WorldWideScience

Sample records for evolutionary synthesis models

  1. Evolutionary Synthesis Models as a Tool and Guide Towards the First Galaxies

    Science.gov (United States)

    Schaerer, Daniel

    We summarize the principles and fundamental ingredients of evolutionary synthesis models, which are stellar evolution, stellar atmospheres, the IMF, star-formation histories, nebular emission, and also attenuation from the ISM and IGM. The chapter focusses in particular on issues of importance for predictions of metal-poor and Population III dominated galaxies.We review recent predictions for the main physical properties and related observables of star-forming galaxies based on up-to-date inputs. The predicted metallicity dependence of these quantities and their physical causes are discussed. The predicted observables include in particular the restframe UV-to-optical domain with continuum emission from stars and the ionized ISM, as well as emission lines from H, He, and metals.Based on these predictions we summarize the main observational signatures (emission line strengths, colors etc.), which can be used to distinguish "normal" stellar populations from very metal-poor objects or even Pop III.Evolutionary synthesis models provide an important and fundamental tool for studies of galaxy formation and evolution, from the nearby Universe back to first galaxies. They are used in many applications to interpret existing observations, to predict and guide future missions/instruments, and to allow direct comparisons between state-of-the-art galaxy simulations and observations.

  2. Probing Evolutionary Population Synthesis Models in the Near Infrared with Early Type Galaxies

    Science.gov (United States)

    Dahmer-Hahn, Luis Gabriel; Riffel, Rogério; Rodríguez-Ardila, Alberto; Martins, Lucimara P.; Kehrig, Carolina; Heckman, Timothy M.; Pastoriza, Miriani G.; Dametto, Natacha Z.

    2018-02-01

    We performed a near-infrared (NIR, ˜1.0μm-2.4μm) stellar population study in a sample of early type galaxies. The synthesis was performed using five different evolutionary population synthesis libraries of models. Our main results can be summarized as follows: low spectral resolution libraries are not able to produce reliable results when applied to the NIR alone, with each library finding a different dominant population. The two newest higher resolution models, on the other hand, perform considerably better, finding consistent results to each other and to literature values. We also found that optical results are consistent with each other even for lower resolution models. We also compared optical and NIR results, and found out that lower resolution models tend to disagree in the optical and in the NIR, with higher fraction of young populations in the NIR and dust extinction ˜1 magnitude higher than optical values. For higher resolution models, optical and NIR results tend do aggree much better, suggesting that a higher spectral resolution is fundamental to improve the quality of the results.

  3. EVOLUTIONARY MODELING PROBLEMS IN STRUCTURAL SYNTHESIS OF INFORMATION NETWORKS OF AUTOMATED CONTROL SYSTEMS

    Directory of Open Access Journals (Sweden)

    N.R.Yusupbekov

    2014-07-01

    Full Text Available This paper provides a new approach for solving a problem of modeling and structural syntheses of information networks of automated control systems by applying fuzzy sets theory, fuzzy logic and genetic algorithms. The procedure of formalizing structural syntheses of multi-level dispersed information networks of automated control systems is proposed. Also, the paper proposes a conceptual model of evolutionary syntheses based on genetic algorithms, which do not require additional information about the characteristics and features of target function. Modified genetic operators of crossover, mutation and algorithms of evolutionary syntheses of information networks systems are developed. Finally, the results of computational experiments on researching the influence of probability of the use of crossover and mutation operators, method of choosing parental pairs, and the size of initial population on the speed and precision of final results are provided.

  4. Why an extended evolutionary synthesis is necessary.

    Science.gov (United States)

    Müller, Gerd B

    2017-10-06

    Since the last major theoretical integration in evolutionary biology-the modern synthesis (MS) of the 1940s-the biosciences have made significant advances. The rise of molecular biology and evolutionary developmental biology, the recognition of ecological development, niche construction and multiple inheritance systems, the '-omics' revolution and the science of systems biology, among other developments, have provided a wealth of new knowledge about the factors responsible for evolutionary change. Some of these results are in agreement with the standard theory and others reveal different properties of the evolutionary process. A renewed and extended theoretical synthesis, advocated by several authors in this issue, aims to unite pertinent concepts that emerge from the novel fields with elements of the standard theory. The resulting theoretical framework differs from the latter in its core logic and predictive capacities. Whereas the MS theory and its various amendments concentrate on genetic and adaptive variation in populations, the extended framework emphasizes the role of constructive processes, ecological interactions and systems dynamics in the evolution of organismal complexity as well as its social and cultural conditions. Single-level and unilinear causation is replaced by multilevel and reciprocal causation. Among other consequences, the extended framework overcomes many of the limitations of traditional gene-centric explanation and entails a revised understanding of the role of natural selection in the evolutionary process. All these features stimulate research into new areas of evolutionary biology.

  5. Structured synthesis of MEMS using evolutionary approaches

    DEFF Research Database (Denmark)

    Fan, Zhun; Wang, Jiachuan; Achiche, Sofiane

    2008-01-01

    In this paper, we discuss the hierarchy that is involved in a typical MEMS design and how evolutionary approaches can be used to automate the hierarchical synthesis process for MEMS. The paper first introduces the flow of a structured MEMS design process and emphasizes that system-level lumped-pa...

  6. An extended synthesis for evolutionary biology.

    Science.gov (United States)

    Pigliucci, Massimo

    2009-06-01

    Evolutionary theory is undergoing an intense period of discussion and reevaluation. This, contrary to the misleading claims of creationists and other pseudoscientists, is no harbinger of a crisis but rather the opposite: the field is expanding dramatically in terms of both empirical discoveries and new ideas. In this essay I briefly trace the conceptual history of evolutionary theory from Darwinism to neo-Darwinism, and from the Modern Synthesis to what I refer to as the Extended Synthesis, a more inclusive conceptual framework containing among others evo-devo, an expanded theory of heredity, elements of complexity theory, ideas about evolvability, and a reevaluation of levels of selection. I argue that evolutionary biology has never seen a paradigm shift, in the philosophical sense of the term, except when it moved from natural theology to empirical science in the middle of the 19th century. The Extended Synthesis, accordingly, is an expansion of the Modern Synthesis of the 1930s and 1940s, and one that--like its predecessor--will probably take decades to complete.

  7. Evolutionary Sound Synthesis Controlled by Gestural Data

    Directory of Open Access Journals (Sweden)

    Jose Fornari

    2011-05-01

    Full Text Available This article focuses on the interdisciplinary research involving Computer Music and Generative Visual Art. We describe the implementation of two interactive artistic systems based on principles of Gestural Data (WILSON, 2002 retrieval and self-organization (MORONI, 2003, to control an Evolutionary Sound Synthesis method (ESSynth. The first implementation uses, as gestural data, image mapping of handmade drawings. The second one uses gestural data from dynamic body movements of dance. The resulting computer output is generated by an interactive system implemented in Pure Data (PD. This system uses principles of Evolutionary Computation (EC, which yields the generation of a synthetic adaptive population of sound objects. Considering that music could be seen as “organized sound” the contribution of our study is to develop a system that aims to generate "self-organized sound" – a method that uses evolutionary computation to bridge between gesture, sound and music.

  8. Life Beyond Earth and the Evolutionary Synthesis

    Science.gov (United States)

    Vakoch, Douglas A.

    For many astronomers, the progressive development of life has been seen as a natural occurrence given proper environmental conditions on a planet: even though such beings would not be identical to humans, there would be significant parallels. A striking contrast is seen in writings of nonphysical scientists, who have held more widely differing views. But within this diversity, reasons for differences become more apparent when we see how views about extraterrestrials can be related to the differential emphasis placed on modern evolutionary theory by scientists of various disciplines. One clue to understanding the differences between the biologists, paleontologists, and anthropologists who speculated on extraterrestrials is suggested by noting who wrote on the subject. Given the relatively small number of commentators on the topic, it seems more than coincidental that four of the major contributors to the evolutionary synthesis in the 1930s and 1940s are among them. Upon closer examination it is evident that the exobiological arguments of Theodosius Dobzhansky and George Gaylord Simpson and, less directly, of H. J. Muller and Ernst Mayr are all related to their earlier work in formulating synthetic evolution. By examining the variety of views held by nonphysical scientists, we can see that there were significant disagreements between them about evolution into the 1960s. By the mid-1980s, many believed that "higher" life, particularly intelligent life, probably occurs quite infrequently in the universe; nevertheless, some held out the possibility that convergence of intelligence could occur across worlds. Regardless of the final conclusions these scientists reached about the likely prevalence of extraterrestrial intelligence, the use of evolutionary arguments to support their positions became increasingly common.

  9. 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.

  10. Defining fitness in evolutionary models

    Indian Academy of Sciences (India)

    The analysis of evolutionary models requires an appropriate definition for fitness. In this paper, I review such definitions in relation to the five major dimensions by which models may be described, namely. finite versus infinite (or very large) population size,; type of environment (constant, fixed length, temporally stochastic, ...

  11. Evolutionary model of stock markets

    Science.gov (United States)

    Kaldasch, Joachim

    2014-12-01

    The paper presents an evolutionary economic model for the price evolution of stocks. Treating a stock market as a self-organized system governed by a fast purchase process and slow variations of demand and supply the model suggests that the short term price distribution has the form a logistic (Laplace) distribution. The long term return can be described by Laplace-Gaussian mixture distributions. The long term mean price evolution is governed by a Walrus equation, which can be transformed into a replicator equation. This allows quantifying the evolutionary price competition between stocks. The theory suggests that stock prices scaled by the price over all stocks can be used to investigate long-term trends in a Fisher-Pry plot. The price competition that follows from the model is illustrated by examining the empirical long-term price trends of two stocks.

  12. Polemics and Synthesis: Ernst Mayr and Evolutionary Biology

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 10; Issue 7. Polemics and Synthesis: Ernst Mayr and Evolutionary Biology. Renee M Borges. General Article Volume 10 Issue 7 July 2005 pp 21-33. Fulltext. Click here to view fulltext PDF. Permanent link:

  13. An Evolutionary Approach for Robust Layout Synthesis of MEMS

    DEFF Research Database (Denmark)

    Fan, Zhun; Wang, Jiachuan; Goodman, Erik

    2005-01-01

    assumptions and treated with multiobjective genetic algorithm (MOGA), a special type of evolutionary computing approaches. Case study based on layout synthesis of a comb-driven MEM resonator shows that the approach proposed in this paper can lead to design results that meet the target performance and are less...

  14. The extended evolutionary synthesis: its structure, assumptions and predictions.

    Science.gov (United States)

    Laland, Kevin N; Uller, Tobias; Feldman, Marcus W; Sterelny, Kim; Müller, Gerd B; Moczek, Armin; Jablonka, Eva; Odling-Smee, John

    2015-08-22

    Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the 'extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism-environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology. © 2015 The Author(s).

