the well-supported MGCA clade (Menyanthaceae + Goodeniaceae + Calyceraceae + Asteraceae). While the basal families share a basic thyrsic/thyrsoid structure of their inflorescences, Asteraceae possesses a capitulum that is widely interpreted as a racemose, condensed inflorescence. Elucidating the poorly known inflorescence structure of Calyceraceae, sister to Asteraceae, should help clarify how the Asteraceae capitulum evolved from thyrsic/thyrsoid inflorescences. The early development and structure of the inflorescence of eight species (five genera) of Calyceraceae were studied by SEM, and patterns of evolutionary change were interpreted via phylogenetic character mapping. The basic inflorescence structure of Calyceraceae is a cephalioid (a very condensed botryoid/thyrsoid). Optimization of inflorescence characters on a DNA sequence-derived tree suggests that the Asteraceae capitulum derives from a simple cephalioid through two morphological changes: loss of the terminal flower and suppression of the cymose branching pattern in the peripheral branches. Widely understood as a condensed raceme, the Asteraceae capitulum is the evolutionary result of a very reduced, condensed thyrsoid. Starting from that point, evolution worked separately only on the racemose developmental control/pattern within Asteraceae and mainly on the cymose developmental control/pattern within Calyceraceae, producing head-like inflorescences in both groups but with very different diversification potential. We also discuss possible remnants of the ancestral cephalioid structure in some Asteraceae.

  10. Evolutionary trade-offs in plants mediate the strength of trophic cascades.

    Science.gov (United States)

    Mooney, Kailen A; Halitschke, Rayko; Kessler, Andre; Agrawal, Anurag A

    2010-03-26

    Predators determine herbivore and plant biomass via so-called trophic cascades, and the strength of such effects is influenced by ecosystem productivity. To determine whether evolutionary trade-offs among plant traits influence patterns of trophic control, we manipulated predators and soil fertility and measured impacts of a major herbivore (the aphid Aphis nerii) on 16 milkweed species (Asclepias spp.) in a phylogenetic field experiment. Herbivore density was determined by variation in predation and trade-offs between herbivore resistance and plant growth strategy. Neither herbivore density nor predator effects on herbivores predicted the cascading effects of predators on plant biomass. Instead, cascade strength was strongly and positively associated with milkweed response to soil fertility. Accordingly, contemporary patterns of trophic control are driven by evolutionary convergent trade-offs faced by plants.

  11. A hybrid firefly algorithm and pattern search technique for SSSC based power oscillation damping controller design

    Directory of Open Access Journals (Sweden)

    Srikanta Mahapatra

    2014-12-01

    Full Text Available In this paper, a novel hybrid Firefly Algorithm and Pattern Search (h-FAPS technique is proposed for a Static Synchronous Series Compensator (SSSC-based power oscillation damping controller design. The proposed h-FAPS technique takes the advantage of global search capability of FA and local search facility of PS. In order to tackle the drawback of using the remote signal that may impact reliability of the controller, a modified signal equivalent to the remote speed deviation signal is constructed from the local measurements. The performances of the proposed controllers are evaluated in SMIB and multi-machine power system subjected to various transient disturbances. To show the effectiveness and robustness of the proposed design approach, simulation results are presented and compared with some recently published approaches such as Differential Evolution (DE and Particle Swarm Optimization (PSO. It is observed that the proposed approach yield superior damping performance compared to some recently reported approaches.

  12. Ecological and evolutionary patterns of freshwater maturation in Pacific and Atlantic salmonines

    Science.gov (United States)

    Sloat, Matthew R.; Fraser, Dylan J.; Dunham, Jason B.; Falke, Jeffery A.; Jordan, Chris E.; McMillan, John R.; Ohms, Haley A.

    2014-01-01

    Reproductive tactics and migratory strategies in Pacific and Atlantic salmonines are inextricably linked through the effects of migration (or lack thereof) on age and size at maturity. In this review, we focus on the ecological and evolutionary patterns of freshwater maturation in salmonines, a key process resulting in the diversification of their life histories. We demonstrate that the energetics of maturation and reproduction provides a unifying theme for understanding both the proximate and ultimate causes of variation in reproductive schedules among species, populations, and the sexes. We use probabilistic maturation reaction norms to illustrate how variation in individual condition, in terms of body size, growth rate, and lipid storage, influences the timing of maturation. This useful framework integrates both genetic and environmental contributions to conditional strategies for maturation and, in doing so, demonstrates how flexible life histories can be both heritable and subject to strong environmental influences. We review evidence that the propensity for freshwater maturation in partially anadromous species is predictable across environmental gradients at geographic and local spatial scales. We note that growth is commonly associated with the propensity for freshwater maturation, but that life-history responses to changes in growth caused by temperature may be strikingly different than changes caused by differences in food availability. We conclude by exploring how contemporary management actions can constrain or promote the diversity of maturation phenotypes in Pacific and Atlantic salmonines and caution against underestimating the role of freshwater maturing forms in maintaining the resiliency of these iconic species.

  13. Social Search: A Taxonomy of, and a User-Centred Approach to, Social Web Search

    Science.gov (United States)

    McDonnell, Michael; Shiri, Ali

    2011-01-01

    Purpose: The purpose of this paper is to introduce the notion of social search as a new concept, drawing upon the patterns of web search behaviour. It aims to: define social search; present a taxonomy of social search; and propose a user-centred social search method. Design/methodology/approach: A mixed method approach was adopted to investigate…

  14. Micro-evolutionary divergence patterns of mandible shapes in wild house mouse (Mus musculus populations

    Directory of Open Access Journals (Sweden)

    Tautz Diethard

    2011-10-01

    Full Text Available Abstract Background Insights into the micro-evolutionary patterns of morphological traits require an assessment of the natural variation of the trait within and between populations and closely related species. The mouse mandible is a particularly suitable morphological trait for such an analysis, since it has long been used as a model to study the quantitative genetics of shape. In addition, many distinct populations, sub-species and closely related species are known for the house mouse. However, morphological comparisons among wild caught animals require an assessment in how far environmental and technical factors could interfere with the shape change measurements. Results Using geometric morphometrics, we have surveyed mandible shapes in 15 natural populations of the genus Mus, with a focus on the subspecies Mus musculus domesticus. In parallel we have carefully assessed possibly confounding technical and biological factors. We find that there are distinct differences on average between populations, subspecies and species, but these differences are smaller than differences between individuals within populations. Populations from summer-dry regions, although more ancestral, are less distinct from each other than are populations from the more recently colonized northern areas. Populations with especially distinct shapes occur in an area of sympatry of M. m. domesticus and M. spretus and on recently colonized sub-antarctic islands. We have also studied a number of inbred strains to assess in how far their mandible shapes resemble those from the wild. We find that they fall indeed into the shape space of natural variation between individuals in populations. Conclusions Although mandible shapes in natural populations can be influenced by environmental variables, these influences are insufficient to explain the average extent of shape differences between populations, such that evolutionary processes must be invoked to explain this level of diversity

  15. What's in a Name: Is “Evolutionary Psychology” Eclipsing “Sociobiology” in the Scientific Literature?

    Directory of Open Access Journals (Sweden)

    Gregory D. Webster

    2007-10-01

    Full Text Available Is the term “evolutionary psychology” supplanting “sociobiology” in the scientific literature? How influential was E. O. Wilson's (1975 book, Sociobiology, in establishing the discipline of the same name? Similarly, how influential were the two Tooby-Cosmides chapters appearing in The Adapted Mind (Cosmides and Tooby, 1992; Tooby and Cosmides, 1992 in establishing evolutionary psychology as a viable outgrowth of sociobiology? The purpose of the present research was to answer these questions using quantitative analyses of publication trends. The Internet search engine Google Scholar was used to count the number of hits (i.e., the number of scholarly works, citations, etc. for “sociobiology” and “evolutionary psychology” separately per year from 1960 to 2003. Interrupted time-series analyses revealed significant increases (intercept shifts for sociobiology hits between 1974 and 1975, and for evolutionary psychology hits between 1991 and 1992. Evolutionary psychology hits also experienced a significant increase in change-over-time (a slope shift between 1991 and 1992. Growth curve analyses revealed that the rate of growth for evolutionary psychology, which was accelerating over time, was significantly greater than that for sociobiology, which was decelerating. The implications of these findings for understanding the histories of sociobiology and evolutionary psychology are discussed.

  16. Evolutionary thinking

    Science.gov (United States)

    Hunt, Tam

    2014-01-01

    Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution—both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place—has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps’ book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging “integral” or “evolutionary” cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps. PMID:26478766

  17. Searching for full power control rod patterns in a boiling water reactor using genetic algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Montes, Jose Luis [Departamento Sistemas Nucleares, ININ, Carr. Mexico-Toluca Km. 36.5, Ocoyoacac, Edo. de Mexico (Mexico)]. E-mail: jlmt@nuclear.inin.mx; Ortiz, Juan Jose [Departamento Sistemas Nucleares, ININ, Carr. Mexico-Toluca Km. 36.5, Ocoyoacac, Edo. de Mexico (Mexico)]. E-mail: jjortiz@nuclear.inin.mx; Requena, Ignacio [Departamento Ciencias Computacion e I.A. ETSII, Informatica, Universidad de Granada, C. Daniel Saucedo Aranda s/n. 18071 Granada (Spain)]. E-mail: requena@decsai.ugr.es; Perusquia, Raul [Departamento Sistemas Nucleares, ININ, Carr. Mexico-Toluca Km. 36.5, Ocoyoacac, Edo. de Mexico (Mexico)]. E-mail: rpc@nuclear.inin.mx

    2004-11-01

    One of the most important questions related to both safety and economic aspects in a nuclear power reactor operation, is without any doubt its reactivity control. During normal operation of a boiling water reactor, the reactivity control of its core is strongly determined by control rods patterns efficiency. In this paper, GACRP system is proposed based on the concepts of genetic algorithms for full power control rod patterns search. This system was carried out using LVNPP transition cycle characteristics, being applied too to an equilibrium cycle. Several operation scenarios, including core water flow variation throughout the cycle and different target axial power distributions, are considered. Genetic algorithm fitness function includes reactor security parameters, such as MLHGR, MCPR, reactor k{sub eff} and axial power density.

  18. Search Strategy of Focused Crawler Based on Adaptive Immune Evolutionary Algorithm%基于自适应免疫进化算法的聚焦爬虫搜索策略

    Institute of Scientific and Technical Information of China (English)

    刘丽杰; 许楠; 李盼池

    2012-01-01

    聚焦爬虫是主题搜索引擎的核心部件。针对目前聚焦爬虫搜索策略的不足,提出基于主题相关度和页面重要性相结合的综合相关度来判别页面主题相关性,并采用自适应免疫进化算法这种搜索策略指导聚焦爬虫的爬行,实验结果证明,该算法下载的主题相关网页数所占比例明显高于最佳搜索和广度优先搜索算法的比例,具有更高的搜索效率。%Focused crawler was a core component of the topic search engine.To overcome the deficiency of focused crawler search strategy,a comprehensive value based on theme relevance and importance of page was proposed to determine the topic relevant of the page,and the adaptive immune evolutionary algorithm of this search strategy was used to guide the crawling strategy of focused crawler.The experiment results showed that the algorithm download the proportion to the number of webpage related to the themes was higher significantly than the best search and breadth first search algorithm and had higher searching efficiency.

  19. Black-Box Search by Unbiased Variation

    DEFF Research Database (Denmark)

    Lehre, Per Kristian; Witt, Carsten

    2012-01-01

    The complexity theory for black-box algorithms, introduced by Droste, Jansen, and Wegener (Theory Comput. Syst. 39:525–544, 2006), describes common limits on the efficiency of a broad class of randomised search heuristics. There is an obvious trade-off between the generality of the black-box model...... and the strength of the bounds that can be proven in such a model. In particular, the original black-box model provides for well-known benchmark problems relatively small lower bounds, which seem unrealistic in certain cases and are typically not met by popular search heuristics.In this paper, we introduce a more...... restricted black-box model for optimisation of pseudo-Boolean functions which we claim captures the working principles of many randomised search heuristics including simulated annealing, evolutionary algorithms, randomised local search, and others. The key concept worked out is an unbiased variation operator...

  20. A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes

    OpenAIRE

    Mukherjee, Krishanu; Brocchieri, Luciano; B?rglin, Thomas R.

    2009-01-01

    The full complement of homeobox transcription factor sequences, including genes and pseudogenes, was determined from the analysis of 10 complete genomes from flowering plants, moss, Selaginella, unicellular green algae, and red algae. Our exhaustive genome-wide searches resulted in the discovery in each class of a greater number of homeobox genes than previously reported. All homeobox genes can be unambiguously classified by sequence evolutionary analysis into 14 distinct classes also charact...

  1. Fitness landscapes, heuristics and technological paradigms: a critique on random search models in evolutionary economics

    NARCIS (Netherlands)

    Frenken, K.

    2001-01-01

    The biological evolution of complex organisms, in which the functioning of genes is interdependent, has been analyzed as "hill-climbing" on NK fitness landscapes through random mutation and natural selection. In evolutionary economics, NK fitness landscapes have been used to simulate the evolution

  2. Compassion: An Evolutionary Analysis and Empirical Review

    OpenAIRE

    Goetz, Jennifer L.; Keltner, Dacher; Simon-Thomas, Emiliana

    2010-01-01

    What is compassion? And how did it evolve? In this review, we integrate three evolutionary arguments that converge on the hypothesis that compassion evolved as a distinct affective experience whose primary function is to facilitate cooperation and protection of the weak and those who suffer. Our empirical review reveals compassion to have distinct appraisal processes attuned to undeserved suffering, distinct signaling behavior related to caregiving patterns of touch, posture, and vocalization...

  3. Evolutionary Stable Strategy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 21; Issue 9. Evolutionary Stable Strategy: Application of Nash Equilibrium in Biology. General Article Volume 21 Issue 9 September 2016 pp 803- ... Keywords. Evolutionary game theory, evolutionary stable state, conflict, cooperation, biological games.

  4. Evolutionary synthesis of optimum light ends recovery unit with exergy analysis application

    International Nuclear Information System (INIS)

    Khalili-Garakani, Amirhossein; Ivakpour, Javad; Kasiri, Norollah

    2016-01-01

    Highlights: • Presenting an evolutionary synthesis algorithm. • Reducing configuration nominees based on exergy loss diagram of distillation columns. • Reduction of search space without decreasing the comprehensiveness and precision of the synthesis algorithm. • Rigorous simulation and optimization of sequences. - Abstract: Exergy analysis proved to be important in understanding of regions with poor energy efficiency and improve the design of distillation processes. In this study a new method based on exergy analysis is developed for the synthesis of a light ends recovery unit. The algorithm is some kinds of evolutionary one which employ total exergy loss diagrams of distillation columns for limiting the search space and reducing configuration nominees. The new method presented here for the light end separation unit, applies exergy loss diagrams as a powerful tool in locating the weak spot in the distillation columns of the Brugma sequence (as a first guess) and change the structure of the sequence step by step to achieve the best sequence. The results show that the new method could reduce the amount of calculations between 16% and 55% of the cases considered in this case study. The reduction of the search space takes place without decreasing the comprehensiveness and precision of the synthesis algorithm. Besides the amount of reduction in total annual cost and exergy loss of the optimum sequence is considerable.

  5. 3rd International Conference on Harmony Search Algorithm

    CERN Document Server

    2017-01-01

    This book presents state-of-the-art technical contributions based around one of the most successful evolutionary optimization algorithms published to date: Harmony Search. Contributions span from novel technical derivations of this algorithm to applications in the broad fields of civil engineering, energy, transportation & mobility and health, among many others and focus not only on its cross-domain applicability, but also on its core evolutionary operators, including elements inspired from other meta-heuristics. The global scientific community is witnessing an upsurge in groundbreaking, new advances in all areas of computational intelligence, with a particular flurry of research focusing on evolutionary computation and bio-inspired optimization. Observed processes in nature and sociology have provided the basis for innovative algorithmic developments aimed at leveraging the inherent capability to adapt characterized by various animals, including ants, fireflies, wolves and humans. However, it is the beha...

  6. Random drift versus selection in academic vocabulary: an evolutionary analysis of published keywords.

    Science.gov (United States)

    Bentley, R Alexander

    2008-08-27

    The evolution of vocabulary in academic publishing is characterized via keyword frequencies recorded in the ISI Web of Science citations database. In four distinct case-studies, evolutionary analysis of keyword frequency change through time is compared to a model of random copying used as the null hypothesis, such that selection may be identified against it. The case studies from the physical sciences indicate greater selection in keyword choice than in the social sciences. Similar evolutionary analyses can be applied to a wide range of phenomena; wherever the popularity of multiple items through time has been recorded, as with web searches, or sales of popular music and books, for example.

  7. The Race for Sponsored Links: Bidding Patterns for Search Advertising

    OpenAIRE

    Zsolt Katona; Miklos Sarvary

    2010-01-01

    Paid placements on search engines reached sales of nearly $11 billion in the United States last year and represent the most rapidly growing form of online advertising today. In its classic form, a search engine sets up an auction for each search word in which competing websites bid for their sponsored links to be displayed next to the search results. We model this advertising market, focusing on two of its key characteristics: (1) the interaction between the list of search results and the lis...

  8. Evolutionary origins of hepatitis A virus in small mammals.

    Science.gov (United States)

    Drexler, Jan Felix; Corman, Victor M; Lukashev, Alexander N; van den Brand, Judith M A; Gmyl, Anatoly P; Brünink, Sebastian; Rasche, Andrea; Seggewiβ, Nicole; Feng, Hui; Leijten, Lonneke M; Vallo, Peter; Kuiken, Thijs; Dotzauer, Andreas; Ulrich, Rainer G; Lemon, Stanley M; Drosten, Christian

    2015-12-08

    Hepatitis A virus (HAV) is an ancient and ubiquitous human pathogen recovered previously only from primates. The sole species of the genus Hepatovirus, existing in both enveloped and nonenveloped forms, and with a capsid structure intermediate between that of insect viruses and mammalian picornaviruses, HAV is enigmatic in its origins. We conducted a targeted search for hepatoviruses in 15,987 specimens collected from 209 small mammal species globally and discovered highly diversified viruses in bats, rodents, hedgehogs, and shrews, which by pairwise sequence distance comprise 13 novel Hepatovirus species. Near-complete genomes from nine of these species show conservation of unique hepatovirus features, including predicted internal ribosome entry site structure, a truncated VP4 capsid protein lacking N-terminal myristoylation, a carboxyl-terminal pX extension of VP1, VP2 late domains involved in membrane envelopment, and a cis-acting replication element within the 3D(pol) sequence. Antibodies in some bat sera immunoprecipitated and neutralized human HAV, suggesting conservation of critical antigenic determinants. Limited phylogenetic cosegregation among hepatoviruses and their hosts and recombination patterns are indicative of major hepatovirus host shifts in the past. Ancestral state reconstructions suggest a Hepatovirus origin in small insectivorous mammals and a rodent origin of human HAV. Patterns of infection in small mammals mimicked those of human HAV in hepatotropism, fecal shedding, acute nature, and extinction of the virus in a closed host population. The evolutionary conservation of hepatovirus structure and pathogenesis provide novel insight into the origins of HAV and highlight the utility of analyzing animal reservoirs for risk assessment of emerging viruses.

  9. PTree: pattern-based, stochastic search for maximum parsimony phylogenies

    OpenAIRE

    Gregor, Ivan; Steinbr?ck, Lars; McHardy, Alice C.

    2013-01-01

    Phylogenetic reconstruction is vital to analyzing the evolutionary relationship of genes within and across populations of different species. Nowadays, with next generation sequencing technologies producing sets comprising thousands of sequences, robust identification of the tree topology, which is optimal according to standard criteria such as maximum parsimony, maximum likelihood or posterior probability, with phylogenetic inference methods is a computationally very demanding task. Here, we ...

  10. Ecological and evolutionary drivers of the elevational gradient of diversity.

    Science.gov (United States)

    Laiolo, Paola; Pato, Joaquina; Obeso, José Ramón

    2018-05-02

    Ecological, evolutionary, spatial and neutral theories make distinct predictions and provide distinct explanations for the mechanisms that control the relationship between diversity and the environment. Here, we test predictions of the elevational diversity gradient focusing on Iberian bumblebees, grasshoppers and birds. Processes mediated by local abundance and regional diversity concur in explaining local diversity patterns along elevation. Effects expressed through variation in abundance were similar among taxa and point to the overriding role of a physical factor, temperature. This determines how energy is distributed among individuals and ultimately how the resulting pattern of abundance affects species incidence. Effects expressed through variation in regional species pools depended instead on taxon-specific evolutionary history, and lead to diverging responses under similar environmental pressures. Local filters and regional variation also explain functional diversity gradients, in line with results from species richness that indicate an (local) ecological and (regional) historical unfolding of diversity-elevation relationships. © 2018 John Wiley & Sons Ltd/CNRS.

  11. DNA evolutionary algorithm (DNAEA) for source term identification in convection-diffusion equation

    International Nuclear Information System (INIS)

    Yang, X-H; Hu, X-X; Shen, Z-Y

    2008-01-01

    The source identification problem is changed into an optimization problem in this paper. This is a complicated nonlinear optimization problem. It is very intractable with traditional optimization methods. So DNA evolutionary algorithm (DNAEA) is presented to solve the discussed problem. In this algorithm, an initial population is generated by a chaos algorithm. With the shrinking of searching range, DNAEA gradually directs to an optimal result with excellent individuals obtained by DNAEA. The position and intensity of pollution source are well found with DNAEA. Compared with Gray-coded genetic algorithm and pure random search algorithm, DNAEA has rapider convergent speed and higher calculation precision

  12. Generalized Pattern Search methods for a class of nonsmooth optimization problems with structure

    Science.gov (United States)

    Bogani, C.; Gasparo, M. G.; Papini, A.

    2009-07-01

    We propose a Generalized Pattern Search (GPS) method to solve a class of nonsmooth minimization problems, where the set of nondifferentiability is included in the union of known hyperplanes and, therefore, is highly structured. Both unconstrained and linearly constrained problems are considered. At each iteration the set of poll directions is enforced to conform to the geometry of both the nondifferentiability set and the boundary of the feasible region, near the current iterate. This is the key issue to guarantee the convergence of certain subsequences of iterates to points which satisfy first-order optimality conditions. Numerical experiments on some classical problems validate the method.

  13. An Evolutionary Approach to the Climate Change Negotiation Game

    Energy Technology Data Exchange (ETDEWEB)

    Courtois, P. [CIRED and University of Paris, Paris (France); Pereau, J.C. [OEP, University of Marne-la-Vallee, Marne-la-Vallee (France); Tazdait, T. [CIRED and OEP, University of Marne-la-Vallee, Marne-la-Vallee (France)

    2001-10-01

    We describe in this paper an evolutionary game theoretic model aiming at representing the climate change negotiation. The model is used to examine the outcome of climate change negotiations in a framework which seeks to closely represent negotiation patterns. Evolutionary setting allows us to consider a decision making structure characterised by agents with bounded knowledge practising mimics and learning from past events and strategies. We show on that framework that a third significant alternative to the binary coordination-defection strategies needs to be considered: a unilateral commitment as precautionary strategy. As a means to widen cooperation, we examine the influence of linking environmental and trade policies via the implementation of a trade penalty on non cooperative behaviours.

  14. An Evolutionary Approach to the Climate Change Negotiation Game

    International Nuclear Information System (INIS)

    Courtois, P.; Pereau, J.C.; Tazdait, T.

    2001-10-01

    We describe in this paper an evolutionary game theoretic model aiming at representing the climate change negotiation. The model is used to examine the outcome of climate change negotiations in a framework which seeks to closely represent negotiation patterns. Evolutionary setting allows us to consider a decision making structure characterised by agents with bounded knowledge practising mimics and learning from past events and strategies. We show on that framework that a third significant alternative to the binary coordination-defection strategies needs to be considered: a unilateral commitment as precautionary strategy. As a means to widen cooperation, we examine the influence of linking environmental and trade policies via the implementation of a trade penalty on non cooperative behaviours

  15. Composite Differential Search Algorithm

    Directory of Open Access Journals (Sweden)

    Bo Liu

    2014-01-01

    Full Text Available Differential search algorithm (DS is a relatively new evolutionary algorithm inspired by the Brownian-like random-walk movement which is used by an organism to migrate. It has been verified to be more effective than ABC, JDE, JADE, SADE, EPSDE, GSA, PSO2011, and CMA-ES. In this paper, we propose four improved solution search algorithms, namely “DS/rand/1,” “DS/rand/2,” “DS/current to rand/1,” and “DS/current to rand/2” to search the new space and enhance the convergence rate for the global optimization problem. In order to verify the performance of different solution search methods, 23 benchmark functions are employed. Experimental results indicate that the proposed algorithm performs better than, or at least comparable to, the original algorithm when considering the quality of the solution obtained. However, these schemes cannot still achieve the best solution for all functions. In order to further enhance the convergence rate and the diversity of the algorithm, a composite differential search algorithm (CDS is proposed in this paper. This new algorithm combines three new proposed search schemes including “DS/rand/1,” “DS/rand/2,” and “DS/current to rand/1” with three control parameters using a random method to generate the offspring. Experiment results show that CDS has a faster convergence rate and better search ability based on the 23 benchmark functions.

  16. Recent advances in swarm intelligence and evolutionary computation

    CERN Document Server

    2015-01-01

    This timely review volume summarizes the state-of-the-art developments in nature-inspired algorithms and applications with the emphasis on swarm intelligence and bio-inspired computation. Topics include the analysis and overview of swarm intelligence and evolutionary computation, hybrid metaheuristic algorithms, bat algorithm, discrete cuckoo search, firefly algorithm, particle swarm optimization, and harmony search as well as convergent hybridization. Application case studies have focused on the dehydration of fruits and vegetables by the firefly algorithm and goal programming, feature selection by the binary flower pollination algorithm, job shop scheduling, single row facility layout optimization, training of feed-forward neural networks, damage and stiffness identification, synthesis of cross-ambiguity functions by the bat algorithm, web document clustering, truss analysis, water distribution networks, sustainable building designs and others. As a timely review, this book can serve as an ideal reference f...

  17. Mathematics and evolutionary biology make bioinformatics education comprehensible

    Science.gov (United States)

    Weisstein, Anton E.

    2013-01-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes—the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software—the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a ‘two-culture’ problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses. PMID:23821621

  18. Mathematics and evolutionary biology make bioinformatics education comprehensible.

    Science.gov (United States)

    Jungck, John R; Weisstein, Anton E

    2013-09-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes-the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software-the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a 'two-culture' problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses.

  19. An Evolutionary Formulation of the Crossing Number Problem

    Directory of Open Access Journals (Sweden)

    Che Sheng Gan

    2009-01-01

    Full Text Available A graph drawing algorithm is presented which results in complete graphs having minimum crossings equal to that of Guy's conjecture. It is then generalized and formulated in an evolutionary algorithm (EA to perform constrained search for the crossing numbers. The main objective of this work is to present a suitable two-dimensional scheme which can greatly reduce the complexity of finding crossing numbers by using computer. Program performance criteria are presented and discussed. It is shown that the EA implementation provides good confirmation of the predicted crossing numbers.

  20. EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data.

    Science.gov (United States)

    Linard, Benjamin; Nguyen, Ngoc Hoan; Prosdocimi, Francisco; Poch, Olivier; Thompson, Julie D

    2012-01-01

    Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutionary histories in large scale studies are currently limited. Here, we propose a new formalism, called EvoluCode (Evolutionary barCode), which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories at the genome scale. The advantages of the approach are demonstrated by constructing barcodes representing the evolution of the complete human proteome. Two large-scale studies are then described: (i) the mapping and visualization of the barcodes on the human chromosomes and (ii) automatic clustering of the barcodes to highlight protein subsets sharing similar evolutionary histories and their functional analysis. The methodologies developed here open the way to the efficient application of other data mining and knowledge extraction techniques in evolutionary systems biology studies. A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes.

  1. Evolutionary change - patterns and processes

    Directory of Open Access Journals (Sweden)

    Francisco M. Salzano

    2005-12-01

    Full Text Available The present review considered: (a the factors that conditioned the early transition from non-life to life; (b genome structure and complexity in prokaryotes, eukaryotes, and organelles; (c comparative human chromosome genomics; and (d the Brazilian contribution to some of these studies. Understanding the dialectical conflict between freedom and organization is fundamental to give meaning to the patterns and processes of organic evolution.A presente revisão considerou: (a os fatores que condicionaram a transição inicial entre não-vida e vida; (b a estrutura e complexidade genômica em procariotos, eucariotos e organelas; (c a genômica comparada dos cromossomos humanos; (d a contribuição brasileira a alguns desses estudos. A compreensão do conflito dialético entre liberdade e organização é fundamental para dar significado aos padrões e processos da evolução orgânica.

  2. Particle Swarm Optimization with Double Learning Patterns.

    Science.gov (United States)

    Shen, Yuanxia; Wei, Linna; Zeng, Chuanhua; Chen, Jian

    2016-01-01

    Particle Swarm Optimization (PSO) is an effective tool in solving optimization problems. However, PSO usually suffers from the premature convergence due to the quick losing of the swarm diversity. In this paper, we first analyze the motion behavior of the swarm based on the probability characteristic of learning parameters. Then a PSO with double learning patterns (PSO-DLP) is developed, which employs the master swarm and the slave swarm with different learning patterns to achieve a trade-off between the convergence speed and the swarm diversity. The particles in the master swarm and the slave swarm are encouraged to explore search for keeping the swarm diversity and to learn from the global best particle for refining a promising solution, respectively. When the evolutionary states of two swarms interact, an interaction mechanism is enabled. This mechanism can help the slave swarm in jumping out of the local optima and improve the convergence precision of the master swarm. The proposed PSO-DLP is evaluated on 20 benchmark functions, including rotated multimodal and complex shifted problems. The simulation results and statistical analysis show that PSO-DLP obtains a promising performance and outperforms eight PSO variants.

  3. Particle Swarm Optimization with Double Learning Patterns

    Science.gov (United States)

    Shen, Yuanxia; Wei, Linna; Zeng, Chuanhua; Chen, Jian

    2016-01-01

    Particle Swarm Optimization (PSO) is an effective tool in solving optimization problems. However, PSO usually suffers from the premature convergence due to the quick losing of the swarm diversity. In this paper, we first analyze the motion behavior of the swarm based on the probability characteristic of learning parameters. Then a PSO with double learning patterns (PSO-DLP) is developed, which employs the master swarm and the slave swarm with different learning patterns to achieve a trade-off between the convergence speed and the swarm diversity. The particles in the master swarm and the slave swarm are encouraged to explore search for keeping the swarm diversity and to learn from the global best particle for refining a promising solution, respectively. When the evolutionary states of two swarms interact, an interaction mechanism is enabled. This mechanism can help the slave swarm in jumping out of the local optima and improve the convergence precision of the master swarm. The proposed PSO-DLP is evaluated on 20 benchmark functions, including rotated multimodal and complex shifted problems. The simulation results and statistical analysis show that PSO-DLP obtains a promising performance and outperforms eight PSO variants. PMID:26858747

  4. The Research of Disease Spots Extraction Based on Evolutionary Algorithm

    Directory of Open Access Journals (Sweden)

    Kangshun Li

    2017-01-01

    Full Text Available According to the characteristics of maize disease spot performance in the image, this paper designs two-histogram segmentation method based on evolutionary algorithm, which combined with the analysis of image of maize diseases and insect pests, with full consideration of color and texture characteristic of the lesion of pests and diseases, the chroma and gray image, composed of two tuples to build a two-dimensional histogram, solves the problem of one-dimensional histograms that cannot be clearly divided into target and background bimodal distribution and improved the traditional two-dimensional histogram application in pest damage lesion extraction. The chromosome coding suitable for the characteristics of lesion image is designed based on second segmentation of the genetic algorithm Otsu. Determining initial population with analysis results of lesion image, parallel selection, optimal preservation strategy, and adaptive mutation operator are used to improve the search efficiency. Finally, by setting the fluctuation threshold, we continue to search for the best threshold in the range of fluctuations for implementation of global search and local search.

  5. Evolutionary design optimization of traffic signals applied to Quito city.

    Science.gov (United States)

    Armas, Rolando; Aguirre, Hernán; Daolio, Fabio; Tanaka, Kiyoshi

    2017-01-01

    This work applies evolutionary computation and machine learning methods to study the transportation system of Quito from a design optimization perspective. It couples an evolutionary algorithm with a microscopic transport simulator and uses the outcome of the optimization process to deepen our understanding of the problem and gain knowledge about the system. The work focuses on the optimization of a large number of traffic lights deployed on a wide area of the city and studies their impact on travel time, emissions and fuel consumption. An evolutionary algorithm with specialized mutation operators is proposed to search effectively in large decision spaces, evolving small populations for a short number of generations. The effects of the operators combined with a varying mutation schedule are studied, and an analysis of the parameters of the algorithm is also included. In addition, hierarchical clustering is performed on the best solutions found in several runs of the algorithm. An analysis of signal clusters and their geolocation, estimation of fuel consumption, spatial analysis of emissions, and an analysis of signal coordination provide an overall picture of the systemic effects of the optimization process.