  15. The extended evolutionary synthesis: its structure, assumptions and predictions

    Science.gov (United States)

    Laland, Kevin N.; Uller, Tobias; Feldman, Marcus W.; Sterelny, Kim; Müller, Gerd B.; Moczek, Armin; Jablonka, Eva; Odling-Smee, John

    2015-01-01

    Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the ‘extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology. PMID:26246559

  16. Regular Network Class Features Enhancement Using an Evolutionary Synthesis Algorithm

    Directory of Open Access Journals (Sweden)

    O. G. Monahov

    2014-01-01

    Full Text Available This paper investigates a solution of the optimization problem concerning the construction of diameter-optimal regular networks (graphs. Regular networks are of practical interest as the graph-theoretical models of reliable communication networks of parallel supercomputer systems, as a basis of the structure in a model of small world in optical and neural networks. It presents a new class of parametrically described regular networks - hypercirculant networks (graphs. An approach that uses evolutionary algorithms for the automatic generation of parametric descriptions of optimal hypercirculant networks is developed. Synthesis of optimal hypercirculant networks is based on the optimal circulant networks with smaller degree of nodes. To construct optimal hypercirculant networks is used a template of circulant network from the known optimal families of circulant networks with desired number of nodes and with smaller degree of nodes. Thus, a generating set of the circulant network is used as a generating subset of the hypercirculant network, and the missing generators are synthesized by means of the evolutionary algorithm, which is carrying out minimization of diameter (average diameter of networks. A comparative analysis of the structural characteristics of hypercirculant, toroidal, and circulant networks is conducted. The advantage hypercirculant networks under such structural characteristics, as diameter, average diameter, and the width of bisection, with comparable costs of the number of nodes and the number of connections is demonstrated. It should be noted the advantage of hypercirculant networks of dimension three over four higher-dimensional tori. Thus, the optimization of hypercirculant networks of dimension three is more efficient than the introduction of an additional dimension for the corresponding toroidal structures. The paper also notes the best structural parameters of hypercirculant networks in comparison with iBT-networks previously

  17. Evolutionary biology today and the call for an extended synthesis.

    Science.gov (United States)

    Futuyma, Douglas J

    2017-10-06

    Evolutionary theory has been extended almost continually since the evolutionary synthesis (ES), but except for the much greater importance afforded genetic drift, the principal tenets of the ES have been strongly supported. Adaptations are attributable to the sorting of genetic variation by natural selection, which remains the only known cause of increase in fitness. Mutations are not adaptively directed, but as principal authors of the ES recognized, the material (structural) bases of biochemistry and development affect the variety of phenotypic variations that arise by mutation and recombination. Against this historical background, I analyse major propositions in the movement for an 'extended evolutionary synthesis'. 'Niche construction' is a new label for a wide variety of well-known phenomena, many of which have been extensively studied, but (as with every topic in evolutionary biology) some aspects may have been understudied. There is no reason to consider it a neglected 'process' of evolution. The proposition that phenotypic plasticity may engender new adaptive phenotypes that are later genetically assimilated or accommodated is theoretically plausible; it may be most likely when the new phenotype is not truly novel, but is instead a slight extension of a reaction norm already shaped by natural selection in similar environments. However, evolution in new environments often compensates for maladaptive plastic phenotypic responses. The union of population genetic theory with mechanistic understanding of developmental processes enables more complete understanding by joining ultimate and proximate causation; but the latter does not replace or invalidate the former. Newly discovered molecular phenomena have been easily accommodated in the past by elaborating orthodox evolutionary theory, and it appears that the same holds today for phenomena such as epigenetic inheritance. In several of these areas, empirical evidence is needed to evaluate enthusiastic speculation

  18. Sport science integration: An evolutionary synthesis.

    Science.gov (United States)

    Balagué, N; Torrents, C; Hristovski, R; Kelso, J A S

    2017-02-01

    The aim of the paper is to point out one way of integrating the supposedly incommensurate disciplines investigated in sports science. General, common principles can be found among apparently unrelated disciplines when the focus is put on the dynamics of sports-related phenomena. Dynamical systems approaches that have recently changed research in biological and social sciences among others, offer key concepts to create a common pluricontextual language in sport science. This common language, far from being homogenising, offers key synthesis between diverse fields, respecting and enabling the theoretical and experimental pluralism. It forms a softly integrated sports science characterised by a basic dynamic explanatory backbone as well as context-dependent theoretical flexibility. After defining the dynamic integration in living systems, unable to be captured by structural static approaches, we show the commonalities between the diversity of processes existing on different levels and time scales in biological and social entities. We justify our interpretation by drawing on some recent scientific contributions that use the same general principles and concepts, and diverse methods and techniques of data analysis, to study different types of phenomena in diverse disciplines. We show how the introduction of the dynamic framework in sport science has started to blur the boundaries between physiology, biomechanics, psychology, phenomenology and sociology. The advantages and difficulties of sport science integration and its consequences in research are also discussed.

  19. Evolutionary genetics: the Drosophila model

    Indian Academy of Sciences (India)

    Unknown

    Evolutionary genetics straddles the two fundamental processes of life, development (the transition from egg to adult) and reproduction (the generation of eggs from adults), and scrutinizes, from an evolu- tionary perspective, the nature .... script profiles in aging and calorically restricted Drosophila melanogaster. Curr. Biol.

  20. The Experimental Study of Bacterial Evolution and Its Implications for the Modern Synthesis of Evolutionary Biology.

    Science.gov (United States)

    O'Malley, Maureen A

    2017-10-04

    Since the 1940s, microbiologists, biochemists and population geneticists have experimented with the genetic mechanisms of microorganisms in order to investigate evolutionary processes. These evolutionary studies of bacteria and other microorganisms gained some recognition from the standard-bearers of the modern synthesis of evolutionary biology, especially Theodosius Dobzhansky and Ledyard Stebbins. A further period of post-synthesis bacterial evolutionary research occurred between the 1950s and 1980s. These experimental analyses focused on the evolution of population and genetic structure, the adaptive gain of new functions, and the evolutionary consequences of competition dynamics. This large body of research aimed to make evolutionary theory testable and predictive, by giving it mechanistic underpinnings. Although evolutionary microbiologists promoted bacterial experiments as methodologically advantageous and a source of general insight into evolution, they also acknowledged the biological differences of bacteria. My historical overview concludes with reflections on what bacterial evolutionary research achieved in this period, and its implications for the still-developing modern synthesis.

  1. 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.

  2. An evolutionary model with Turing machines

    CERN Document Server

    Feverati, Giovanni

    2007-01-01

    The development of a large non-coding fraction in eukaryotic DNA and the phenomenon of the code-bloat in the field of evolutionary computations show a striking similarity. This seems to suggest that (in the presence of mechanisms of code growth) the evolution of a complex code can't be attained without maintaining a large inactive fraction. To test this hypothesis we performed computer simulations of an evolutionary toy model for Turing machines, studying the relations among fitness and coding/non-coding ratio while varying mutation and code growth rates. The results suggest that, in our model, having a large reservoir of non-coding states constitutes a great (long term) evolutionary advantage.

  3. Towards an evolutionary model of transcription networks.

    Directory of Open Access Journals (Sweden)

    Dan Xie

    2011-06-01

    Full Text Available DNA evolution models made invaluable contributions to comparative genomics, although it seemed formidable to include non-genomic features into these models. In order to build an evolutionary model of transcription networks (TNs, we had to forfeit the substitution model used in DNA evolution and to start from modeling the evolution of the regulatory relationships. We present a quantitative evolutionary model of TNs, subjecting the phylogenetic distance and the evolutionary changes of cis-regulatory sequence, gene expression and network structure to one probabilistic framework. Using the genome sequences and gene expression data from multiple species, this model can predict regulatory relationships between a transcription factor (TF and its target genes in all species, and thus identify TN re-wiring events. Applying this model to analyze the pre-implantation development of three mammalian species, we identified the conserved and re-wired components of the TNs downstream to a set of TFs including Oct4, Gata3/4/6, cMyc and nMyc. Evolutionary events on the DNA sequence that led to turnover of TF binding sites were identified, including a birth of an Oct4 binding site by a 2nt deletion. In contrast to recent reports of large interspecies differences of TF binding sites and gene expression patterns, the interspecies difference in TF-target relationship is much smaller. The data showed increasing conservation levels from genomic sequences to TF-DNA interaction, gene expression, TN, and finally to morphology, suggesting that evolutionary changes are larger at molecular levels and smaller at functional levels. The data also showed that evolutionarily older TFs are more likely to have conserved target genes, whereas younger TFs tend to have larger re-wiring rates.

  4. Context dependent DNA evolutionary models

    DEFF Research Database (Denmark)

    Jensen, Jens Ledet

    in this paper, and a time discretization of the process is presented in order to make the calculations more feasible. Apart from the time discretization we introduce a set of simple estimating equations, together with an EM type algorithm, for finding the parameter estimates. A detailed derivation......This paper is about stochastic models for the evolution of DNA. For a set of aligned DNA sequences, connected in a phylogenetic tree, the models should be able to explain - in probabilistic terms - the differences seen in the sequences. From the estimates of the parameters in the model one can...... studying models on spaces with 4n (or 64n) number of states with n well above one hundred, say. For such models it is no longer possible to calculate the transition probability analytically, and often Markov chain Monte Carlo is used in connection with likelihood analysis. This is also the approach taken...

  5. An Evolutionary Model of DNA Substring Distribution

    Science.gov (United States)

    Kull, Meelis; Tretyakov, Konstantin; Vilo, Jaak

    DNA sequence analysis methods, such as motif discovery, gene detection or phylogeny reconstruction, can often provide important input for biological studies. Many of such methods require a background model, representing the expected distribution of short substrings in a given DNA region. Most current techniques for modeling this distribution disregard the evolutionary processes underlying DNA formation. We propose a novel approach for modeling DNA k-mer distribution that is capable of taking the notions of evolution and natural selection into account. We derive a computionally tractable approximation for estimating k-mer probabilities at genetic equilibrium, given a description of evolutionary processes in terms of fitness and mutation probabilities. We assess the goodness of this approximation via numerical experiments. Besides providing a generative model for DNA sequences, our method has further applications in motif discovery.