  6. A new greedy search method for the design of digital IIR filter

    Directory of Open Access Journals (Sweden)

    Ranjit Kaur

    2015-07-01

    Full Text Available A new greedy search method is applied in this paper to design the optimal digital infinite impulse response (IIR filter. The greedy search method is based on binary successive approximation (BSA and evolutionary search (ES. The suggested greedy search method optimizes the magnitude response and the phase response simultaneously and also finds the lowest order of the filter. The order of the filter is controlled by a control gene whose value is also optimized along with the filter coefficients to obtain optimum order of designed IIR filter. The stability constraints of IIR filter are taken care of during the design procedure. To determine the trade-off relationship between conflicting objectives in the non-inferior domain, the weighting method is exploited. The proposed approach is effectively applied to solve the multiobjective optimization problems of designing the digital low-pass (LP, high-pass (HP, bandpass (BP, and bandstop (BS filters. It has been demonstrated that this technique not only fulfills all types of filter performance requirements, but also the lowest order of the filter can be found. The computational experiments show that the proposed approach gives better digital IIR filters than the existing evolutionary algorithm (EA based methods.

  7. Evolutionary conceptual analysis: faith community nursing.

    Science.gov (United States)

    Ziebarth, Deborah

    2014-12-01

    The aim of the study was to report an evolutionary concept analysis of faith community nursing (FCN). FCN is a source of healthcare delivery in the USA which has grown in comprehensiveness and complexity. With increasing healthcare cost and a focus on access and prevention, FCN has extended beyond the physical walls of the faith community building. Faith communities and healthcare organizations invest in FCN and standardized training programs exist. Using Rodgers' evolutionary analysis, the literature was examined for antecedents, attributes, and consequences of the concept. This design allows for understanding the historical and social nature of the concept and how it changes over time. A search of databases using the keywords FCN, faith community nurse, parish nursing, and parish nurse was done. The concept of FCN was explored using research and theoretical literature. A theoretical definition and model were developed with relevant implications. The search results netted a sample of 124 reports of research and theoretical articles from multiple disciplines: medicine, education, religion and philosophy, international health, and nursing. Theoretical definition: FCN is a method of healthcare delivery that is centered in a relationship between the nurse and client (client as person, family, group, or community). The relationship occurs in an iterative motion over time when the client seeks or is targeted for wholistic health care with the goal of optimal wholistic health functioning. Faith integrating is a continuous occurring attribute. Health promoting, disease managing, coordinating, empowering and accessing health care are other essential attributes. All essential attributes occur with intentionality in a faith community, home, health institution and other community settings with fluidity as part of a community, national, or global health initiative. A new theoretical definition and corresponding conceptual model of FCN provides a basis for future nursing

  8. SEDRIO/INCORE, an automatic optimal loading pattern search system for PWR NPP reload core using an expert system

    International Nuclear Information System (INIS)

    Xian Chunyu; Zhang Zongyao

    2003-01-01

    The expert knowledge library for Daya Bay and Qinshan phase II NPP has been established based on expert knowledge, and the reload core loading pattern heuristic search is performed. The in-core fuel management code system INCORE that has been used in engineering design is employed for neutron calculation, and loading pattern is evaluated by using of cycle length and core radial power peaking factor. The developed system SEDRIO/INCORE has been applied in cycle 4 for unit 2 of Daya Bay NPP and cycle 4 for Phase II in Qinshan NPP. The application demonstrated that the loading patterns obtained by SEDRIO/INCORE system are much better than reference ones from the view of the radial power peak and the cycle length

  9. Exploring social influence on evolutionary prisoner’s dilemma games in networks

    Science.gov (United States)

    Zong, Hengshan; Jia, Guozhu; Cheng, Yang

    2015-11-01

    Though numerous studies demonstrate the importance of social influence in deciding individual decision-making process in networks, little has been done to explore its impact on players’ behavioral patterns in evolutionary prisoner’s dilemma games (PDGs). This study investigates how social influenced strategy updating rules may affect the final equilibrium of game dynamics. The results show that weak social influence usually inhibits cooperation, while strong social influence has a mediating effect. The impacts of network structure and the existence of rebels in social influence scenarios are also tested. The paper provides a comprehensive interpretation on social influence effects on evolutionary PDGs in networks.

  10. 2nd International Conference on Harmony Search Algorithm

    CERN Document Server

    Geem, Zong

    2016-01-01

    The Harmony Search Algorithm (HSA) is one of the most well-known techniques in the field of soft computing, an important paradigm in the science and engineering community.  This volume, the proceedings of the 2nd International Conference on Harmony Search Algorithm 2015 (ICHSA 2015), brings together contributions describing the latest developments in the field of soft computing with a special focus on HSA techniques. It includes coverage of new methods that have potentially immense application in various fields. Contributed articles cover aspects of the following topics related to the Harmony Search Algorithm: analytical studies; improved, hybrid and multi-objective variants; parameter tuning; and large-scale applications.  The book also contains papers discussing recent advances on the following topics: genetic algorithms; evolutionary strategies; the firefly algorithm and cuckoo search; particle swarm optimization and ant colony optimization; simulated annealing; and local search techniques.   This book ...

  11. A fully automatic peak-search program for the evaluation of Gauss-shaped diffraction patterns

    International Nuclear Information System (INIS)

    Lauterjung, J.; Will, G.; Hinze, E.

    1985-01-01

    Diffraction patterns (X-rays or neutrons) often contain regions of overlapping, unresolved peaks. When using energy-dispersive techniques with solid state detectors the degree of overlap is especially high because of the poor resolution of such detectors. Profile analysis then offers the possibility to overcome, or at least reduce this drawback. In this paper a peak-search program is represented for fully automatic separation of the individual peaks. Only the instrumental parameter fwhm (full width at half-maximum) and the recorded spectrum are required as input for the program. Results are given for orthorhombic MnSO 4 . (orig.)

  12. System optimization for HVAC energy management using the robust evolutionary algorithm

    International Nuclear Information System (INIS)

    Fong, K.F.; Hanby, V.I.; Chow, T.T.

    2009-01-01

    For an installed centralized heating, ventilating and air conditioning (HVAC) system, appropriate energy management measures would achieve energy conservation targets through the optimal control and operation. The performance optimization of conventional HVAC systems may be handled by operation experience, but it may not cover different optimization scenarios and parameters in response to a variety of load and weather conditions. In this regard, it is common to apply the suitable simulation-optimization technique to model the system then determine the required operation parameters. The particular plant simulation models can be built up by either using the available simulation programs or a system of mathematical expressions. To handle the simulation models, iterations would be involved in the numerical solution methods. Since the gradient information is not easily available due to the complex nature of equations, the traditional gradient-based optimization methods are not applicable for this kind of system models. For the heuristic optimization methods, the continual search is commonly necessary, and the system function call is required for each search. The frequency of simulation function calls would then be a time-determining step, and an efficient optimization method is crucial, in order to find the solution through a number of function calls in a reasonable computational period. In this paper, the robust evolutionary algorithm (REA) is presented to tackle this nature of the HVAC simulation models. REA is based on one of the paradigms of evolutionary algorithm, evolution strategy, which is a stochastic population-based searching technique emphasized on mutation. The REA, which incorporates the Cauchy deterministic mutation, tournament selection and arithmetic recombination, would provide a synergetic effect for optimal search. The REA is effective to cope with the complex simulation models, as well as those represented by explicit mathematical expressions of

  13. Evolutionary plant physiology: Charles Darwin's forgotten synthesis

    Science.gov (United States)

    Kutschera, Ulrich; Niklas, Karl J.

    2009-11-01

    Charles Darwin dedicated more than 20 years of his life to a variety of investigations on higher plants (angiosperms). It has been implicitly assumed that these studies in the fields of descriptive botany and experimental plant physiology were carried out to corroborate his principle of descent with modification. However, Darwin’s son Francis, who was a professional plant biologist, pointed out that the interests of his father were both of a physiological and an evolutionary nature. In this article, we describe Darwin’s work on the physiology of higher plants from a modern perspective, with reference to the following topics: circumnutations, tropisms and the endogenous oscillator model; the evolutionary patterns of auxin action; the root-brain hypothesis; phloem structure and photosynthesis research; endosymbioses and growth-promoting bacteria; photomorphogenesis and phenotypic plasticity; basal metabolic rate, the Pfeffer-Kleiber relationship and metabolic optimality theory with respect to adaptive evolution; and developmental constraints versus functional equivalence in relationship to directional natural selection. Based on a review of these various fields of inquiry, we deduce the existence of a Darwinian (evolutionary) approach to plant physiology and define this emerging scientific discipline as the experimental study and theoretical analysis of the functions of green, sessile organisms from a phylogenetic perspective.

  14. Evolutionary plant physiology: Charles Darwin's forgotten synthesis.

    Science.gov (United States)

    Kutschera, Ulrich; Niklas, Karl J

    2009-11-01

    Charles Darwin dedicated more than 20 years of his life to a variety of investigations on higher plants (angiosperms). It has been implicitly assumed that these studies in the fields of descriptive botany and experimental plant physiology were carried out to corroborate his principle of descent with modification. However, Darwin's son Francis, who was a professional plant biologist, pointed out that the interests of his father were both of a physiological and an evolutionary nature. In this article, we describe Darwin's work on the physiology of higher plants from a modern perspective, with reference to the following topics: circumnutations, tropisms and the endogenous oscillator model; the evolutionary patterns of auxin action; the root-brain hypothesis; phloem structure and photosynthesis research; endosymbioses and growth-promoting bacteria; photomorphogenesis and phenotypic plasticity; basal metabolic rate, the Pfeffer-Kleiber relationship and metabolic optimality theory with respect to adaptive evolution; and developmental constraints versus functional equivalence in relationship to directional natural selection. Based on a review of these various fields of inquiry, we deduce the existence of a Darwinian (evolutionary) approach to plant physiology and define this emerging scientific discipline as the experimental study and theoretical analysis of the functions of green, sessile organisms from a phylogenetic perspective.

  15. Evolutionary games on multilayer networks: a colloquium

    Science.gov (United States)

    Wang, Zhen; Wang, Lin; Szolnoki, Attila; Perc, Matjaž

    2015-05-01

    Networks form the backbone of many complex systems, ranging from the Internet to human societies. Accordingly, not only is the range of our interactions limited and thus best described and modeled by networks, it is also a fact that the networks that are an integral part of such models are often interdependent or even interconnected. Networks of networks or multilayer networks are therefore a more apt description of social systems. This colloquium is devoted to evolutionary games on multilayer networks, and in particular to the evolution of cooperation as one of the main pillars of modern human societies. We first give an overview of the most significant conceptual differences between single-layer and multilayer networks, and we provide basic definitions and a classification of the most commonly used terms. Subsequently, we review fascinating and counterintuitive evolutionary outcomes that emerge due to different types of interdependencies between otherwise independent populations. The focus is on coupling through the utilities of players, through the flow of information, as well as through the popularity of different strategies on different network layers. The colloquium highlights the importance of pattern formation and collective behavior for the promotion of cooperation under adverse conditions, as well as the synergies between network science and evolutionary game theory.

  16. Levy Foraging in a Dynamic Environment – Extending the Levy Search

    Directory of Open Access Journals (Sweden)

    Vincenzo Fioriti

    2015-07-01

    Full Text Available A common task for robots is the patrolling of an unknown area with inadequate information about target locations. Under these circumstances it has been suggested that animal foraging could provide an optimal or at least sub-optimal search methodology, namely the Levy flight search. Although still in debate, it seems that predators somehow follow this search pattern when foraging, because it avoids being trapped in a local search if the food is beyond the sensory range. A Levy flight is a particular case of the random walk. Its displacements on a 2-D surface are drawn from the Pareto-Levy probability distribution, characterized by power law tails. The Levy flight search has many applications in optical material, ladars, optics, large database search, earthquake data analysis, location of DNA sites, human mobility, stock return analysis, online auctions, astronomy, ecology and biology. Almost all studies and simulations concerning the Levy flight foraging examine static or slowly moving (with respect to the forager uniformly distributed resources. Moreover, in recent works a small swarm of underwater autonomous vehicles has been used to test the standard Levy search in the underwater environment, with good results. In this paper we extend the classical Levy foraging framework taking into consideration a moving target allocated on a 2-D surface according to a radial probability distribution and comparing its performance with the random walk search. The metric used in the numerical simulations is the detection rate. Simulations include the sensor resolution, intended as the maximum detection distance of the forager from the target. Furthermore, contrarily to the usual Levy foraging framework, we use only one target. Results show that Levy flight outperforms the random walk if the sensor detection radius is not too small or too large. We also find the Levy flight in the velocity of the center of mass model of a fish school according the Kuramoto

  17. Evolutionary responses of native plant species to invasive plants: a review.

    Science.gov (United States)

    Oduor, Ayub M O

    2013-12-01

    Strong competition from invasive plant species often leads to declines in abundances and may, in certain cases, cause localized extinctions of native plant species. Nevertheless, studies have shown that certain populations of native plant species can co-exist with invasive plant species,suggesting the possibility of adaptive evolutionary responses of those populations to the invasive plants. Empirical inference of evolutionary responses of the native plant species to invasive plants has involved experiments comparing two conspecific groups of native plants for differences in expression of growth/reproductive traits: populations that have experienced competition from the invasive plant species (i.e. experienced natives) versus populations with no known history of interactions with the invasive plant species (i.e. naıve natives). Here, I employ a meta-analysis to obtain a general pattern of inferred evolutionary responses of native plant species from 53 such studies. In general, the experienced natives had significantly higher growth/reproductive performances than naıve natives, when grown with or without competition from invasive plants.While the current results indicate that certain populations of native plant species could potentially adapt evolutionarily to invasive plant species, the ecological and evolutionary mechanisms that probably underlie such evolutionary responses remain unexplored and should be the focus of future studies.

  18. More efficient evolutionary strategies for model calibration with watershed model for demonstration

    Science.gov (United States)

    Baggett, J. S.; Skahill, B. E.

    2008-12-01

    Evolutionary strategies allow automatic calibration of more complex models than traditional gradient based approaches, but they are more computationally intensive. We present several efficiency enhancements for evolution strategies, many of which are not new, but when combined have been shown to dramatically decrease the number of model runs required for calibration of synthetic problems. To reduce the number of expensive model runs we employ a surrogate objective function for an adaptively determined fraction of the population at each generation (Kern et al., 2006). We demonstrate improvements to the adaptive ranking strategy that increase its efficiency while sacrificing little reliability and further reduce the number of model runs required in densely sampled parts of parameter space. Furthermore, we include a gradient individual in each generation that is usually not selected when the search is in a global phase or when the derivatives are poorly approximated, but when selected near a smooth local minimum can dramatically increase convergence speed (Tahk et al., 2007). Finally, the selection of the gradient individual is used to adapt the size of the population near local minima. We show, by incorporating these enhancements into the Covariance Matrix Adaption Evolution Strategy (CMAES; Hansen, 2006), that their synergetic effect is greater than their individual parts. This hybrid evolutionary strategy exploits smooth structure when it is present but degrades to an ordinary evolutionary strategy, at worst, if smoothness is not present. Calibration of 2D-3D synthetic models with the modified CMAES requires approximately 10%-25% of the model runs of ordinary CMAES. Preliminary demonstration of this hybrid strategy will be shown for watershed model calibration problems. Hansen, N. (2006). The CMA Evolution Strategy: A Comparing Review. In J.A. Lozano, P. Larrañga, I. Inza and E. Bengoetxea (Eds.). Towards a new evolutionary computation. Advances in estimation of

  19. Random drift versus selection in academic vocabulary: an evolutionary analysis of published keywords.

    Directory of Open Access Journals (Sweden)

    R Alexander Bentley

    Full Text Available The evolution of vocabulary in academic publishing is characterized via keyword frequencies recorded in the ISI Web of Science citations database. In four distinct case-studies, evolutionary analysis of keyword frequency change through time is compared to a model of random copying used as the null hypothesis, such that selection may be identified against it. The case studies from the physical sciences indicate greater selection in keyword choice than in the social sciences. Similar evolutionary analyses can be applied to a wide range of phenomena; wherever the popularity of multiple items through time has been recorded, as with web searches, or sales of popular music and books, for example.

  20. Analyses of Evolutionary Characteristics of the Hemagglutinin-Esterase Gene of Influenza C Virus during a Period of 68 Years Reveals Evolutionary Patterns Different from Influenza A and B Viruses

    Directory of Open Access Journals (Sweden)

    Yuki Furuse

    2016-11-01

    Full Text Available Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses. Along with our data, we obtained public sequence data of the hemagglutinin-esterase gene of the virus; the dataset consists of 218 unique sequences of the virus collected from 14 countries between 1947 and 2014. Informatics analyses revealed that (1 multiple lineages have been circulating globally; (2 there have been weak and infrequent selective bottlenecks; (3 the evolutionary rate is low because of weak positive selection and a low capability to induce mutations; and (4 there is no significant positive selection although a few mutations affecting its antigenicity have been induced. The unique evolutionary dynamics of the influenza C virus must be shaped by multiple factors, including virological, immunological, and epidemiological characteristics.

  1. Joy and happiness: a simultaneous and evolutionary concept analysis.

    Science.gov (United States)

    Cottrell, Laura

    2016-07-01

    To report a simultaneous and evolutionary analysis of the concepts of joy and long-term happiness. Joy and happiness are underrepresented in the nursing literature, though negative concepts are well represented. When mentioned in the literature, neither joy nor happiness is adequately defined, explained, or clearly understood. To promote further investigation of these concepts in nursing and to explore their relationship with health and healing, conceptual clarity is an essential first step. Concept analysis. The following databases were searched, without time restrictions, for articles in English: Academic Search Complete, Anthropology Plus; ATLA Religious Database with ATLASerials; Cumulative Index of Nursing and Allied Health Literature (CINAHL); Education Research Complete; Humanities International Complete; Psych EXTRA; and SocINDEX with Full Text. The final sample size consists of 61 articles and one book, published between 1978-2014. An adapted combination of Rodgers' Evolutionary Model and Haase et al.'s Simultaneous Concept Analysis (SCA) method. Though both are positive concepts, joy and happiness have significant differences. Attributes of joy describe a spontaneous, sudden and transient concept associated with connection, awareness, and freedom. Attributes of happiness describe a pursued, long-lasting, stable mental state associated with virtue and self-control. Further exploration of joy and happiness is necessary to ascertain their relationship with health and their value to nursing practice and theory development. Nurses are encouraged to consider the value of positive concepts to all areas of nursing. © 2016 John Wiley & Sons Ltd.

  2. Polymorphic Evolutionary Games.

    Science.gov (United States)

    Fishman, Michael A

    2016-06-07

    In this paper, I present an analytical framework for polymorphic evolutionary games suitable for explicitly modeling evolutionary processes in diploid populations with sexual reproduction. The principal aspect of the proposed approach is adding diploid genetics cum sexual recombination to a traditional evolutionary game, and switching from phenotypes to haplotypes as the new game׳s pure strategies. Here, the relevant pure strategy׳s payoffs derived by summing the payoffs of all the phenotypes capable of producing gametes containing that particular haplotype weighted by the pertinent probabilities. The resulting game is structurally identical to the familiar Evolutionary Games with non-linear pure strategy payoffs (Hofbauer and Sigmund, 1998. Cambridge University Press), and can be analyzed in terms of an established analytical framework for such games. And these results can be translated into the terms of genotypic, and whence, phenotypic evolutionary stability pertinent to the original game. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. THE THEORY OF THE FIRM AND THE EVOLUTIONARY GAMES

    Directory of Open Access Journals (Sweden)

    Sirghi Nicoleta

    2013-07-01

    Full Text Available The neoclassical theory of the firm deals with the pattern of perfect competition, within which the perfect information available to economic agents provides instant allocation of production factors and access to economic goods. The Austrian School (C. Menger, L. von Mises, Hayek, etc. supported the idea of minimal state intervention on the markets, bringing important conceptual developments on the theory of the firm. Hirschleifer (1982 put forward the model of social and institutional functioning, arguing that the game theory is able to predict the outcome of the collective behavior and the human characteristics necessary for building the respective institutions.The evolutionary theory provides the firm and the entrepreneur the recognition of the functions of innovation, of generating and exploiting information and of organizing and coordinating production. The evolutionary perspective of the firm assumes the existence of a body of knowledge that is acquired through and builds up the organizational memory, subsequently found in routines, all choices being made based on these routines (Nelson and Winter, 2002. The evolution of the firm is considered to be similar to natural selection, but unlike the classic market selection, the evolutionists suggest the existence of a plurality of selection media. The present research is structured as follows: a brief introduction into the theories of the firm, the second part of the paper analyzes the theories of the firm from an institutional, neo-institutional and evolutionary perspective. In the third part of the paper the evolutionary games are described and analyzed from the evolutionary perspective of the firm. The last part of the paper represents a study of the “hawk-dove” game dynamic replicator. The final conclusions of the paper show that the evolutionary theory brings valuable contributions to the foundation of explanations regarding economic phenomena, indicating new directions for advanced

  4. Remembering the evolutionary Freud.

    Science.gov (United States)

    Young, Allan

    2006-03-01

    Throughout his career as a writer, Sigmund Freud maintained an interest in the evolutionary origins of the human mind and its neurotic and psychotic disorders. In common with many writers then and now, he believed that the evolutionary past is conserved in the mind and the brain. Today the "evolutionary Freud" is nearly forgotten. Even among Freudians, he is regarded to be a red herring, relevant only to the extent that he diverts attention from the enduring achievements of the authentic Freud. There are three ways to explain these attitudes. First, the evolutionary Freud's key work is the "Overview of the Transference Neurosis" (1915). But it was published at an inopportune moment, forty years after the author's death, during the so-called "Freud wars." Second, Freud eventually lost interest in the "Overview" and the prospect of a comprehensive evolutionary theory of psychopathology. The publication of The Ego and the Id (1923), introducing Freud's structural theory of the psyche, marked the point of no return. Finally, Freud's evolutionary theory is simply not credible. It is based on just-so stories and a thoroughly discredited evolutionary mechanism, Lamarckian use-inheritance. Explanations one and two are probably correct but also uninteresting. Explanation number three assumes that there is a fundamental difference between Freud's evolutionary narratives (not credible) and the evolutionary accounts of psychopathology that currently circulate in psychiatry and mainstream journals (credible). The assumption is mistaken but worth investigating.

  5. Understanding the mind from an evolutionary perspective: an overview of evolutionary psychology.

    Science.gov (United States)

    Shackelford, Todd K; Liddle, James R

    2014-05-01

    The theory of evolution by natural selection provides the only scientific explanation for the existence of complex adaptations. The design features of the brain, like any organ, are the result of selection pressures operating over deep time. Evolutionary psychology posits that the human brain comprises a multitude of evolved psychological mechanisms, adaptations to specific and recurrent problems of survival and reproduction faced over human evolutionary history. Although some mistakenly view evolutionary psychology as promoting genetic determinism, evolutionary psychologists appreciate and emphasize the interactions between genes and environments. This approach to psychology has led to a richer understanding of a variety of psychological phenomena, and has provided a powerful foundation for generating novel hypotheses. Critics argue that evolutionary psychologists resort to storytelling, but as with any branch of science, empirical testing is a vital component of the field, with hypotheses standing or falling with the weight of the evidence. Evolutionary psychology is uniquely suited to provide a unifying theoretical framework for the disparate subdisciplines of psychology. An evolutionary perspective has provided insights into several subdisciplines of psychology, while simultaneously demonstrating the arbitrary nature of dividing psychological science into such subdisciplines. Evolutionary psychologists have amassed a substantial empirical and theoretical literature, but as a relatively new approach to psychology, many questions remain, with several promising directions for future research. For further resources related to this article, please visit the WIREs website. The authors have declared no conflicts of interest for this article. © 2014 John Wiley & Sons, Ltd.

  6. Application of network methods for understanding evolutionary dynamics in discrete habitats.

    Science.gov (United States)

    Greenbaum, Gili; Fefferman, Nina H

    2017-06-01

    In populations occupying discrete habitat patches, gene flow between habitat patches may form an intricate population structure. In such structures, the evolutionary dynamics resulting from interaction of gene-flow patterns with other evolutionary forces may be exceedingly complex. Several models describing gene flow between discrete habitat patches have been presented in the population-genetics literature; however, these models have usually addressed relatively simple settings of habitable patches and have stopped short of providing general methodologies for addressing nontrivial gene-flow patterns. In the last decades, network theory - a branch of discrete mathematics concerned with complex interactions between discrete elements - has been applied to address several problems in population genetics by modelling gene flow between habitat patches using networks. Here, we present the idea and concepts of modelling complex gene flows in discrete habitats using networks. Our goal is to raise awareness to existing network theory applications in molecular ecology studies, as well as to outline the current and potential contribution of network methods to the understanding of evolutionary dynamics in discrete habitats. We review the main branches of network theory that have been, or that we believe potentially could be, applied to population genetics and molecular ecology research. We address applications to theoretical modelling and to empirical population-genetic studies, and we highlight future directions for extending the integration of network science with molecular ecology. © 2017 John Wiley & Sons Ltd.

  7. Low emittance lattice optimization using a multi-objective evolutionary algorithm

    International Nuclear Information System (INIS)

    Gao Weiwei; Wang Lin; Li Weimin; He Duohui

    2011-01-01

    A low emittance lattice design and optimization procedure are systematically studied with a non-dominated sorting-based multi-objective evolutionary algorithm which not only globally searches the low emittance lattice, but also optimizes some beam quantities such as betatron tunes, momentum compaction factor and dispersion function simultaneously. In this paper the detailed algorithm and lattice design procedure are presented. The Hefei light source upgrade project storage ring lattice, with fixed magnet layout, is designed to illustrate this optimization procedure. (authors)

  8. SEARCHING FOR URBAN PATTERNS; AN ASSESSMENT OF HISTORIC EDGES AND ITS SURROUNDING CONTEXT: HISTORIC CAIRO AS A CASE STUDY

    Directory of Open Access Journals (Sweden)

    Nabil Mohareb

    2016-07-01

    Full Text Available This paper analyzes the urban edges of historic cities. Managing these edges would enhance the success of any intervention projects inside the historic fabric. The paper develops and tests a method of analytical assessment framework that is applicable for quantitative analysis within an urban edge. It is capable of measuring micro and macro levels of analysis of historic urban edges with reference to their spatial configuration. In addition, the paper searches for repetitive spatial configuration patterns. The main case study is Historic Cairo. The paper reveals that there are apparent patterns of cause and effect of both spatial configurations and related activities along the urban edges, forming different type of barriers. The paper discovers the repetitive spatial, architectural, and land-use patterns that exist on various edges. These patterns enable the possibility of learning and acquiring from other successful interventions that have been applied to similar patterns, without being limited to cultural or contextual differences.

  9. Looking at the origin of phenotypic variation from pattern formation ...

    Indian Academy of Sciences (India)

    Prakash

    evolutionary considerations, a large number of researchers, ... This article critically reviews some widespread views about the overall functioning of development. ... Thus, a great deal about the evolution and functioning of ... variants and thus take patterns of phenotypic variation as ..... Evolutionary thinking to the rescue.

  10. An Enhanced Differential Evolution with Elite Chaotic Local Search

    Directory of Open Access Journals (Sweden)

    Zhaolu Guo

    2015-01-01

    Full Text Available Differential evolution (DE is a simple yet efficient evolutionary algorithm for real-world engineering problems. However, its search ability should be further enhanced to obtain better solutions when DE is applied to solve complex optimization problems. This paper presents an enhanced differential evolution with elite chaotic local search (DEECL. In DEECL, it utilizes a chaotic search strategy based on the heuristic information from the elite individuals to promote the exploitation power. Moreover, DEECL employs a simple and effective parameter adaptation mechanism to enhance the robustness. Experiments are conducted on a set of classical test functions. The experimental results show that DEECL is very competitive on the majority of the test functions.

  11. DrawCompileEvolve: Sparking interactive evolutionary art with human creations

    DEFF Research Database (Denmark)

    Zhang, Jinhong; Taarnby, Rasmus; Liapis, Antonios

    2015-01-01

    This paper presents DrawCompileEvolve, a web-based drawing tool which allows users to draw simple primitive shapes, group them together or define patterns in their groupings (e.g. symmetry, repetition). The user’s vector drawing is then compiled into an indirectly encoded genetic representation......, which can be evolved interactively, allowing the user to change the image’s colors, patterns and ultimately transform it. The human artist has direct control while drawing the initial seed of an evolutionary run and indirect control while interactively evolving it, thus making DrawCompileEvolve a mixed...

  12. Concentrated Hitting Times of Randomized Search Heuristics with Variable Drift

    DEFF Research Database (Denmark)

    Lehre, Per Kristian; Witt, Carsten

    2014-01-01

    Drift analysis is one of the state-of-the-art techniques for the runtime analysis of randomized search heuristics (RSHs) such as evolutionary algorithms (EAs), simulated annealing etc. The vast majority of existing drift theorems yield bounds on the expected value of the hitting time for a target...

  13. [Evolutionary medicine].

    Science.gov (United States)

    Wjst, M

    2013-12-01

    Evolutionary medicine allows new insights into long standing medical problems. Are we "really stoneagers on the fast lane"? This insight might have enormous consequences and will allow new answers that could never been provided by traditional anthropology. Only now this is made possible using data from molecular medicine and systems biology. Thereby evolutionary medicine takes a leap from a merely theoretical discipline to practical fields - reproductive, nutritional and preventive medicine, as well as microbiology, immunology and psychiatry. Evolutionary medicine is not another "just so story" but a serious candidate for the medical curriculum providing a universal understanding of health and disease based on our biological origin. © Georg Thieme Verlag KG Stuttgart · New York.

  14. Core principles of evolutionary medicine

    Science.gov (United States)

    Grunspan, Daniel Z; Nesse, Randolph M; Barnes, M Elizabeth; Brownell, Sara E

    2018-01-01

    Abstract Background and objectives Evolutionary medicine is a rapidly growing field that uses the principles of evolutionary biology to better understand, prevent and treat disease, and that uses studies of disease to advance basic knowledge in evolutionary biology. Over-arching principles of evolutionary medicine have been described in publications, but our study is the first to systematically elicit core principles from a diverse panel of experts in evolutionary medicine. These principles should be useful to advance recent recommendations made by The Association of American Medical Colleges and the Howard Hughes Medical Institute to make evolutionary thinking a core competency for pre-medical education. Methodology The Delphi method was used to elicit and validate a list of core principles for evolutionary medicine. The study included four surveys administered in sequence to 56 expert panelists. The initial open-ended survey created a list of possible core principles; the three subsequent surveys winnowed the list and assessed the accuracy and importance of each principle. Results Fourteen core principles elicited at least 80% of the panelists to agree or strongly agree that they were important core principles for evolutionary medicine. These principles over-lapped with concepts discussed in other articles discussing key concepts in evolutionary medicine. Conclusions and implications This set of core principles will be helpful for researchers and instructors in evolutionary medicine. We recommend that evolutionary medicine instructors use the list of core principles to construct learning goals. Evolutionary medicine is a young field, so this list of core principles will likely change as the field develops further. PMID:29493660

  15. Evolutionary tracks of extended radio sources

    International Nuclear Information System (INIS)

    Baldwin, J.E.

    1982-01-01

    We know almost nothing about the evolutionary tracks of extragalactic radio sources but those tracks are, however, strongly constrained by the distribution of sources in the radio luminosity, P, overall physical size, D, diagram. The P-D diagram for the 3CR 166 source sample of Jenkins et al. (1977) is presented with later additions. Most of the sources are identified and have known redshifts. Because of doubts about the completeness of the sample in this region, the author has made searches in the 6C 151MHz survey for sources with specific surface brightnesses. The numbers found to a limiting flux density of 1-2 Jy suggest that there is no serious underestimate of the numbers in 166 source sample. (Auth.)

  16. Obtention control bars patterns for a BWR using Tabo search; Obtencion de patrones de barras de control para un BWR usando busqueda Tabu

    Energy Technology Data Exchange (ETDEWEB)

    Castillo, A.; Ortiz, J.J.; Alonso, G. [Instituto Nacional de Investigaciones Nucleares, Km. 36.5 Carretera Mexico-Toluca, Ocoyoacac, Estado de Mexico 52045 (Mexico); Morales, L.B. [UNAM, IIMAS, Ciudad Universitaria, D. F. 04510 (Mexico); Valle, E. del [IPN, ESFM, Unidad Profesional ' Adolfo Lopez Mateos' , Col. Lindavista 07738, D. F. (Mexico)]. e-mail: jacm@nuclear.inin.mx

    2004-07-01

    The obtained results when implementing the technique of tabu search, for to optimize patterns of control bars in a BWR type reactor, using the CM-PRESTO code are presented. The patterns of control bars were obtained for the designs of fuel reloads obtained in a previous work, using the same technique. The obtained results correspond to a cycle of 18 months using 112 fresh fuels enriched at the 3.53 of U-235. The used technique of tabu search, prohibits recently visited movements, in the position that correspond to the axial positions of the control bars, additionally the tiempo{sub t}abu matrix is used for to manage a size of variable tabu list and the objective function is punished with the frequency of the forbidden movements. The obtained patterns of control bars improve the longitude of the cycle with regard to the reference values and they complete the restrictions of safety. (Author)

  17. Searching for patterns in TJ-II time evolution signals

    International Nuclear Information System (INIS)

    Farias, G.; Dormido-Canto, S.; Vega, J.; Sanchez, J.; Duro, N.; Dormido, R.; Ochando, M.; Santos, M.; Pajares, G.