  6. Incorporating evolutionary processes into population viability models.

    Science.gov (United States)

    Pierson, Jennifer C; Beissinger, Steven R; Bragg, Jason G; Coates, David J; Oostermeijer, J Gerard B; Sunnucks, Paul; Schumaker, Nathan H; Trotter, Meredith V; Young, Andrew G

    2015-06-01

    We examined how ecological and evolutionary (eco-evo) processes in population dynamics could be better integrated into population viability analysis (PVA). Complementary advances in computation and population genomics can be combined into an eco-evo PVA to offer powerful new approaches to understand the influence of evolutionary processes on population persistence. We developed the mechanistic basis of an eco-evo PVA using individual-based models with individual-level genotype tracking and dynamic genotype-phenotype mapping to model emergent population-level effects, such as local adaptation and genetic rescue. We then outline how genomics can allow or improve parameter estimation for PVA models by providing genotypic information at large numbers of loci for neutral and functional genome regions. As climate change and other threatening processes increase in rate and scale, eco-evo PVAs will become essential research tools to evaluate the effects of adaptive potential, evolutionary rescue, and locally adapted traits on persistence. © 2014 Society for Conservation Biology.

  7. Evolutionary models of in-group favoritism.

    Science.gov (United States)

    Masuda, Naoki; Fu, Feng

    2015-01-01

    In-group favoritism is the tendency for individuals to cooperate with in-group members more strongly than with out-group members. Similar concepts have been described across different domains, including in-group bias, tag-based cooperation, parochial altruism, and ethnocentrism. Both humans and other animals show this behavior. Here, we review evolutionary mechanisms for explaining this phenomenon by covering recently developed mathematical models. In fact, in-group favoritism is not easily realized on its own in theory, although it can evolve under some conditions. We also discuss the implications of these modeling results in future empirical and theoretical research.

  8. Modeling Poker Challenges by Evolutionary Game Theory

    Directory of Open Access Journals (Sweden)

    Marco Alberto Javarone

    2016-12-01

    Full Text Available We introduce a model for studying the evolutionary dynamics of Poker. Notably, despite its wide diffusion and the raised scientific interest around it, Poker still represents an open challenge. Recent attempts for uncovering its real nature, based on statistical physics, showed that Poker in some conditions can be considered as a skill game. In addition, preliminary investigations reported a neat difference between tournaments and ‘cash game’ challenges, i.e., between the two main configurations for playing Poker. Notably, these previous models analyzed populations composed of rational and irrational agents, identifying in the former those that play Poker by using a mathematical strategy, while in the latter those playing randomly. Remarkably, tournaments require very few rational agents to make Poker a skill game, while ‘cash game’ may require several rational agents for not being classified as gambling. In addition, when the agent interactions are based on the ‘cash game’ configuration, the population shows an interesting bistable behavior that deserves further attention. In the proposed model, we aim to study the evolutionary dynamics of Poker by using the framework of Evolutionary Game Theory, in order to get further insights on its nature, and for better clarifying those points that remained open in the previous works (as the mentioned bistable behavior. In particular, we analyze the dynamics of an agent population composed of rational and irrational agents, that modify their behavior driven by two possible mechanisms: self-evaluation of the gained payoff, and social imitation. Results allow to identify a relation between the mechanisms for updating the agents’ behavior and the final equilibrium of the population. Moreover, the proposed model provides further details on the bistable behavior observed in the ‘cash game’ configuration.

  9. An Evolutionary Optimizer of libsvm Models

    Directory of Open Access Journals (Sweden)

    Dragos Horvath

    2014-11-01

    Full Text Available This user guide describes the rationale behind, and the modus operandi of a Unix script-driven package for evolutionary searching of optimal Support Vector Machine model parameters as computed by the libsvm package, leading to support vector machine models of maximal predictive power and robustness. Unlike common libsvm parameterizing engines, the current distribution includes the key choice of best-suited sets of attributes/descriptors, in addition to the classical libsvm operational parameters (kernel choice, kernel parameters, cost, and so forth, allowing a unified search in an enlarged problem space. It relies on an aggressive, repeated cross-validation scheme to ensure a rigorous assessment of model quality. Primarily designed for chemoinformatics applications, it also supports the inclusion of decoy instances, for which the explained property (bioactivity is, strictly speaking, unknown but presumably “inactive”, thus additionally testing the robustness of a model to noise. The package was developed with parallel computing in mind, supporting execution on both multi-core workstations as well as compute cluster environments. It can be downloaded from http://infochim.u-strasbg.fr/spip.php?rubrique178.

  10. Evaluation of models generated via hybrid evolutionary algorithms ...

    African Journals Online (AJOL)

    2016-04-02

    Apr 2, 2016 ... Evaluation of models generated via hybrid evolutionary algorithms for the prediction of Microcystis concentrations ... evolutionary algorithms (HEA) proved to be highly applica- ble to the hypertrophic reservoirs of .... Principal component analysis (PCA) was carried out on the input dataset used for the model ...

  11. Toward a synthesis of developmental biology with evolutionary theory and ecology.

    Science.gov (United States)

    Sommer, Ralf J; Mayer, Melanie G

    2015-01-01

    The evolutionary conservation of developmental mechanisms is a truism in biology, but few attempts have been made to integrate development with evolutionary theory and ecology. To work toward such a synthesis, we summarize studies in the nematode model Pristionchus pacificus, focusing on the development of the dauer, a stress-resistant, alternative larval stage. Integrative approaches combining molecular and genetic principles of development with natural variation and ecological studies in wild populations have identified a key role for a developmental switch mechanism in dauer development and evolution, one that involves the nuclear hormone receptor DAF-12. DAF-12 is a crucial regulator and convergence point for different signaling inputs, and its function is conserved among free-living and parasitic nematodes. Furthermore, DAF-12 is the target of regulatory loops that rely on novel or fast-evolving components to control the intraspecific competition of dauer larvae. We propose developmental switches as paradigms for understanding the integration of development, evolution, and ecology at the molecular level.

  12. Polemics and Synthesis: Ernst Mayr and Evolutionary Biology

    Indian Academy of Sciences (India)

    during his life that spanned a century, Ernst Mayr (1904-2005) made outstanding contributions to our understanding of the pat- tern and process of evolution. An ornithologist and systematist by training, Mayr embraced Darwinism and championed the cause of evolutionary biology throughout his long and highly productive.

  13. Evolutionary model of the personal income distribution

    Science.gov (United States)

    Kaldasch, Joachim

    2012-11-01

    The aim of this work is to develop a qualitative picture of the personal income distribution. Treating an economy as a self-organized system the key idea of the model is that the income distribution contains competitive and non-competitive contributions. The presented model distinguishes between three main income classes. 1. Capital income from private firms is shown to be the result of an evolutionary competition between products. A direct consequence of this competition is Gibrat’s law suggesting a lognormal income distribution for small private firms. Taking into account an additional preferential attachment mechanism for large private firms the income distribution is supplemented by a power law (Pareto) tail. 2. Due to the division of labor a diversified labor market is seen as a non-competitive market. In this case wage income exhibits an exponential distribution. 3. Also included is income from a social insurance system. It can be approximated by a Gaussian peak. A consequence of this theory is that for short time intervals a fixed ratio of total labor (total capital) to net income exists (Cobb-Douglas relation). A comparison with empirical high resolution income data confirms this pattern of the total income distribution. The theory suggests that competition is the ultimate origin of the uneven income distribution.

  14. Evolutionary triplet models of structured RNA.

    Directory of Open Access Journals (Sweden)

    Robert K Bradley

    2009-08-01

    Full Text Available The reconstruction and synthesis of ancestral RNAs is a feasible goal for paleogenetics. This will require new bioinformatics methods, including a robust statistical framework for reconstructing histories of substitutions, indels and structural changes. We describe a "transducer composition" algorithm for extending pairwise probabilistic models of RNA structural evolution to models of multiple sequences related by a phylogenetic tree. This algorithm draws on formal models of computational linguistics as well as the 1985 protosequence algorithm of David Sankoff. The output of the composition algorithm is a multiple-sequence stochastic context-free grammar. We describe dynamic programming algorithms, which are robust to null cycles and empty bifurcations, for parsing this grammar. Example applications include structural alignment of non-coding RNAs, propagation of structural information from an experimentally-characterized sequence to its homologs, and inference of the ancestral structure of a set of diverged RNAs. We implemented the above algorithms for a simple model of pairwise RNA structural evolution; in particular, the algorithms for maximum likelihood (ML alignment of three known RNA structures and a known phylogeny and inference of the common ancestral structure. We compared this ML algorithm to a variety of related, but simpler, techniques, including ML alignment algorithms for simpler models that omitted various aspects of the full model and also a posterior-decoding alignment algorithm for one of the simpler models. In our tests, incorporation of basepair structure was the most important factor for accurate alignment inference; appropriate use of posterior-decoding was next; and fine details of the model were least important. Posterior-decoding heuristics can be substantially faster than exact phylogenetic inference, so this motivates the use of sum-over-pairs heuristics where possible (and approximate sum-over-pairs. For more exact

  15. Modelling Evolutionary Algorithms with Stochastic Differential Equations.

    Science.gov (United States)

    Heredia, Jorge Pérez

    2017-11-20

    There has been renewed interest in modelling the behaviour of evolutionary algorithms (EAs) by more traditional mathematical objects, such as ordinary differential equations or Markov chains. The advantage is that the analysis becomes greatly facilitated due to the existence of well established methods. However, this typically comes at the cost of disregarding information about the process. Here, we introduce the use of stochastic differential equations (SDEs) for the study of EAs. SDEs can produce simple analytical results for the dynamics of stochastic processes, unlike Markov chains which can produce rigorous but unwieldy expressions about the dynamics. On the other hand, unlike ordinary differential equations (ODEs), they do not discard information about the stochasticity of the process. We show that these are especially suitable for the analysis of fixed budget scenarios and present analogues of the additive and multiplicative drift theorems from runtime analysis. In addition, we derive a new more general multiplicative drift theorem that also covers non-elitist EAs. This theorem simultaneously allows for positive and negative results, providing information on the algorithm's progress even when the problem cannot be optimised efficiently. Finally, we provide results for some well-known heuristics namely Random Walk (RW), Random Local Search (RLS), the (1+1) EA, the Metropolis algorithm (MA) and the Strong Selection Weak Mutation (SSWM) algorithm.

  16. [Symbiogenesis and Synthetic Evolutionary Theory: The Third Synthesis].

    Science.gov (United States)

    Provoro, N A; Tikhonovich, I A; Vorobyov, N I

    2015-06-01

    Integration of the concepts of symbiogenesis and synthetic evolutionary theory is the main path for the development of evolutionary biology. It is based on the analysis of cooperative adaptations that evolve under the impact of symbiotic-specific selective pressures responsible for the formation of super-species hereditary systems--metagenomes, symbiogenomes, and hologenomes. The genetic integration of nonrelated organisms (symbiogenesis) is determined by the inheritance of microsymbionts by hosts resulted in the complication of mutualistic interactions according to the scheme: pleiotropic symbiosis --> mutual partner's exploitation --> interspecies altruism. This evolution may result in the loss of genetic individuality in microsymbionts; this loss is expressed as a deep reduction in their genomes. A significant number of these may be exported to the host, resulting in the transformation of symbiotic systems into novel, genetically integral organisms.

  17. A Modeling Approach to Teaching Evolutionary Biology in High Schools.

    Science.gov (United States)

    Passmore, Cynthia; Stewart, Jim

    2002-01-01

    Describes the commitments and research that went into the design of a 9-week high school course in evolutionary biology designed to bring students to an understanding of the practice of evolutionary biology by engaging them in developing, elaborating, and using one of the discipline's most important explanatory models. (Contains 39 references.)…

  18. Incorporating evolutionary processes into population viability models

    NARCIS (Netherlands)

    Pierson, J.C.; Beissinger, S.R.; Bragg, J.G.; Coates, D.J.; Oostermeijer, J.G.B.; Sunnucks, P.; Schumaker, N.H.; Trotter, M.V.; Young, A.G.

    2015-01-01

    We examined how ecological and evolutionary (eco-evo) processes in population dynamics could be better integrated into population viability analysis (PVA). Complementary advances in computation and population genomics can be combined into an eco-evo PVA to offer powerful new approaches to understand

  19. An Evolutionary Game Theory Model of Spontaneous Brain Functioning

    National Research Council Canada - National Science Library

    Dario Madeo; Agostino Talarico; Alvaro Pascual-Leone; Chiara Mocenni; Emiliano Santarnecchi

    2017-01-01

    ... conditions, making its understanding of fundamental importance in modern neuroscience. Here we present a theoretical and mathematical model based on an extension of evolutionary game theory on networks (EGN...

  20. The uncertain foundation of neo-Darwinism: metaphysical and epistemological pluralism in the evolutionary synthesis.

    Science.gov (United States)

    Delisle, Richard G

    2009-06-01

    The Evolutionary Synthesis is often seen as a unification process in evolutionary biology, one which provided this research area with a solid common theoretical foundation. As such, neo-Darwinism is believed to constitute from this time onward a single, coherent, and unified movement offering research guidelines for investigations. While this may be true if evolutionary biology is solely understood as centred around evolutionary mechanisms, an entirely different picture emerges once other aspects of the founding neo-Darwinists' views are taken into consideration, aspects potentially relevant to the elaboration of an evolutionary worldview: the tree of life, the ontological distinctions of the main cosmic entities (inert matter, biological organisms, mind), the inherent properties of self-organizing matter, evolutionary ethics, and so on. Profound tensions and inconsistencies are immediately revealed in the neo-Darwinian movement once this broader perspective is adopted. This pluralism is such that it is possible to identify at least three distinct and quasi-incommensurable epistemological/metaphysical frameworks as providing a proper foundation for neo-Darwinism. The analysis of the views of Theodosius Dobzhansky, Bernhard Rensch, and Ernst Mayr will illustrate this untenable pluralism, one which requires us to conceive of the neo-Darwinian research agenda as being conducted in more than one research programme or research tradition at the same time.

  1. Modeling evolutionary games in populations with demographic structure

    DEFF Research Database (Denmark)

    Li, Xiang-Yi; Giaimo, Stefano; Baudisch, Annette

    2015-01-01

    Classic life history models are often based on optimization algorithms, focusing on the adaptation of survival and reproduction to the environment, while neglecting frequency dependent interactions in the population. Evolutionary game theory, on the other hand, studies frequency dependent strategy...... interactions, but usually omits life history and the demographic structure of the population. Here we show how an integration of both aspects can substantially alter the underlying evolutionary dynamics. We study the replicator dynamics of strategy interactions in life stage structured populations. Individuals...

  2. Evaluation of Generation Alternation Models in Evolutionary Robotics

    Science.gov (United States)

    Oiso, Masashi; Matsumura, Yoshiyuki; Yasuda, Toshiyuki; Ohkura, Kazuhiro

    For efficient implementation of Evolutionary Algorithms (EA) to a desktop grid computing environment, we propose a new generation alternation model called Grid-Oriented-Deletion (GOD) based on comparison with the conventional techniques. In previous research, generation alternation models are generally evaluated by using test functions. However, their exploration performance on the real problems such as Evolutionary Robotics (ER) has not been made very clear yet. Therefore we investigate the relationship between the exploration performance of EA on an ER problem and its generation alternation model. We applied four generation alternation models to the Evolutionary Multi-Robotics (EMR), which is the package-pushing problem to investigate their exploration performance. The results show that GOD is more effective than the other conventional models.

  3. Mouse Models as Predictors of Human Responses: Evolutionary Medicine.

    Science.gov (United States)

    Uhl, Elizabeth W; Warner, Natalie J

    Mice offer a number of advantages and are extensively used to model human diseases and drug responses. Selective breeding and genetic manipulation of mice have made many different genotypes and phenotypes available for research. However, in many cases, mouse models have failed to be predictive. Important sources of the prediction problem have been the failure to consider the evolutionary basis for species differences, especially in drug metabolism, and disease definitions that do not reflect the complexity of gene expression underlying disease phenotypes. Incorporating evolutionary insights into mouse models allow for unique opportunities to characterize the effects of diet, different gene expression profiles, and microbiomics underlying human drug responses and disease phenotypes.

  4. Individual-based modeling of ecological and evolutionary processes

    NARCIS (Netherlands)

    DeAngelis, D.L.; Mooij, W.M.

    2005-01-01

    Individual-based models (IBMs) allow the explicit inclusion of individual variation in greater detail than do classical differential and difference equation models. Inclusion of such variation is important for continued progress in ecological and evolutionary theory. We provide a conceptual basis

  5. Evolutionary systems biology: historical and philosophical perspectives on an emerging synthesis.

    Science.gov (United States)

    O'Malley, Maureen A

    2012-01-01

    Systems biology (SB) is at least a decade old now and maturing rapidly. A more recent field, evolutionary systems biology (ESB), is in the process of further developing system-level approaches through the expansion of their explanatory and potentially predictive scope. This chapter will outline the varieties of ESB existing today by tracing the diverse roots and fusions that make up this integrative project. My approach is philosophical and historical. As well as examining the recent origins of ESB, I will reflect on its central features and the different clusters of research it comprises. In its broadest interpretation, ESB consists of five overlapping approaches: comparative and correlational ESB; network architecture ESB; network property ESB; population genetics ESB; and finally, standard evolutionary questions answered with SB methods. After outlining each approach with examples, I will examine some strong general claims about ESB, particularly that it can be viewed as the next step toward a fuller modern synthesis of evolutionary biology (EB), and that it is also the way forward for evolutionary and systems medicine. I will conclude with a discussion of whether the emerging field of ESB has the capacity to combine an even broader scope of research aims and efforts than it presently does.

  6. Instrument Modeling and Synthesis

    Science.gov (United States)

    Horner, Andrew B.; Beauchamp, James W.

    During the 1970s and 1980s, before synthesizers based on direct sampling of musical sounds became popular, replicating musical instruments using frequency modulation (FM) or wavetable synthesis was one of the “holy grails” of music synthesis. Synthesizers such as the Yamaha DX7 allowed users great flexibility in mixing and matching sounds, but were notoriously difficult to coerce into producing sounds like those of a given instrument. Instrument design wizards practiced the mysteries of FM instrument design.

  7. Individual-based modeling of ecological and evolutionary processes

    Science.gov (United States)

    DeAngelis, Donald L.; Mooij, Wolf M.

    2005-01-01

    Individual-based models (IBMs) allow the explicit inclusion of individual variation in greater detail than do classical differential-equation and difference-equation models. Inclusion of such variation is important for continued progress in ecological and evolutionary theory. We provide a conceptual basis for IBMs by describing five major types of individual variation in IBMs: spatial, ontogenetic, phenotypic, cognitive, and genetic. IBMs are now used in almost all subfields of ecology and evolutionary biology. We map those subfields and look more closely at selected key papers on fish recruitment, forest dynamics, sympatric speciation, metapopulation dynamics, maintenance of diversity, and species conservation. Theorists are currently divided on whether IBMs represent only a practical tool for extending classical theory to more complex situations, or whether individual-based theory represents a radically new research program. We feel that the tension between these two poles of thinking can be a source of creativity in ecology and evolutionary theory.

  8. [Debating Darwin in Spain: anti-Darwinian evolutionary theories and modern synthesis].

    Science.gov (United States)

    Pelayo, Francisco

    2009-01-01

    Centenary celebrations of Darwin's birth were held in Valencia and Lorca in 1909. Fifty years later, the meetings and the publications of the Spanish scientific community on the occasion of the centenary of the publication of "On the Origin of Species" showed a proximity and an acceptance towards the theses of the evolutionary modern synthesis. During the first half of the 20th century, there were controversies in Spain between the Darwinian and anti-Darwinian positions. In addition, non-Darwinian evolutionary theories were spread and supported. Though the assumptions of the synthetic theory of evolution were soon known, commented and discussed, the majority trend in the 40s and 50s was to incline towards finalist and vitalist interpretations of evolution.

  9. SYNTHESIS OF DUAL RADIATION PATTERN OF RECTANGULAR PLANAR ARRAY ANTENNA USING EVOLUTIONARY ALGORITHM

    Directory of Open Access Journals (Sweden)

    Debasis Mandal

    2015-09-01

    Full Text Available A pattern synthesis method based on Evolutionary Algorithm is presented to generate a dual radiation pattern from a planar array of isotropic antennas. The desired patterns are obtained by finding out optimum set of elements excitations. Flat-top and Pencil beams share a common optimum amplitude distribution among the array elements. Flat-top beam is generated by updating the zero phases with the optimum phases among the elements. 4 bit discrete amplitudes and 5 bit discrete phases have been taken to simplify the design of the feed network. Results clearly show the effectiveness of the proposed method.

  10. Debating Darwin in Spain: anti-darwinian evolutionary theories and modern synthesis

    OpenAIRE

    Pelayo, Francisco

    2009-01-01

    Centenary celebrations of Darwin’s birth were held in Valencia and Lorca in 1909. Fifty years later, the meetings and the publications of the Spanish scientific community on the occasion of the centenary of the publication of On the Origin of Species showed a proximity and an acceptance towards the theses of the evolutionary modern synthesis. During the first half of the 20th century, there were controversies in Spain between the Darwinian and anti-Darwinian positions. In a...

  11. New advances in spatial network modelling: towards evolutionary algorithms

    NARCIS (Netherlands)

    Reggiani, A; Nijkamp, P.; Sabella, E.

    2001-01-01

    This paper discusses analytical advances in evolutionary methods with a view towards their possible applications in the space-economy. For this purpose, we present a brief overview and illustration of models actually available in the spatial sciences which attempt to map the complex patterns of

  12. Sciara as an experimental model for studies on the evolutionary ...

    Indian Academy of Sciences (India)

    Sciara as an experimental model for studies on the evolutionary relationships between the zygotic, maternal and environmental primary signals for sexual development. Lucas Sánchez. Review Article Volume ... Lucas Sánchez1. Centro de Investigaciones Biol´ogicas (C. S. I. C.), Ramiro de Maeztu 9, 28040 Madrid, Spain ...