    2006-01-01

    Since fusion plasma experiments generate hundreds of signals, it is important for their analysis to have automatic mechanisms for searching for similarities and retrieving specific data from the signal database. This paper describes a technique for searching in the TJ-II database that combines support vector machines and similarity query methods. Firstly, plasma signals are pre-processed by wavelet transform or discrete Fourier transform to reduce the dimensionality of the problem and to extract their main features. Secondly, support vector machines are used to classify a set of signals by reference to an input signal. Finally, similarity query methods (Euclidean distance and bounding envelope) are used to search the set of signals that best matches the input signal

  18. Evolved finite state controller for hybrid system in reduced search space

    DEFF Research Database (Denmark)

    Dupuis, Jean-Francois; Fan, Zhun

    2009-01-01

    This paper presents an evolutionary methodology to automatically generate finite state automata (FSA) controllers to control hybrid systems. The proposed approach reduces the search space using an invariant analysis of the system. FSA controllers for a case study of two-tank system have been...

  19. Applying evolutionary anthropology.

    Science.gov (United States)

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

    Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. © 2015 Wiley Periodicals, Inc.

  20. Applying Evolutionary Anthropology

    Science.gov (United States)

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

    Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. PMID:25684561

  1. Local Orientation and the Evolution of Foraging: Changes in Decision Making Can Eliminate Evolutionary Trade-offs

    Science.gov (United States)

    van der Post, Daniel J.; Semmann, Dirk

    2011-01-01

    Information processing is a major aspect of the evolution of animal behavior. In foraging, responsiveness to local feeding opportunities can generate patterns of behavior which reflect or “recognize patterns” in the environment beyond the perception of individuals. Theory on the evolution of behavior generally neglects such opportunity-based adaptation. Using a spatial individual-based model we study the role of opportunity-based adaptation in the evolution of foraging, and how it depends on local decision making. We compare two model variants which differ in the individual decision making that can evolve (restricted and extended model), and study the evolution of simple foraging behavior in environments where food is distributed either uniformly or in patches. We find that opportunity-based adaptation and the pattern recognition it generates, plays an important role in foraging success, particularly in patchy environments where one of the main challenges is “staying in patches”. In the restricted model this is achieved by genetic adaptation of move and search behavior, in light of a trade-off on within- and between-patch behavior. In the extended model this trade-off does not arise because decision making capabilities allow for differentiated behavioral patterns. As a consequence, it becomes possible for properties of movement to be specialized for detection of patches with more food, a larger scale information processing not present in the restricted model. Our results show that changes in decision making abilities can alter what kinds of pattern recognition are possible, eliminate an evolutionary trade-off and change the adaptive landscape. PMID:21998571

  2. Self-organized modularization in evolutionary algorithms.

    Science.gov (United States)

    Dauscher, Peter; Uthmann, Thomas

    2005-01-01

    The principle of modularization has proven to be extremely successful in the field of technical applications and particularly for Software Engineering purposes. The question to be answered within the present article is whether mechanisms can also be identified within the framework of Evolutionary Computation that cause a modularization of solutions. We will concentrate on processes, where modularization results only from the typical evolutionary operators, i.e. selection and variation by recombination and mutation (and not, e.g., from special modularization operators). This is what we call Self-Organized Modularization. Based on a combination of two formalizations by Radcliffe and Altenberg, some quantitative measures of modularity are introduced. Particularly, we distinguish Built-in Modularity as an inherent property of a genotype and Effective Modularity, which depends on the rest of the population. These measures can easily be applied to a wide range of present Evolutionary Computation models. It will be shown, both theoretically and by simulation, that under certain conditions, Effective Modularity (as defined within this paper) can be a selection factor. This causes Self-Organized Modularization to take place. The experimental observations emphasize the importance of Effective Modularity in comparison with Built-in Modularity. Although the experimental results have been obtained using a minimalist toy model, they can lead to a number of consequences for existing models as well as for future approaches. Furthermore, the results suggest a complex self-amplification of highly modular equivalence classes in the case of respected relations. Since the well-known Holland schemata are just the equivalence classes of respected relations in most Simple Genetic Algorithms, this observation emphasizes the role of schemata as Building Blocks (in comparison with arbitrary subsets of the search space).

  3. Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions.

    Science.gov (United States)

    Peer, Asaf; Margalit, Hanah

    2014-07-01

    Most bacterial small RNAs (sRNAs) are post-transcriptional regulators of gene expression, exerting their regulatory function by base-pairing with their target mRNAs. While it has become evident that sRNAs play central regulatory roles in the cell, little is known about their evolution and the evolution of their regulatory interactions. Here we used the prokaryotic phylogenetic tree to reconstruct the evolutionary history of Escherichia coli sRNAs and their binding sites on target mRNAs. We discovered that sRNAs currently present in E. coli mainly accumulated inside the Enterobacteriales order, succeeding the appearance of other types of noncoding RNAs and concurrently with the evolution of a variant of the Hfq protein exhibiting a longer C-terminal region. Our analysis of the evolutionary ages of sRNA-mRNA interactions revealed that while all sRNAs were evolutionarily older than most of their known binding sites on mRNA targets, for quite a few sRNAs there was at least one binding site that coappeared with or preceded them. It is conceivable that the establishment of these first interactions forced selective pressure on the sRNAs, after which additional targets were acquired by fitting a binding site to the active region of the sRNA. This conjecture is supported by the appearance of many binding sites on target mRNAs only after the sRNA gain, despite the prior presence of the target gene in ancestral genomes. Our results suggest a selective mechanism that maintained the sRNAs across the phylogenetic tree, and shed light on the evolution of E. coli post-transcriptional regulatory network. © 2014 Peer and Margalit; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  4. Search and optimization by metaheuristics techniques and algorithms inspired by nature

    CERN Document Server

    Du, Ke-Lin

    2016-01-01

    This textbook provides a comprehensive introduction to nature-inspired metaheuristic methods for search and optimization, including the latest trends in evolutionary algorithms and other forms of natural computing. Over 100 different types of these methods are discussed in detail. The authors emphasize non-standard optimization problems and utilize a natural approach to the topic, moving from basic notions to more complex ones. An introductory chapter covers the necessary biological and mathematical backgrounds for understanding the main material. Subsequent chapters then explore almost all of the major metaheuristics for search and optimization created based on natural phenomena, including simulated annealing, recurrent neural networks, genetic algorithms and genetic programming, differential evolution, memetic algorithms, particle swarm optimization, artificial immune systems, ant colony optimization, tabu search and scatter search, bee and bacteria foraging algorithms, harmony search, biomolecular computin...

  5. Evolutionary Expectations

    DEFF Research Database (Denmark)

    Nash, Ulrik William

    2014-01-01

    , they are correlated among people who share environments because these individuals satisfice within their cognitive bounds by using cues in order of validity, as opposed to using cues arbitrarily. Any difference in expectations thereby arise from differences in cognitive ability, because two individuals with identical...... cognitive bounds will perceive business opportunities identically. In addition, because cues provide information about latent causal structures of the environment, changes in causality must be accompanied by changes in cognitive representations if adaptation is to be maintained. The concept of evolutionary......The concept of evolutionary expectations descends from cue learning psychology, synthesizing ideas on rational expectations with ideas on bounded rationality, to provide support for these ideas simultaneously. Evolutionary expectations are rational, but within cognitive bounds. Moreover...

  6. Evolutionary Awareness

    Directory of Open Access Journals (Sweden)

    Gregory Gorelik

    2014-10-01

    Full Text Available In this article, we advance the concept of “evolutionary awareness,” a metacognitive framework that examines human thought and emotion from a naturalistic, evolutionary perspective. We begin by discussing the evolution and current functioning of the moral foundations on which our framework rests. Next, we discuss the possible applications of such an evolutionarily-informed ethical framework to several domains of human behavior, namely: sexual maturation, mate attraction, intrasexual competition, culture, and the separation between various academic disciplines. Finally, we discuss ways in which an evolutionary awareness can inform our cross-generational activities—which we refer to as “intergenerational extended phenotypes”—by helping us to construct a better future for ourselves, for other sentient beings, and for our environment.

  7. Short-term economic environmental hydrothermal scheduling using improved multi-objective gravitational search algorithm

    International Nuclear Information System (INIS)

    Li, Chunlong; Zhou, Jianzhong; Lu, Peng; Wang, Chao

    2015-01-01

    Highlights: • Improved multi-objective gravitational search algorithm. • An elite archive set is proposed to guide evolutionary process. • Neighborhood searching mechanism to improve local search ability. • Adopt chaotic mutation for avoiding premature convergence. • Propose feasible space method to handle hydro plant constrains. - Abstract: With growing concerns about energy and environment, short-term economic environmental hydrothermal scheduling (SEEHS) plays a more and more important role in power system. Because of the two objectives and various constraints, SEEHS is a complex multi-objective optimization problem (MOOP). In order to solve the problem, we propose an improved multi-objective gravitational search algorithm (IMOGSA) in this paper. In IMOGSA, the mass of the agent is redefined by multiple objectives to make it suitable for MOOP. An elite archive set is proposed to keep Pareto optimal solutions and guide evolutionary process. For balancing exploration and exploitation, a neighborhood searching mechanism is presented to cooperate with chaotic mutation. Moreover, a novel method based on feasible space is proposed to handle hydro plant constraints during SEEHS, and a violation adjustment method is adopted to handle power balance constraint. For verifying its effectiveness, the proposed IMOGSA is applied to a hydrothermal system in two different case studies. The simulation results show that IMOGSA has a competitive performance in SEEHS when compared with other established algorithms

  8. Evolutionary Developmental Robotics: Improving Morphology and Control of Physical Robots.

    Science.gov (United States)

    Vujovic, Vuk; Rosendo, Andre; Brodbeck, Luzius; Iida, Fumiya

    2017-01-01

    Evolutionary algorithms have previously been applied to the design of morphology and control of robots. The design space for such tasks can be very complex, which can prevent evolution from efficiently discovering fit solutions. In this article we introduce an evolutionary-developmental (evo-devo) experiment with real-world robots. It allows robots to grow their leg size to simulate ontogenetic morphological changes, and this is the first time that such an experiment has been performed in the physical world. To test diverse robot morphologies, robot legs of variable shapes were generated during the evolutionary process and autonomously built using additive fabrication. We present two cases with evo-devo experiments and one with evolution, and we hypothesize that the addition of a developmental stage can be used within robotics to improve performance. Moreover, our results show that a nonlinear system-environment interaction exists, which explains the nontrivial locomotion patterns observed. In the future, robots will be present in our daily lives, and this work introduces for the first time physical robots that evolve and grow while interacting with the environment.

  9. Implementation of strength pareto evolutionary algorithm II in the multiobjective burnable poison placement optimization of KWU pressurized water reactor

    International Nuclear Information System (INIS)

    Gharari, Rahman; Poursalehi, Navid; Abbasi, Mohmmadreza; Aghale, Mahdi

    2016-01-01

    In this research, for the first time, a new optimization method, i.e., strength Pareto evolutionary algorithm II (SPEA-II), is developed for the burnable poison placement (BPP) optimization of a nuclear reactor core. In the BPP problem, an optimized placement map of fuel assemblies with burnable poison is searched for a given core loading pattern according to defined objectives. In this work, SPEA-II coupled with a nodal expansion code is used for solving the BPP problem of Kraftwerk Union AG (KWU) pressurized water reactor. Our optimization goal for the BPP is to achieve a greater multiplication factor (K-e-f-f) for gaining possible longer operation cycles along with more flattening of fuel assembly relative power distribution, considering a safety constraint on the radial power peaking factor. For appraising the proposed methodology, the basic approach, i.e., SPEA, is also developed in order to compare obtained results. In general, results reveal the acceptance performance and high strength of SPEA, particularly its new version, i.e., SPEA-II, in achieving a semioptimized loading pattern for the BPP optimization of KWU pressurized water reactor

  10. Implementation of strength pareto evolutionary algorithm II in the multiobjective burnable poison placement optimization of KWU pressurized water reactor

    Energy Technology Data Exchange (ETDEWEB)

    Gharari, Rahman [Nuclear Science and Technology Research Institute (NSTRI), Tehran (Iran, Islamic Republic of); Poursalehi, Navid; Abbasi, Mohmmadreza; Aghale, Mahdi [Nuclear Engineering Dept, Shahid Beheshti University, Tehran (Iran, Islamic Republic of)

    2016-10-15

    In this research, for the first time, a new optimization method, i.e., strength Pareto evolutionary algorithm II (SPEA-II), is developed for the burnable poison placement (BPP) optimization of a nuclear reactor core. In the BPP problem, an optimized placement map of fuel assemblies with burnable poison is searched for a given core loading pattern according to defined objectives. In this work, SPEA-II coupled with a nodal expansion code is used for solving the BPP problem of Kraftwerk Union AG (KWU) pressurized water reactor. Our optimization goal for the BPP is to achieve a greater multiplication factor (K-e-f-f) for gaining possible longer operation cycles along with more flattening of fuel assembly relative power distribution, considering a safety constraint on the radial power peaking factor. For appraising the proposed methodology, the basic approach, i.e., SPEA, is also developed in order to compare obtained results. In general, results reveal the acceptance performance and high strength of SPEA, particularly its new version, i.e., SPEA-II, in achieving a semioptimized loading pattern for the BPP optimization of KWU pressurized water reactor.

  11. Hough transform search for continuous gravitational waves

    International Nuclear Information System (INIS)

    Krishnan, Badri; Papa, Maria Alessandra; Sintes, Alicia M.; Schutz, Bernard F.; Frasca, Sergio; Palomba, Cristiano

    2004-01-01

    This paper describes an incoherent method to search for continuous gravitational waves based on the Hough transform, a well-known technique used for detecting patterns in digital images. We apply the Hough transform to detect patterns in the time-frequency plane of the data produced by an earth-based gravitational wave detector. Two different flavors of searches will be considered, depending on the type of input to the Hough transform: either Fourier transforms of the detector data or the output of a coherent matched-filtering type search. We present the technical details for implementing the Hough transform algorithm for both kinds of searches, their statistical properties, and their sensitivities

  12. EVOLUTIONARY FOUNDATIONS FOR MOLECULAR MEDICINE

    Science.gov (United States)

    Nesse, Randolph M.; Ganten, Detlev; Gregory, T. Ryan; Omenn, Gilbert S.

    2015-01-01

    Evolution has long provided a foundation for population genetics, but many major advances in evolutionary biology from the 20th century are only now being applied in molecular medicine. They include the distinction between proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are further transforming evolutionary biology and creating yet more opportunities for progress at the interface of evolution with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and others to speed the development of evolutionary molecular medicine. PMID:22544168

  13. Temporal stability of visual search-driven biometrics

    Science.gov (United States)

    Yoon, Hong-Jun; Carmichael, Tandy R.; Tourassi, Georgia

    2015-03-01

    Previously, we have shown the potential of using an individual's visual search pattern as a possible biometric. That study focused on viewing images displaying dot-patterns with different spatial relationships to determine which pattern can be more effective in establishing the identity of an individual. In this follow-up study we investigated the temporal stability of this biometric. We performed an experiment with 16 individuals asked to search for a predetermined feature of a random-dot pattern as we tracked their eye movements. Each participant completed four testing sessions consisting of two dot patterns repeated twice. One dot pattern displayed concentric circles shifted to the left or right side of the screen overlaid with visual noise, and participants were asked which side the circles were centered on. The second dot-pattern displayed a number of circles (between 0 and 4) scattered on the screen overlaid with visual noise, and participants were asked how many circles they could identify. Each session contained 5 untracked tutorial questions and 50 tracked test questions (200 total tracked questions per participant). To create each participant's "fingerprint", we constructed a Hidden Markov Model (HMM) from the gaze data representing the underlying visual search and cognitive process. The accuracy of the derived HMM models was evaluated using cross-validation for various time-dependent train-test conditions. Subject identification accuracy ranged from 17.6% to 41.8% for all conditions, which is significantly higher than random guessing (1/16 = 6.25%). The results suggest that visual search pattern is a promising, temporally stable personalized fingerprint of perceptual organization.

  14. Temporal Stability of Visual Search-Driven Biometrics

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Hong-Jun [ORNL; Carmichael, Tandy [Tennessee Technological University; Tourassi, Georgia [ORNL

    2015-01-01

    Previously, we have shown the potential of using an individual s visual search pattern as a possible biometric. That study focused on viewing images displaying dot-patterns with different spatial relationships to determine which pattern can be more effective in establishing the identity of an individual. In this follow-up study we investigated the temporal stability of this biometric. We performed an experiment with 16 individuals asked to search for a predetermined feature of a random-dot pattern as we tracked their eye movements. Each participant completed four testing sessions consisting of two dot patterns repeated twice. One dot pattern displayed concentric circles shifted to the left or right side of the screen overlaid with visual noise, and participants were asked which side the circles were centered on. The second dot-pattern displayed a number of circles (between 0 and 4) scattered on the screen overlaid with visual noise, and participants were asked how many circles they could identify. Each session contained 5 untracked tutorial questions and 50 tracked test questions (200 total tracked questions per participant). To create each participant s "fingerprint", we constructed a Hidden Markov Model (HMM) from the gaze data representing the underlying visual search and cognitive process. The accuracy of the derived HMM models was evaluated using cross-validation for various time-dependent train-test conditions. Subject identification accuracy ranged from 17.6% to 41.8% for all conditions, which is significantly higher than random guessing (1/16 = 6.25%). The results suggest that visual search pattern is a promising, fairly stable personalized fingerprint of perceptual organization.

  15. Surveillance Tools Emerging From Search Engines and Social Media Data for Determining Eye Disease Patterns.

    Science.gov (United States)

    Deiner, Michael S; Lietman, Thomas M; McLeod, Stephen D; Chodosh, James; Porco, Travis C

    2016-09-01

    Internet-based search engine and social media data may provide a novel complementary source for better understanding the epidemiologic factors of infectious eye diseases, which could better inform eye health care and disease prevention. To assess whether data from internet-based social media and search engines are associated with objective clinic-based diagnoses of conjunctivitis. Data from encounters of 4143 patients diagnosed with conjunctivitis from June 3, 2012, to April 26, 2014, at the University of California San Francisco (UCSF) Medical Center, were analyzed using Spearman rank correlation of each weekly observation to compare demographics and seasonality of nonallergic conjunctivitis with allergic conjunctivitis. Data for patient encounters with diagnoses for glaucoma and influenza were also obtained for the same period and compared with conjunctivitis. Temporal patterns of Twitter and Google web search data, geolocated to the United States and associated with these clinical diagnoses, were compared with the clinical encounters. The a priori hypothesis was that weekly internet-based searches and social media posts about conjunctivitis may reflect the true weekly clinical occurrence of conjunctivitis. Weekly total clinical diagnoses at UCSF of nonallergic conjunctivitis, allergic conjunctivitis, glaucoma, and influenza were compared using Spearman rank correlation with equivalent weekly data on Tweets related to disease or disease-related keyword searches obtained from Google Trends. Seasonality of clinical diagnoses of nonallergic conjunctivitis among the 4143 patients (2364 females [57.1%] and 1776 males [42.9%]) with 5816 conjunctivitis encounters at UCSF correlated strongly with results of Google searches in the United States for the term pink eye (ρ, 0.68 [95% CI, 0.52 to 0.78]; P < .001) and correlated moderately with Twitter results about pink eye (ρ, 0.38 [95% CI, 0.16 to 0.56]; P < .001) and with clinical diagnosis of influenza (ρ, 0

  16. Heuristic Search Theory and Applications

    CERN Document Server

    Edelkamp, Stefan

    2011-01-01

    Search has been vital to artificial intelligence from the very beginning as a core technique in problem solving. The authors present a thorough overview of heuristic search with a balance of discussion between theoretical analysis and efficient implementation and application to real-world problems. Current developments in search such as pattern databases and search with efficient use of external memory and parallel processing units on main boards and graphics cards are detailed. Heuristic search as a problem solving tool is demonstrated in applications for puzzle solving, game playing, constra

  17. Attractive evolutionary equilibria

    NARCIS (Netherlands)

    Joosten, Reinoud A.M.G.; Roorda, Berend

    2011-01-01

    We present attractiveness, a refinement criterion for evolutionary equilibria. Equilibria surviving this criterion are robust to small perturbations of the underlying payoff system or the dynamics at hand. Furthermore, certain attractive equilibria are equivalent to others for certain evolutionary

  18. Cognition and Culture in Evolutionary Context.

    Science.gov (United States)

    Colmenares, Fernando; Hernández-Lloreda, María Victoria

    2017-01-09

    In humans and other animals, the individuals' ability to adapt efficiently and effectively to the niches they have actively contributed to construct relies heavily on an evolved psychology which has been shaped by biological, social, and cultural processes over evolutionary time. As expected, although many of the behavioral and cognitive components of this evolved psychology are widely shared across species, many others are species-unique. Although many animal species are known to acquire group-specific traditions (or cultures) via social learning, human culture is unique in terms of its contents and characteristics (observable and unobservable products, cumulative effects, norm conformity, and norm enforcement) and of its cognitive underpinnings (imitation, instructed teaching, and language). Here we provide a brief overview of some of the issues that are currently tackled in the field. We also highlight some of the strengths of a biological, comparative, non-anthropocentric and evolutionarily grounded approach to the study of culture. The main contributions of this approach to the science of culture are its emphasis (a) on the integration of information on mechanisms, function, and evolution, and on mechanistic factors located at different levels of the biological hierarchy, and (b) on the search for general principles that account for commonalities and differences between species, both in the cultural products and in the processes of innovation, dissemination, and accumulation involved that operate during developmental and evolutionary timespans.

  19. MDTS: automatic complex materials design using Monte Carlo tree search

    Science.gov (United States)

    Dieb, Thaer M.; Ju, Shenghong; Yoshizoe, Kazuki; Hou, Zhufeng; Shiomi, Junichiro; Tsuda, Koji

    2017-12-01

    Complex materials design is often represented as a black-box combinatorial optimization problem. In this paper, we present a novel python library called MDTS (Materials Design using Tree Search). Our algorithm employs a Monte Carlo tree search approach, which has shown exceptional performance in computer Go game. Unlike evolutionary algorithms that require user intervention to set parameters appropriately, MDTS has no tuning parameters and works autonomously in various problems. In comparison to a Bayesian optimization package, our algorithm showed competitive search efficiency and superior scalability. We succeeded in designing large Silicon-Germanium (Si-Ge) alloy structures that Bayesian optimization could not deal with due to excessive computational cost. MDTS is available at https://github.com/tsudalab/MDTS.

  20. IDEA: Interactive Display for Evolutionary Analyses.

    Science.gov (United States)

    Egan, Amy; Mahurkar, Anup; Crabtree, Jonathan; Badger, Jonathan H; Carlton, Jane M; Silva, Joana C

    2008-12-08

    The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are codeml and baseml, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency. We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with codeml and baseml for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly. IDEA provides a graphical user interface that allows the user to follow a codeml or baseml analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.

  1. Evolutionary psychology is compatible with equity feminism, but not with gender feminism: a reply to Eagly and Wood (2011).

    Science.gov (United States)

    Kuhle, Barry X

    2012-01-11

    I comment on Eagly and Wood's biosocial constructionist evolutionary theory (2011; DOI: 10.1007/s11199-011-9949-9). Although this gender feminist theory allows for evolved physical differences between men and women and evolved psychological similarities for men and women, it fails to consider evolutionary accounts of psychological sex differences. I hypothesize that gender feminists' reluctance to acknowledge that evolution has left different fingerprints on men's and women's bodies and brains stems from two common misunderstandings of evolutionary psychology: the myth of immutability and the naturalistic fallacy. I conclude that although evolutionary psychology is eminently compatible with equity feminism, evolutionary psychology and feminist psychology will conflict as long as the latter adheres to gender feminism and its unwillingness to acknowledge the evidence for evolved psychological sex differences.  Gender feminism's dualistic view of evolution hinders the search for and understanding of the proximate and ultimate causes of inequality. Feminist psychology needs to evolve by embracing equity feminism, which has no a priori stance on the origin or existence of differences between the sexes.

  2. Evolutionary Psychology is Compatible with Equity Feminism, but Not with Gender Feminism: A Reply to Eagly and Wood (2011

    Directory of Open Access Journals (Sweden)

    Barry X. Kuhle

    2012-01-01

    Full Text Available I comment on Eagly and Wood's biosocial constructionist evolutionary theory (2011; DOI: 10.1007/s11199-011-9949-9. Although this gender feminist theory allows for evolved physical differences between men and women and evolved psychological similarities for men and women, it fails to consider evolutionary accounts of psychological sex differences. I hypothesize that gender feminists' reluctance to acknowledge that evolution has left different fingerprints on men's and women's bodies and brains stems from two common misunderstandings of evolutionary psychology: the myth of immutability and the naturalistic fallacy. I conclude that although evolutionary psychology is eminently compatible with equity feminism, evolutionary psychology and feminist psychology will conflict as long as the latter adheres to gender feminism and its unwillingness to acknowledge the evidence for evolved psychological sex differences. Gender feminism's dualistic view of evolution hinders the search for and understanding of the proximate and ultimate causes of inequality. Feminist psychology needs to evolve by embracing equity feminism, which has no a priori stance on the origin or existence of differences between the sexes.

  3. Generative models versus underlying symmetries to explain biological pattern.

    Science.gov (United States)

    Frank, S A

    2014-06-01

    Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative models confirm the plausibility of an explanation and make testable hypotheses for further experiments. However, studies rarely consider the broad family of alternative models that match the same observed pattern. The symmetries that define the broad class of matching models are in fact the only aspects of information truly revealed by observed pattern. Commonly observed patterns derive from simple underlying symmetries. This article illustrates the problem by showing the symmetry associated with the observed rate of increase in fitness in a constant environment. That underlying symmetry reveals how each particular generative model defines a single example within the broad class of matching models. Further progress on the relation between pattern and process requires deeper consideration of the underlying symmetries. © 2014 The Author. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  4. Yin and yang surfaces: an evolutionary perspective.

    Science.gov (United States)

    Legge, David

    2014-12-01

    A search of the Chinese medicine literature reveals several conflicting explanations of the division of the body into yin and yang surfaces. This paper attempts to clarify this basic concept and reconcile the differing descriptions of it through an exploration of material from other disciplines. A remarkable similarity exists between the surfaces on the human body that are defined by the pathways of the yin and yang meridians and those that have evolved from the ventral and the dorsal aspects of early vertebrate structure. Many of the evolutionary changes described have parallels in our embryological development and are evident in the underlying anatomy of our limbs. The degree of convergence between the two descriptions strongly supports the definition of the yin and yang surfaces as those traversed by the yin and yang meridians. It also goes a long way towards reconciling the conflicting definitions found in the literature. Finding a solution to this question of yin and yang surfaces that is based on anatomy and evolutionary theories has several advantages. It can throw light on differences in the clinical effects of points on the yin and yang meridians and enable the identification of anomalies in the pathways of the main meridian network. Copyright © 2014. Published by Elsevier B.V.

  5. Genetic algorithms and artificial neural networks for loading pattern optimisation of advanced gas-cooled reactors

    Energy Technology Data Exchange (ETDEWEB)

    Ziver, A.K. E-mail: a.k.ziver@imperial.ac.uk; Pain, C.C; Carter, J.N.; Oliveira, C.R.E. de; Goddard, A.J.H.; Overton, R.S

    2004-03-01

    A non-generational genetic algorithm (GA) has been developed for fuel management optimisation of Advanced Gas-Cooled Reactors, which are operated by British Energy and produce around 20% of the UK's electricity requirements. An evolutionary search is coded using the genetic operators; namely selection by tournament, two-point crossover, mutation and random assessment of population for multi-cycle loading pattern (LP) optimisation. A detailed description of the chromosomes in the genetic algorithm coded is presented. Artificial Neural Networks (ANNs) have been constructed and trained to accelerate the GA-based search during the optimisation process. The whole package, called GAOPT, is linked to the reactor analysis code PANTHER, which performs fresh fuel loading, burn-up and power shaping calculations for each reactor cycle by imposing station-specific safety and operational constraints. GAOPT has been verified by performing a number of tests, which are applied to the Hinkley Point B and Hartlepool reactors. The test results giving loading pattern (LP) scenarios obtained from single and multi-cycle optimisation calculations applied to realistic reactor states of the Hartlepool and Hinkley Point B reactors are discussed. The results have shown that the GA/ANN algorithms developed can help the fuel engineer to optimise loading patterns in an efficient and more profitable way than currently available for multi-cycle refuelling of AGRs. Research leading to parallel GAs applied to LP optimisation are outlined, which can be adapted to present day LWR fuel management problems.

  6. Open Issues in Evolutionary Robotics.

    Science.gov (United States)

    Silva, Fernando; Duarte, Miguel; Correia, Luís; Oliveira, Sancho Moura; Christensen, Anders Lyhne

    2016-01-01

    One of the long-term goals in evolutionary robotics is to be able to automatically synthesize controllers for real autonomous robots based only on a task specification. While a number of studies have shown the applicability of evolutionary robotics techniques for the synthesis of behavioral control, researchers have consistently been faced with a number of issues preventing the widespread adoption of evolutionary robotics for engineering purposes. In this article, we review and discuss the open issues in evolutionary robotics. First, we analyze the benefits and challenges of simulation-based evolution and subsequent deployment of controllers versus evolution on real robotic hardware. Second, we discuss specific evolutionary computation issues that have plagued evolutionary robotics: (1) the bootstrap problem, (2) deception, and (3) the role of genomic encoding and genotype-phenotype mapping in the evolution of controllers for complex tasks. Finally, we address the absence of standard research practices in the field. We also discuss promising avenues of research. Our underlying motivation is the reduction of the current gap between evolutionary robotics and mainstream robotics, and the establishment of evolutionary robotics as a canonical approach for the engineering of autonomous robots.

  7. Models for Evolutionary Algorithms and Their Applications in System Identification and Control Optimization

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    population and many generations, which essentially turns the problem into a series of related static problems. To our surprise, the control problem could easily be solved when optimized like this. To further examine this, we compared the EA with a particle swarm and a local search approach, which we...... simulate an evolutionary process where the goal is to evolve solutions by means of crossover, mutation, and selection based on their quality (fitness) with respect to the optimization problem at hand. Evolutionary algorithms (EAs) are highly relevant for industrial applications, because they are capable...... of handling problems with non-linear constraints, multiple objectives, and dynamic components – properties that frequently appear in real-world problems. This thesis presents research in three fundamental areas of EC; fitness function design, methods for parameter control, and techniques for multimodal...

  8. An encoding technique for multiobjective evolutionary algorithms applied to power distribution system reconfiguration.

    Science.gov (United States)

    Guardado, J L; Rivas-Davalos, F; Torres, J; Maximov, S; Melgoza, E

    2014-01-01

    Network reconfiguration is an alternative to reduce power losses and optimize the operation of power distribution systems. In this paper, an encoding scheme for evolutionary algorithms is proposed in order to search efficiently for the Pareto-optimal solutions during the reconfiguration of power distribution systems considering multiobjective optimization. The encoding scheme is based on the edge window decoder (EWD) technique, which was embedded in the Strength Pareto Evolutionary Algorithm 2 (SPEA2) and the Nondominated Sorting Genetic Algorithm II (NSGA-II). The effectiveness of the encoding scheme was proved by solving a test problem for which the true Pareto-optimal solutions are known in advance. In order to prove the practicability of the encoding scheme, a real distribution system was used to find the near Pareto-optimal solutions for different objective functions to optimize.

  9. XTALOPT: An open-source evolutionary algorithm for crystal structure prediction

    Science.gov (United States)

    Lonie, David C.; Zurek, Eva

    2011-02-01

    The implementation and testing of XTALOPT, an evolutionary algorithm for crystal structure prediction, is outlined. We present our new periodic displacement (ripple) operator which is ideally suited to extended systems. It is demonstrated that hybrid operators, which combine two pure operators, reduce the number of duplicate structures in the search. This allows for better exploration of the potential energy surface of the system in question, while simultaneously zooming in on the most promising regions. A continuous workflow, which makes better use of computational resources as compared to traditional generation based algorithms, is employed. Various parameters in XTALOPT are optimized using a novel benchmarking scheme. XTALOPT is available under the GNU Public License, has been interfaced with various codes commonly used to study extended systems, and has an easy to use, intuitive graphical interface. Program summaryProgram title:XTALOPT Catalogue identifier: AEGX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL v2.1 or later [1] No. of lines in distributed program, including test data, etc.: 36 849 No. of bytes in distributed program, including test data, etc.: 1 149 399 Distribution format: tar.gz Programming language: C++ Computer: PCs, workstations, or clusters Operating system: Linux Classification: 7.7 External routines: QT [2], OpenBabel [3], AVOGADRO [4], SPGLIB [8] and one of: VASP [5], PWSCF [6], GULP [7]. Nature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics. Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum on their potential energy surface. Our evolutionary algorithm, XTALOPT, is freely

  10. Multi-step-prediction of chaotic time series based on co-evolutionary recurrent neural network

    International Nuclear Information System (INIS)

    Ma Qianli; Zheng Qilun; Peng Hong; Qin Jiangwei; Zhong Tanwei

    2008-01-01

    This paper proposes a co-evolutionary recurrent neural network (CERNN) for the multi-step-prediction of chaotic time series, it estimates the proper parameters of phase space reconstruction and optimizes the structure of recurrent neural networks by co-evolutionary strategy. The searching space was separated into two subspaces and the individuals are trained in a parallel computational procedure. It can dynamically combine the embedding method with the capability of recurrent neural network to incorporate past experience due to internal recurrence. The effectiveness of CERNN is evaluated by using three benchmark chaotic time series data sets: the Lorenz series, Mackey-Glass series and real-world sun spot series. The simulation results show that CERNN improves the performances of multi-step-prediction of chaotic time series

  11. C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search.

    Science.gov (United States)

    Sowpati, Divya Tej; Srivastava, Surabhi; Dhawan, Jyotsna; Mishra, Rakesh K

    2017-09-13

    Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of novel epigenetic patterns and their visualization across gene subsets remains a challenge. We developed a fast and interactive web app, C-State (Chromatin-State), to query and plot chromatin landscapes across multiple loci and cell types. C-State has an interactive, JavaScript-based graphical user interface and runs locally in modern web browsers that are pre-installed on all computers, thus eliminating the need for cumbersome data transfer, pre-processing and prior programming knowledge. C-State is unique in its ability to extract and analyze multi-gene epigenetic information. It allows for powerful GUI-based pattern searching and visualization. We include a case study to demonstrate its potential for identifying user-defined epigenetic trends in context of gene expression profiles.