  13. Preventing clonal evolutionary processes in cancer: Insights from mathematical models.

    Science.gov (United States)

    Rodriguez-Brenes, Ignacio A; Wodarz, Dominik

    2015-07-21

    Clonal evolutionary processes can drive pathogenesis in human diseases, with cancer being a prominent example. To prevent or treat cancer, mechanisms that can potentially interfere with clonal evolutionary processes need to be understood better. Mathematical modeling is an important research tool that plays an ever-increasing role in cancer research. This paper discusses how mathematical models can be useful to gain insights into mechanisms that can prevent disease initiation, help analyze treatment responses, and aid in the design of treatment strategies to combat the emergence of drug-resistant cells. The discussion will be done in the context of specific examples. Among defense mechanisms, we explore how replicative limits and cellular senescence induced by telomere shortening can influence the emergence and evolution of tumors. Among treatment approaches, we consider the targeted treatment of chronic lymphocytic leukemia (CLL) with tyrosine kinase inhibitors. We illustrate how basic evolutionary mathematical models have the potential to make patient-specific predictions about disease and treatment outcome, and argue that evolutionary models could become important clinical tools in the field of personalized medicine.

  14. Evolutionary thinking in microeconomic models: prestige bias and market bubbles.

    Science.gov (United States)

    Bell, Adrian Viliami

    2013-01-01

    Evolutionary models broadly support a number of social learning strategies likely important in economic behavior. Using a simple model of price dynamics, I show how prestige bias, or copying of famed (and likely successful) individuals, influences price equilibria and investor disposition in a way that exacerbates or creates market bubbles. I discuss how integrating the social learning and demographic forces important in cultural evolution with economic models provides a fruitful line of inquiry into real-world behavior.

  15. AN ADAPTATIVE EVOLUTIONARY MODEL OF FINANCIAL INVESTORS

    Directory of Open Access Journals (Sweden)

    Stanculescu Mircea

    2009-05-01

    Full Text Available The main purpose of the paper is to determine a general behavior of a multi-agent model capable of describing the process of deliberation of an investors group witch may repeatedly decide whether to buy or sell an asset. Each adaptive agent was modeled as

  16. A stochastic evolutionary model for survival dynamics

    Science.gov (United States)

    Fenner, Trevor; Levene, Mark; Loizou, George

    2014-09-01

    The recent interest in human dynamics has led researchers to investigate the stochastic processes that explain human behaviour in different contexts. Here we propose a generative model to capture the essential dynamics of survival analysis, traditionally employed in clinical trials and reliability analysis in engineering. In our model, the only implicit assumption made is that the longer an actor has been in the system, the more likely it is to have failed. We derive a power-law distribution for the process and provide preliminary empirical evidence for the validity of the model from two well-known survival analysis data sets.

  17. An Evolutionary Model of Spatial Competition

    DEFF Research Database (Denmark)

    Knudsen, Thorbjørn; Winter, Sidney G.

    as well in the new environment as they did in the old; the firm may respond with effort to locate appropriate environments or by modification of its routines.  Tradeoffs are presented between the complexity of a business model and its replication costs,  as well as issues involving response...... to environmental change.  Formally, the model builds on the NK framework for organizational analysis, with firm policy choices and environmental conditions represented by segments of a string of N bits; it joins this structure to an abstract representation of space based on the idea of a cellular automaton....... Randomly generated firm policies are tested first by a local market environment, and then, if success leads the firm to grow spatially, in a gradually expanding environment.  In the initial experiments reported here, we show that the model generates configurations that reflect features of the exogenous...

  18. Evolutionary and Ecological Genomics of Non-Model Plants

    OpenAIRE

    Song, Bao-Hua; Mitchell-Olds, Thomas

    2011-01-01

    Dissecting evolutionary dynamics of ecologically important traits is a long-term challenge for biologists. Attempts to understand natural variation and molecular mechanisms have motivated a move from laboratory model systems to non-model systems in diverse natural environments. Next generation sequencing methods, along with an expansion of genomic resources and tools, have fostered new links between diverse disciplines, including molecular biology, evolution, and ecology, and genomics. Great ...

  19. Charophytes: Evolutionary Giants and Emerging Model Organisms

    Directory of Open Access Journals (Sweden)

    David Domozych

    2016-10-01

    Full Text Available Charophytes are the group of green algae whose ancestral lineage gave rise to land plants in what resulted in a profoundly transformative event in the natural history of the planet. Extant charophytes exhibit many features that are similar to those found in land plants and their relatively simple phenotypes make them efficacious organisms for the study of many fundamental biological phenomena. Several taxa including Micrasterias, Penium, Chara and Coleochaete are valuable model organisms for the study of cell biology, development, physiology and ecology of plants. New and rapidly expanding molecular studies are increasing the use of charophytes that in turn, will dramatically enhance our understanding of the evolution of plants and the adaptations that allowed for survival on land. The Frontiers in Plant Science series on Charophytes provides an assortment of new research reports and reviews on charophytes and their emerging significance as model plants.

  20. Lamprey: a model for vertebrate evolutionary research

    Science.gov (United States)

    XU, Yang; ZHU, Si-Wei; LI, Qing-Wei

    2016-01-01

    Lampreys belong to the superclass Cyclostomata and represent the most ancient group of vertebrates. Existing for over 360 million years, they are known as living fossils due to their many evolutionally conserved features. They are not only a keystone species for studying the origin and evolution of vertebrates, but also one of the best models for researching vertebrate embryonic development and organ differentiation. From the perspective of genetic information, the lamprey genome remains primitive compared with that of other higher vertebrates, and possesses abundant functional genes. Through scientific and technological progress, scientists have conducted in-depth studies on the nervous, endocrine, and immune systems of lampreys. Such research has significance for understanding and revealing the origin and evolution of vertebrates, and could contribute to a greater understanding of human diseases and treatments. This review presents the current progress and significance of lamprey research. PMID:27686784

  1. Evolutionary model of the growth and size of firms

    Science.gov (United States)

    Kaldasch, Joachim

    2012-07-01

    The key idea of this model is that firms are the result of an evolutionary process. Based on demand and supply considerations the evolutionary model presented here derives explicitly Gibrat's law of proportionate effects as the result of the competition between products. Applying a preferential attachment mechanism for firms, the theory allows to establish the size distribution of products and firms. Also established are the growth rate and price distribution of consumer goods. Taking into account the characteristic property of human activities to occur in bursts, the model allows also an explanation of the size-variance relationship of the growth rate distribution of products and firms. Further the product life cycle, the learning (experience) curve and the market size in terms of the mean number of firms that can survive in a market are derived. The model also suggests the existence of an invariant of a market as the ratio of total profit to total revenue. The relationship between a neo-classic and an evolutionary view of a market is discussed. The comparison with empirical investigations suggests that the theory is able to describe the main stylized facts concerning the size and growth of firms.

  2. Evolutionary dynamics in a simple model of self-assembly

    Science.gov (United States)

    Johnston, Iain G.; Ahnert, Sebastian E.; Doye, Jonathan P. K.; Louis, Ard A.

    2011-06-01

    We investigate the evolutionary dynamics of an idealized model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between sets of square tiles that drive the self-assembly process. The relationship between the model’s rule set and its resulting self-assembled structure can be viewed as a genotype-phenotype map and incorporated into a genetic algorithm. The rule sets evolve under selection for specified target structures. The corresponding complex fitness landscape generates rich evolutionary dynamics as a function of parameters such as the population size, search space size, mutation rate, and method of recombination. Furthermore, these systems are simple enough that in some cases the associated model genome space can be completely characterized, shedding light on how the evolutionary dynamics depends on the detailed structure of the fitness landscape. Finally, we apply the model to study the emergence of the preference for dihedral over cyclic symmetry observed for homomeric protein tetramers.

  3. Synthesis of porous-acoustic absorbing systems by an evolutionary optimization method

    Science.gov (United States)

    Silva, F. I.; Pavanello, R.

    2010-10-01

    Topology optimization is frequently used to design structures and acoustic systems in a large range of engineering applications. In this work, a method is proposed for maximizing the absorbing performance of acoustic panels by using a coupled finite element model and evolutionary strategies. The goal is to find the best distribution of porous material for sound absorbing panels. The absorbing performance of the porous material samples in a Kundt tube is simulated using a coupled porous-acoustic finite element model. The equivalent fluid model is used to represent the foam material. The porous material model is coupled to a wave guide using a modal superposition technique. A sensitivity number indicating the optimum locations for porous material to be removed is derived and used in a numerical hard kill scheme. The sensitivity number is used to form an evolutionary porous material optimization algorithm which is verified through examples.

  4. Evolutionary Development of the Simulation by Logical Modeling System (SIBYL)

    Science.gov (United States)

    Wu, Helen

    1995-01-01

    Through the evolutionary development of the Simulation by Logical Modeling System (SIBYL) we have re-engineered the expensive and complex IBM mainframe based Long-term Hardware Projection Model (LHPM) to a robust cost-effective computer based mode that is easy to use. We achieved significant cost reductions and improved productivity in preparing long-term forecasts of Space Shuttle Main Engine (SSME) hardware. The LHPM for the SSME is a stochastic simulation model that projects the hardware requirements over 10 years. SIBYL is now the primary modeling tool for developing SSME logistics proposals and Program Operating Plan (POP) for NASA and divisional marketing studies.

  5. Sticklebacks as model hosts in ecological and evolutionary parasitology.

    Science.gov (United States)

    Barber, Iain

    2013-11-01

    The three-spined stickleback is a small teleost fish, native to coastal regions of the Northern Hemisphere, which has emerged as a key model organism in evolutionary biology and ecology. Sticklebacks possess a well-documented and experimentally amenable parasite fauna, and are well suited to both laboratory and field parasitological investigation. As a consequence, sticklebacks have been extensively used as model hosts in studies of host-parasite interactions, and these studies have provided considerable insight into the roles of parasites in ecology and evolutionary biology. In this review, I discuss key advances in our understanding of host-parasite interactions that have arisen from studies involving stickleback hosts, highlight areas of current research activity, and identify potentially promising areas for future research. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Evolutionary and Ecological Genomics of Non-Model Plants

    Science.gov (United States)

    Song, Bao-Hua; Mitchell-Olds, Thomas

    2011-01-01

    Dissecting evolutionary dynamics of ecologically important traits is a long-term challenge for biologists. Attempts to understand natural variation and molecular mechanisms have motivated a move from laboratory model systems to non-model systems in diverse natural environments. Next generation sequencing methods, along with an expansion of genomic resources and tools, have fostered new links between diverse disciplines, including molecular biology, evolution, and ecology, and genomics. Great progress has been made in a few non-model wild plants, such as Arabidopsis relatives, monkey flowers, and wild sunflowers. Until recently, the lack of comprehensive genomic information has limited evolutionary and ecological studies to larger QTL regions rather than single gene resolution, and has hindered recognition of general patterns of natural variation and local adaptation. Further efforts in accumulating genomic data and developing bioinformatic and biostatistical tools are now poised to move this field forward. Integrative national and international collaborations and research communities are needed to facilitate development in the field of evolutionary and ecological genomics. PMID:21394233

  7. Lyapunov stability in an evolutionary game theory model of the labour market

    Directory of Open Access Journals (Sweden)

    Ricardo Azevedo Araujo

    2014-01-01

    Full Text Available In this paper the existence and stability of equilibriums in an evolutionary game theory model of the labour market is studied by using the Lyapunov method. The model displays multiple equilibriums and it is shown that the Nash equilibriums of the static game are evolutionary stable equilibrium in the game theory evolutionary set up. A complete characterization of the dynamics of an evolutionary model of the labour market is provided.