  12. Patterns in Orthoptera biodiversity. I. Adaptations in ecological and evolutionary contexts

    Directory of Open Access Journals (Sweden)

    Claudio J. Bidau

    2014-10-01

    Full Text Available The Orthoptera have inhabited the Earth for ca 300 million years and today include about 25,000 described species. Although orthopterans are mainly known to the general public by their most conspicuous species such as rangeland grasshoppers, locusts, katydids and crickets, they include an amazing diversity of forms and life-styles. In this review, I bring together a series of facts about orthopteran biology that demonstrate their enormous biodiversity, concentrating on ecological and evolutionary characteristics such as habitat variation, modes of feeding, defense mechanisms and phase transformation. In a second part of this review I will consider subjects of more direct human interest as their use as food, their importance in folk medicine and their role as entertainment.

  13. Gene Coexpression and Evolutionary Conservation Analysis of the Human Preimplantation Embryos

    Directory of Open Access Journals (Sweden)

    Tiancheng Liu

    2015-01-01

    Full Text Available Evolutionary developmental biology (EVO-DEVO tries to decode evolutionary constraints on the stages of embryonic development. Two models—the “funnel-like” model and the “hourglass” model—have been proposed by investigators to illustrate the fluctuation of selective pressure on these stages. However, selective indices of stages corresponding to mammalian preimplantation embryonic development (PED were undetected in previous studies. Based on single cell RNA sequencing of stages during human PED, we used coexpression method to identify gene modules activated in each of these stages. Through measuring the evolutionary indices of gene modules belonging to each stage, we observed change pattern of selective constraints on PED for the first time. The selective pressure decreases from the zygote stage to the 4-cell stage and increases at the 8-cell stage and then decreases again from 8-cell stage to the late blastocyst stages. Previous EVO-DEVO studies concerning the whole embryo development neglected the fluctuation of selective pressure in these earlier stages, and the fluctuation was potentially correlated with events of earlier stages, such as zygote genome activation (ZGA. Such oscillation in an earlier stage would further affect models of the evolutionary constraints on whole embryo development. Therefore, these earlier stages should be measured intensively in future EVO-DEVO studies.

  14. Shelves around the Iberian Peninsula (II): Evolutionary sedimentary patterns; Las plataformas continentales de la Peninsula Iberica (II): Patrones sedimentarios evolutivos

    Energy Technology Data Exchange (ETDEWEB)

    Lobo, F. J.; Duran, R.; Roque, C.; Ribo, M.; Carrera, G.; Mendes, I.; Ferrin, A.; Fernandez-Salas, L. M.; Garcia-Gil, S.; Galpalsoro, I.; Rosa, F.; Barcenas, P.

    2015-07-01

    We present a synthetic view of continental-shelf evolutionary patterns around the Iberian Peninsula, focusing on proposed sequence stratigraphy interpretations and attempting a comparison between Atlantic- and Mediterranean-type shelf-margin constructions. Most of the studied shelves show a dominance of regressive to low stand deposition through successive pro gradations, particularly evident in the Pliocene-Quaternary, documenting the influence of glacio-eustasy. Transgressive to high stand development predating the Last Glacial Maximum seems to be favoured off major rivers, but the highest variability is seen during post glacial evolution. Transgressive deposits tend to show a higher spatial variability, ranging from pro graded para sequences to extensive sand sheets. Holocene high- stand deposits usually show a more homogeneous character, with development of proximal wedge-shaped deposits and a distal sheet-like deposition. Atlantic continental shelves off Iberia display three different types of shelf growth: depositional shelves, shelves with restricted pro gradation and erosional shelves. They result from the interplay between depositional and hydrodynamic regimes, with the occurrence of a latitudinal gradation from erosional shelves in the Cantabrian continental shelf to depositional shelves in the northern Gulf of Cadiz shelf. Some shelf sectors do not correspond to this general pattern, as shelf sedimentation is mainly controlled by morpho-structural features (e.g., ria environments and shelves crossed by major tectonic accidents). The Mediterranean continental shelves of Iberia show two basic types, high- versus low-supply shelves, and their growth patterns are mainly a response to the amount of fluvial supply. The low-supply style is clearly the most frequent type, and it may show further complexity according to the occurrence of submarine canyons and/or morpho-structural control. (Author)

  15. Optimizing Visual Properties of Game Content through Neuroevolution

    DEFF Research Database (Denmark)

    Liapis, Antonios; Yannakakis, Georgios N.; Togelius, Julian

    This paper presents a search-based approach to generating game content that satisfies both gameplay requirements and user-expressed aesthetic criteria. Using evolutionary constraint satisfaction, we search for spaceships (for a space combat game) represented as compositional pattern...

  16. Numerical and Evolutionary Optimization Workshop

    CERN Document Server

    Trujillo, Leonardo; Legrand, Pierrick; Maldonado, Yazmin

    2017-01-01

    This volume comprises a selection of works presented at the Numerical and Evolutionary Optimization (NEO) workshop held in September 2015 in Tijuana, Mexico. The development of powerful search and optimization techniques is of great importance in today’s world that requires researchers and practitioners to tackle a growing number of challenging real-world problems. In particular, there are two well-established and widely known fields that are commonly applied in this area: (i) traditional numerical optimization techniques and (ii) comparatively recent bio-inspired heuristics. Both paradigms have their unique strengths and weaknesses, allowing them to solve some challenging problems while still failing in others. The goal of the NEO workshop series is to bring together people from these and related fields to discuss, compare and merge their complimentary perspectives in order to develop fast and reliable hybrid methods that maximize the strengths and minimize the weaknesses of the underlying paradigms. Throu...

  17. Evolutionary Pattern of Improved 1-Mile Running Performance

    NARCIS (Netherlands)

    Foster, C.S.; de Koning, J.J.; Thiel, C.

    2014-01-01

    The official world records (WR) for the 1-mile run for men (3: 43.13) and for women (4: 12.58) have improved 12.2% and 32.3%, respectively, since the first WR recognized by the International Association of Athletics Federations. Previous observations have suggested that the pacing pattern for

  18. Cube search, revisited

    Science.gov (United States)

    Zhang, Xuetao; Huang, Jie; Yigit-Elliott, Serap; Rosenholtz, Ruth

    2015-01-01

    Observers can quickly search among shaded cubes for one lit from a unique direction. However, replace the cubes with similar 2-D patterns that do not appear to have a 3-D shape, and search difficulty increases. These results have challenged models of visual search and attention. We demonstrate that cube search displays differ from those with “equivalent” 2-D search items in terms of the informativeness of fairly low-level image statistics. This informativeness predicts peripheral discriminability of target-present from target-absent patches, which in turn predicts visual search performance, across a wide range of conditions. Comparing model performance on a number of classic search tasks, cube search does not appear unexpectedly easy. Easy cube search, per se, does not provide evidence for preattentive computation of 3-D scene properties. However, search asymmetries derived from rotating and/or flipping the cube search displays cannot be explained by the information in our current set of image statistics. This may merely suggest a need to modify the model's set of 2-D image statistics. Alternatively, it may be difficult cube search that provides evidence for preattentive computation of 3-D scene properties. By attributing 2-D luminance variations to a shaded 3-D shape, 3-D scene understanding may slow search for 2-D features of the target. PMID:25780063

  19. Nature-inspired Cuckoo Search Algorithm for Side Lobe Suppression in a Symmetric Linear Antenna Array

    Directory of Open Access Journals (Sweden)

    K. N. Abdul Rani

    2012-09-01

    Full Text Available In this paper, we proposed a newly modified cuckoo search (MCS algorithm integrated with the Roulette wheel selection operator and the inertia weight controlling the search ability towards synthesizing symmetric linear array geometry with minimum side lobe level (SLL and/or nulls control. The basic cuckoo search (CS algorithm is primarily based on the natural obligate brood parasitic behavior of some cuckoo species in combination with the Levy flight behavior of some birds and fruit flies. The CS metaheuristic approach is straightforward and capable of solving effectively general N-dimensional, linear and nonlinear optimization problems. The array geometry synthesis is first formulated as an optimization problem with the goal of SLL suppression and/or null prescribed placement in certain directions, and then solved by the newly MCS algorithm for the optimum element or isotropic radiator locations in the azimuth-plane or xy-plane. The study also focuses on the four internal parameters of MCS algorithm specifically on their implicit effects in the array synthesis. The optimal inter-element spacing solutions obtained by the MCS-optimizer are validated through comparisons with the standard CS-optimizer and the conventional array within the uniform and the Dolph-Chebyshev envelope patterns using MATLABTM. Finally, we also compared the fine-tuned MCS algorithm with two popular evolutionary algorithm (EA techniques include particle swarm optimization (PSO and genetic algorithms (GA.

  20. Synergistic Coherence of Bifurcation Evolutionary Processes of Mergers and Acquisitions of Enterprises

    Directory of Open Access Journals (Sweden)

    Ivanchenko Hennadii F.

    2016-08-01

    Full Text Available The aim of the article is developing information tools for the economic and mathematical modeling of the dynamics of evolutionary processes concerning trophic relationships of populations of enterprises, which allowed to conduct the phase and bifurcation analysis of possible dynamic regimes of the populations’ evolution, determine the mechanisms of influence of the external environment and the internal structure of the system, identify patterns and limits of stability of M&A processes. In the work the main provisions of the evolutionary concept concerning development of the population of enterprises as an economic system are analyzed, the provisions of the evolutionary concept of population systems’ development are considered, the basis of evolutionary modeling methods allowing to analyze the functioning of populations of enterprises in terms of individual strategies of each enterprise’s behavior is studied. The basic principles of synergy of the life cycle evolution for populations of enterprises are determined. An evolutionary approach to the evaluation of a synergistic effect of M & A is proposed. The evolutionary modeling of the scenario for self-organization of populations of dairy industry enterprises through a combination of statistical and expert data is applied. There also created a model of the population of firms reflecting behavioral and resource and technological characteristics of the studied in the work real population of industrial enterprises, which form the input flows of matter, energy and information to the dairy industry, which allows to combine the reflection of main possible options in terms of the external conditions of the population functioning and its internal structure.

  1. Chaos Enhanced Differential Evolution in the Task of Evolutionary Control of Selected Set of Discrete Chaotic Systems

    Directory of Open Access Journals (Sweden)

    Roman Senkerik

    2014-01-01

    Full Text Available Evolutionary technique differential evolution (DE is used for the evolutionary tuning of controller parameters for the stabilization of set of different chaotic systems. The novelty of the approach is that the selected controlled discrete dissipative chaotic system is used also as the chaotic pseudorandom number generator to drive the mutation and crossover process in the DE. The idea was to utilize the hidden chaotic dynamics in pseudorandom sequences given by chaotic map to help differential evolution algorithm search for the best controller settings for the very same chaotic system. The optimizations were performed for three different chaotic systems, two types of case studies and developed cost functions.

  2. Oxidation-specific epitopes are danger-associated molecular patterns recognized by pattern recognition receptors of innate immunity

    DEFF Research Database (Denmark)

    Miller, Yury I; Choi, Soo-Ho; Wiesner, Philipp

    2011-01-01

    are a major target of innate immunity, recognized by a variety of "pattern recognition receptors" (PRRs). By analogy with microbial "pathogen-associated molecular patterns" (PAMPs), we postulate that host-derived, oxidation-specific epitopes can be considered to represent "danger (or damage......)-associated molecular patterns" (DAMPs). We also argue that oxidation-specific epitopes present on apoptotic cells and their cellular debris provided the primary evolutionary pressure for the selection of such PRRs. Furthermore, because many PAMPs on microbes share molecular identity and/or mimicry with oxidation...

  3. Preventive maintenance scheduling by variable dimension evolutionary algorithms

    International Nuclear Information System (INIS)

    Limbourg, Philipp; Kochs, Hans-Dieter

    2006-01-01

    Black box optimization strategies have been proven to be useful tools for solving complex maintenance optimization problems. There has been a considerable amount of research on the right choice of optimization strategies for finding optimal preventive maintenance schedules. Much less attention is turned to the representation of the schedule to the algorithm. Either the search space is represented as a binary string leading to highly complex combinatorial problem or maintenance operations are defined by regular intervals which may restrict the search space to suboptimal solutions. An adequate representation however is vitally important for result quality. This work presents several nonstandard input representations and compares them to the standard binary representation. An evolutionary algorithm with extensions to handle variable length genomes is used for the comparison. The results demonstrate that two new representations perform better than the binary representation scheme. A second analysis shows that the performance may be even more increased using modified genetic operators. Thus, the choice of alternative representations leads to better results in the same amount of time and without any loss of accuracy

  4. Induction Motor Parameter Identification Using a Gravitational Search Algorithm

    Directory of Open Access Journals (Sweden)

    Omar Avalos

    2016-04-01

    Full Text Available The efficient use of electrical energy is a topic that has attracted attention for its environmental consequences. On the other hand, induction motors represent the main component in most industries. They consume the highest energy percentages in industrial facilities. This energy consumption depends on the operation conditions of the induction motor imposed by its internal parameters. Since the internal parameters of an induction motor are not directly measurable, an identification process must be conducted to obtain them. In the identification process, the parameter estimation is transformed into a multidimensional optimization problem where the internal parameters of the induction motor are considered as decision variables. Under this approach, the complexity of the optimization problem tends to produce multimodal error surfaces for which their cost functions are significantly difficult to minimize. Several algorithms based on evolutionary computation principles have been successfully applied to identify the optimal parameters of induction motors. However, most of them maintain an important limitation: They frequently obtain sub-optimal solutions as a result of an improper equilibrium between exploitation and exploration in their search strategies. This paper presents an algorithm for the optimal parameter identification of induction motors. To determine the parameters, the proposed method uses a recent evolutionary method called the gravitational search algorithm (GSA. Different from most of the existent evolutionary algorithms, the GSA presents a better performance in multimodal problems, avoiding critical flaws such as the premature convergence to sub-optimal solutions. Numerical simulations have been conducted on several models to show the effectiveness of the proposed scheme.

  5. Animal egg as evolutionary innovation: a solution to the "embryonic hourglass" puzzle.

    Science.gov (United States)

    Newman, Stuart A

    2011-11-15

    The evolutionary origin of the egg stage of animal development presents several difficulties for conventional developmental and evolutionary narratives. If the egg's internal organization represents a template for key features of the developed organism, why can taxa within a given phylum exhibit very different egg types, pass through a common intermediate morphology (the so-called "phylotypic stage"), only to diverge again, thus exemplifying the embryonic "hourglass"? Moreover, if different egg types typically represent adaptations to different environmental conditions, why do birds and mammals, for example, have such vastly different eggs with respect to size, shape, and postfertilization dynamics, whereas all these features are more similar for ascidians and mammals? Here, I consider the possibility that different body plans had their origin in self-organizing physical processes in ancient clusters of cells, and suggest that eggs represented a set of independent evolutionary innovations subsequently inserted into the developmental trajectories of such aggregates. I first describe how "dynamical patterning modules" (DPMs) associations between components of the metazoan developmental-genetic toolkit and certain physical processes and effects may have organized primitive animal body plans independently of an egg stage. Next, I describe how adaptive specialization of cells released from such aggregates could have become "proto-eggs," which regenerated the parental cell clusters by cleavage, conserving the characteristic DPMs available to a lineage. Then, I show how known processes of cytoplasmic reorganization following fertilization are often based on spontaneous, self-organizing physical effects ("egg-patterning processes": EPPs). I suggest that rather than acting as developmental blueprints or prepatterns, the EPPs refine the phylotypic body plans determined by the DPMs by setting the boundary and initial conditions under which these multicellular patterning

  6. Deciphering the evolutionary history of open and closed mitosis.

    Science.gov (United States)

    Sazer, Shelley; Lynch, Michael; Needleman, Daniel

    2014-11-17

    The origin of the nucleus at the prokaryote-to-eukaryote transition represents one of the most important events in the evolution of cellular organization. The nuclear envelope encircles the chromosomes in interphase and is a selectively permeable barrier between the nucleoplasm and cytoplasm and an organizational scaffold for the nucleus. It remains intact in the 'closed' mitosis of some yeasts, but loses its integrity in the 'open' mitosis of mammals. Instances of both types of mitosis within two evolutionary clades indicate multiple evolutionary transitions between open and closed mitosis, although the underlying genetic changes that influenced these transitions remain unknown. A survey of the diversity of mitotic nuclei that fall between these extremes is the starting point from which to determine the physiologically relevant characteristics distinguishing open from closed mitosis and to understand how they evolved and why they are retained in present-day organisms. The field is now poised to begin addressing these issues by defining and documenting patterns of mitotic nuclear variation within and among species and mapping them onto a phylogenic tree. Deciphering the evolutionary history of open and closed mitosis will complement cell biological and genetic approaches aimed at deciphering the fundamental organizational principles of the nucleus. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. An Analytical Framework for Runtime of a Class of Continuous Evolutionary Algorithms

    Directory of Open Access Journals (Sweden)

    Yushan Zhang

    2015-01-01

    Full Text Available Although there have been many studies on the runtime of evolutionary algorithms in discrete optimization, relatively few theoretical results have been proposed on continuous optimization, such as evolutionary programming (EP. This paper proposes an analysis of the runtime of two EP algorithms based on Gaussian and Cauchy mutations, using an absorbing Markov chain. Given a constant variation, we calculate the runtime upper bound of special Gaussian mutation EP and Cauchy mutation EP. Our analysis reveals that the upper bounds are impacted by individual number, problem dimension number n, searching range, and the Lebesgue measure of the optimal neighborhood. Furthermore, we provide conditions whereby the average runtime of the considered EP can be no more than a polynomial of n. The condition is that the Lebesgue measure of the optimal neighborhood is larger than a combinatorial calculation of an exponential and the given polynomial of n.

  8. Intermittent search strategies

    Science.gov (United States)

    Bénichou, O.; Loverdo, C.; Moreau, M.; Voituriez, R.

    2011-01-01

    This review examines intermittent target search strategies, which combine phases of slow motion, allowing the searcher to detect the target, and phases of fast motion during which targets cannot be detected. It is first shown that intermittent search strategies are actually widely observed at various scales. At the macroscopic scale, this is, for example, the case of animals looking for food; at the microscopic scale, intermittent transport patterns are involved in a reaction pathway of DNA-binding proteins as well as in intracellular transport. Second, generic stochastic models are introduced, which show that intermittent strategies are efficient strategies that enable the minimization of search time. This suggests that the intrinsic efficiency of intermittent search strategies could justify their frequent observation in nature. Last, beyond these modeling aspects, it is proposed that intermittent strategies could also be used in a broader context to design and accelerate search processes.

  9. IDEA: Interactive Display for Evolutionary Analyses

    Directory of Open Access Journals (Sweden)

    Carlton Jane M

    2008-12-01

    Full Text Available Abstract Background The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are codeml and baseml, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency. Results We have developed IDEA (Interactive Display for Evolutionary Analyses, an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with codeml and baseml for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly. Conclusion IDEA provides a graphical user interface that allows the user to follow a codeml or baseml analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.

  10. Automatic boiling water reactor control rod pattern design using particle swarm optimization algorithm and local search

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Cheng-Der, E-mail: jdwang@iner.gov.tw [Nuclear Engineering Division, Institute of Nuclear Energy Research, No. 1000, Wenhua Rd., Jiaan Village, Longtan Township, Taoyuan County 32546, Taiwan, ROC (China); Lin, Chaung [National Tsing Hua University, Department of Engineering and System Science, 101, Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan (China)

    2013-02-15

    Highlights: ► The PSO algorithm was adopted to automatically design a BWR CRP. ► The local search procedure was added to improve the result of PSO algorithm. ► The results show that the obtained CRP is the same good as that in the previous work. -- Abstract: This study developed a method for the automatic design of a boiling water reactor (BWR) control rod pattern (CRP) using the particle swarm optimization (PSO) algorithm. The PSO algorithm is more random compared to the rank-based ant system (RAS) that was used to solve the same BWR CRP design problem in the previous work. In addition, the local search procedure was used to make improvements after PSO, by adding the single control rod (CR) effect. The design goal was to obtain the CRP so that the thermal limits and shutdown margin would satisfy the design requirement and the cycle length, which is implicitly controlled by the axial power distribution, would be acceptable. The results showed that the same acceptable CRP found in the previous work could be obtained.

  11. MetaCompose: A Compositional Evolutionary Music Composer

    DEFF Research Database (Denmark)

    Scirea, Marco; Togelius, Julian; Eklund, Peter

    2016-01-01

    This paper describes a compositional, extensible framework for music composition and a user study to systematically evaluate its core components. These components include a graph traversal-based chord sequence generator, a search-based melody generator and a pattern-based accompaniment generator...

  12. Evolutionary Demography

    DEFF Research Database (Denmark)

    Levitis, Daniel

    2015-01-01

    of biological and cultural evolution. Demographic variation within and among human populations is influenced by our biology, and therefore by natural selection and our evolutionary background. Demographic methods are necessary for studying populations of other species, and for quantifying evolutionary fitness......Demography is the quantitative study of population processes, while evolution is a population process that influences all aspects of biological organisms, including their demography. Demographic traits common to all human populations are the products of biological evolution or the interaction...

  13. An Encoding Technique for Multiobjective Evolutionary Algorithms Applied to Power Distribution System Reconfiguration

    Directory of Open Access Journals (Sweden)

    J. L. Guardado

    2014-01-01

    Full Text Available Network reconfiguration is an alternative to reduce power losses and optimize the operation of power distribution systems. In this paper, an encoding scheme for evolutionary algorithms is proposed in order to search efficiently for the Pareto-optimal solutions during the reconfiguration of power distribution systems considering multiobjective optimization. The encoding scheme is based on the edge window decoder (EWD technique, which was embedded in the Strength Pareto Evolutionary Algorithm 2 (SPEA2 and the Nondominated Sorting Genetic Algorithm II (NSGA-II. The effectiveness of the encoding scheme was proved by solving a test problem for which the true Pareto-optimal solutions are known in advance. In order to prove the practicability of the encoding scheme, a real distribution system was used to find the near Pareto-optimal solutions for different objective functions to optimize.

  14. Proteomics in evolutionary ecology.

    Science.gov (United States)

    Baer, B; Millar, A H

    2016-03-01

    Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein

  15. EvolQG - An R package for evolutionary quantitative genetics [version 2; referees: 1 approved, 2 approved with reservations

    Directory of Open Access Journals (Sweden)

    Diogo Melo

    2016-06-01

    Full Text Available We present an open source package for performing evolutionary quantitative genetics analyses in the R environment for statistical computing. Evolutionary theory shows that evolution depends critically on the available variation in a given population. When dealing with many quantitative traits this variation is expressed in the form of a covariance matrix, particularly the additive genetic covariance matrix or sometimes the phenotypic matrix, when the genetic matrix is unavailable and there is evidence the phenotypic matrix is sufficiently similar to the genetic matrix. Given this mathematical representation of available variation, the EvolQG package provides functions for calculation of relevant evolutionary statistics; estimation of sampling error; corrections for this error; matrix comparison via correlations, distances and matrix decomposition; analysis of modularity patterns; and functions for testing evolutionary hypotheses on taxa diversification.

  16. Evolutionary analysis of groundwater flow: Application of multivariate statistical analysis to hydrochemical data in the Densu Basin, Ghana

    Science.gov (United States)

    Yidana, Sandow Mark; Bawoyobie, Patrick; Sakyi, Patrick; Fynn, Obed Fiifi

    2018-02-01

    An evolutionary trend has been postulated through the analysis of hydrochemical data of a crystalline rock aquifer system in the Densu Basin, Southern Ghana. Hydrochemcial data from 63 groundwater samples, taken from two main groundwater outlets (Boreholes and hand dug wells) were used to postulate an evolutionary theory for the basin. Sequential factor and hierarchical cluster analysis were used to disintegrate the data into three factors and five clusters (spatial associations). These were used to characterize the controls on groundwater hydrochemistry and its evolution in the terrain. The dissolution of soluble salts and cation exchange processes are the dominant processes controlling groundwater hydrochemistry in the terrain. The trend of evolution of this set of processes follows the pattern of groundwater flow predicted by a calibrated transient groundwater model in the area. The data suggest that anthropogenic activities represent the second most important process in the hydrochemistry. Silicate mineral weathering is the third most important set of processes. Groundwater associations resulting from Q-mode hierarchical cluster analysis indicate an evolutionary pattern consistent with the general groundwater flow pattern in the basin. These key findings are at variance with results of previous investigations and indicate that when carefully done, groundwater hydrochemical data can be very useful for conceptualizing groundwater flow in basins.

  17. A Guiding Evolutionary Algorithm with Greedy Strategy for Global Optimization Problems

    Directory of Open Access Journals (Sweden)

    Leilei Cao

    2016-01-01

    Full Text Available A Guiding Evolutionary Algorithm (GEA with greedy strategy for global optimization problems is proposed. Inspired by Particle Swarm Optimization, the Genetic Algorithm, and the Bat Algorithm, the GEA was designed to retain some advantages of each method while avoiding some disadvantages. In contrast to the usual Genetic Algorithm, each individual in GEA is crossed with the current global best one instead of a randomly selected individual. The current best individual served as a guide to attract offspring to its region of genotype space. Mutation was added to offspring according to a dynamic mutation probability. To increase the capability of exploitation, a local search mechanism was applied to new individuals according to a dynamic probability of local search. Experimental results show that GEA outperformed the other three typical global optimization algorithms with which it was compared.

  18. Assessing fluctuating evolutionary pressure in yeast and mammal evolutionary rate covariation using bioinformatics of meiotic protein genetic sequences

    Science.gov (United States)

    Dehipawala, Sunil; Nguyen, A.; Tremberger, G.; Cheung, E.; Holden, T.; Lieberman, D.; Cheung, T.

    2013-09-01

    The evolutionary rate co-variation in meiotic proteins has been reported for yeast and mammal using phylogenic branch lengths which assess retention, duplication and mutation. The bioinformatics of the corresponding DNA sequences could be classified as a diagram of fractal dimension and Shannon entropy. Results from biomedical gene research provide examples on the diagram methodology. The identification of adaptive selection using entropy marker and functional-structural diversity using fractal dimension would support a regression analysis where the coefficient of determination would serve as evolutionary pathway marker for DNA sequences and be an important component in the astrobiology community. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, clinical trial targeted cancer gene CD47, SIRT6 in spermatogenesis, and HLA-C in mosquito bite immunology demonstrate the diagram classification methodology. Comparisons to the SEPT4-XIAP pair in stem cell apoptosis, testesexpressed taste genes TAS1R3-GNAT3 pair, and amyloid beta APLP1-APLP2 pair with the yeast-mammal DNA sequences for meiotic proteins RAD50-MRE11 pair and NCAPD2-ICK pair have accounted for the observed fluctuating evolutionary pressure systematically. Regression with high R-sq values or a triangular-like cluster pattern for concordant pairs in co-variation among the studied species could serve as evidences for the possible location of common ancestors in the entropy-fractal dimension diagram, consistent with an example of the human-chimp common ancestor study using the FOXP2 regulated genes reported in human fetal brain study. The Deinococcus radiodurans R1 Rad-A could be viewed as an outlier in the RAD50 diagram and also in the free energy versus fractal dimension regression Cook's distance, consistent with a non-Earth source for this radiation resistant bacterium. Convergent and divergent fluctuating evolutionary

  19. Using SQL Databases for Sequence Similarity Searching and Analysis.

    Science.gov (United States)

    Pearson, William R; Mackey, Aaron J

    2017-09-13

    Relational databases can integrate diverse types of information and manage large sets of similarity search results, greatly simplifying genome-scale analyses. By focusing on taxonomic subsets of sequences, relational databases can reduce the size and redundancy of sequence libraries and improve the statistical significance of homologs. In addition, by loading similarity search results into a relational database, it becomes possible to explore and summarize the relationships between all of the proteins in an organism and those in other biological kingdoms. This unit describes how to use relational databases to improve the efficiency of sequence similarity searching and demonstrates various large-scale genomic analyses of homology-related data. It also describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. The unit also introduces search_demo, a database that stores sequence similarity search results. The search_demo database is then used to explore the evolutionary relationships between E. coli proteins and proteins in other organisms in a large-scale comparative genomic analysis. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  20. Deterministic network interdiction optimization via an evolutionary approach

    International Nuclear Information System (INIS)

    Rocco S, Claudio M.; Ramirez-Marquez, Jose Emmanuel

    2009-01-01

    This paper introduces an evolutionary optimization approach that can be readily applied to solve deterministic network interdiction problems. The network interdiction problem solved considers the minimization of the maximum flow that can be transmitted between a source node and a sink node for a fixed network design when there is a limited amount of resources available to interdict network links. Furthermore, the model assumes that the nominal capacity of each network link and the cost associated with their interdiction can change from link to link. For this problem, the solution approach developed is based on three steps that use: (1) Monte Carlo simulation, to generate potential network interdiction strategies, (2) Ford-Fulkerson algorithm for maximum s-t flow, to analyze strategies' maximum source-sink flow and, (3) an evolutionary optimization technique to define, in probabilistic terms, how likely a link is to appear in the final interdiction strategy. Examples for different sizes of networks and network behavior are used throughout the paper to illustrate the approach. In terms of computational effort, the results illustrate that solutions are obtained from a significantly restricted solution search space. Finally, the authors discuss the need for a reliability perspective to network interdiction, so that solutions developed address more realistic scenarios of such problem

  1. Global analyses of evolutionary dynamics and exhaustive search for social norms that maintain cooperation by reputation.

    Science.gov (United States)

    Ohtsuki, Hisashi; Iwasa, Yoh

    2007-02-07

    Reputation formation is a key to understanding indirect reciprocity. In particular, the way to assign reputation to each individual, namely a norm that describes who is good and who is bad, greatly affects the possibility of sustained cooperation in the population. Previously, we have exhaustively studied reputation dynamics that are able to maintain a high level of cooperation at the ESS. However, this analysis examined the stability of monomorphic population and did not investigate polymorphic population where several strategies coexist. Here, we study the evolutionary dynamics of multiple behavioral strategies by replicator dynamics. We exhaustively study all 16 possible norms under which the reputation of a player in the next round is determined by the action of the self and the reputation of the opponent. For each norm, we explore evolutionary dynamics of three strategies: unconditional cooperators, unconditional defectors, and conditional cooperators. We find that only three norms, simple-standing, Kandori, and shunning, can make conditional cooperation evolutionarily stable, hence, realize sustained cooperation. The other 13 norms, including scoring, ultimately lead to the invasion by defectors. Also, we study the model in which private reputation errors exist to a small extent. In this case, we find the stable coexistence of unconditional and conditional cooperators under the three norms.

  2. Attractive evolutionary equilibria

    OpenAIRE

    Roorda, Berend; Joosten, Reinoud

    2011-01-01

    We present attractiveness, a refinement criterion for evolutionary equilibria. Equilibria surviving this criterion are robust to small perturbations of the underlying payoff system or the dynamics at hand. Furthermore, certain attractive equilibria are equivalent to others for certain evolutionary dynamics. For instance, each attractive evolutionarily stable strategy is an attractive evolutionarily stable equilibrium for certain barycentric ray-projection dynamics, and vice versa.

  3. A multilevel evolutionary framework for sustainability analysis

    Directory of Open Access Journals (Sweden)

    Timothy M. Waring

    2015-06-01

    Full Text Available Sustainability theory can help achieve desirable social-ecological states by generalizing lessons across contexts and improving the design of sustainability interventions. To accomplish these goals, we argue that theory in sustainability science must (1 explain the emergence and persistence of social-ecological states, (2 account for endogenous cultural change, (3 incorporate cooperation dynamics, and (4 address the complexities of multilevel social-ecological interactions. We suggest that cultural evolutionary theory broadly, and cultural multilevel selection in particular, can improve on these fronts. We outline a multilevel evolutionary framework for describing social-ecological change and detail how multilevel cooperative dynamics can determine outcomes in environmental dilemmas. We show how this framework complements existing sustainability frameworks with a description of the emergence and persistence of sustainable institutions and behavior, a means to generalize causal patterns across social-ecological contexts, and a heuristic for designing and evaluating effective sustainability interventions. We support these assertions with case examples from developed and developing countries in which we track cooperative change at multiple levels of social organization as they impact social-ecological outcomes. Finally, we make suggestions for further theoretical development, empirical testing, and application.

  4. Cyclic dominance in evolutionary games: a review

    Science.gov (United States)

    Szolnoki, Attila; Mobilia, Mauro; Jiang, Luo-Luo; Szczesny, Bartosz; Rucklidge, Alastair M.; Perc, Matjaž

    2014-01-01

    Rock is wrapped by paper, paper is cut by scissors and scissors are crushed by rock. This simple game is popular among children and adults to decide on trivial disputes that have no obvious winner, but cyclic dominance is also at the heart of predator–prey interactions, the mating strategy of side-blotched lizards, the overgrowth of marine sessile organisms and competition in microbial populations. Cyclical interactions also emerge spontaneously in evolutionary games entailing volunteering, reward, punishment, and in fact are common when the competing strategies are three or more, regardless of the particularities of the game. Here, we review recent advances on the rock–paper–scissors (RPS) and related evolutionary games, focusing, in particular, on pattern formation, the impact of mobility and the spontaneous emergence of cyclic dominance. We also review mean-field and zero-dimensional RPS models and the application of the complex Ginzburg–Landau equation, and we highlight the importance and usefulness of statistical physics for the successful study of large-scale ecological systems. Directions for future research, related, for example, to dynamical effects of coevolutionary rules and invasion reversals owing to multi-point interactions, are also outlined. PMID:25232048

  5. Phylogenetic niche conservatism and the evolutionary basis of ecological speciation.

    Science.gov (United States)

    Pyron, R Alexander; Costa, Gabriel C; Patten, Michael A; Burbrink, Frank T

    2015-11-01

    Phylogenetic niche conservatism (PNC) typically refers to the tendency of closely related species to be more similar to each other in terms of niche than they are to more distant relatives. This has been implicated as a potential driving force in speciation and other species-richness patterns, such as latitudinal gradients. However, PNC has not been very well defined in most previous studies. Is it a pattern or a process? What are the underlying endogenous (e.g. genetic) and exogenous (e.g. ecological) factors that cause niches to be conserved? What degree of similarity is necessary to qualify as PNC? Is it possible for the evolutionary processes causing niches to be conserved to also result in niche divergence in different habitats? Here, we revisit these questions, codifying a theoretical and operational definition of PNC as a mechanistic evolutionary process resulting from several factors. We frame this both from a macroevolutionary and population-genetic perspective. We discuss how different axes of physical (e.g. geographic) and environmental (e.g. climatic) heterogeneity interact with the fundamental process of PNC to produce different outcomes of ecological speciation. We also review tests for PNC, and suggest ways that these could be improved or better utilized in future studies. Ultimately, PNC as a process has a well-defined mechanistic basis in organisms, and future studies investigating ecological speciation would be well served to consider this, and frame hypothesis testing in terms of the processes and expected patterns described herein. The process of PNC may lead to patterns where niches are conserved (more similar than expected), constrained (divergent within a limited subset of available niches), or divergent (less similar than expected), based on degree of phylogenetic relatedness between species. © 2014 Cambridge Philosophical Society.

  6. Evolutionary principles and their practical application.

    Science.gov (United States)

    Hendry, Andrew P; Kinnison, Michael T; Heino, Mikko; Day, Troy; Smith, Thomas B; Fitt, Gary; Bergstrom, Carl T; Oakeshott, John; Jørgensen, Peter S; Zalucki, Myron P; Gilchrist, George; Southerton, Simon; Sih, Andrew; Strauss, Sharon; Denison, Robert F; Carroll, Scott P

    2011-03-01

    Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology.

  7. A chaos-based evolutionary algorithm for general nonlinear programming problems

    International Nuclear Information System (INIS)

    El-Shorbagy, M.A.; Mousa, A.A.; Nasr, S.M.

    2016-01-01

    In this paper we present a chaos-based evolutionary algorithm (EA) for solving nonlinear programming problems named chaotic genetic algorithm (CGA). CGA integrates genetic algorithm (GA) and chaotic local search (CLS) strategy to accelerate the optimum seeking operation and to speed the convergence to the global solution. The integration of global search represented in genetic algorithm and CLS procedures should offer the advantages of both optimization methods while offsetting their disadvantages. By this way, it is intended to enhance the global convergence and to prevent to stick on a local solution. The inherent characteristics of chaos can enhance optimization algorithms by enabling it to escape from local solutions and increase the convergence to reach to the global solution. Twelve chaotic maps have been analyzed in the proposed approach. The simulation results using the set of CEC’2005 show that the application of chaotic mapping may be an effective strategy to improve the performances of EAs.

  8. Energy-Efficient Scheduling Problem Using an Effective Hybrid Multi-Objective Evolutionary Algorithm

    Directory of Open Access Journals (Sweden)

    Lvjiang Yin

    2016-12-01

    Full Text Available Nowadays, manufacturing enterprises face the challenge of just-in-time (JIT production and energy saving. Therefore, study of JIT production and energy consumption is necessary and important in manufacturing sectors. Moreover, energy saving can be attained by the operational method and turn off/on idle machine method, which also increases the complexity of problem solving. Thus, most researchers still focus on small scale problems with one objective: a single machine environment. However, the scheduling problem is a multi-objective optimization problem in real applications. In this paper, a single machine scheduling model with controllable processing and sequence dependence setup times is developed for minimizing the total earliness/tardiness (E/T, cost, and energy consumption simultaneously. An effective multi-objective evolutionary algorithm called local multi-objective evolutionary algorithm (LMOEA is presented to tackle this multi-objective scheduling problem. To accommodate the characteristic of the problem, a new solution representation is proposed, which can convert discrete combinational problems into continuous problems. Additionally, a multiple local search strategy with self-adaptive mechanism is introduced into the proposed algorithm to enhance the exploitation ability. The performance of the proposed algorithm is evaluated by instances with comparison to other multi-objective meta-heuristics such as Nondominated Sorting Genetic Algorithm II (NSGA-II, Strength Pareto Evolutionary Algorithm 2 (SPEA2, Multiobjective Particle Swarm Optimization (OMOPSO, and Multiobjective Evolutionary Algorithm Based on Decomposition (MOEA/D. Experimental results demonstrate that the proposed LMOEA algorithm outperforms its counterparts for this kind of scheduling problems.

  9. Differential trends in the codon usage patterns in HIV-1 genes.

    Directory of Open Access Journals (Sweden)

    Aridaman Pandit

    Full Text Available Host-pathogen interactions underlie one of the most complex evolutionary phenomena resulting in continual adaptive genetic changes, where pathogens exploit the host's molecular resources for growth and survival, while hosts try to eliminate the pathogen. Deciphering the molecular basis of host-pathogen interactions is useful in understanding the factors governing pathogen evolution and disease propagation. In host-pathogen context, a balance between mutation, selection, and genetic drift is known to maintain codon bias in both organisms. Studies revealing determinants of the bias and its dynamics are central to the understanding of host-pathogen evolution. We considered the Human Immunodeficiency Virus (HIV type 1 and its human host to search for evolutionary signatures in the viral genome. Positive selection is known to dominate intra-host evolution of HIV-1, whereas high genetic variability underlies the belief that neutral processes drive inter-host differences. In this study, we analyze the codon usage patterns of HIV-1 genomes across all subtypes and clades sequenced over a period of 23 years. We show presence of unique temporal correlations in the codon bias of three HIV-1 genes illustrating differential adaptation of the HIV-1 genes towards the host preferred codons. Our results point towards gene-specific translational selection to be an important force driving the evolution of HIV-1 at the population level.

  10. Evolutionary relationships between miRNA genes and their activity.

    Science.gov (United States)

    Zhu, Yan; Skogerbø, Geir; Ning, Qianqian; Wang, Zhen; Li, Biqing; Yang, Shuang; Sun, Hong; Li, Yixue

    2012-12-22

    The emergence of vertebrates is characterized by a strong increase in miRNA families. MicroRNAs interact broadly with many transcripts, and the evolution of such a system is intriguing. However, evolutionary questions concerning the origin of miRNA genes and their subsequent evolution remain unexplained. In order to systematically understand the evolutionary relationship between miRNAs gene and their function, we classified human known miRNAs into eight groups based on their evolutionary ages estimated by maximum parsimony method. New miRNA genes with new functional sequences accumulated more dynamically in vertebrates than that observed in Drosophila. Different levels of evolutionary selection were observed over miRNA gene sequences with different time of origin. Most genic miRNAs differ from their host genes in time of origin, there is no particular relationship between the age of a miRNA and the age of its host genes, genic miRNAs are mostly younger than the corresponding host genes. MicroRNAs originated over different time-scales are often predicted/verified to target the same or overlapping sets of genes, opening the possibility of substantial functional redundancy among miRNAs of different ages. Higher degree of tissue specificity and lower expression level was found in young miRNAs. Our data showed that compared with protein coding genes, miRNA genes are more dynamic in terms of emergence and decay. Evolution patterns are quite different between miRNAs of different ages. MicroRNAs activity is under tight control with well-regulated expression increased and targeting decreased over time. Our work calls attention to the study of miRNA activity with a consideration of their origin time.

  11. Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention.

    Science.gov (United States)

    Johnston, Iain G; Williams, Ben P

    2016-02-24

    Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modeling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins comprising the structural cores of the electron transport chain are preferentially encoded within mitochondrial genomes across eukaryotes. A combination of high GC content and high protein hydrophobicity is required to explain patterns of mtDNA gene retention; a model that accounts for these selective pressures can also predict the success of artificial gene transfer experiments in vivo. This work provides a general method for data-driven inference of the ordering of evolutionary and progressive events, here identifying the distinct features shaping mitochondrial genomes of present-day species. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Changes in users' Web search performance after ten years ...

    African Journals Online (AJOL)

    The changes in users' Web search performance using search engines over ten years was investigated in this study. Matched data obtained from samples in 2000 and 2010 were used for the comparative analysis. The patterns of Web search engine use suggested a dominance in using a particular search engine. Statistical ...

  13. Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae.

    Science.gov (United States)

    Westneat, Mark W; Alfaro, Michael E; Wainwright, Peter C; Bellwood, David R; Grubich, Justin R; Fessler, Jennifer L; Clements, Kendall D; Smith, Lydia L

    2005-05-22

    The Labridae is one of the most structurally and functionally diversified fish families on coral and rocky reefs around the world, providing a compelling system for examination of evolutionary patterns of functional change. Labrid fishes have evolved a diverse array of skull forms for feeding on prey ranging from molluscs, crustaceans, plankton, detritus, algae, coral and other fishes. The species richness and diversity of feeding ecology in the Labridae make this group a marine analogue to the cichlid fishes. Despite the importance of labrids to coastal reef ecology, we lack evolutionary analysis of feeding biomechanics among labrids. Here, we combine a molecular phylogeny of the Labridae with the biomechanics of skull function to reveal a broad pattern of repeated convergence in labrid feeding systems. Mechanically fast jaw systems have evolved independently at least 14 times from ancestors with forceful jaws. A repeated phylogenetic pattern of functional divergence in local regions of the labrid tree produces an emergent family-wide pattern of global convergence in jaw function. Divergence of close relatives, convergence among higher clades and several unusual 'breakthroughs' in skull function characterize the evolution of functional complexity in one of the most diverse groups of reef fishes.

  14. The search for understanding: the role of paradigms.

    Science.gov (United States)

    Kelly, Marcella; Dowling, Maura; Millar, Michelle

    2018-03-16

    Kuhn's ( 1962 ) acknowledgement of a paradigm as a way that scientists make sense of their world and its reality gave recognition to the idea of 'paradigm shift'. This shift exposes the transience of paradigm development shaped by societal and scientific evolution. This ongoing evolutionary development provides the researcher with many paradigms to consider regarding how research is undertaken and the search for understanding achieved. An understanding of paradigm development is necessary when planning a study and can shape the search for understanding. It is hoped that the discussion presented here will assist novice and experienced researchers in articulating the rationales for their paradigm choices. An overview of the dominant paradigms is presented, reflecting ongoing paradigm development shaped by ontological, epistemological and methodological perspectives. Potential paradigm choices that shape research aims, objectives and focus in the search for understanding are considered. The inherent debates about paradigm shift, division, war and synthesis leave the researcher many perspectives to consider. Articulating the world views underpinning constructivism, interpretivism and pragmatism is particularly challenging because of the blurring of boundaries between them. The evolutionary nature of paradigmatic development has provided nurse researchers with the opportunity for methodological openness to the myriad research approaches, methods and designs that they may choose to answer their research question. However, it is imperative that researchers consider their ontological stances and the nature of their research questions. This is challenging in constructivism, interpretivism and pragmatism, where there is often an overlap of paradigm world views. ©2018 RCN Publishing Company Ltd. All rights reserved. Not to be copied, transmitted or recorded in any way, in whole or part, without prior permission of the publishers.

  15. Investigating User Search Tactic Patterns and System Support in Using Digital Libraries

    Science.gov (United States)

    Joo, Soohyung

    2013-01-01

    This study aims to investigate users' search tactic application and system support in using digital libraries. A user study was conducted with sixty digital library users. The study was designed to answer three research questions: 1) How do users engage in a search process by applying different types of search tactics while conducting different…

  16. A Novel Evolutionary Algorithm for Designing Robust Analog Filters

    Directory of Open Access Journals (Sweden)

    Shaobo Li

    2018-03-01

    Full Text Available Designing robust circuits that withstand environmental perturbation and device degradation is critical for many applications. Traditional robust circuit design is mainly done by tuning parameters to improve system robustness. However, the topological structure of a system may set a limit on the robustness achievable through parameter tuning. This paper proposes a new evolutionary algorithm for robust design that exploits the open-ended topological search capability of genetic programming (GP coupled with bond graph modeling. We applied our GP-based robust design (GPRD algorithm to evolve robust lowpass and highpass analog filters. Compared with a traditional robust design approach based on a state-of-the-art real-parameter genetic algorithm (GA, our GPRD algorithm with a fitness criterion rewarding robustness, with respect to parameter perturbations, can evolve more robust filters than what was achieved through parameter tuning alone. We also find that inappropriate GA tuning may mislead the search process and that multiple-simulation and perturbed fitness evaluation methods for evolving robustness have complementary behaviors with no absolute advantage of one over the other.

  17. Cooperative random Levy flight searches and the flight patterns of honeybees

    International Nuclear Information System (INIS)

    Reynolds, A.M.

    2006-01-01

    The most efficient Levy flight (scale-free) searching strategy for N independent searchers to adopt when target sites are randomly and sparsely distributed is identified. For N=1, it is well known that the optimal searching strategy is attained when μ=2, where the exponent μ characterizes the Levy distribution, P(l)=l -μ , of flight-lengths. For N>1, the optimal searching strategy is attained as μ->1. It is suggested that the orientation flights of honeybees can be understood within the context of such an optimal cooperative random Levy flight searching strategy. Upon returning to their hive after surveying a landscape honeybees can exchange information about the locations of target sites through the waggle dance. In accordance with observations it is predicted that the waggle dance can be disrupted without noticeable influence on a hive's ability to maintain weight when forage is plentiful

  18. Seasonal variation in Internet searches for vitamin D.

    Science.gov (United States)

    Moon, Rebecca J; Curtis, Elizabeth M; Davies, Justin H; Cooper, Cyrus; Harvey, Nicholas C

    2017-12-01

    Internet search rates for "vitamin D" were explored using Google Trends. Search rates increased from 2004 until 2010 and thereafter displayed a seasonal pattern peaking in late winter. This knowledge could help guide the timing of public health interventions aimed at managing vitamin D deficiency. The Internet is an important source of health information. Analysis of Internet search activity rates can provide information on disease epidemiology, health related behaviors and public interest. We explored Internet search rates for vitamin D to determine whether this reflects the increasing scientific interest in this topic. Google Trends is a publically available tool that provides data on Internet searches using Google. Search activity for the term "vitamin D" from 1st January 2004 until 31st October 2016 was obtained. Comparison was made to other bone and nutrition related terms. Worldwide, searches for "vitamin D" increased from 2004 until 2010 and thereafter a statistically significant (p Internet search activity, did increase from 2004 to 2010, likely reflecting the growing scientific interest, but now displays a seasonal pattern with peak interest during late winter. This information could be used to guide public health approaches to managing vitamin D deficiency.

  19. Evolutionary traces decode molecular mechanism behind fast pace of myosin XI

    Directory of Open Access Journals (Sweden)

    Syamaladevi Divya P

    2011-09-01

    Full Text Available Abstract Background Cytoplasmic class XI myosins are the fastest processive motors known. This class functions in high-velocity cytoplasmic streaming in various plant cells from algae to angiosperms. The velocities at which they process are ten times faster than its closest class V homologues. Results To provide sequence determinants and structural rationale for the molecular mechanism of this fast pace myosin, we have compared the sequences from myosin class V and XI through Evolutionary Trace (ET analysis. The current study identifies class-specific residues of myosin XI spread over the actin binding site, ATP binding site and light chain binding neck region. Sequences for ET analysis were accumulated from six plant genomes, using literature based text search and sequence searches, followed by triple validation viz. CDD search, string-based searches and phylogenetic clustering. We have identified nine myosin XI genes in sorghum and seven in grape by sequence searches. Both the plants possess one gene product each belonging to myosin type VIII as well. During this process, we have re-defined the gene boundaries for three sorghum myosin XI genes using fgenesh program. Conclusion Molecular modelling and subsequent analysis of putative interactions involving these class-specific residues suggest a structural basis for the molecular mechanism behind high velocity of plant myosin XI. We propose a model of a more flexible switch I region that contributes to faster ADP release leading to high velocity movement of the algal myosin XI.

  20. Chess players' eye movements reveal rapid recognition of complex visual patterns: Evidence from a chess-related visual search task.

    Science.gov (United States)

    Sheridan, Heather; Reingold, Eyal M

    2017-03-01

    To explore the perceptual component of chess expertise, we monitored the eye movements of expert and novice chess players during a chess-related visual search task that tested anecdotal reports that a key differentiator of chess skill is the ability to visualize the complex moves of the knight piece. Specifically, chess players viewed an array of four minimized chessboards, and they rapidly searched for the target board that allowed a knight piece to reach a target square in three moves. On each trial, there was only one target board (i.e., the "Yes" board), and for the remaining "lure" boards, the knight's path was blocked on either the first move (the "Easy No" board) or the second move (i.e., "the Difficult No" board). As evidence that chess experts can rapidly differentiate complex chess-related visual patterns, the experts (but not the novices) showed longer first-fixation durations on the "Yes" board relative to the "Difficult No" board. Moreover, as hypothesized, the task strongly differentiated chess skill: Reaction times were more than four times faster for the experts relative to novices, and reaction times were correlated with within-group measures of expertise (i.e., official chess ratings, number of hours of practice). These results indicate that a key component of chess expertise is the ability to rapidly recognize complex visual patterns.

  1. Evolutionary Cellular Automata for Image Segmentation and Noise Filtering Using Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Sihem SLATNIA

    2011-01-01

    Full Text Available We use an evolutionary process to seek a specialized set of rules among a wide range of rules to be used by Cellular Automata (CA for a range of tasks,extracting edges in a given gray or colour image, noise filtering applied to black-white image. This is the best set of local rules determine the future state of CA in an asynchronous way. The Genetic Algorithm (GA is applied to search the best CA rules that can realize the best edge detection and noise filtering.

  2. Evolutionary Cellular Automata for Image Segmentation and Noise Filtering Using Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Okba Kazar

    2011-01-01

    Full Text Available We use an evolutionary process to seek a specialized set of rules among a wide range of rules to be used by Cellular Automata (CA for a range of tasks, extracting edges in a given gray or colour image, noise filtering applied to black-white image. This is the best set of local rules determine the future state of CA in an asynchronous way. The Genetic Algorithm (GA is applied to search the best CA rules that can realize the best edge detection and noise filtering.

  3. Evolutionary Explanations of Eating Disorders

    Directory of Open Access Journals (Sweden)

    Igor Kardum

    2008-12-01

    Full Text Available This article reviews several most important evolutionary mechanisms that underlie eating disorders. The first part clarifies evolutionary foundations of mental disorders and various mechanisms leading to their development. In the second part selective pressures and evolved adaptations causing contemporary epidemic of obesity as well as differences in dietary regimes and life-style between modern humans and their ancestors are described. Concerning eating disorders, a number of current evolutionary explanations of anorexia nervosa are presented together with their main weaknesses. Evolutionary explanations of eating disorders based on the reproductive suppression hypothesis and its variants derived from kin selection theory and the model of parental manipulation were elaborated. The sexual competition hypothesis of eating disorder, adapted to flee famine hypothesis as well as explanation based on the concept of social attention holding power and the need to belonging were also explained. The importance of evolutionary theory in modern conceptualization and research of eating disorders is emphasized.

  4. A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs

    Directory of Open Access Journals (Sweden)

    Guoqin Mai

    2016-01-01

    Full Text Available Motivation. Clustered regularly interspaced short palindromic repeat (CRISPR is a genetic element with active regulation roles for foreign invasive genes in the prokaryotic genomes and has been engineered to work with the CRISPR-associated sequence (Cas gene Cas9 as one of the modern genome editing technologies. Due to inconsistent definitions, the existing CRISPR detection programs seem to have missed some weak CRISPR signals. Results. This study manually curates all the currently annotated CRISPR elements in the prokaryotic genomes and proposes 95 updates to the annotations. A new definition is proposed to cover all the CRISPRs. The comprehensive comparison of CRISPR numbers on the taxonomic levels of both domains and genus shows high variations for closely related species even in the same genus. The detailed investigation of how CRISPRs are evolutionarily manipulated in the 8 completely sequenced species in the genus Thermoanaerobacter demonstrates that transposons act as a frequent tool for splitting long CRISPRs into shorter ones along a long evolutionary history.

  5. A novel directional asymmetric sampling search algorithm for fast block-matching motion estimation

    Science.gov (United States)

    Li, Yue-e.; Wang, Qiang

    2011-11-01

    This paper proposes a novel directional asymmetric sampling search (DASS) algorithm for video compression. Making full use of the error information (block distortions) of the search patterns, eight different direction search patterns are designed for various situations. The strategy of local sampling search is employed for the search of big-motion vector. In order to further speed up the search, early termination strategy is adopted in procedure of DASS. Compared to conventional fast algorithms, the proposed method has the most satisfactory PSNR values for all test sequences.

  6. The citation field of evolutionary economics

    NARCIS (Netherlands)

    Dolfsma, Wilfred; Leydesdorff, Loet

    2010-01-01

    Evolutionary economics has developed into an academic field of its own, institutionalized around, amongst others, the Journal of Evolutionary Economics (JEE). This paper analyzes the way and extent to which evolutionary economics has become an interdisciplinary journal, as its aim was: a journal

  7. Towards a mechanistic foundation of evolutionary theory.

    Science.gov (United States)

    Doebeli, Michael; Ispolatov, Yaroslav; Simon, Burt

    2017-02-15

    Most evolutionary thinking is based on the notion of fitness and related ideas such as fitness landscapes and evolutionary optima. Nevertheless, it is often unclear what fitness actually is, and its meaning often depends on the context. Here we argue that fitness should not be a basal ingredient in verbal or mathematical descriptions of evolution. Instead, we propose that evolutionary birth-death processes, in which individuals give birth and die at ever-changing rates, should be the basis of evolutionary theory, because such processes capture the fundamental events that generate evolutionary dynamics. In evolutionary birth-death processes, fitness is at best a derived quantity, and owing to the potential complexity of such processes, there is no guarantee that there is a simple scalar, such as fitness, that would describe long-term evolutionary outcomes. We discuss how evolutionary birth-death processes can provide useful perspectives on a number of central issues in evolution.

  8. Evolutionary thinking: "A conversation with Carter Phipps about the role of evolutionary thinking in modern culture".

    Science.gov (United States)

    Hunt, Tam

    2014-12-01

    Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution-both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place-has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps' book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging "integral" or "evolutionary" cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps.

  9. Signatures of active and passive optimized Lévy searching in jellyfish.

    Science.gov (United States)

    Reynolds, Andy M

    2014-10-06

    Some of the strongest empirical support for Lévy search theory has come from telemetry data for the dive patterns of marine predators (sharks, bony fishes, sea turtles and penguins). The dive patterns of the unusually large jellyfish Rhizostoma octopus do, however, sit outside of current Lévy search theory which predicts that a single search strategy is optimal. When searching the water column, the movement patterns of these jellyfish change over time. Movement bouts can be approximated by a variety of Lévy and Brownian (exponential) walks. The adaptive value of this variation is not known. On some occasions movement pattern data are consistent with the jellyfish prospecting away from a preferred depth, not finding an improvement in conditions elsewhere and so returning to their original depth. This 'bounce' behaviour also sits outside of current Lévy walk search theory. Here, it is shown that the jellyfish movement patterns are consistent with their using optimized 'fast simulated annealing'--a novel kind of Lévy walk search pattern--to locate the maximum prey concentration in the water column and/or to locate the strongest of many olfactory trails emanating from more distant prey. Fast simulated annealing is a powerful stochastic search algorithm for locating a global maximum that is hidden among many poorer local maxima in a large search space. This new finding shows that the notion of active optimized Lévy walk searching is not limited to the search for randomly and sparsely distributed resources, as previously thought, but can be extended to embrace other scenarios, including that of the jellyfish R. octopus. In the presence of convective currents, it could become energetically favourable to search the water column by riding the convective currents. Here, it is shown that these passive movements can be represented accurately by Lévy walks of the type occasionally seen in R. octopus. This result vividly illustrates that Lévy walks are not necessarily

  10. Where Evolutionary Psychology Meets Cognitive Neuroscience: A Précis to Evolutionary Cognitive Neuroscience1

    Directory of Open Access Journals (Sweden)

    Austen L. Krill

    2007-01-01

    Full Text Available Cognitive neuroscience, the study of brain-behavior relationships, has long attempted to map the brain. The discipline is flourishing, with an increasing number of functional neuroimaging studies appearing in the scientific literature daily. Unlike biology and even psychology, the cognitive neurosciences have only recently begun to apply evolutionary meta-theory and methodological guidance. Approaching cognitive neuroscience from an evolutionary perspective allows scientists to apply biologically based theoretical guidance to their investigations and can be conducted in both humans and nonhuman animals. In fact, several investigations of this sort are underway in laboratories around the world. This paper and two new volumes (Platek, Keenan, and Shackelford [Eds.], 2007; Platek and Shackelford [Eds.], under contract represent the first formal attempts to document the burgeoning field of evolutionary cognitive neuroscience. Here, we briefly review the current state of the science of evolutionary cognitive neuroscience, the methods available to the evolutionary cognitive neuroscientist, and what we foresee as the future directions of the discipline.

  11. Object Detection and Tracking using Modified Diamond Search Block Matching Motion Estimation Algorithm

    Directory of Open Access Journals (Sweden)

    Apurva Samdurkar

    2018-06-01

    Full Text Available Object tracking is one of the main fields within computer vision. Amongst various methods/ approaches for object detection and tracking, the background subtraction approach makes the detection of object easier. To the detected object, apply the proposed block matching algorithm for generating the motion vectors. The existing diamond search (DS and cross diamond search algorithms (CDS are studied and experiments are carried out on various standard video data sets and user defined data sets. Based on the study and analysis of these two existing algorithms a modified diamond search pattern (MDS algorithm is proposed using small diamond shape search pattern in initial step and large diamond shape (LDS in further steps for motion estimation. The initial search pattern consists of five points in small diamond shape pattern and gradually grows into a large diamond shape pattern, based on the point with minimum cost function. The algorithm ends with the small shape pattern at last. The proposed MDS algorithm finds the smaller motion vectors and fewer searching points than the existing DS and CDS algorithms. Further, object detection is carried out by using background subtraction approach and finally, MDS motion estimation algorithm is used for tracking the object in color video sequences. The experiments are carried out by using different video data sets containing a single object. The results are evaluated and compared by using the evaluation parameters like average searching points per frame and average computational time per frame. The experimental results show that the MDS performs better than DS and CDS on average search point and average computation time.

  12. Essays on nonlinear evolutionary game dynamics

    NARCIS (Netherlands)

    Ochea, M.I.

    2010-01-01

    Evolutionary game theory has been viewed as an evolutionary repair of rational actor game theory in the hope that a population of boundedly rational players may attain convergence to classic rational solutions, such as the Nash Equilibrium, via some learning or evolutionary process. In this thesis

  13. Approaches to understanding the impact of life-history features on plant-pathogen co-evolutionary dynamics

    Science.gov (United States)

    Jeremy J. Burdon; Peter H. Thrall; Adnane Nemri

    2012-01-01

    Natural plant-pathogen associations are complex interactions in which the interplay of environment, host, and pathogen factors results in spatially heterogeneous ecological and epidemiological dynamics. The evolutionary patterns that result from the interaction of these factors are still relatively poorly understood. Recently, integration of the appropriate spatial and...

  14. Design of Spiking Central Pattern Generators for Multiple Locomotion Gaits in Hexapod Robots by Christiansen Grammar Evolution.

    Science.gov (United States)

    Espinal, Andres; Rostro-Gonzalez, Horacio; Carpio, Martin; Guerra-Hernandez, Erick I; Ornelas-Rodriguez, Manuel; Sotelo-Figueroa, Marco

    2016-01-01

    This paper presents a method to design Spiking Central Pattern Generators (SCPGs) to achieve locomotion at different frequencies on legged robots. It is validated through embedding its designs into a Field-Programmable Gate Array (FPGA) and implemented on a real hexapod robot. The SCPGs are automatically designed by means of a Christiansen Grammar Evolution (CGE)-based methodology. The CGE performs a solution for the configuration (synaptic weights and connections) for each neuron in the SCPG. This is carried out through the indirect representation of candidate solutions that evolve to replicate a specific spike train according to a locomotion pattern (gait) by measuring the similarity between the spike trains and the SPIKE distance to lead the search to a correct configuration. By using this evolutionary approach, several SCPG design specifications can be explicitly added into the SPIKE distance-based fitness function, such as looking for Spiking Neural Networks (SNNs) with minimal connectivity or a Central Pattern Generator (CPG) able to generate different locomotion gaits only by changing the initial input stimuli. The SCPG designs have been successfully implemented on a Spartan 6 FPGA board and a real time validation on a 12 Degrees Of Freedom (DOFs) hexapod robot is presented.

  15. Species packing in eco-evolutionary models of seasonally fluctuating environments.

    Science.gov (United States)

    Kremer, Colin T; Klausmeier, Christopher A

    2017-09-01

    As ecology and evolution become ever more entwined, many areas of ecological theory are being re-examined. Eco-evolutionary analyses of classic coexistence mechanisms are yielding new insights into the structure and stability of communities. We examine fluctuation-dependent coexistence models, identifying communities that are both ecologically and evolutionarily stable. Members of these communities possess distinct environmental preferences, revealing widespread patterns of limiting similarity. This regularity leads to consistent changes in the structure of communities across fluctuation regimes. However, at high amplitudes, subtle differences in the form of fluctuations dramatically affect the collapse of communities. We also show that identical fluctuations can support multiple evolutionarily stable communities - a novel example of alternative stable states within eco-evolutionary systems. Consequently, the configuration of communities will depend on historical contingencies, including details of the adaptive process. Integrating evolution into the study of coexistence offers new insights, while enriching our understanding of ecology. © 2017 John Wiley & Sons Ltd/CNRS.

  16. Evolutionary and developmental modules.

    Science.gov (United States)

    Lacquaniti, Francesco; Ivanenko, Yuri P; d'Avella, Andrea; Zelik, Karl E; Zago, Myrka

    2013-01-01

    The identification of biological modules at the systems level often follows top-down decomposition of a task goal, or bottom-up decomposition of multidimensional data arrays into basic elements or patterns representing shared features. These approaches traditionally have been applied to mature, fully developed systems. Here we review some results from two other perspectives on modularity, namely the developmental and evolutionary perspective. There is growing evidence that modular units of development were highly preserved and recombined during evolution. We first consider a few examples of modules well identifiable from morphology. Next we consider the more difficult issue of identifying functional developmental modules. We dwell especially on modular control of locomotion to argue that the building blocks used to construct different locomotor behaviors are similar across several animal species, presumably related to ancestral neural networks of command. A recurrent theme from comparative studies is that the developmental addition of new premotor modules underlies the postnatal acquisition and refinement of several different motor behaviors in vertebrates.

  17. Blackout risk prevention in a smart grid based flexible optimal strategy using Grey Wolf-pattern search algorithms

    International Nuclear Information System (INIS)

    Mahdad, Belkacem; Srairi, K.