  8. Evolutionary model of an anonymous consumer durable market

    Science.gov (United States)

    Kaldasch, Joachim

    2011-07-01

    An analytic model is presented that considers the evolution of a market of durable goods. The model suggests that after introduction goods spread always according to a Bass diffusion. However, this phase will be followed by a diffusion process for durable consumer goods governed by a variation-selection-reproduction mechanism and the growth dynamics can be described by a replicator equation. The theory suggests that products play the role of species in biological evolutionary models. It implies that the evolution of man-made products can be arranged into an evolutionary tree. The model suggests that each product can be characterized by its product fitness. The fitness space contains elements of both sites of the market, supply and demand. The unit sales of products with a higher product fitness compared to the mean fitness increase. Durables with a constant fitness advantage replace other goods according to a logistic law. The model predicts in particular that the mean price exhibits an exponential decrease over a long time period for durable goods. The evolutionary diffusion process is directly related to this price decline and is governed by Gompertz equation. Therefore it is denoted as Gompertz diffusion. Describing the aggregate sales as the sum of first, multiple and replacement purchase the product life cycle can be derived. Replacement purchase causes periodic variations of the sales determined by the finite lifetime of the good (Juglar cycles). The model suggests that both, Bass- and Gompertz diffusion may contribute to the product life cycle of a consumer durable. The theory contains the standard equilibrium view of a market as a special case. It depends on the time scale, whether an equilibrium or evolutionary description is more appropriate. The evolutionary framework is used to derive also the size, growth rate and price distribution of manufacturing business units. It predicts that the size distribution of the business units (products) is lognormal

  9. 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.

  10. Biochemistry and physiology within the framework of the extended synthesis of evolutionary biology.

    Science.gov (United States)

    Vianello, Angelo; Passamonti, Sabina

    2016-02-09

    Functional biologists, like Claude Bernard, ask "How?", meaning that they investigate the mechanisms underlying the emergence of biological functions (proximal causes), while evolutionary biologists, like Charles Darwin, asks "Why?", meaning that they search the causes of adaptation, survival and evolution (remote causes). Are these divergent views on what is life? The epistemological role of functional biology (molecular biology, but also biochemistry, physiology, cell biology and so forth) appears essential, for its capacity to identify several mechanisms of natural selection of new characters, individuals and populations. Nevertheless, several issues remain unsolved, such as orphan metabolic activities, i.e., adaptive functions still missing the identification of the underlying genes and proteins, and orphan genes, i.e., genes that bear no signature of evolutionary history, yet provide an organism with improved adaptation to environmental changes. In the framework of the Extended Synthesis, we suggest that the adaptive roles of any known function/structure are reappraised in terms of their capacity to warrant constancy of the internal environment (homeostasis), a concept that encompasses both proximal and remote causes.

  11. An Evolutionary Modelling Approach To Understanding The Factors Behind Plant Invasiveness And Community Susceptibility To Invasion

    DEFF Research Database (Denmark)

    Warren, John; Topping, Christopher John; James, Penri

    2011-01-01

    Ecologists have had limited success in understanding which introduced species may become invasive. An evolutionary model is used to investigate which traits are associated with invasiveness. Translocation experiments were simulated in which species were moved into similar but evolutionary younger...

  12. Preference learning with evolutionary Multivariate Adaptive Regression Spline model

    DEFF Research Database (Denmark)

    Abou-Zleikha, Mohamed; Shaker, Noor; Christensen, Mads Græsbøll

    2015-01-01

    This paper introduces a novel approach for pairwise preference learning through combining an evolutionary method with Multivariate Adaptive Regression Spline (MARS). Collecting users' feedback through pairwise preferences is recommended over other ranking approaches as this method is more appealing...... for human decision making. Learning models from pairwise preference data is however an NP-hard problem. Therefore, constructing models that can effectively learn such data is a challenging task. Models are usually constructed with accuracy being the most important factor. Another vitally important aspect...... that is usually given less attention is expressiveness, i.e. how easy it is to explain the relationship between the model input and output. Most machine learning techniques are focused either on performance or on expressiveness. This paper employ MARS models which have the advantage of being a powerful method...

  13. A Dynamic Evolutionary Game Model of Modular Production Network

    Directory of Open Access Journals (Sweden)

    Wei He

    2016-01-01

    Full Text Available As a new organization mode of production in the 21st century, modular production network is deemed extensively to be a source of competitiveness for lead firms in manufacturing industries. However, despite the abundant studies on the modular production network, there are very few studies from a dynamic perspective to discuss the conditions on which a modular production network develops. Based on the dynamic evolutionary game theory, this paper constructs a model, which incorporates several main factors influencing the development of modular production network. By calculating the replicator dynamics equations and analyzing the evolutionary stable strategies, this paper discusses the evolution process of cooperation strategies of member enterprises in a modular production network. Furthermore, by using NetLogo software to simulate the model, this paper verifies the effectiveness of the model. From the model, we can find that the final stable equilibrium strategy is related to such factors as the initial cost, the extra payoff, the cooperation willingness of both parties, the cooperation efforts, and the proportion each party can get from the extra payoff. To encourage the cooperation of production integrator and modular supplier, some suggestions are also provided.

  14. Debating Darwin in Spain: anti-darwinian evolutionary theories and modern synthesis

    Directory of Open Access Journals (Sweden)

    Pelayo, Francisco

    2009-12-01

    Full Text Available Centenary celebrations of Darwin’s birth were held in Valencia and Lorca in 1909. Fifty years later, the meetings and the publications of the Spanish scientific community on the occasion of the centenary of the publication of On the Origin of Species showed a proximity and an acceptance towards the theses of the evolutionary modern synthesis. During the first half of the 20th century, there were controversies in Spain between the Darwinian and anti-Darwinian positions. In addition, non-Darwinian evolutionary theories were spread and supported. Though the assumptions of the synthetic theory of evolution were soon known, commented and discussed, the majority trend in the 40’s and 50’s was to incline towards finalist and vitalist interpretations of evolution.

    En 1909 se celebraron en Valencia y Lorca homenajes a Darwin en el primer centenario del nacimiento. Medio siglo después, los actos y publicaciones de la comunidad científica española con motivo del centenario de la publicación de On the Origin of Species, coincidieron en mostrar una cercanía y aceptación hacia las tesis de la síntesis moderna de la evolución. Durante la primera mitad del siglo XX, en España se desarrollaron controversias entre las posturas darwinistas y antidarwinistas y se difundieron y apoyaron teorías evolucionistas no darwinistas. Aunque pronto se conocieron, comentaron y discutieron los supuestos de la teoría sintética de la evolución, la tendencia mayoritaria en los años cuarenta y cincuenta fue inclinarse por interpretaciones vitalistas y finalistas.

  15. Evolving the Topology of Hidden Markov Models using Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Thomsen, Réne

    2002-01-01

    Hidden Markov models (HMM) are widely used for speech recognition and have recently gained a lot of attention in the bioinformatics community, because of their ability to capture the information buried in biological sequences. Usually, heuristic algorithms such as Baum-Welch are used to estimate...... the model parameters. However, Baum-Welch has a tendency to stagnate on local optima. Furthermore, designing an optimal HMM topology usually requires a priori knowledge from a field expert and is usually found by trial-and-error. In this study, we present an evolutionary algorithm capable of evolving both...... the topology and the model parameters of HMMs. The applicability of the method is exemplified on a secondary structure prediction problem....

  16. Comparison of evolutionary algorithms in gene regulatory network model inference.

    LENUS (Irish Health Repository)

    2010-01-01

    ABSTRACT: BACKGROUND: The evolution of high throughput technologies that measure gene expression levels has created a data base for inferring GRNs (a process also known as reverse engineering of GRNs). However, the nature of these data has made this process very difficult. At the moment, several methods of discovering qualitative causal relationships between genes with high accuracy from microarray data exist, but large scale quantitative analysis on real biological datasets cannot be performed, to date, as existing approaches are not suitable for real microarray data which are noisy and insufficient. RESULTS: This paper performs an analysis of several existing evolutionary algorithms for quantitative gene regulatory network modelling. The aim is to present the techniques used and offer a comprehensive comparison of approaches, under a common framework. Algorithms are applied to both synthetic and real gene expression data from DNA microarrays, and ability to reproduce biological behaviour, scalability and robustness to noise are assessed and compared. CONCLUSIONS: Presented is a comparison framework for assessment of evolutionary algorithms, used to infer gene regulatory networks. Promising methods are identified and a platform for development of appropriate model formalisms is established.

  17. An Evolutionary Game Theory Model of Spontaneous Brain Functioning.

    Science.gov (United States)

    Madeo, Dario; Talarico, Agostino; Pascual-Leone, Alvaro; Mocenni, Chiara; Santarnecchi, Emiliano

    2017-11-22

    Our brain is a complex system of interconnected regions spontaneously organized into distinct networks. The integration of information between and within these networks is a continuous process that can be observed even when the brain is at rest, i.e. not engaged in any particular task. Moreover, such spontaneous dynamics show predictive value over individual cognitive profile and constitute a potential marker in neurological and psychiatric conditions, making its understanding of fundamental importance in modern neuroscience. Here we present a theoretical and mathematical model based on an extension of evolutionary game theory on networks (EGN), able to capture brain's interregional dynamics by balancing emulative and non-emulative attitudes among brain regions. This results in the net behavior of nodes composing resting-state networks identified using functional magnetic resonance imaging (fMRI), determining their moment-to-moment level of activation and inhibition as expressed by positive and negative shifts in BOLD fMRI signal. By spontaneously generating low-frequency oscillatory behaviors, the EGN model is able to mimic functional connectivity dynamics, approximate fMRI time series on the basis of initial subset of available data, as well as simulate the impact of network lesions and provide evidence of compensation mechanisms across networks. Results suggest evolutionary game theory on networks as a new potential framework for the understanding of human brain network dynamics.