    2015-01-01

    Highlights: • A generalized optimal security power system planning strategy for blackout risk prevention is proposed. • A Grey Wolf Optimizer dynamically coordinated with Pattern Search algorithm is proposed. • A useful optimized database dynamically generated considering margin loading stability under severe faults. • The robustness and feasibility of the proposed strategy is validated in the standard IEEE 30 Bus system. • The proposed planning strategy will be useful for power system protection coordination and control. - Abstract: Developing a flexible and reliable power system planning strategy under critical situations is of great importance to experts and industrials to minimize the probability of blackouts occurrence. This paper introduces the first stage of this practical strategy by the application of Grey Wolf Optimizer coordinated with pattern search algorithm for solving the security smart grid power system management under critical situations. The main objective of this proposed planning strategy is to prevent the practical power system against blackout due to the apparition of faults in generating units or important transmission lines. At the first stage the system is pushed to its margin stability limit, the critical loads shedding are selected using voltage stability index. In the second stage the generator control variables, the reactive power of shunt and dynamic compensators are adjusted in coordination with minimization the active and reactive power at critical loads to maintain the system at security state to ensure service continuity. The feasibility and efficiency of the proposed strategy is applied to IEEE 30-Bus test system. Results are promising and prove the practical efficiency of the proposed strategy to ensure system security under critical situations

  18. Integrating genomics into evolutionary medicine.

    Science.gov (United States)

    Rodríguez, Juan Antonio; Marigorta, Urko M; Navarro, Arcadi

    2014-12-01

    The application of the principles of evolutionary biology into medicine was suggested long ago and is already providing insight into the ultimate causes of disease. However, a full systematic integration of medical genomics and evolutionary medicine is still missing. Here, we briefly review some cases where the combination of the two fields has proven profitable and highlight two of the main issues hindering the development of evolutionary genomic medicine as a mature field, namely the dissociation between fitness and health and the still considerable difficulties in predicting phenotypes from genotypes. We use publicly available data to illustrate both problems and conclude that new approaches are needed for evolutionary genomic medicine to overcome these obstacles. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Form of an evolutionary tradeoff affects eco-evolutionary dynamics in a predator-prey system.

    Science.gov (United States)

    Kasada, Minoru; Yamamichi, Masato; Yoshida, Takehito

    2014-11-11

    Evolution on a time scale similar to ecological dynamics has been increasingly recognized for the last three decades. Selection mediated by ecological interactions can change heritable phenotypic variation (i.e., evolution), and evolution of traits, in turn, can affect ecological interactions. Hence, ecological and evolutionary dynamics can be tightly linked and important to predict future dynamics, but our understanding of eco-evolutionary dynamics is still in its infancy and there is a significant gap between theoretical predictions and empirical tests. Empirical studies have demonstrated that the presence of genetic variation can dramatically change ecological dynamics, whereas theoretical studies predict that eco-evolutionary dynamics depend on the details of the genetic variation, such as the form of a tradeoff among genotypes, which can be more important than the presence or absence of the genetic variation. Using a predator-prey (rotifer-algal) experimental system in laboratory microcosms, we studied how different forms of a tradeoff between prey defense and growth affect eco-evolutionary dynamics. Our experimental results show for the first time to our knowledge that different forms of the tradeoff produce remarkably divergent eco-evolutionary dynamics, including near fixation, near extinction, and coexistence of algal genotypes, with quantitatively different population dynamics. A mathematical model, parameterized from completely independent experiments, explains the observed dynamics. The results suggest that knowing the details of heritable trait variation and covariation within a population is essential for understanding how evolution and ecology will interact and what form of eco-evolutionary dynamics will result.

  20. New insights into the phylogenetic relationships, character evolution, and phytogeographic patterns of Calceolaria (Calceolariaceae).

    Science.gov (United States)

    Cosacov, Andrea; Sérsic, Alicia N; Sosa, Victoria; De-Nova, J Arturo; Nylinder, Stephan; Cocucci, Andrea A

    2009-12-01

    Biogeographical patterns and diversification processes in Andean and Patagonian flora are not yet well understood. Calceolaria is a highly diversified genus of these areas, representing one of the most specialized plant-pollinator systems because flowers produce nonvolatile oils, a very unusual floral reward. Phylogenetic analyses with molecular (ITS and matK) and morphological characters from 103 Calceolaria species were conducted to examine relationships, to understand biogeographic patterns, and to detect evolutionary patterns of floral and ecological characters. Total evidence analysis retrieved three major clades, which strongly correspond to the three previously recognized subgenera, although only subgenus Rosula was retrieved as a monophyletic group. A single historical event explains the expansion from the southern to central Andes, while different parallel evolutionary lines show a northward expansion from the central to northern Andes across the Huancabamba Deflection, an important geographical barrier in northern Peru. Polyploidy, acquisition of elaiophores, and a nototribic pollination mechanism are key aspects of the evolutionary history of Calceolaria. Pollination interactions were more frequently established with Centris than with Chalepogenus oil-collecting bee species. The repeated loss of the oil gland and shifts to pollen as the only reward suggest an evolutionary tendency from highly to moderately specialized pollination systems.

  1. A loading pattern optimization method for nuclear fuel management

    International Nuclear Information System (INIS)

    Argaud, J.P.

    1997-01-01

    Nuclear fuel reload of PWR core leads to the search of an optimal nuclear fuel assemblies distribution, namely of loading pattern. This large discrete optimization problem is here expressed as a cost function minimization. To deal with this problem, an approach based on gradient information is used to direct the search in the patterns discrete space. A method using an adjoint state formulation is then developed, and final results of complete patterns search tests by this method are presented. (author)

  2. Different evolutionary pathways underlie the morphology of wrist bones in hominoids.

    Science.gov (United States)

    Kivell, Tracy L; Barros, Anna P; Smaers, Jeroen B

    2013-10-23

    The hominoid wrist has been a focus of numerous morphological analyses that aim to better understand long-standing questions about the evolution of human and hominoid hand use. However, these same analyses also suggest various scenarios of complex and mosaic patterns of morphological evolution within the wrist and potentially multiple instances of homoplasy that would benefit from require formal analysis within a phylogenetic context.We identify morphological features that principally characterize primate - and, in particular, hominoid (apes, including humans) - wrist evolution and reveal the rate, process and evolutionary timing of patterns of morphological change on individual branches of the primate tree of life. Linear morphological variables of five wrist bones - the scaphoid, lunate, triquetrum, capitate and hamate - are analyzed in a diverse sample of extant hominoids (12 species, 332 specimens), Old World (8 species, 43 specimens) and New World (4 species, 26 specimens) monkeys, fossil Miocene apes (8 species, 20 specimens) and Plio-Pleistocene hominins (8 species, 18 specimens). Results reveal a combination of parallel and synapomorphic morphology within haplorrhines, and especially within hominoids, across individual wrist bones. Similar morphology of some wrist bones reflects locomotor behaviour shared between clades (scaphoid, triquetrum and capitate) while others (lunate and hamate) indicate clade-specific synapomorphic morphology. Overall, hominoids show increased variation in wrist bone morphology compared with other primate clades, supporting previous analyses, and demonstrate several occurrences of parallel evolution, particularly between orangutans and hylobatids, and among hominines (extant African apes, humans and fossil hominins). Our analyses indicate that different evolutionary processes can underlie the evolution of a single anatomical unit (the wrist) to produce diversity in functional and morphological adaptations across individual wrist

  3. Evolutionary dynamics of cooperation in neutral populations

    Science.gov (United States)

    Szolnoki, Attila; Perc, Matjaž

    2018-01-01

    Cooperation is a difficult proposition in the face of Darwinian selection. Those that defect have an evolutionary advantage over cooperators who should therefore die out. However, spatial structure enables cooperators to survive through the formation of homogeneous clusters, which is the hallmark of network reciprocity. Here we go beyond this traditional setup and study the spatiotemporal dynamics of cooperation in a population of populations. We use the prisoner's dilemma game as the mathematical model and show that considering several populations simultaneously gives rise to fascinating spatiotemporal dynamics and pattern formation. Even the simplest assumption that strategies between different populations are payoff-neutral with one another results in the spontaneous emergence of cyclic dominance, where defectors of one population become prey of cooperators in the other population, and vice versa. Moreover, if social interactions within different populations are characterized by significantly different temptations to defect, we observe that defectors in the population with the largest temptation counterintuitively vanish the fastest, while cooperators that hang on eventually take over the whole available space. Our results reveal that considering the simultaneous presence of different populations significantly expands the complexity of evolutionary dynamics in structured populations, and it allows us to understand the stability of cooperation under adverse conditions that could never be bridged by network reciprocity alone.

  4. Characterization and evolutionary analysis of tributyltin-binding protein and pufferfish saxitoxin and tetrodotoxin-binding protein genes in toxic and nontoxic pufferfishes.

    Science.gov (United States)

    Hashiguchi, Y; Lee, J M; Shiraishi, M; Komatsu, S; Miki, S; Shimasaki, Y; Mochioka, N; Kusakabe, T; Oshima, Y

    2015-05-01

    Understanding the evolutionary mechanisms of toxin accumulation in pufferfishes has been long-standing problem in toxicology and evolutionary biology. Pufferfish saxitoxin and tetrodotoxin-binding protein (PSTBP) is involved in the transport and accumulation of tetrodotoxin and is one of the most intriguing proteins related to the toxicity of pufferfishes. PSTBPs are fusion proteins consisting of two tandem repeated tributyltin-binding protein type 2 (TBT-bp2) domains. In this study, we examined the evolutionary dynamics of TBT-bp2 and PSTBP genes to understand the evolution of toxin accumulation in pufferfishes. Database searches and/or PCR-based cDNA cloning in nine pufferfish species (6 toxic and 3 nontoxic) revealed that all species possessed one or more TBT-bp2 genes, but PSTBP genes were found only in 5 toxic species belonging to genus Takifugu. These toxic Takifugu species possessed two or three copies of PSTBP genes. Phylogenetic analysis of TBT-bp2 and PSTBP genes suggested that PSTBPs evolved in the common ancestor of Takifugu species by repeated duplications and fusions of TBT-bp2 genes. In addition, a detailed comparison of Takifugu TBT-bp2 and PSTBP gene sequences detected a signature of positive selection under the pressure of gene conversion. The complicated evolutionary dynamics of TBT-bp2 and PSTBP genes may reflect the diversity of toxicity in pufferfishes. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

  5. Climate variability slows evolutionary responses of Colias butterflies to recent climate change.

    Science.gov (United States)

    Kingsolver, Joel G; Buckley, Lauren B

    2015-03-07

    How does recent climate warming and climate variability alter fitness, phenotypic selection and evolution in natural populations? We combine biophysical, demographic and evolutionary models with recent climate data to address this question for the subalpine and alpine butterfly, Colias meadii, in the southern Rocky Mountains. We focus on predicting patterns of selection and evolution for a key thermoregulatory trait, melanin (solar absorptivity) on the posterior ventral hindwings, which affects patterns of body temperature, flight activity, adult and egg survival, and reproductive success in Colias. Both mean annual summer temperatures and thermal variability within summers have increased during the past 60 years at subalpine and alpine sites. At the subalpine site, predicted directional selection on wing absorptivity has shifted from generally positive (favouring increased wing melanin) to generally negative during the past 60 years, but there is substantial variation among years in the predicted magnitude and direction of selection and the optimal absorptivity. The predicted magnitude of directional selection at the alpine site declined during the past 60 years and varies substantially among years, but selection has generally been positive at this site. Predicted evolutionary responses to mean climate warming at the subalpine site since 1980 is small, because of the variability in selection and asymmetry of the fitness function. At both sites, the predicted effects of adaptive evolution on mean population fitness are much smaller than the fluctuations in mean fitness due to climate variability among years. Our analyses suggest that variation in climate within and among years may strongly limit evolutionary responses of ectotherms to mean climate warming in these habitats. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  6. Searching for Complex Patterns Using Disjunctive Anomaly Detection

    OpenAIRE

    Sabhnani, Maheshkumar; Dubrawski, Artur; Schneider, Jeff

    2013-01-01

    Objective Disjunctive anomaly detection (DAD) algorithm [1] can efficiently search across multidimensional biosurveillance data to find multiple simultaneously occurring (in time) and overlapping (across different data dimensions) anomalous clusters. We introduce extensions of DAD to handle rich cluster interactions and diverse data distributions. Introduction Modern biosurveillance data contains thousands of unique time series defined across various categorical dimensions (zipcode, age group...

  7. Calculating evolutionary dynamics in structured populations.

    Directory of Open Access Journals (Sweden)

    Charles G Nathanson

    2009-12-01

    Full Text Available Evolution is shaping the world around us. At the core of every evolutionary process is a population of reproducing individuals. The outcome of an evolutionary process depends on population structure. Here we provide a general formula for calculating evolutionary dynamics in a wide class of structured populations. This class includes the recently introduced "games in phenotype space" and "evolutionary set theory." There can be local interactions for determining the relative fitness of individuals, but we require global updating, which means all individuals compete uniformly for reproduction. We study the competition of two strategies in the context of an evolutionary game and determine which strategy is favored in the limit of weak selection. We derive an intuitive formula for the structure coefficient, sigma, and provide a method for efficient numerical calculation.

  8. Evolutionary Multiplayer Games

    OpenAIRE

    Gokhale, Chaitanya S.; Traulsen, Arne

    2014-01-01

    Evolutionary game theory has become one of the most diverse and far reaching theories in biology. Applications of this theory range from cell dynamics to social evolution. However, many applications make it clear that inherent non-linearities of natural systems need to be taken into account. One way of introducing such non-linearities into evolutionary games is by the inclusion of multiple players. An example is of social dilemmas, where group benefits could e.g.\\ increase less than linear wi...

  9. The evolutionary history of colour polymorphism in Ischnura damselflies.

    Science.gov (United States)

    Sánchez-Guillén, Rosa A; Cordero-Rivera, Adolfo; Rivas-Torres, Anais; Wellenreuther, Maren; Bybee, Seth; Hansson, Bengt; Velasquez-Vélez, María I; Realpe, Emilio; Chávez-Ríos, Jesús R; Villalobos, Fabricio; Dumont, Henri

    2018-05-10

    A major challenge in evolutionary biology consists of understanding how genetic and phenotypic variation is created and maintained. In the present study, we investigated the origin(s) and evolutionary patterns of the female-limited colour polymorphism in ischnuran damselflies. These consist of the presence of one to three colour morphs: one androchrome morph with a colouration that is similar to the male, and two gynochrome morphs (infuscans and aurantiaca) with female-specific colouration. We (i) documented the colour and mating system of 44 of the 75 taxa within the genus Ischnura, (ii) reconstructed the evolutionary history of colour and mating system to identify the ancestral state, (iii) evaluated the stability of the colour morph status over time, and (iv) tested for a correlation between colour and mating system. We found that the ances tral female colour of Ischnura was monomorphic and aurantiaca and that colour morph status changed over time; characterised by many gains and losses across the species tree. Our results further showed that colour polymorphism is significantly more frequent among polyandric species, whereas monandric species tend to be monomorphic. Research on some Ischnura species has shown that colour morphs have evolved to reduce male mating harassment, and our finding that the same phenotypic morphs have evolved multiple times (convergent evolution) suggests that several species in this genus might be experiencing similar selective pressures. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  10. Applying Cuckoo Search for analysis of LFSR based cryptosystem

    Directory of Open Access Journals (Sweden)

    Maiya Din

    2016-09-01

    Full Text Available Cryptographic techniques are employed for minimizing security hazards to sensitive information. To make the systems more robust, cyphers or crypts being used need to be analysed for which cryptanalysts require ways to automate the process, so that cryptographic systems can be tested more efficiently. Evolutionary algorithms provide one such resort as these are capable of searching global optimal solution very quickly. Cuckoo Search (CS Algorithm has been used effectively in cryptanalysis of conventional systems like Vigenere and Transposition cyphers. Linear Feedback Shift Register (LFSR is a crypto primitive used extensively in design of cryptosystems. In this paper, we analyse LFSR based cryptosystem using Cuckoo Search to find correct initial states of used LFSR. Primitive polynomials of degree 11, 13, 17 and 19 are considered to analyse text crypts of length 200, 300 and 400 characters. Optimal solutions were obtained for the following CS parameters: Levy distribution parameter (β = 1.5 and Alien eggs discovering probability (pa = 0.25.

  11. Asymmetric Evolutionary Games

    Science.gov (United States)

    McAvoy, Alex; Hauert, Christoph

    2015-01-01

    Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner’s Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games. PMID:26308326

  12. Phylogeography in Nassarius mud snails: Complex patterns in congeneric species.

    Directory of Open Access Journals (Sweden)

    Chuanliang Pu

    Full Text Available One major goal for phylogeographical studies is to elucidate respective roles of multiple evolutionary and ecological forces that shape the current distribution patterns. In marine and coastal ecosystems, it has been generated a common realization that species with enormous population size and pelagic larval stages can disperse across broad geographical scales, leading to weak or even no phylogeographical structure across large geographical scales. However, the violation of such realization has been frequently reported, and it remains largely unexplored on mechanisms responsible for various phylogeographical patterns observed in different species at varied geographical scales. Here, we used a species-rich genus Nassarius to assess and compare phylogeographical patterns in congeneric species, and discuss causes and consequences underlying varied phylogeographical patterns. Interestingly, we observed complex phylogeographical patterns both within single species and across multiple species, and multiple analyses showed varied levels of genetic heterogeneity among sites within and across species. Available evidence suggests that related species with similar biological characteristics may not be necessary to result in consistent phylogeographical patterns. Multiple factors, including larval ecology, interactions between dispersal and natural selection, and human activity-mediated dispersal, can partially explain the complex patterns observed in this study. Deep investigations should be performed on these factors, particularly their respective roles in determining evolutionary/ecological processes to form phylogeographical patterns in species with high dispersal capacities in marine and coastal ecosystems.

  13. SIRW: A web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches.

    Science.gov (United States)

    Ramu, Chenna

    2003-07-01

    SIRW (http://sirw.embl.de/) is a World Wide Web interface to the Simple Indexing and Retrieval System (SIR) that is capable of parsing and indexing various flat file databases. In addition it provides a framework for doing sequence analysis (e.g. motif pattern searches) for selected biological sequences through keyword search. SIRW is an ideal tool for the bioinformatics community for searching as well as analyzing biological sequences of interest.

  14. Industrial Applications of Evolutionary Algorithms

    CERN Document Server

    Sanchez, Ernesto; Tonda, Alberto

    2012-01-01

    This book is intended as a reference both for experienced users of evolutionary algorithms and for researchers that are beginning to approach these fascinating optimization techniques. Experienced users will find interesting details of real-world problems, and advice on solving issues related to fitness computation, modeling and setting appropriate parameters to reach optimal solutions. Beginners will find a thorough introduction to evolutionary computation, and a complete presentation of all evolutionary algorithms exploited to solve different problems. The book could fill the gap between the

  15. An evolutionary firefly algorithm for the estimation of nonlinear biological model parameters.

    Directory of Open Access Journals (Sweden)

    Afnizanfaizal Abdullah

    Full Text Available The development of accurate computational models of biological processes is fundamental to computational systems biology. These models are usually represented by mathematical expressions that rely heavily on the system parameters. The measurement of these parameters is often difficult. Therefore, they are commonly estimated by fitting the predicted model to the experimental data using optimization methods. The complexity and nonlinearity of the biological processes pose a significant challenge, however, to the development of accurate and fast optimization methods. We introduce a new hybrid optimization method incorporating the Firefly Algorithm and the evolutionary operation of the Differential Evolution method. The proposed method improves solutions by neighbourhood search using evolutionary procedures. Testing our method on models for the arginine catabolism and the negative feedback loop of the p53 signalling pathway, we found that it estimated the parameters with high accuracy and within a reasonable computation time compared to well-known approaches, including Particle Swarm Optimization, Nelder-Mead, and Firefly Algorithm. We have also verified the reliability of the parameters estimated by the method using an a posteriori practical identifiability test.

  16. An evolutionary firefly algorithm for the estimation of nonlinear biological model parameters.

    Science.gov (United States)

    Abdullah, Afnizanfaizal; Deris, Safaai; Anwar, Sohail; Arjunan, Satya N V

    2013-01-01

    The development of accurate computational models of biological processes is fundamental to computational systems biology. These models are usually represented by mathematical expressions that rely heavily on the system parameters. The measurement of these parameters is often difficult. Therefore, they are commonly estimated by fitting the predicted model to the experimental data using optimization methods. The complexity and nonlinearity of the biological processes pose a significant challenge, however, to the development of accurate and fast optimization methods. We introduce a new hybrid optimization method incorporating the Firefly Algorithm and the evolutionary operation of the Differential Evolution method. The proposed method improves solutions by neighbourhood search using evolutionary procedures. Testing our method on models for the arginine catabolism and the negative feedback loop of the p53 signalling pathway, we found that it estimated the parameters with high accuracy and within a reasonable computation time compared to well-known approaches, including Particle Swarm Optimization, Nelder-Mead, and Firefly Algorithm. We have also verified the reliability of the parameters estimated by the method using an a posteriori practical identifiability test.

  17. Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management.

    Science.gov (United States)

    Savory, Elizabeth A; Fuller, Skylar L; Weisberg, Alexandra J; Thomas, William J; Gordon, Michael I; Stevens, Danielle M; Creason, Allison L; Belcher, Michael S; Serdani, Maryna; Wiseman, Michele S; Grünwald, Niklaus J; Putnam, Melodie L; Chang, Jeff H

    2017-12-12

    Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of Rhodococcus and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of Rhodococcus , and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks. We demonstrate that isolates lacking virulence genes promote beneficial plant growth, and that the acquisition of a virulence plasmid is sufficient to transition beneficial symbionts to phytopathogens. This evolutionary transition, along with the distribution patterns of plasmids, reveals the impact of horizontal gene transfer in rapidly generating new pathogenic lineages and provides an alternative explanation for pathogen transmission patterns. Results also uncovered a misdiagnosed epidemic that implicated beneficial Rhodococcus bacteria as pathogens of pistachio. The misdiagnosis perpetuated the unnecessary removal of trees and exacerbated economic losses.

  18. Stochastic optimization of loading pattern for PWR

    International Nuclear Information System (INIS)

    Smuc, T.; Pevec, D.

    1994-01-01

    The application of stochastic optimization methods in solving in-core fuel management problems is restrained by the need for a large number of proposed solutions loading patterns, if a high quality final solution is wanted. Proposed loading patterns have to be evaluated by core neutronics simulator, which can impose unrealistic computer time requirements. A new loading pattern optimization code Monte Carlo Loading Pattern Search has been developed by coupling the simulated annealing optimization algorithm with a fast one-and-a-half dimensional core depletion simulator. The structure of the optimization method provides more efficient performance and allows the user to empty precious experience in the search process, thus reducing the search space size. Hereinafter, we discuss the characteristics of the method and illustrate them on the results obtained by solving the PWR reload problem. (authors). 7 refs., 1 tab., 1 fig

  19. Core principles of evolutionary medicine: A Delphi study.

    Science.gov (United States)

    Grunspan, Daniel Z; Nesse, Randolph M; Barnes, M Elizabeth; Brownell, Sara E

    2018-01-01

    Evolutionary medicine is a rapidly growing field that uses the principles of evolutionary biology to better understand, prevent and treat disease, and that uses studies of disease to advance basic knowledge in evolutionary biology. Over-arching principles of evolutionary medicine have been described in publications, but our study is the first to systematically elicit core principles from a diverse panel of experts in evolutionary medicine. These principles should be useful to advance recent recommendations made by The Association of American Medical Colleges and the Howard Hughes Medical Institute to make evolutionary thinking a core competency for pre-medical education. The Delphi method was used to elicit and validate a list of core principles for evolutionary medicine. The study included four surveys administered in sequence to 56 expert panelists. The initial open-ended survey created a list of possible core principles; the three subsequent surveys winnowed the list and assessed the accuracy and importance of each principle. Fourteen core principles elicited at least 80% of the panelists to agree or strongly agree that they were important core principles for evolutionary medicine. These principles over-lapped with concepts discussed in other articles discussing key concepts in evolutionary medicine. This set of core principles will be helpful for researchers and instructors in evolutionary medicine. We recommend that evolutionary medicine instructors use the list of core principles to construct learning goals. Evolutionary medicine is a young field, so this list of core principles will likely change as the field develops further.

  20. Conceptual Barriers to Progress Within Evolutionary Biology.

    Science.gov (United States)

    Laland, Kevin N; Odling-Smee, John; Feldman, Marcus W; Kendal, Jeremy

    2009-08-01

    In spite of its success, Neo-Darwinism is faced with major conceptual barriers to further progress, deriving directly from its metaphysical foundations. Most importantly, neo-Darwinism fails to recognize a fundamental cause of evolutionary change, "niche construction". This failure restricts the generality of evolutionary theory, and introduces inaccuracies. It also hinders the integration of evolutionary biology with neighbouring disciplines, including ecosystem ecology, developmental biology, and the human sciences. Ecology is forced to become a divided discipline, developmental biology is stubbornly difficult to reconcile with evolutionary theory, and the majority of biologists and social scientists are still unhappy with evolutionary accounts of human behaviour. The incorporation of niche construction as both a cause and a product of evolution removes these disciplinary boundaries while greatly generalizing the explanatory power of evolutionary theory.

  1. Evolutionary Statistical Procedures

    CERN Document Server

    Baragona, Roberto; Poli, Irene

    2011-01-01

    This proposed text appears to be a good introduction to evolutionary computation for use in applied statistics research. The authors draw from a vast base of knowledge about the current literature in both the design of evolutionary algorithms and statistical techniques. Modern statistical research is on the threshold of solving increasingly complex problems in high dimensions, and the generalization of its methodology to parameters whose estimators do not follow mathematically simple distributions is underway. Many of these challenges involve optimizing functions for which analytic solutions a

  2. How can we estimate natural selection on endocrine traits? Lessons from evolutionary biology.

    Science.gov (United States)

    Bonier, Frances; Martin, Paul R

    2016-11-30

    An evolutionary perspective can enrich almost any endeavour in biology, providing a deeper understanding of the variation we see in nature. To this end, evolutionary endocrinologists seek to describe the fitness consequences of variation in endocrine traits. Much of the recent work in our field, however, follows a flawed approach to the study of how selection shapes endocrine traits. Briefly, this approach relies on among-individual correlations between endocrine phenotypes (often circulating hormone levels) and fitness metrics to estimate selection on those endocrine traits. Adaptive plasticity in both endocrine and fitness-related traits can drive these correlations, generating patterns that do not accurately reflect natural selection. We illustrate why this approach to studying selection on endocrine traits is problematic, referring to work from evolutionary biologists who, decades ago, described this problem as it relates to a variety of other plastic traits. We extend these arguments to evolutionary endocrinology, where the likelihood that this flaw generates bias in estimates of selection is unusually high due to the exceptional responsiveness of hormones to environmental conditions, and their function to induce adaptive life-history responses to environmental variation. We end with a review of productive approaches for investigating the fitness consequences of variation in endocrine traits that we expect will generate exciting advances in our understanding of endocrine system evolution. © 2016 The Author(s).

  3. DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors

    NARCIS (Netherlands)

    T. Mazor (Tali); A. Pankov (Aleksandr); B.E. Johnson (Brett E.); C. Hong (Chibo); E.G. Hamilton (Emily G.); R.J.A. Bell (Robert J.A.); I.V. Smirnov (Ivan V.); G.F. Reis (Gerald F.); J.J. Phillips (Joanna J.); M.J. Barnes (Michael); A. Idbaih (Ahmed); A. Alentorn (Agusti); J.J. Kloezeman (Jenneke); M.L.M. Lamfers (Martine); A.W. Bollen (Andrew W.); B.S. Taylor (Barry S.); A.M. Molinaro (Annette M.); A. Olshen (Adam); S.M. Chang (Susan); J.S. Song (Jun S.); J.F. Costello (Joseph F.)

    2015-01-01

    textabstractThe evolutionary history of tumor cell populations can be reconstructed from patterns of genetic alterations. In contrast to stable genetic events, epigenetic states are reversible and sensitive to the microenvironment, prompting the question whether epigenetic information can similarly

  4. Behavioural, ecological, and evolutionary aspects of diversity in frog colour patterns

    OpenAIRE

    Rojas Zuluaga, Bibiana

    2017-01-01

    The role of colours and colour patterns in behavioural ecology has been extensively studied in a variety of contexts and taxa, while almost overlooked in many others. For decades anurans have been the focus of research on acoustic signalling due to the prominence of vocalisations in their communication. Much less attention has been paid to the enormous diversity of colours, colour patterns, and other types of putative visual signals exhibited by frogs. With the exception of some anecdotal obs...

  5. Contemporary issues in evolutionary biology

    Indian Academy of Sciences (India)

    These discussions included, among others, the possible consequences of nonDNA-based inheritance—epigenetics and cultural evolution, niche construction, and developmental mechanisms on our understanding of the evolutionary process, speciation, complexity in biology, and constructing a formal evolutionary theory.

  6. A Problem-Reduction Evolutionary Algorithm for Solving the Capacitated Vehicle Routing Problem

    Directory of Open Access Journals (Sweden)

    Wanfeng Liu

    2015-01-01

    Full Text Available Assessment of the components of a solution helps provide useful information for an optimization problem. This paper presents a new population-based problem-reduction evolutionary algorithm (PREA based on the solution components assessment. An individual solution is regarded as being constructed by basic elements, and the concept of acceptability is introduced to evaluate them. The PREA consists of a searching phase and an evaluation phase. The acceptability of basic elements is calculated in the evaluation phase and passed to the searching phase. In the searching phase, for each individual solution, the original optimization problem is reduced to a new smaller-size problem. With the evolution of the algorithm, the number of common basic elements in the population increases until all individual solutions are exactly the same which is supposed to be the near-optimal solution of the optimization problem. The new algorithm is applied to a large variety of capacitated vehicle routing problems (CVRP with customers up to nearly 500. Experimental results show that the proposed algorithm has the advantages of fast convergence and robustness in solution quality over the comparative algorithms.

  7. Evolutionary Co-Option of Floral Meristem Identity Genes for Patterning of the Flower-Like Asteraceae Inflorescence.

    Science.gov (United States)

    Zhao, Yafei; Zhang, Teng; Broholm, Suvi K; Tähtiharju, Sari; Mouhu, Katriina; Albert, Victor A; Teeri, Teemu H; Elomaa, Paula

    2016-09-01

    The evolutionary success of Asteraceae, the largest family of flowering plants, has been attributed to the unique inflorescence architecture of the family, which superficially resembles an individual flower. Here, we show that Asteraceae inflorescences (flower heads, or capitula) resemble solitary flowers not only morphologically but also at the molecular level. By conducting functional analyses for orthologs of the flower meristem identity genes LEAFY (LFY) and UNUSUAL FLORAL ORGANS (UFO) in Gerbera hybrida, we show that GhUFO is the master regulator of flower meristem identity, while GhLFY has evolved a novel, homeotic function during the evolution of head-like inflorescences. Resembling LFY expression in a single flower meristem, uniform expression of GhLFY in the inflorescence meristem defines the capitulum as a determinate structure that can assume floral fate upon ectopic GhUFO expression. We also show that GhLFY uniquely regulates the ontogeny of outer, expanded ray flowers but not inner, compact disc flowers, indicating that the distinction of different flower types in Asteraceae is connected with their independent evolutionary origins from separate branching systems. © 2016 American Society of Plant Biologists. All rights reserved.

  8. An Evolutionary Algorithm to Mine High-Utility Itemsets

    Directory of Open Access Journals (Sweden)

    Jerry Chun-Wei Lin

    2015-01-01

    Full Text Available High-utility itemset mining (HUIM is a critical issue in recent years since it can be used to reveal the profitable products by considering both the quantity and profit factors instead of frequent itemset mining (FIM of association rules (ARs. In this paper, an evolutionary algorithm is presented to efficiently mine high-utility itemsets (HUIs based on the binary particle swarm optimization. A maximal pattern (MP-tree strcutrue is further designed to solve the combinational problem in the evolution process. Substantial experiments on real-life datasets show that the proposed binary PSO-based algorithm has better results compared to the state-of-the-art GA-based algorithm.

  9. Research traditions and evolutionary explanations in medicine.

    Science.gov (United States)

    Méthot, Pierre-Olivier

    2011-02-01

    In this article, I argue that distinguishing 'evolutionary' from 'Darwinian' medicine will help us assess the variety of roles that evolutionary explanations can play in a number of medical contexts. Because the boundaries of evolutionary and Darwinian medicine overlap to some extent, however, they are best described as distinct 'research traditions' rather than as competing paradigms. But while evolutionary medicine does not stand out as a new scientific field of its own, Darwinian medicine is united by a number of distinctive theoretical and methodological claims. For example, evolutionary medicine and Darwinian medicine can be distinguished with respect to the styles of evolutionary explanations they employ. While the former primarily involves 'forward looking' explanations, the latter depends mostly on 'backward looking' explanations. A forward looking explanation tries to predict the effects of ongoing evolutionary processes on human health and disease in contemporary environments (e.g., hospitals). In contrast, a backward looking explanation typically applies evolutionary principles from the vantage point of humans' distant biological past in order to assess present states of health and disease. Both approaches, however, are concerned with the prevention and control of human diseases. In conclusion, I raise some concerns about the claim that 'nothing in medicine makes sense except in the light of evolution'.

  10. Applications of evolutionary economic geography

    NARCIS (Netherlands)

    Boschma, R.A.; Frenken, K.; Puranam, Krishna Kishore; Ravi Kumar Jain B., xx

    2008-01-01

    This paper is written as the first chapter of an edited volume on evolutionary economics and economic geography (Frenken, K., editor, Applied Evolutionary Economics and Economic Geography, Cheltenham: Edward Elgar, expected publication date February 2007). The paper reviews empirical applications of

  11. How visual search relates to visual diagnostic performance: a narrative systematic review of eye-tracking research in radiology.