  18. Goldfish morphology as a model for evolutionary developmental biology.

    Science.gov (United States)

    Ota, Kinya G; Abe, Gembu

    2016-01-01

    Morphological variation of the goldfish is known to have been established by artificial selection for ornamental purposes during the domestication process. Chinese texts that date to the Song dynasty contain descriptions of goldfish breeding for ornamental purposes, indicating that the practice originated over one thousand years ago. Such a well-documented goldfish breeding process, combined with the phylogenetic and embryological proximities of this species with zebrafish, would appear to make the morphologically diverse goldfish strains suitable models for evolutionary developmental (evodevo) studies. However, few modern evodevo studies of goldfish have been conducted. In this review, we provide an overview of the historical background of goldfish breeding, and the differences between this teleost and zebrafish from an evolutionary perspective. We also summarize recent progress in the field of molecular developmental genetics, with a particular focus on the twin-tail goldfish morphology. Furthermore, we discuss unanswered questions relating to the evolution of the genome, developmental robustness, and morphologies in the goldfish lineage, with the goal of blazing a path toward an evodevo study paradigm using this teleost species as a new model species. For further resources related to this article, please visit the WIREs website. © 2016 The Authors. WIREs Developmental Biology published by Wiley Periodicals, Inc.

  19. Modeling evolutionary games in populations with demographic structure.

    Science.gov (United States)

    Li, Xiang-Yi; Giaimo, Stefano; Baudisch, Annette; Traulsen, Arne

    2015-09-07

    Classic life history models are often based on optimization algorithms, focusing on the adaptation of survival and reproduction to the environment, while neglecting frequency dependent interactions in the population. Evolutionary game theory, on the other hand, studies frequency dependent strategy interactions, but usually omits life history and the demographic structure of the population. Here we show how an integration of both aspects can substantially alter the underlying evolutionary dynamics. We study the replicator dynamics of strategy interactions in life stage structured populations. Individuals have two basic strategic behaviours, interacting in pairwise games. A player may condition behaviour on the life stage of its own, or that of the opponent, or the matching of life stages between both players. A strategy is thus defined as the set of rules that determines a player׳s life stage dependent behaviours. We show that the diversity of life stage structures and life stage dependent strategies can promote each other, and the stable frequency of basic strategic behaviours can deviate from game equilibrium in populations with life stage structures. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Kernel method based human model for enhancing interactive evolutionary optimization.

    Science.gov (United States)

    Pei, Yan; 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.

  1. The evolutionary potential of paramutation: a population-epigenetic model.

    Science.gov (United States)

    Geoghegan, Jemma L; Spencer, Hamish G

    2013-09-01

    Paramutation involves an interaction between homologous alleles resulting in a heritable change in gene expression without altering the DNA sequence. Initially believed to be restricted to plants, paramutation has recently been observed in animal models, and a paramutation-like event has been noted in humans. Despite the accumulating evidence suggesting that trans-acting epigenetic effects can be inherited transgenerationally and therefore generate non-genomic phenotypic variation, these effects have been largely ignored in the context of evolutionary theory. The model presented here incorporates paramutation into the standard model of viability selection at one locus and demonstrates that paramutation can create long-term biological diversity in the absence of genetic change, and even in the absence of the original paramutagenic allele. Therefore, if paramutation is present, attributing evolution to only a traditional genetic model may fail to encompass the broad scope of phenotypic differences observed in nature. Moreover, we show also that an unusual mathematical behaviour, analogous to "Ewens' gap" of the two-locus two-allele symmetric-selection model, occurs: when the rate of one parameter-for example, the rate of paramutation-is increased, a pair of equilibria may disappear only to reappear as this parameter increases further. In summary, by incorporating even the simplest epigenetic parameters into the standard population-genetic model of selection, we show how this type of inheritance system can profoundly alter the course of evolution. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. A Study On Traditional And Evolutionary Software Development Models

    Directory of Open Access Journals (Sweden)

    Kamran Rasheed

    2017-07-01

    Full Text Available Today Computing technologies are becoming the pioneers of the organizations and helpful in individual functionality i.e. added to computing device we need to add softwares. Set of instruction or computer program is known as software. The development of software is done through some traditional or some new or evolutionary models. Software development is becoming a key and a successful business nowadays. Without software all hardware is useless. Some collective steps that are performed in the development of these are known as Software development life cycle SDLC. There are some adaptive and predictive models for developing software. Predictive mean already known like WATERFALL Spiral Prototype and V-shaped models while Adaptive model include agile Scrum. All methodologies of both adaptive and predictive have their own procedure and steps. Predictive are Static and Adaptive are dynamic mean change cannot be made to the predictive while adaptive have the capability of changing. The purpose of this study is to get familiar with all these and discuss their uses and steps of development. This discussion will be helpful in deciding which model they should use in which circumstance and what are the development step including in each model.

  3. Social norms and illicit behavior: an evolutionary model of compliance.

    Science.gov (United States)

    Haab, Timothy C; McConnell, Kenneth E

    2002-09-01

    Economists have viewed the presence of externalities and other market failures as leading to a private equilibrium that would not be Pareto optimal. In the exploitation of common-pool resources, especially biological resources, this would lead to the much-discussed 'tragedy of the commons'. A challenge to this traditional view has emerged from a careful study of the theory and practice of the exploitation of common-pool resources. The existence of a social norm may provide an individual with information on the extent of external costs associated with a behavior, and thus provides an imperfect means of internalizing the external costs. In this paper we propose an evolutionary model of compliance that allows for the existence of a social norm. The impact of the social norm on public policy towards externalities is examined.

  4. How altruism works: An evolutionary model of supply networks

    Science.gov (United States)

    Ge, Zehui; Zhang, Zi-Ke; Lü, Linyuan; Zhou, Tao; Xi, Ning

    2012-02-01

    Recently, supply networks have attracted increasing attention from the scientific community. However, it lacks serious consideration of social preference in Supply Chain Management. In this paper, we develop an evolutionary decision-making model to characterize the effects of suppliers' altruism in supply networks, and find that the performances of both suppliers and supply chains are improved by introducing the role of altruism. Furthermore, an interesting and reasonable phenomenon is discovered that the suppliers' and whole network's profits do not change monotonously with suppliers' altruistic preference, η, but reach the best at η=0.6 and η=0.4, respectively. This work may shed some light on the in-depth understanding of the effects of altruism for both research and commercial applications.

  5. Cultural evolutionary modeling of patterns in language change : exercises in evolutionary linguistics

    NARCIS (Netherlands)

    Landsbergen, Frank

    2009-01-01

    This thesis describes the use of an evolutionary linguistic approach in the study of language change in a series of case studies. The main purpose of this exercise is to get a better insight in the mechanisms that have played a role in the respective cases of change. Human language can be

  6. Basic emotions and adaptation. A computational and evolutionary model.

    Science.gov (United States)

    Pacella, Daniela; Ponticorvo, Michela; Gigliotta, Onofrio; Miglino, Orazio

    2017-01-01

    The core principles of the evolutionary theories of emotions declare that affective states represent crucial drives for action selection in the environment and regulated the behavior and adaptation of natural agents in ancestrally recurrent situations. While many different studies used autonomous artificial agents to simulate emotional responses and the way these patterns can affect decision-making, few are the approaches that tried to analyze the evolutionary emergence of affective behaviors directly from the specific adaptive problems posed by the ancestral environment. A model of the evolution of affective behaviors is presented using simulated artificial agents equipped with neural networks and physically inspired on the architecture of the iCub humanoid robot. We use genetic algorithms to train populations of virtual robots across generations, and investigate the spontaneous emergence of basic emotional behaviors in different experimental conditions. In particular, we focus on studying the emotion of fear, therefore the environment explored by the artificial agents can contain stimuli that are safe or dangerous to pick. The simulated task is based on classical conditioning and the agents are asked to learn a strategy to recognize whether the environment is safe or represents a threat to their lives and select the correct action to perform in absence of any visual cues. The simulated agents have special input units in their neural structure whose activation keep track of their actual "sensations" based on the outcome of past behavior. We train five different neural network architectures and then test the best ranked individuals comparing their performances and analyzing the unit activations in each individual's life cycle. We show that the agents, regardless of the presence of recurrent connections, spontaneously evolved the ability to cope with potentially dangerous environment by collecting information about the environment and then switching their behavior

  7. Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors.

    Directory of Open Access Journals (Sweden)

    Andrea Sottoriva

    2011-05-01

    Full Text Available The cancer stem cell (CSC concept is a highly debated topic in cancer research. While experimental evidence in favor of the cancer stem cell theory is apparently abundant, the results are often criticized as being difficult to interpret. An important reason for this is that most experimental data that support this model rely on transplantation studies. In this study we use a novel cellular Potts model to elucidate the dynamics of established malignancies that are driven by a small subset of CSCs. Our results demonstrate that epigenetic mutations that occur during mitosis display highly altered dynamics in CSC-driven malignancies compared to a classical, non-hierarchical model of growth. In particular, the heterogeneity observed in CSC-driven tumors is considerably higher. We speculate that this feature could be used in combination with epigenetic (methylation sequencing studies of human malignancies to prove or refute the CSC hypothesis in established tumors without the need for transplantation. Moreover our tumor growth simulations indicate that CSC-driven tumors display evolutionary features that can be considered beneficial during tumor progression. Besides an increased heterogeneity they also exhibit properties that allow the escape of clones from local fitness peaks. This leads to more aggressive phenotypes in the long run and makes the neoplasm more adaptable to stringent selective forces such as cancer treatment. Indeed when therapy is applied the clone landscape of the regrown tumor is more aggressive with respect to the primary tumor, whereas the classical model demonstrated similar patterns before and after therapy. Understanding these often counter-intuitive fundamental properties of (non-hierarchically organized malignancies is a crucial step in validating the CSC concept as well as providing insight into the therapeutical consequences of this model.

  8. Gnarled-trunk evolutionary model of influenza A virus hemagglutinin.

    Directory of Open Access Journals (Sweden)

    Kimihito Ito

    Full Text Available Human influenza A viruses undergo antigenic changes with gradual accumulation of amino acid substitutions on the hemagglutinin (HA molecule. A strong antigenic mismatch between vaccine and epidemic strains often requires the replacement of influenza vaccines worldwide. To establish a practical model enabling us to predict the future direction of the influenza virus evolution, relative distances of amino acid sequences among past epidemic strains were analyzed by multidimensional scaling (MDS. We found that human influenza viruses have evolved along a gnarled evolutionary pathway with an approximately constant curvature in the MDS-constructed 3D space. The gnarled pathway indicated that evolution on the trunk favored multiple substitutions at the same amino acid positions on HA. The constant curvature was reasonably explained by assuming that the rate of amino acid substitutions varied from one position to another according to a gamma distribution. Furthermore, we utilized the estimated parameters of the gamma distribution to predict the amino acid substitutions on HA in subsequent years. Retrospective prediction tests for 12 years from 1997 to 2009 showed that 70% of actual amino acid substitutions were correctly predicted, and that 45% of predicted amino acid substitutions have been actually observed. Although it remains unsolved how to predict the exact timing of antigenic changes, the present results suggest that our model may have the potential to recognize emerging epidemic strains.