    Science.gov (United States)

    van der Gijp, A; Ravesloot, C J; Jarodzka, H; van der Schaaf, M F; van der Schaaf, I C; van Schaik, J P J; Ten Cate, Th J

    2017-08-01

    Eye tracking research has been conducted for decades to gain understanding of visual diagnosis such as in radiology. For educational purposes, it is important to identify visual search patterns that are related to high perceptual performance and to identify effective teaching strategies. This review of eye-tracking literature in the radiology domain aims to identify visual search patterns associated with high perceptual performance. Databases PubMed, EMBASE, ERIC, PsycINFO, Scopus and Web of Science were searched using 'visual perception' OR 'eye tracking' AND 'radiology' and synonyms. Two authors independently screened search results and included eye tracking studies concerning visual skills in radiology published between January 1, 1994 and July 31, 2015. Two authors independently assessed study quality with the Medical Education Research Study Quality Instrument, and extracted study data with respect to design, participant and task characteristics, and variables. A thematic analysis was conducted to extract and arrange study results, and a textual narrative synthesis was applied for data integration and interpretation. The search resulted in 22 relevant full-text articles. Thematic analysis resulted in six themes that informed the relation between visual search and level of expertise: (1) time on task, (2) eye movement characteristics of experts, (3) differences in visual attention, (4) visual search patterns, (5) search patterns in cross sectional stack imaging, and (6) teaching visual search strategies. Expert search was found to be characterized by a global-focal search pattern, which represents an initial global impression, followed by a detailed, focal search-to-find mode. Specific task-related search patterns, like drilling through CT scans and systematic search in chest X-rays, were found to be related to high expert levels. One study investigated teaching of visual search strategies, and did not find a significant effect on perceptual performance. Eye

  12. Diversity and evolutionary patterns of immune genes in free-ranging Namibian leopards (Panthera pardus pardus).

    Science.gov (United States)

    Castro-Prieto, Aines; Wachter, Bettina; Melzheimer, Joerg; Thalwitzer, Susanne; Sommer, Simone

    2011-01-01

    The genes of the major histocompatibility complex (MHC) are a key component of the mammalian immune system and have become important molecular markers for fitness-related genetic variation in wildlife populations. Currently, no information about the MHC sequence variation and constitution in African leopards exists. In this study, we isolated and characterized genetic variation at the adaptively most important region of MHC class I and MHC class II-DRB genes in 25 free-ranging African leopards from Namibia and investigated the mechanisms that generate and maintain MHC polymorphism in the species. Using single-stranded conformation polymorphism analysis and direct sequencing, we detected 6 MHC class I and 6 MHC class II-DRB sequences, which likely correspond to at least 3 MHC class I and 3 MHC class II-DRB loci. Amino acid sequence variation in both MHC classes was higher or similar in comparison to other reported felids. We found signatures of positive selection shaping the diversity of MHC class I and MHC class II-DRB loci during the evolutionary history of the species. A comparison of MHC class I and MHC class II-DRB sequences of the leopard to those of other felids revealed a trans-species mode of evolution. In addition, the evolutionary relationships of MHC class II-DRB sequences between African and Asian leopard subspecies are discussed.

  13. Evolutionary dynamics of incubation periods.

    Science.gov (United States)

    Ottino-Loffler, Bertrand; Scott, Jacob G; Strogatz, Steven H

    2017-12-21

    The incubation period for typhoid, polio, measles, leukemia and many other diseases follows a right-skewed, approximately lognormal distribution. Although this pattern was discovered more than sixty years ago, it remains an open question to explain its ubiquity. Here, we propose an explanation based on evolutionary dynamics on graphs. For simple models of a mutant or pathogen invading a network-structured population of healthy cells, we show that skewed distributions of incubation periods emerge for a wide range of assumptions about invader fitness, competition dynamics, and network structure. The skewness stems from stochastic mechanisms associated with two classic problems in probability theory: the coupon collector and the random walk. Unlike previous explanations that rely crucially on heterogeneity, our results hold even for homogeneous populations. Thus, we predict that two equally healthy individuals subjected to equal doses of equally pathogenic agents may, by chance alone, show remarkably different time courses of disease.

  14. Evolutionary adaptations to dietary changes.

    Science.gov (United States)

    Luca, F; Perry, G H; Di Rienzo, A

    2010-08-21

    Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area.

  15. Reconstructing the Evolutionary History of Paralogous APETALA1/FRUITFULL-Like Genes in Grasses (Poaceae)

    Science.gov (United States)

    Preston, Jill C.; Kellogg, Elizabeth A.

    2006-01-01

    Gene duplication is an important mechanism for the generation of evolutionary novelty. Paralogous genes that are not silenced may evolve new functions (neofunctionalization) that will alter the developmental outcome of preexisting genetic pathways, partition ancestral functions (subfunctionalization) into divergent developmental modules, or function redundantly. Functional divergence can occur by changes in the spatio-temporal patterns of gene expression and/or by changes in the activities of their protein products. We reconstructed the evolutionary history of two paralogous monocot MADS-box transcription factors, FUL1 and FUL2, and determined the evolution of sequence and gene expression in grass AP1/FUL-like genes. Monocot AP1/FUL-like genes duplicated at the base of Poaceae and codon substitutions occurred under relaxed selection mostly along the branch leading to FUL2. Following the duplication, FUL1 was apparently lost from early diverging taxa, a pattern consistent with major changes in grass floral morphology. Overlapping gene expression patterns in leaves and spikelets indicate that FUL1 and FUL2 probably share some redundant functions, but that FUL2 may have become temporally restricted under partial subfunctionalization to particular stages of floret development. These data have allowed us to reconstruct the history of AP1/FUL-like genes in Poaceae and to hypothesize a role for this gene duplication in the evolution of the grass spikelet. PMID:16816429

  16. Preliminary Results on Uncertainty Quantification for Pattern Analytics

    Energy Technology Data Exchange (ETDEWEB)

    Stracuzzi, David John [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Brost, Randolph [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Chen, Maximillian Gene [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Malinas, Rebecca [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Peterson, Matthew Gregor [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Phillips, Cynthia A. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Robinson, David G. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Woodbridge, Diane [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

    2015-09-01

    This report summarizes preliminary research into uncertainty quantification for pattern ana- lytics within the context of the Pattern Analytics to Support High-Performance Exploitation and Reasoning (PANTHER) project. The primary focus of PANTHER was to make large quantities of remote sensing data searchable by analysts. The work described in this re- port adds nuance to both the initial data preparation steps and the search process. Search queries are transformed from does the specified pattern exist in the data? to how certain is the system that the returned results match the query? We show example results for both data processing and search, and discuss a number of possible improvements for each.

  17. Chaos Enhanced Differential Evolution in the Task of Evolutionary Control of Discrete Chaotic LOZI Map

    Directory of Open Access Journals (Sweden)

    Roman Senkerik

    2016-01-01

    Full Text Available In this paper, evolutionary technique Differential Evolution (DE is used for the evolutionary tuning of controller parameters for the stabilization of selected discrete chaotic system, which is the two-dimensional Lozi map. The novelty of the approach is that the selected controlled discrete dissipative chaotic system is used within Chaos enhanced heuristic concept as the chaotic pseudo-random number generator to drive the mutation and crossover process in the DE. The idea was to utilize the hidden chaotic dynamics in pseudo-random sequences given by chaotic map to help Differential evolution algorithm in searching for the best controller settings for the same chaotic system. The optimizations were performed for three different required final behavior of the chaotic system, and two types of developed cost function. To confirm the robustness of presented approach, comparisons with canonical DE strategy and PSO algorithm have been performed.

  18. Urban Evolutionary Ecology and the Potential Benefits of Implementing Genomics.

    Science.gov (United States)

    Schell, Christopher J

    2018-02-14

    Urban habitats are quickly becoming exceptional models to address adaptation under rapid environmental change, given the expansive temporal and spatial scales with which anthropogenic landscape conversion occurs. Urban ecologists in the last 10-15 years have done an extraordinary job of highlighting phenotypic patterns that correspond with urban living, as well as delineating urban population structure using traditional genetic markers. The underpinning genetic mechanisms that govern those phenotypic patterns, however, are less well established. Moreover, the power of traditional molecular studies is constrained by the number of markers being evaluated, which limits the potential to assess fine-scale population structure potentially common in urban areas. With the recent proliferation of low-cost, high-throughput sequencing methods, we can begin to address an emerging question in urban ecology: are species adapted to local optima within cities or are they expressing latent phenotypic plasticity? Here, I provide a comprehensive review of previous urban ecological studies, with special focus on the molecular ecology and phenotypic adjustments documented in urban terrestrial and amphibious fauna. I subsequently pinpoint areas in the literature that could benefit from a genomic investigation and briefly discuss the suitability of specific techniques in addressing eco-evolutionary questions within urban ecology. Though many challenges exist with implementing genomics into urban ecology, such studies provide an exceptional opportunity to advance our understanding of eco-evolutionary processes in metropolitan areas. © The American Genetic Association 2018. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. Revising the recent evolutionary history of equids using ancient DNA.

    Science.gov (United States)

    Orlando, Ludovic; Metcalf, Jessica L; Alberdi, Maria T; Telles-Antunes, Miguel; Bonjean, Dominique; Otte, Marcel; Martin, Fabiana; Eisenmann, Véra; Mashkour, Marjan; Morello, Flavia; Prado, Jose L; Salas-Gismondi, Rodolfo; Shockey, Bruce J; Wrinn, Patrick J; Vasil'ev, Sergei K; Ovodov, Nikolai D; Cherry, Michael I; Hopwood, Blair; Male, Dean; Austin, Jeremy J; Hänni, Catherine; Cooper, Alan

    2009-12-22

    The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.

  20. An improved Pattern Search based algorithm to solve the Dynamic Economic Dispatch problem with valve-point effect

    International Nuclear Information System (INIS)

    Alsumait, J.S.; Qasem, M.; Sykulski, J.K.; Al-Othman, A.K.

    2010-01-01

    In this paper, an improved algorithm based on Pattern Search method (PS) to solve the Dynamic Economic Dispatch is proposed. The algorithm maintains the essential unit ramp rate constraint, along with all other necessary constraints, not only for the time horizon of operation (24 h), but it preserves these constraints through the transaction period to the next time horizon (next day) in order to avoid the discontinuity of the power system operation. The Dynamic Economic and Emission Dispatch problem (DEED) is also considered. The load balance constraints, operating limits, valve-point loading and network losses are included in the models of both DED and DEED. The numerical results clarify the significance of the improved algorithm and verify its performance.

  1. Evolutionary growth process of highly conserved sequences in vertebrate genomes.

    Science.gov (United States)

    Ishibashi, Minaka; Noda, Akiko Ogura; Sakate, Ryuichi; Imanishi, Tadashi

    2012-08-01

    Genome sequence comparison between evolutionarily distant species revealed ultraconserved elements (UCEs) among mammals under strong purifying selection. Most of them were also conserved among vertebrates. Because they tend to be located in the flanking regions of developmental genes, they would have fundamental roles in creating vertebrate body plans. However, the evolutionary origin and selection mechanism of these UCEs remain unclear. Here we report that UCEs arose in primitive vertebrates, and gradually grew in vertebrate evolution. We searched for UCEs in two teleost fishes, Tetraodon nigroviridis and Oryzias latipes, and found 554 UCEs with 100% identity over 100 bps. Comparison of teleost and mammalian UCEs revealed 43 pairs of common, jawed-vertebrate UCEs (jUCE) with high sequence identities, ranging from 83.1% to 99.2%. Ten of them retain lower similarities to the Petromyzon marinus genome, and the substitution rates of four non-exonic jUCEs were reduced after the teleost-mammal divergence, suggesting that robust conservation had been acquired in the jawed vertebrate lineage. Our results indicate that prototypical UCEs originated before the divergence of jawed and jawless vertebrates and have been frozen as perfect conserved sequences in the jawed vertebrate lineage. In addition, our comparative sequence analyses of UCEs and neighboring regions resulted in a discovery of lineage-specific conserved sequences. They were added progressively to prototypical UCEs, suggesting step-wise acquisition of novel regulatory roles. Our results indicate that conserved non-coding elements (CNEs) consist of blocks with distinct evolutionary history, each having been frozen since different evolutionary era along the vertebrate lineage. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. Evolutionary disarmament in interspecific competition.

    Science.gov (United States)

    Kisdi, E; Geritz, S A

    2001-12-22

    Competitive asymmetry, which is the advantage of having a larger body or stronger weaponry than a contestant, drives spectacular evolutionary arms races in intraspecific competition. Similar asymmetries are well documented in interspecific competition, yet they seldom lead to exaggerated traits. Here we demonstrate that two species with substantially different size may undergo parallel coevolution towards a smaller size under the same ecological conditions where a single species would exhibit an evolutionary arms race. We show that disarmament occurs for a wide range of parameters in an ecologically explicit model of competition for a single shared resource; disarmament also occurs in a simple Lotka-Volterra competition model. A key property of both models is the interplay between evolutionary dynamics and population density. The mechanism does not rely on very specific features of the model. Thus, evolutionary disarmament may be widespread and may help to explain the lack of interspecific arms races.

  3. Searching Process with Raita Algorithm and its Application

    Science.gov (United States)

    Rahim, Robbi; Saleh Ahmar, Ansari; Abdullah, Dahlan; Hartama, Dedy; Napitupulu, Darmawan; Putera Utama Siahaan, Andysah; Hasan Siregar, Muhammad Noor; Nasution, Nurliana; Sundari, Siti; Sriadhi, S.

    2018-04-01

    Searching is a common process performed by many computer users, Raita algorithm is one algorithm that can be used to match and find information in accordance with the patterns entered. Raita algorithm applied to the file search application using java programming language and the results obtained from the testing process of the file search quickly and with accurate results and support many data types.

  4. Incorporating evolutionary principles into environmental management and policy

    DEFF Research Database (Denmark)

    Lankau, Richard; Jørgensen, Peter Søgaard; Harris, David J.

    2011-01-01

    As policymakers and managers work to mitigate the effects of rapid anthropogenic environmental changes, they need to consider organisms’ responses. In light of recent evidence that evolution can be quite rapid, this now includes evolutionary responses. Evolutionary principles have a long history...... in conservation biology, and the necessary next step for the field is to consider ways in which conservation policy makers and managers can proactively manipulate evolutionary processes to achieve their goals. In this review, we aim to illustrate the potential conservation benefits of an increased understanding...... of evolutionary history and prescriptive manipulation of three basic evolutionary factors: selection, variation, and gene flow. For each, we review and propose ways that policy makers and managers can use evolutionary thinking to preserve threatened species, combat pest species, or reduce undesirable evolutionary...

  5. Analysis of Nondeterministic Search Patterns for Minimization of UAV Counter-Targeting

    Science.gov (United States)

    2013-03-01

    64 Figure 4.9 Procerus Unicorn UAV [48] used in multi-UAV look-ahead Levy search demonstration conducted at 13-2 JIFX in February, 2013...minimum time or coverage path, minimal overlap, increased robustness to localization errors, etc. [3–5]. The role of randomized coverage and search...to the Procerus Unicorn UAV employed during these flight experiments, shown in Figure 4.9. Figure 4.10 shows the straight-line path between the major

  6. Google vs. the Library (Part II): Student Search Patterns and Behaviors When Using Google and a Federated Search Tool

    Science.gov (United States)

    Georgas, Helen

    2014-01-01

    This study examines the information-seeking behavior of undergraduate students within a research context. Student searches were recorded while the participants used Google and a library (federated) search tool to find sources (one book, two articles, and one other source of their choosing) for a selected topic. The undergraduates in this study…

  7. An evolutionary concept analysis of futility in health care.

    Science.gov (United States)

    Morata, Lauren

    2018-06-01

    To report a concept analysis of futility in health care. Each member of the healthcare team: the physician, the nurse, the patient, the family and all others involved perceive futility differently. The current evidence and knowledge in regard to futility in health care manifest a plethora of definitions, meanings and interpretations without consensus. Concept analysis. Databases searched included Medline, Cumulative Index of Nursing and Allied Health Literature, Academic Search Premier, Cochrane Database of Systematic Reviews and PsycINFO. Search terms included "futil*," "concept analysis," "concept," "inefficacious," "non-beneficial," "ineffective" and "fruitless" from 1935-2016 to ensure a historical perspective of the concept. A total of 106 articles were retained to develop the concept. Rogers' evolutionary concept analysis was used to evaluate the concept of futility from ancient medicine to the present. Seven antecedents (the patient/family autonomy, surrogate decision-making movement, the patient-family/physician relationship, physician authority, legislation and court rulings, catastrophic events and advancing medical technology) lead to four major attributes (quantitative, physiologic, qualitative, and disease-specific). Ultimately, futile care could lead to consequences such as litigation, advancing technology, increasing healthcare costs, rationing, moral distress and ethical dilemmas. Futility in health care demonstrates components of a cyclical process and a consensus definition is proposed. A framework is developed to clarify the concept and articulate relationships among attributes, antecedents and consequences. Further testing of the proposed definition and framework are needed. © 2018 John Wiley & Sons Ltd.

  8. Evolutionary economics and industry location

    NARCIS (Netherlands)

    Boschma, R.A.; Frenken, K.

    2003-01-01

    This paper aims to provide the outlines of an evolutionary economic geography of industry location. We discuss two evolutionary explanations of industry location, that is, one that concentrates on spin-offs, and one that focuses attention on knowledge and agglomeration economies. We claim that both

  9. High activity and Levy searches: jellyfish can search the water column like fish.

    Science.gov (United States)

    Hays, Graeme C; Bastian, Thomas; Doyle, Thomas K; Fossette, Sabrina; Gleiss, Adrian C; Gravenor, Michael B; Hobson, Victoria J; Humphries, Nicolas E; Lilley, Martin K S; Pade, Nicolas G; Sims, David W

    2012-02-07

    Over-fishing may lead to a decrease in fish abundance and a proliferation of jellyfish. Active movements and prey search might be thought to provide a competitive advantage for fish, but here we use data-loggers to show that the frequently occurring coastal jellyfish (Rhizostoma octopus) does not simply passively drift to encounter prey. Jellyfish (327 days of data from 25 jellyfish with depth collected every 1 min) showed very dynamic vertical movements, with their integrated vertical movement averaging 619.2 m d(-1), more than 60 times the water depth where they were tagged. The majority of movement patterns were best approximated by exponential models describing normal random walks. However, jellyfish also showed switching behaviour from exponential patterns to patterns best fitted by a truncated Lévy distribution with exponents (mean μ=1.96, range 1.2-2.9) close to the theoretical optimum for searching for sparse prey (μopt≈2.0). Complex movements in these 'simple' animals may help jellyfish to compete effectively with fish for plankton prey, which may enhance their ability to increase in dominance in perturbed ocean systems.

  10. Evolutionary institutionalism.

    Science.gov (United States)

    Fürstenberg, Dr Kai

    Institutions are hard to define and hard to study. Long prominent in political science have been two theories: Rational Choice Institutionalism (RCI) and Historical Institutionalism (HI). Arising from the life sciences is now a third: Evolutionary Institutionalism (EI). Comparative strengths and weaknesses of these three theories warrant review, and the value-to-be-added by expanding the third beyond Darwinian evolutionary theory deserves consideration. Should evolutionary institutionalism expand to accommodate new understanding in ecology, such as might apply to the emergence of stability, and in genetics, such as might apply to political behavior? Core arguments are reviewed for each theory with more detailed exposition of the third, EI. Particular attention is paid to EI's gene-institution analogy; to variation, selection, and retention of institutional traits; to endogeneity and exogeneity; to agency and structure; and to ecosystem effects, institutional stability, and empirical limitations in behavioral genetics. RCI, HI, and EI are distinct but complementary. Institutional change, while amenable to rational-choice analysis and, retrospectively, to criticaljuncture and path-dependency analysis, is also, and importantly, ecological. Stability, like change, is an emergent property of institutions, which tend to stabilize after change in a manner analogous to allopatric speciation. EI is more than metaphorically biological in that institutional behaviors are driven by human behaviors whose evolution long preceded the appearance of institutions themselves.

  11. Evolutionary foundations for cancer biology.

    Science.gov (United States)

    Aktipis, C Athena; Nesse, Randolph M

    2013-01-01

    New applications of evolutionary biology are transforming our understanding of cancer. The articles in this special issue provide many specific examples, such as microorganisms inducing cancers, the significance of within-tumor heterogeneity, and the possibility that lower dose chemotherapy may sometimes promote longer survival. Underlying these specific advances is a large-scale transformation, as cancer research incorporates evolutionary methods into its toolkit, and asks new evolutionary questions about why we are vulnerable to cancer. Evolution explains why cancer exists at all, how neoplasms grow, why cancer is remarkably rare, and why it occurs despite powerful cancer suppression mechanisms. Cancer exists because of somatic selection; mutations in somatic cells result in some dividing faster than others, in some cases generating neoplasms. Neoplasms grow, or do not, in complex cellular ecosystems. Cancer is relatively rare because of natural selection; our genomes were derived disproportionally from individuals with effective mechanisms for suppressing cancer. Cancer occurs nonetheless for the same six evolutionary reasons that explain why we remain vulnerable to other diseases. These four principles-cancers evolve by somatic selection, neoplasms grow in complex ecosystems, natural selection has shaped powerful cancer defenses, and the limitations of those defenses have evolutionary explanations-provide a foundation for understanding, preventing, and treating cancer.

  12. A solution to energy and environmental problems of electric power system using hybrid harmony search-random search optimization algorithm

    Directory of Open Access Journals (Sweden)

    Vikram Kumar Kamboj

    2016-04-01

    Full Text Available In recent years, global warming and carbon dioxide (CO2 emission reduction have become important issues in India, as CO2 emission levels are continuing to rise in accordance with the increased volume of Indian national energy consumption under the pressure of global warming, it is crucial for Indian government to impose the effective policy to promote CO2 emission reduction. Challenge of supplying the nation with high quality and reliable electrical energy at a reasonable cost, converted government policy into deregulation and restructuring environment. This research paper presents aims to presents an effective solution for energy and environmental problems of electric power using an efficient and powerful hybrid optimization algorithm: Hybrid Harmony search-random search algorithm. The proposed algorithm is tested for standard IEEE-14 bus, -30 bus and -56 bus system. The effectiveness of proposed hybrid algorithm is compared with others well known evolutionary, heuristics and meta-heuristics search algorithms. For multi-objective unit commitment, it is found that as there are conflicting relationship between cost and emission, if the performance in cost criterion is improved, performance in the emission is seen to deteriorate.

  13. Culture belief based multi-objective hybrid differential evolutionary algorithm in short term hydrothermal scheduling

    International Nuclear Information System (INIS)

    Zhang Huifeng; Zhou Jianzhong; Zhang Yongchuan; Lu Youlin; Wang Yongqiang

    2013-01-01

    Highlights: ► Culture belief is integrated into multi-objective differential evolution. ► Chaotic sequence is imported to improve evolutionary population diversity. ► The priority of convergence rate is proved in solving hydrothermal problem. ► The results show the quality and potential of proposed algorithm. - Abstract: A culture belief based multi-objective hybrid differential evolution (CB-MOHDE) is presented to solve short term hydrothermal optimal scheduling with economic emission (SHOSEE) problem. This problem is formulated for compromising thermal cost and emission issue while considering its complicated non-linear constraints with non-smooth and non-convex characteristics. The proposed algorithm integrates a modified multi-objective differential evolutionary algorithm into the computation model of culture algorithm (CA) as well as some communication protocols between population space and belief space, three knowledge structures in belief space are redefined according to these problem-solving characteristics, and in the differential evolution a chaotic factor is embedded into mutation operator for avoiding the premature convergence by enlarging the search scale when the search trajectory reaches local optima. Furthermore, a new heuristic constraint-handling technique is utilized to handle those complex equality and inequality constraints of SHOSEE problem. After the application on hydrothermal scheduling system, the efficiency and stability of the proposed CB-MOHDE is verified by its more desirable results in comparison to other method established recently, and the simulation results also reveal that CB-MOHDE can be a promising alternative for solving SHOSEE.

  14. Evolutionary principles and their practical application

    DEFF Research Database (Denmark)

    Hendry, A. P.; Kinnison, M. T.; Heino, M.

    2011-01-01

    Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles...... are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design...... of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently...

  15. Motion Vector Estimation Using Line-Square Search Block Matching Algorithm for Video Sequences

    Directory of Open Access Journals (Sweden)

    Guo Bao-long

    2004-09-01

    Full Text Available Motion estimation and compensation techniques are widely used for video coding applications but the real-time motion estimation is not easily achieved due to its enormous computations. In this paper, a new fast motion estimation algorithm based on line search is presented, in which computation complexity is greatly reduced by using the line search strategy and a parallel search pattern. Moreover, the accurate search is achieved because the small square search pattern is used. It has a best-case scenario of only 9 search points, which is 4 search points less than the diamond search algorithm. Simulation results show that, compared with the previous techniques, the LSPS algorithm significantly reduces the computational requirements for finding motion vectors, and also produces close performance in terms of motion compensation errors.

  16. Evolutionary Co-Option of Floral Meristem Identity Genes for Patterning of the Flower-Like Asteraceae Inflorescence1

    Science.gov (United States)

    Broholm, Suvi K.; Tähtiharju, Sari

    2016-01-01

    The evolutionary success of Asteraceae, the largest family of flowering plants, has been attributed to the unique inflorescence architecture of the family, which superficially resembles an individual flower. Here, we show that Asteraceae inflorescences (flower heads, or capitula) resemble solitary flowers not only morphologically but also at the molecular level. By conducting functional analyses for orthologs of the flower meristem identity genes LEAFY (LFY) and UNUSUAL FLORAL ORGANS (UFO) in Gerbera hybrida, we show that GhUFO is the master regulator of flower meristem identity, while GhLFY has evolved a novel, homeotic function during the evolution of head-like inflorescences. Resembling LFY expression in a single flower meristem, uniform expression of GhLFY in the inflorescence meristem defines the capitulum as a determinate structure that can assume floral fate upon ectopic GhUFO expression. We also show that GhLFY uniquely regulates the ontogeny of outer, expanded ray flowers but not inner, compact disc flowers, indicating that the distinction of different flower types in Asteraceae is connected with their independent evolutionary origins from separate branching systems. PMID:27382139

  17. Academic search in response to major scientific events

    NARCIS (Netherlands)

    Li, X.; de Rijke, M.

    2017-01-01

    In this paper, we look at the search behavior of users of an academic search engine and in particular, their query patterns following the occurrence of major scientific events. We select Nobel Prize announcements as major scientific events and observe how academic searchers behave in response to

  18. A Fuzzy Gravitational Search Algorithm to Design Optimal IIR Filters

    Directory of Open Access Journals (Sweden)

    Danilo Pelusi

    2018-03-01

    Full Text Available The goodness of Infinite Impulse Response (IIR digital filters design depends on pass band ripple, stop band ripple and transition band values. The main problem is defining a suitable error fitness function that depends on these parameters. This fitness function can be optimized by search algorithms such as evolutionary algorithms. This paper proposes an intelligent algorithm for the design of optimal 8th order IIR filters. The main contribution is the design of Fuzzy Inference Systems able to tune key parameters of a revisited version of the Gravitational Search Algorithm (GSA. In this way, a Fuzzy Gravitational Search Algorithm (FGSA is designed. The optimization performances of FGSA are compared with those of Differential Evolution (DE and GSA. The results show that FGSA is the algorithm that gives the best compromise between goodness, robustness and convergence rate for the design of 8th order IIR filters. Moreover, FGSA assures a good stability of the designed filters.

  19. Evolutionary and developmental implications of asymmetric brain folding in a large primate pedigree

    OpenAIRE

    Atkinson, Elizabeth G.; Rogers, Jeffrey; Cheverud, James M.

    2016-01-01

    Bilateral symmetry is a fundamental property of the vertebrate central nervous system. Local deviations from symmetry provide various types of information about the development, evolution and function of elements within the CNS, especially the cerebral hemispheres. Here, we quantify the pattern and extent of asymmetry in cortical folding within the cerebrum of Papio baboons and assess the evolutionary and developmental implications of the findings. Analyses of directional asymmetry show a pop...

  20. Gender Inequality in Interaction--An Evolutionary Account

    Science.gov (United States)

    Hopcroft, Rosemary L.

    2009-01-01

    In this article I argue that evolutionary theorizing can help sociologists and feminists better understand gender inequality. Evolutionary theory explains why control of the sexuality of young women is a priority across most human societies both past and present. Evolutionary psychology has extended our understanding of male violence against…

  1. Identification of volatile and semivolatile compounds in chemical ionization GC-MS using a mass-to-structure (MTS) Search Engine with integral isotope pattern ranking.

    Science.gov (United States)

    Liao, Wenta; Draper, William M

    2013-02-21

    The mass-to-structure or MTS Search Engine is an Access 2010 database containing theoretical molecular mass information for 19,438 compounds assembled from common sources such as the Merck Index, pesticide and pharmaceutical compilations, and chemical catalogues. This database, which contains no experimental mass spectral data, was developed as an aid to identification of compounds in atmospheric pressure ionization (API)-LC-MS. This paper describes a powerful upgrade to this database, a fully integrated utility for filtering or ranking candidates based on isotope ratios and patterns. The new MTS Search Engine is applied here to the identification of volatile and semivolatile compounds including pesticides, nitrosoamines and other pollutants. Methane and isobutane chemical ionization (CI) GC-MS spectra were obtained from unit mass resolution mass spectrometers to determine MH(+) masses and isotope ratios. Isotopes were measured accurately with errors of Search Engine and details performance testing with over 50 model compounds.

  2. The eco-evolutionary impacts of domestication and agricultural practices on wild species.

    Science.gov (United States)

    Turcotte, Martin M; Araki, Hitoshi; Karp, Daniel S; Poveda, Katja; Whitehead, Susan R

    2017-01-19

    Agriculture is a dominant evolutionary force that drives the evolution of both domesticated and wild species. However, the various mechanisms of agriculture-induced evolution and their socio-ecological consequences are not often synthetically discussed. Here, we explore how agricultural practices and evolutionary changes in domesticated species cause evolution in wild species. We do so by examining three processes by which agriculture drives evolution. First, differences in the traits of domesticated species, compared with their wild ancestors, alter the selective environment and create opportunities for wild species to specialize. Second, selection caused by agricultural practices, including both those meant to maximize productivity and those meant to control pest species, can lead to pest adaptation. Third, agriculture can cause non-selective changes in patterns of gene flow in wild species. We review evidence for these processes and then discuss their ecological and sociological impacts. We finish by identifying important knowledge gaps and future directions related to the eco-evolutionary impacts of agriculture including their extent, how to prevent the detrimental evolution of wild species, and finally, how to use evolution to minimize the ecological impacts of agriculture.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'. © 2016 The Author(s).

  3. Evolutionary and genetic analysis of the VP2 gene of canine parvovirus.

    Science.gov (United States)

    Li, Gairu; Ji, Senlin; Zhai, Xiaofeng; Zhang, Yuxiang; Liu, Jie; Zhu, Mengyan; Zhou, Jiyong; Su, Shuo

    2017-07-17

    Canine parvovirus (CPV) type 2 emerged in 1978 in the USA and quickly spread among dog populations all over the world with high morbidity. Although CPV is a DNA virus, its genomic substitution rate is similar to some RNA viruses. Therefore, it is important to trace the evolution of CPV to monitor the appearance of mutations that might affect vaccine effectiveness. Our analysis shows that the VP2 genes of CPV isolated from 1979 to 2016 are divided into six groups: GI, GII, GIII, GIV, GV, and GVI. Amino acid mutation analysis revealed several undiscovered important mutation sites: F267Y, Y324I, and T440A. Of note, the evolutionary rate of the CPV VP2 gene from Asia and Europe decreased. Codon usage analysis showed that the VP2 gene of CPV exhibits high bias with an ENC ranging from 34.93 to 36.7. Furthermore, we demonstrate that natural selection plays a major role compared to mutation pressure driving CPV evolution. There are few studies on the codon usage of CPV. Here, we comprehensively studied the genetic evolution, codon usage pattern, and evolutionary characterization of the VP2 gene of CPV. The novel findings revealing the evolutionary process of CPV will greatly serve future CPV research.

  4. The origins and evolutionary history of human non-coding RNA regulatory networks.

    Science.gov (United States)

    Sherafatian, Masih; Mowla, Seyed Javad

    2017-04-01

    The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human. We were able to recognize evolutionary hallmarks of ncRNA targets by phylostratigraphic analysis. We found the conventional 3'-UTR and lesser known 5'-UTR targets of miRNAs to be enriched at three consecutive phylostrata. Firstly, in eukaryata phylostratum corresponding to the emergence of miRNAs, our study revealed that miRNA targets function primarily in cell cycle processes. Moreover, the same overrepresentation of the targets observed in the next two consecutive phylostrata, opisthokonta and eumetazoa, corresponded to the expansion periods of miRNAs in animals evolution. Coding sequence targets of miRNAs showed a delayed rise at opisthokonta phylostratum, compared to the 3' and 5' UTR targets of miRNAs. LncRNA regulatory network was the latest to evolve at eumetazoa.

  5. A new search for R Coronae Borealis stars in the SMC

    Directory of Open Access Journals (Sweden)

    Nikzat Fatemeh

    2017-01-01

    Full Text Available R Coronae Borealis (RCB stars are rare, and their evolutionary origin is not well understood. Since they are obscured due to formation of carbon dust around the star during their mass loss events, RCB stars can be classified as self-eclipsing variable stars. The purpose of this work is to present a new search for RCB stars in the Small Magellanic Cloud (SMC, by analysing VI data from the OGLE project.

  6. A dynamic parking charge optimal control model under perspective of commuters' evolutionary game behavior

    Science.gov (United States)

    Lin, XuXun; Yuan, PengCheng

    2018-01-01

    In this research we consider commuters' dynamic learning effect by modeling the trip mode choice behavior from a new perspective of dynamic evolutionary game theory. We explore the behavior pattern of different types of commuters and study the evolution path and equilibrium properties under different traffic conditions. We further establish a dynamic parking charge optimal control (referred to as DPCOC) model to alter commuters' trip mode choice while minimizing the total social cost. Numerical tests show. (1) Under fixed parking fee policy, the evolutionary results are completely decided by the travel time and the only method for public transit induction is to increase the parking charge price. (2) Compared with fixed parking fee policy, DPCOC policy proposed in this research has several advantages. Firstly, it can effectively turn the evolutionary path and evolutionary stable strategy to a better situation while minimizing the total social cost. Secondly, it can reduce the sensitivity of trip mode choice behavior to traffic congestion and improve the ability to resist interferences and emergencies. Thirdly, it is able to control the private car proportion to a stable state and make the trip behavior more predictable for the transportation management department. The research results can provide theoretical basis and decision-making references for commuters' mode choice prediction, dynamic setting of urban parking charge prices and public transit induction.

  7. An Artificial Immune System-Inspired Multiobjective Evolutionary Algorithm with Application to the Detection of Distributed Computer Network Intrusions

    Science.gov (United States)

    2007-03-01

    Optimization Coello, Van Veldhuizen , and Lamont define global optimization as, “the process of finding the global minimum4 within some search space S [CVL02...Technology, Shapes Markets, and Manages People, Simon & Schuster, New York, 1995. [CVL02] Coello, C., Van Veldhuizen , D., Lamont, G.B., Evolutionary...Anomaly Detection, Technical Report CS- 2003-02, Computer Science Department, Florida Institute of Technology, 2003. [Marmelstein99] Marmelstein, R., Van

  8. Making evolutionary biology a basic science for medicine

    Science.gov (United States)

    Nesse, Randolph M.; Bergstrom, Carl T.; Ellison, Peter T.; Flier, Jeffrey S.; Gluckman, Peter; Govindaraju, Diddahally R.; Niethammer, Dietrich; Omenn, Gilbert S.; Perlman, Robert L.; Schwartz, Mark D.; Thomas, Mark G.; Stearns, Stephen C.; Valle, David

    2010-01-01

    New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease. PMID:19918069

  9. A search for photometric and spectroscopic evolutionary changes in the young planetary nebula Vy 2-2

    Science.gov (United States)

    Arkhipova, V. P.; Burlak, M. A.; Esipov, V. F.; Ikonnikova, N. P.; Komissarova, G. V.

    2017-12-01

    The results of long-term photometric and spectroscopic observations of the young compact planetary nebula Vy 2-2 (PNG 045.4-02.7) are presented. The UBV photometry in 1990-2016 has revealed a slight brightness trend in the yearly averaged data, most pronounced in the V band. We have measured the relative fluxes of optical emission lines on the spectrograms taken with the 1.25-m telescope at the Southern Station of the SAI MSU in 1999-2016, estimated the absolute flux in the Hβ line to be F(H β) = (2.1 ± 0.4) × 10-12 erg cm-2 s-1, and determined the interstellar extinction constant c(Hβ) = 1.8. The electron temperature and density in the nebula have been estimated from diagnostic line ratios: Te = (10-12) × 103 K and Ne ≥ 105 cm-3. To detect any possible evolutionary changes, we have compared the new observations with the archival data obtained over the entire history of spectroscopic observations of Vy 2-2. No significant changes in the relative intensities of the strongest emission lines and the integrated flux in the H β line exceeding the observational errors have been found. We have revealed a tendency for the intensity ratio F(λ4363)/F(λ4959) to decrease with time, which may be related to a decrease in the electron density in the nebula. Based on our photometric and spectroscopic data, we have estimated the luminosity of the central star of Vy 2-2, which corresponds to the evolutionary tracks for the most massive post-AGB stars of the O-rich sequence.

  10. Evolutionary constraints shape caste-specific gene expression across 15 ant species.

    Science.gov (United States)

    Morandin, Claire; Mikheyev, Alexander S; Pedersen, Jes Søe; Helanterä, Heikki

    2017-05-01

    Development of polymorphic phenotypes from similar genomes requires gene expression differences. However, little is known about how morph-specific gene expression patterns vary on a broad phylogenetic scale. We hypothesize that evolution of morph-specific gene expression, and consequently morph-specific phenotypic evolution, may be constrained by gene essentiality and the amount of pleiotropic constraints. Here, we use comparative transcriptomics of queen and worker morphs, that is, castes, from 15 ant species to understand the constraints of morph-biased gene expression. In particular, we investigate how measures of evolutionary constraints at the sequence level (expression level, connectivity, and number of gene ontology [GO] terms) correlate with morph-biased expression. Our results show that genes indeed vary in their potential to become morph-biased. The existence of genes that are constrained in becoming caste-biased potentially limits the evolutionary decoupling of the caste phenotypes, that is, it might result in "caste load" occasioning from antagonistic fitness variation, similarly to sexually antagonistic fitness variation between males and females. On the other hand, we suggest that genes under low constraints are released from antagonistic variation and thus more likely to be co-opted for morph specific use. Overall, our results suggest that the factors that affect sequence evolutionary rates and evolution of plastic expression may largely overlap. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  11. Combining evolutionary algorithms with oblique decision trees to detect bent-double galaxies

    Science.gov (United States)

    Cantu-Paz, Erick; Kamath, Chandrika

    2000-10-01

    Decision tress have long been popular in classification as they use simple and easy-to-understand tests at each node. Most variants of decision trees test a single attribute at a node, leading to axis- parallel trees, where the test results in a hyperplane which is parallel to one of the dimensions in the attribute space. These trees can be rather large and inaccurate in cases where the concept to be learned is best approximated by oblique hyperplanes. In such cases, it may be more appropriate to use an oblique decision tree, where the decision at each node is a linear combination of the attributes. Oblique decision trees have not gained wide popularity in part due to the complexity of constructing good oblique splits and the tendency of existing splitting algorithms to get stuck in local minima. Several alternatives have been proposed to handle these problems including randomization in conjunction wiht deterministic hill-climbing and the use of simulated annealing. In this paper, we use evolutionary algorithms (EAs) to determine the split. EAs are well suited for this problem because of their global search properties, their tolerance to noisy fitness evaluations, and their scalability to large dimensional search spaces. We demonstrate our technique on a synthetic data set, and then we apply it to a practical problem from astronomy, namely, the classification of galaxies with a bent-double morphology. In addition, we describe our experiences with several split evaluation criteria. Our results suggest that, in some cases, the evolutionary approach is faster and more accurate than existing oblique decision tree algorithms. However, for our astronomical data, the accuracy is not significantly different than the axis-parallel trees.

  12. Contemporary issues in evolutionary biology

    Indian Academy of Sciences (India)

    We are delighted to bring to the readers, a set of peer-reviewed papers on evolutionary biology, published as a special issue of the Journal of Genetics. These papers emanated from ruminations upon and discussions at the Foundations of. Evolutionary Theory: the Ongoing Synthesis meeting at Coorg, India, in February ...

  13. Molecular evolutionary rates are not correlated with temperature and latitude in Squamata: an exception to the metabolic theory of ecology?

    Science.gov (United States)

    Rolland, Jonathan; Loiseau, Oriane; Romiguier, Jonathan; Salamin, Nicolas

    2016-05-20

    The metabolic theory of ecology stipulates that molecular evolutionary rates should correlate with temperature and latitude in ectothermic organisms. Previous studies have shown that most groups of vertebrates, such as amphibians, turtles and even endothermic mammals, have higher molecular evolutionary rates in regions where temperature is high. However, the association between molecular evolutionary rates and temperature or latitude has never been tested in Squamata. We used a large dataset including the spatial distributions and environmental variables for 1,651 species of Squamata and compared the contrast of the rates of molecular evolution with the contrast of temperature and latitude between sister species. Using major axis regressions and a new algorithm to choose independent sister species pairs, we found that temperature and absolute latitude were not associated with molecular evolutionary rates. This absence of association in such a diverse ectothermic group questions the mechanisms explaining current pattern of species diversity in Squamata and challenges the presupposed universality of the metabolic theory of ecology.

  14. Public Awareness of Uterine Power Morcellation Through US Food and Drug Administration Communications: Analysis of Google Trends Search Term Patterns.

    Science.gov (United States)

    Wood, Lauren N; Jamnagerwalla, Juzar; Markowitz, Melissa A; Thum, D Joseph; McCarty, Philip; Medendorp, Andrew R; Raz, Shlomo; Kim, Ja-Hong

    2018-04-26

    Uterine power morcellation, where the uterus is shred into smaller pieces, is a widely used technique for removal of uterine specimens in patients undergoing minimally invasive abdominal hysterectomy or myomectomy. Complications related to power morcellation of uterine specimens led to US Food and Drug Administration (FDA) communications in 2014 ultimately recommending against the use of power morcellation for women undergoing minimally invasive hysterectomy. Subsequently, practitioners drastically decreased the use of morcellation. We aimed to determine the effect of increased patient awareness on the decrease in use of the morcellator. Google Trends is a public tool that provides data on temporal patterns of search terms, and we correlated this data with the timing of the FDA communication. Weekly relative search volume (RSV) was obtained from Google Trends using the term “morcellation.” Higher RSV corresponds to increases in weekly search volume. Search volumes were divided into 3 groups: the 2 years prior to the FDA communication, a 1-year period following, and thereafter, with the distribution of the weekly RSV over the 3 periods tested using 1-way analysis of variance. Additionally, we analyzed the total number of websites containing the term “morcellation” over this time. The mean RSV prior to the FDA communication was 12.0 (SD 15.8), with the RSV being 60.3 (SD 24.7) in the 1-year after and 19.3 (SD 5.2) thereafter (PGoogle search activity about morcellation of uterine specimens increased significantly after the FDA communications. This trend indicates an increased public awareness regarding morcellation and its complications. More extensive preoperative counseling and alteration of surgical technique and clinician practice may be necessary. ©Lauren N Wood, Juzar Jamnagerwalla, Melissa A Markowitz, D Joseph Thum, Philip McCarty, Andrew R Medendorp, Shlomo Raz, Ja-Hong Kim. Originally published in JMIR Public Health and Surveillance (http

  15. Neurocranium versus Face: A Morphometric Approach with Classical Anthropometric Variables for Characterizing Patterns of Cranial Integration in Extant Hominoids and Extinct Hominins.

    Directory of Open Access Journals (Sweden)

    Juan Antonio Pérez-Claros

    Full Text Available The relative importance of the two main cranial complexes, the neurocranium and the splanchnocranium, has been examined in the five species of extant hominoids and in a huge sample of extinct hominins using six standard craniometric variables that measure the length, width and height of each cranial module. Factor analysis and two-block partial least squares were used for establishing the major patterns of developmental and evolutionary integration between both cranial modules. The results obtained show that all extant hominoids (including the anatomically modern humans share a conserved pattern of developmental integration, a result that agrees with previous studies. The pattern of evolutionary integration between both cranial modules in australopiths runs in parallel to developmental integration. In contrast, the pattern of evolutionary and developmental integration of the species of the genus Homo is the opposite, which is probably the consequence of distinctive selective regimes for both hominin groups.

  16. Neurocranium versus Face: A Morphometric Approach with Classical Anthropometric Variables for Characterizing Patterns of Cranial Integration in Extant Hominoids and Extinct Hominins.

    Science.gov (United States)

    Pérez-Claros, Juan Antonio; Jiménez-Arenas, Juan Manuel; Palmqvist, Paul

    2015-01-01

    The relative importance of the two main cranial complexes, the neurocranium and the splanchnocranium, has been examined in the five species of extant hominoids and in a huge sample of extinct hominins using six standard craniometric variables that measure the length, width and height of each cranial module. Factor analysis and two-block partial least squares were used for establishing the major patterns of developmental and evolutionary integration between both cranial modules. The results obtained show that all extant hominoids (including the anatomically modern humans) share a conserved pattern of developmental integration, a result that agrees with previous studies. The pattern of evolutionary integration between both cranial modules in australopiths runs in parallel to developmental integration. In contrast, the pattern of evolutionary and developmental integration of the species of the genus Homo is the opposite, which is probably the consequence of distinctive selective regimes for both hominin groups.

  17. Virus evolutionary genetic algorithm for task collaboration of logistics distribution

    Science.gov (United States)

    Ning, Fanghua; Chen, Zichen; Xiong, Li

    2005-12-01

    In order to achieve JIT (Just-In-Time) level and clients' maximum satisfaction in logistics collaboration, a Virus Evolutionary Genetic Algorithm (VEGA) was put forward under double constraints of logistics resource and operation sequence. Based on mathematic description of a multiple objective function, the algorithm was designed to schedule logistics tasks with different due dates and allocate them to network members. By introducing a penalty item, make span and customers' satisfaction were expressed in fitness function. And a dynamic adaptive probability of infection was used to improve performance of local search. Compared to standard Genetic Algorithm (GA), experimental result illustrates the performance superiority of VEGA. So the VEGA can provide a powerful decision-making technique for optimizing resource configuration in logistics network.

  18. Simulation Optimization by Genetic Search: A Comprehensive Study with Applications to Production Management

    National Research Council Canada - National Science Library

    Yunker, James

    2003-01-01

    In this report, a relatively new simulation optimization technique, the genetic search, is compared to two more established simulation techniques-the pattern search and the response surface methodology search...

  19. Designing Search UX Strategies for eCommerce Success

    CERN Document Server

    Nudelman, Greg

    2011-01-01

    Best practices, practical advice, and design ideas for successful ecommerce search A glaring gap has existed in the market for a resource that offers a comprehensive, actionable design patterns and design strategies for ecommerce search-but no longer. With this invaluable book, user experience designer and user researcher Greg Nudelman shares his years of experience working on popular ecommerce sites as he tackles even the most difficult ecommerce search design problems. Nudelman helps you create highly effective and intuitive ecommerce search design solutions and he takes a unique forward-thi

  20. Improved quantum-behaved particle swarm optimization with local search strategy

    Directory of Open Access Journals (Sweden)

    Maolong Xi

    2017-03-01

    Full Text Available Quantum-behaved particle swarm optimization, which was motivated by analysis of particle swarm optimization and quantum system, has shown compared performance in finding the optimal solutions for many optimization problems to other evolutionary algorithms. To address the problem of premature, a local search strategy is proposed to improve the performance of quantum-behaved particle swarm optimization. In proposed local search strategy, a super particle is presented which is a collection body of randomly selected particles’ dimension information in the swarm. The selected probability of particles in swarm is different and determined by their fitness values. To minimization problems, the fitness value of one particle is smaller; the selected probability is more and will contribute more information in constructing the super particle. In addition, in order to investigate the influence on algorithm performance with different local search space, four methods of computing the local search radius are applied in local search strategy and propose four variants of local search quantum-behaved particle swarm optimization. Empirical studies on a suite of well-known benchmark functions are undertaken in order to make an overall performance comparison among the proposed methods and other quantum-behaved particle swarm optimization. The simulation results show that the proposed quantum-behaved particle swarm optimization variants have better advantages over the original quantum-behaved particle swarm optimization.

  1. An evolutionary programming based simulated annealing method for solving the unit commitment problem

    Energy Technology Data Exchange (ETDEWEB)

    Christober Asir Rajan, C. [Department of EEE, Pondicherry Engineering College, Pondicherry 605014 (India); Mohan, M.R. [Department of EEE, Anna University, Chennai 600 025 (India)

    2007-09-15

    This paper presents a new approach to solve the short-term unit commitment problem using an evolutionary programming based simulated annealing method. The objective of this paper is to find the generation scheduling such that the total operating cost can be minimized, when subjected to a variety of constraints. This also means that it is desirable to find the optimal generating unit commitment in the power system for the next H hours. Evolutionary programming, which happens to be a global optimisation technique for solving unit commitment Problem, operates on a system, which is designed to encode each unit's operating schedule with regard to its minimum up/down time. In this, the unit commitment schedule is coded as a string of symbols. An initial population of parent solutions is generated at random. Here, each schedule is formed by committing all the units according to their initial status (''flat start''). Here the parents are obtained from a pre-defined set of solution's, i.e. each and every solution is adjusted to meet the requirements. Then, a random recommitment is carried out with respect to the unit's minimum down times. And SA improves the status. The best population is selected by evolutionary strategy. The Neyveli Thermal Power Station (NTPS) Unit-II in India demonstrates the effectiveness of the proposed approach; extensive studies have also been performed for different power systems consists of 10, 26, 34 generating units. Numerical results are shown comparing the cost solutions and computation time obtained by using the Evolutionary Programming method and other conventional methods like Dynamic Programming, Lagrangian Relaxation and Simulated Annealing and Tabu Search in reaching proper unit commitment. (author)

  2. MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

    Science.gov (United States)

    Tamura, Koichiro; Peterson, Daniel; Peterson, Nicholas; Stecher, Glen; Nei, Masatoshi; Kumar, Sudhir

    2011-01-01

    Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net. PMID:21546353

  3. Mean-Potential Law in Evolutionary Games

    Science.gov (United States)

    Nałecz-Jawecki, Paweł; Miekisz, Jacek

    2018-01-01

    The Letter presents a novel way to connect random walks, stochastic differential equations, and evolutionary game theory. We introduce a new concept of a potential function for discrete-space stochastic systems. It is based on a correspondence between one-dimensional stochastic differential equations and random walks, which may be exact not only in the continuous limit but also in finite-state spaces. Our method is useful for computation of fixation probabilities in discrete stochastic dynamical systems with two absorbing states. We apply it to evolutionary games, formulating two simple and intuitive criteria for evolutionary stability of pure Nash equilibria in finite populations. In particular, we show that the 1 /3 law of evolutionary games, introduced by Nowak et al. [Nature, 2004], follows from a more general mean-potential law.

  4. Is evolutionary psychology a metatheory for psychology? A discussion of four major issues in psychology from an evolutionary developmental perspective

    NARCIS (Netherlands)

    Ploeger, A.; van der Maas, H.L.J.; Raijmakers, M.E.J.

    2008-01-01

    Evolutionary psychology has been proposed as a metatheoretical framework for psychology. We argue that evolutionary psychology should be expanded if it is to offer new insights regarding the major issues in psychology. Evolutionary developmental biology can provide valuable new insights into issues

  5. Comparison of evolutionary computation algorithms for solving bi ...

    Indian Academy of Sciences (India)

    failure probability. Multiobjective Evolutionary Computation algorithms (MOEAs) are well-suited for Multiobjective task scheduling on heterogeneous environment. The two Multi-Objective Evolutionary Algorithms such as Multiobjective Genetic. Algorithm (MOGA) and Multiobjective Evolutionary Programming (MOEP) with.

  6. Species co-evolutionary algorithm: a novel evolutionary algorithm based on the ecology and environments for optimization

    DEFF Research Database (Denmark)

    Li, Wuzhao; Wang, Lei; Cai, Xingjuan

    2015-01-01

    and affect each other in many ways. The relationships include competition, predation, parasitism, mutualism and pythogenesis. In this paper, we consider the five relationships between solutions to propose a co-evolutionary algorithm termed species co-evolutionary algorithm (SCEA). In SCEA, five operators...

  7. The Effects of Fatigue From Overnight Shifts on Radiology Search Patterns and Diagnostic Performance.

    Science.gov (United States)

    Hanna, Tarek N; Zygmont, Matthew E; Peterson, Ryan; Theriot, David; Shekhani, Haris; Johnson, Jamlik-Omari; Krupinski, Elizabeth A

    2018-01-20

    The aim of this study was to assess the effect of overnight shifts (ONS) on radiologist fatigue, visual search pattern, and diagnostic performance. This experimental study was approved by the institutional review board. Twelve radiologists (five faculty members and seven residents) each completed two sessions: one during a normal workday ("not fatigued") and another in the morning after an ONS ("fatigued"). Each radiologist completed the Swedish Occupational Fatigue Inventory. During each session, radiologists viewed 20 bone radiographs consisting of normal and abnormal findings. Viewing time, diagnostic confidence, and eye-tracking data were recorded. Swedish Occupational Fatigue Inventory results demonstrated worsening in all five variables (lack of energy, physical exertion, physical discomfort, lack of motivation, and sleepiness) after ONS (P radiologists were more fatigued with worse diagnostic performance, a 45% increase in view time per case, a 60% increase in total gaze fixations, and a 34% increase in time to fixate on the fracture. The effects of fatigue were more pronounced in residents. Copyright © 2017 American College of Radiology. Published by Elsevier Inc. All rights reserved.

  8. Alternative Evolutionary Paths to Bacterial Antibiotic Resistance Cause Distinct Collateral Effects.

    Science.gov (United States)

    Barbosa, Camilo; Trebosc, Vincent; Kemmer, Christian; Rosenstiel, Philip; Beardmore, Robert; Schulenburg, Hinrich; Jansen, Gunther

    2017-09-01

    When bacteria evolve resistance against a particular antibiotic, they may simultaneously gain increased sensitivity against a second one. Such collateral sensitivity may be exploited to develop novel, sustainable antibiotic treatment strategies aimed at containing the current, dramatic spread of drug resistance. To date, the presence and molecular basis of collateral sensitivity has only been studied in few bacterial species and is unknown for opportunistic human pathogens such as Pseudomonas aeruginosa. In the present study, we assessed patterns of collateral effects by experimentally evolving 160 independent populations of P. aeruginosa to high levels of resistance against eight commonly used antibiotics. The bacteria evolved resistance rapidly and expressed both collateral sensitivity and cross-resistance. The pattern of such collateral effects differed to those previously reported for other bacterial species, suggesting interspecific differences in the underlying evolutionary trade-offs. Intriguingly, we also identified contrasting patterns of collateral sensitivity and cross-resistance among the replicate populations adapted to the same drug. Whole-genome sequencing of 81 independently evolved populations revealed distinct evolutionary paths of resistance to the selective drug, which determined whether bacteria became cross-resistant or collaterally sensitive towards others. Based on genomic and functional genetic analysis, we demonstrate that collateral sensitivity can result from resistance mutations in regulatory genes such as nalC or mexZ, which mediate aminoglycoside sensitivity in β-lactam-adapted populations, or the two-component regulatory system gene pmrB, which enhances penicillin sensitivity in gentamicin-resistant populations. Our findings highlight substantial variation in the evolved collateral effects among replicates, which in turn determine their potential in antibiotic therapy. © The Author 2017. Published by Oxford University Press on

  9. Adaptive developmental delay in Chagas disease vectors: an evolutionary ecology approach.

    Directory of Open Access Journals (Sweden)

    Frédéric Menu

    2010-05-01

    Full Text Available The developmental time of vector insects is important in population dynamics, evolutionary biology, epidemiology and in their responses to global climatic change. In the triatomines (Triatominae, Reduviidae, vectors of Chagas disease, evolutionary ecology concepts, which may allow for a better understanding of their biology, have not been applied. Despite delay in the molting in some individuals observed in triatomines, no effort was made to explain this variability.We applied four methods: (1 an e-mail survey sent to 30 researchers with experience in triatomines, (2 a statistical description of the developmental time of eleven triatomine species, (3 a relationship between development time pattern and climatic inter-annual variability, (4 a mathematical optimization model of evolution of developmental delay (diapause.85.6% of responses informed on prolonged developmental times in 5(th instar nymphs, with 20 species identified with remarkable developmental delays. The developmental time analysis showed some degree of bi-modal pattern of the development time of the 5(th instars in nine out of eleven species but no trend between development time pattern and climatic inter-annual variability was observed. Our optimization model predicts that the developmental delays could be due to an adaptive risk-spreading diapause strategy, only if survival throughout the diapause period and the probability of random occurrence of "bad" environmental conditions are sufficiently high.Developmental delay may not be a simple non-adaptive phenotypic plasticity in development time, and could be a form of adaptive diapause associated to a physiological mechanism related to the postponement of the initiation of reproduction, as an adaptation to environmental stochasticity through a spreading of risk (bet-hedging strategy. We identify a series of parameters that can be measured in the field and laboratory to test this hypothesis. The importance of these findings is

  10. Fast Structural Search in Phylogenetic Databases

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    William H. Piel

    2005-01-01

    Full Text Available As the size of phylogenetic databases grows, the need for efficiently searching these databases arises. Thanks to previous and ongoing research, searching by attribute value and by text has become commonplace in these databases. However, searching by topological or physical structure, especially for large databases and especially for approximate matches, is still an art. We propose structural search techniques that, given a query or pattern tree P and a database of phylogenies D, find trees in D that are sufficiently close to P . The “closeness” is a measure of the topological relationships in P that are found to be the same or similar in a tree D in D. We develop a filtering technique that accelerates searches and present algorithms for rooted and unrooted trees where the trees can be weighted or unweighted. Experimental results on comparing the similarity measure with existing tree metrics and on evaluating the efficiency of the search techniques demonstrate that the proposed approach is promising

  11. Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts.

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    Cécile Troupin

    2016-12-01

    Full Text Available The natural evolution of rabies virus (RABV provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics.

  12. Fixation Time for Evolutionary Graphs

    Science.gov (United States)

    Nie, Pu-Yan; Zhang, Pei-Ai

    Evolutionary graph theory (EGT) is recently proposed by Lieberman et al. in 2005. EGT is successful for explaining biological evolution and some social phenomena. It is extremely important to consider the time of fixation for EGT in many practical problems, including evolutionary theory and the evolution of cooperation. This study characterizes the time to asymptotically reach fixation.

  13. Statistical Pattern Recognition

    CERN Document Server

    Webb, Andrew R

    2011-01-01

    Statistical pattern recognition relates to the use of statistical techniques for analysing data measurements in order to extract information and make justified decisions.  It is a very active area of study and research, which has seen many advances in recent years. Applications such as data mining, web searching, multimedia data retrieval, face recognition, and cursive handwriting recognition, all require robust and efficient pattern recognition techniques. This third edition provides an introduction to statistical pattern theory and techniques, with material drawn from a wide range of fields,

  14. MONSS: A multi-objective nonlinear simplex search approach

    Science.gov (United States)

    Zapotecas-Martínez, Saúl; Coello Coello, Carlos A.

    2016-01-01

    This article presents a novel methodology for dealing with continuous box-constrained multi-objective optimization problems (MOPs). The proposed algorithm adopts a nonlinear simplex search scheme in order to obtain multiple elements of the Pareto optimal set. The search is directed by a well-distributed set of weight vectors, each of which defines a scalarization problem that is solved by deforming a simplex according to the movements described by Nelder and Mead's method. Considering an MOP with n decision variables, the simplex is constructed using n+1 solutions which minimize different scalarization problems defined by n+1 neighbor weight vectors. All solutions found in the search are used to update a set of solutions considered to be the minima for each separate problem. In this way, the proposed algorithm collectively obtains multiple trade-offs among the different conflicting objectives, while maintaining a proper representation of the Pareto optimal front. In this article, it is shown that a well-designed strategy using just mathematical programming techniques can be competitive with respect to the state-of-the-art multi-objective evolutionary algorithms against which it was compared.

  15. Evolutionary computation in zoology and ecology.

    Science.gov (United States)

    Boone, Randall B

    2017-12-01

    Evolutionary computational methods have adopted attributes of natural selection and evolution to solve problems in computer science, engineering, and other fields. The method is growing in use in zoology and ecology. Evolutionary principles may be merged with an agent-based modeling perspective to have individual animals or other agents compete. Four main categories are discussed: genetic algorithms, evolutionary programming, genetic programming, and evolutionary strategies. In evolutionary computation, a population is represented in a way that allows for an objective function to be assessed that is relevant to the problem of interest. The poorest performing members are removed from the population, and remaining members reproduce and may be mutated. The fitness of the members is again assessed, and the cycle continues until a stopping condition is met. Case studies include optimizing: egg shape given different clutch sizes, mate selection, migration of wildebeest, birds, and elk, vulture foraging behavior, algal bloom prediction, and species richness given energy constraints. Other case studies simulate the evolution of species and a means to project shifts in species ranges in response to a changing climate that includes competition and phenotypic plasticity. This introduction concludes by citing other uses of evolutionary computation and a review of the flexibility of the methods. For example, representing species' niche spaces subject to selective pressure allows studies on cladistics, the taxon cycle, neutral versus niche paradigms, fundamental versus realized niches, community structure and order of colonization, invasiveness, and responses to a changing climate.

  16. Evolutionary Naturalism and the Logical Structure of Valuation: The Other Side of Error Theory

    Directory of Open Access Journals (Sweden)

    Richard A Richards

    2006-01-01

    Full Text Available On one standard philosophical position adopted by evolutionary naturalists, human ethical systems are nothing more than evolutionary adaptations that facilitate social behavior. Belief in an absolute moral foundation is therefore in error. But evolutionary naturalism, by its commitment to the basic valutional concept of fitness, reveals another, logical error: standard conceptions of value in terms of simple predication and properties are mistaken. Valuation has instead, a relational structure that makes reference to respects, subjects and environments. This relational nature is illustrated by the analogy commonly drawn between value and color. Color perception, as recognized by the ecological concept, is relational and dependent on subject and environment. In a similar way, value is relational and dependent on subject and environment. This makes value subjective, but also objective in that it is grounded on facts about mattering. At bottom, values are complex relational facts. The view presented here, unlike other prominent relational and naturalistic conceptions of value, recognizes the full range of valuation in nature. The advantages of this relational conception are first, that it gets valuation right; second, it provides a framework to better explain and understand valuation in all its varieties and patterns.

  17. Evolutionary Naturalism and the Logical Structure of Valuation: The Other Side of Error Theory

    Directory of Open Access Journals (Sweden)

    Richard A Richards

    2005-01-01

    Full Text Available On one standard philosophical position adopted by evolutionary naturalists, human ethical systems are nothing more than evolutionary adaptations that facilitate social behavior. Belief in an absolute moral foundation is therefore in error. But evolutionary naturalism, by its commitment to the basic valutional concept of fitness, reveals another, logical error: standard conceptions of value in terms of simple predication and properties are mistaken. Valuation has instead, a relational structure that makes reference to respects, subjects and environments. This relational nature is illustrated by the analogy commonly drawn between value and color. Color perception, as recognized by the ecological concept, is relational and dependent on subject and environment. In a similar way, value is relational and dependent on subject and environment. This makes value subjective, but also objective in that it is grounded on facts about mattering. At bottom, values are complex relational facts. The view presented here, unlike other prominent relational and naturalistic conceptions of value, recognizes the full range of valuation in nature. The advantages of this relational conception are first, that it gets valuation right; second, it provides a framework to better explain and understand valuation in all its varieties and patterns.

  18. Evolutionary accounts of human behavioural diversity

    Science.gov (United States)

    Brown, Gillian R.; Dickins, Thomas E.; Sear, Rebecca; Laland, Kevin N.

    2011-01-01

    Human beings persist in an extraordinary range of ecological settings, in the process exhibiting enormous behavioural diversity, both within and between populations. People vary in their social, mating and parental behaviour and have diverse and elaborate beliefs, traditions, norms and institutions. The aim of this theme issue is to ask whether, and how, evolutionary theory can help us to understand this diversity. In this introductory article, we provide a background to the debate surrounding how best to understand behavioural diversity using evolutionary models of human behaviour. In particular, we examine how diversity has been viewed by the main subdisciplines within the human evolutionary behavioural sciences, focusing in particular on the human behavioural ecology, evolutionary psychology and cultural evolution approaches. In addition to differences in focus and methodology, these subdisciplines have traditionally varied in the emphasis placed on human universals, ecological factors and socially learned behaviour, and on how they have addressed the issue of genetic variation. We reaffirm that evolutionary theory provides an essential framework for understanding behavioural diversity within and between human populations, but argue that greater integration between the subfields is critical to developing a satisfactory understanding of diversity. PMID:21199836

  19. Evolutionary equations with applications in natural sciences

    CERN Document Server

    Mokhtar-Kharroubi, Mustapha

    2015-01-01

    With the unifying theme of abstract evolutionary equations, both linear and nonlinear, in a complex environment, the book presents a multidisciplinary blend of topics, spanning the fields of theoretical and applied functional analysis, partial differential equations, probability theory and numerical analysis applied to various models coming from theoretical physics, biology, engineering and complexity theory. The unique features of the book are: the first simultaneous presentation of two complementary approaches to fragmentation and coagulation problems, by weak compactness methods and by using semigroup techniques, comprehensive exposition of probabilistic methods of analysis of long term dynamics of dynamical systems, semigroup analysis of biological problems and cutting edge pattern formation theory. The book will appeal to postgraduate students and researchers specializing in applications of mathematics to problems arising in natural sciences and engineering.

  20. ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

    Science.gov (United States)

    Sablok, Gaurav; Chen, Ting-Wen; Lee, Chi-Ching; Yang, Chi; Gan, Ruei-Chi; Wegrzyn, Jill L; Porta, Nicola L; Nayak, Kinshuk C; Huang, Po-Jung; Varotto, Claudio; Tang, Petrus

    2017-06-01

    Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.