  9. The Zipf Law revisited: An evolutionary model of emerging classification

    Energy Technology Data Exchange (ETDEWEB)

    Levitin, L.B. [Boston Univ., MA (United States); Schapiro, B. [TINA, Brandenburg (Germany); Perlovsky, L. [NRC, Wakefield, MA (United States)

    1996-12-31

    Zipf`s Law is a remarkable rank-frequency relationship observed in linguistics (the frequencies of the use of words are approximately inversely proportional to their ranks in the decreasing frequency order) as well as in the behavior of many complex systems of surprisingly different nature. We suggest an evolutionary model of emerging classification of objects into classes corresponding to concepts and denoted by words. The evolution of the system is derived from two basic assumptions: first, the probability to recognize an object as belonging to a known class is proportional to the number of objects in this class already recognized, and, second, there exists a small probability to observe an object that requires creation of a new class ({open_quotes}mutation{close_quotes} that gives birth to a new {open_quotes}species{close_quotes}). It is shown that the populations of classes in such a system obey the Zipf Law provided that the rate of emergence of new classes is small. The model leads also to the emergence of a second-tier structure of {open_quotes}super-classes{close_quotes} - groups of classes with almost equal populations.

  10. Marmosets as model species in neuroscience and evolutionary anthropology.

    Science.gov (United States)

    Burkart, Judith M; Finkenwirth, Christa

    2015-04-01

    Marmosets are increasingly used as model species by both neuroscientists and evolutionary anthropologists, but with a different rationale for doing so. Whereas neuroscientists stress that marmosets share many cognitive traits with humans due to common descent, anthropologists stress those traits shared with marmosets - and callitrichid monkeys in general - due to convergent evolution, as a consequence of the cooperative breeding system that characterizes both humans and callitrichids. Similarities in socio-cognitive abilities due to convergence, rather than homology, raise the question whether these similarities also extend to the proximate regulatory mechanisms, which is particularly relevant for neuroscientific investigations. In this review, we first provide an overview of the convergent adaptations to cooperative breeding at the psychological and cognitive level in primates, which bear important implications for our understanding of human cognitive evolution. In the second part, we zoom in on two of these convergent adaptations, proactive prosociality and social learning, and compare their proximate regulation in marmosets and humans with regard to oxytocin and cognitive top down regulation. Our analysis suggests considerable similarity in these regulatory mechanisms presumably because the convergent traits emerged due to small motivational changes that define how pre-existing cognitive mechanisms are quantitatively combined. This finding reconciles the prima facie contradictory rationale for using marmosets as high priority model species in neuroscience and anthropology. Copyright © 2014 Elsevier Ireland Ltd and the Japan Neuroscience Society. All rights reserved.

  11. Use of genome-scale metabolic models in evolutionary systems biology.

    Science.gov (United States)

    Papp, Balázs; Szappanos, Balázs; Notebaart, Richard A

    2011-01-01

    One of the major aims of the nascent field of evolutionary systems biology is to test evolutionary hypotheses that are not only realistic from a population genetic point of view but also detailed in terms of molecular biology mechanisms. By providing a mapping between genotype and phenotype for hundreds of genes, genome-scale systems biology models of metabolic networks have already provided valuable insights into the evolution of metabolic gene contents and phenotypes of yeast and other microbial species. Here we review the recent use of these computational models to predict the fitness effect of mutations, genetic interactions, evolutionary outcomes, and to decipher the mechanisms of mutational robustness. While these studies have demonstrated that even simplified models of biochemical reaction networks can be highly informative for evolutionary analyses, they have also revealed the weakness of this modeling framework to quantitatively predict mutational effects, a challenge that needs to be addressed for future progress in evolutionary systems biology.

  12. Invisible hand effect in an evolutionary minority game model

    Science.gov (United States)

    Sysi-Aho, Marko; Saramäki, Jari; Kaski, Kimmo

    2005-03-01

    In this paper, we study the properties of a minority game with evolution realized by using genetic crossover to modify fixed-length decision-making strategies of agents. Although the agents in this evolutionary game act selfishly by trying to maximize their own performances only, it turns out that the whole society will eventually be rewarded optimally. This “invisible hand” effect is what Adam Smith over two centuries ago expected to take place in the context of free market mechanism. However, this behaviour of the society of agents is realized only under idealized conditions, where all agents are utilizing the same efficient evolutionary mechanism. If on the other hand part of the agents are adaptive, but not evolutionary, the system does not reach optimum performance, which is also the case if part of the evolutionary agents form a uniformly acting “cartel”.

  13. Basic emotions and adaptation. A computational and evolutionary model.

    Directory of Open Access Journals (Sweden)

    Daniela Pacella

    Full Text Available The core principles of the evolutionary theories of emotions declare that affective states represent crucial drives for action selection in the environment and regulated the behavior and adaptation of natural agents in ancestrally recurrent situations. While many different studies used autonomous artificial agents to simulate emotional responses and the way these patterns can affect decision-making, few are the approaches that tried to analyze the evolutionary emergence of affective behaviors directly from the specific adaptive problems posed by the ancestral environment. A model of the evolution of affective behaviors is presented using simulated artificial agents equipped with neural networks and physically inspired on the architecture of the iCub humanoid robot. We use genetic algorithms to train populations of virtual robots across generations, and investigate the spontaneous emergence of basic emotional behaviors in different experimental conditions. In particular, we focus on studying the emotion of fear, therefore the environment explored by the artificial agents can contain stimuli that are safe or dangerous to pick. The simulated task is based on classical conditioning and the agents are asked to learn a strategy to recognize whether the environment is safe or represents a threat to their lives and select the correct action to perform in absence of any visual cues. The simulated agents have special input units in their neural structure whose activation keep track of their actual "sensations" based on the outcome of past behavior. We train five different neural network architectures and then test the best ranked individuals comparing their performances and analyzing the unit activations in each individual's life cycle. We show that the agents, regardless of the presence of recurrent connections, spontaneously evolved the ability to cope with potentially dangerous environment by collecting information about the environment and then

  14. Towards an Evolutionary Model of Animal-Associated Microbiomes

    Directory of Open Access Journals (Sweden)

    Bryan A. White

    2011-02-01

    Full Text Available Second-generation sequencing technologies have granted us greater access to the diversity and genetics of microbial communities that naturally reside endo- and ecto-symbiotically with animal hosts. Substantial research has emerged describing the diversity and broader trends that exist within and between host species and their associated microbial ecosystems, yet the application of these data to our evolutionary understanding of microbiomes appears fragmented. For the most part biological perspectives are based on limited observations of oversimplified communities, while mathematical and/or computational modeling of these concepts often lack biological precedence. In recognition of this disconnect, both fields have attempted to incorporate ecological theories, although their applicability is currently a subject of debate because most ecological theories were developed based on observations of macro-organisms and their ecosystems. For the purposes of this review, we attempt to transcend the biological, ecological and computational realms, drawing on extensive literature, to forge a useful framework that can, at a minimum be built upon, but ideally will shape the hypotheses of each field as they move forward. In evaluating the top-down selection pressures that are exerted on a microbiome we find cause to warrant reconsideration of the much-maligned theory of multi-level selection and reason that complexity must be underscored by modularity.

  15. Economic Modeling Using Evolutionary Algorithms: The Effect of a Binary Encoding of Strategies

    NARCIS (Netherlands)

    L. Waltman (Ludo); N.J.P. van Eck (Nees Jan); R. Dekker (Rommert); U. Kaymak (Uzay)

    2009-01-01

    textabstractWe are concerned with evolutionary algorithms that are employed for economic modeling purposes. We focus in particular on evolutionary algorithms that use a binary encoding of strategies. These algorithms, commonly referred to as genetic algorithms, are popular in agent-based

  16. On parameter synthesis by parallel model checking.

    Science.gov (United States)

    Barnat, Jirí; Brim, Lubos; Krejcí, Adam; Streck, Adam; Safránek, David; Vejnár, Martin; Vejpustek, Tomás

    2012-01-01

    An important problem in current computational systems biology is to analyze models of biological systems dynamics under parameter uncertainty. This paper presents a novel algorithm for parameter synthesis based on parallel model checking. The algorithm is conceptually universal with respect to the modeling approach employed. We introduce the algorithm, show its scalability, and examine its applicability on several biological models.

  17. An Evolutionary Model of the Environmental Conditions that Shape the Development of Prosociality

    Directory of Open Access Journals (Sweden)

    Daniel Tumminelli O'Brien

    2014-04-01

    Full Text Available The current review presents a model for how prosocial development is driven by sociocognitive mechanisms that have been shaped by natural selection to translate critical environmental factors into locally adaptive levels of prosociality. This is done through a synthesis of two existing literatures. Evolutionary developmental psychologists have demonstrated a biological basis for the emergence of prosocial behavior early in youth, and work based on social learning theory has explored how social experiences can influence prosociality across development. The model forwarded organizes this latter literature in a way that is specific to how the biological mechanisms underpinning prosociality have evolved. This consists of two main psychological mechanisms. 1 A domain-specific program that is responsive to environmental factors that determine the relative success of different levels of prosociality. It uses the local prevalence of prosocial others (i.e., support and expectations for prosocial behavior (i.e., structure to guide prosocial development. 2 The domain-general process of cultural learning, by which youth adopt local social norms based on the examples of others. Implications and hypotheses are articulated for both the sociocognitive structure of the individual and the role of social contexts.

  18. Loss of lipid synthesis as an evolutionary consequence of a parasitic lifestyle.

    NARCIS (Netherlands)

    Visser, B.; Le Lann, C.; den Blanken, F.J.; Harvey, J.A.; van Alphen, J.J.M.; Ellers, J.

    2010-01-01

    Evolutionary loss of traits can result from negative selection on a specific phenotype, or if the trait is selectively neutral, because the phenotype associated with the trait has become redundant. Even essential traits may be lost, however, if the resulting phenotypic deficiencies can be

  19. A Philosophical Perspective on Evolutionary Systems Biology.

    Science.gov (United States)

    O'Malley, Maureen A; Soyer, Orkun S; Siegal, Mark L

    2015-03-01

    Evolutionary systems biology (ESB) is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis. We locate these discussions in the context of long-running philosophical deliberations on explanation, modeling, and theoretical synthesis. We show how many of the issues central to ESB's progress can be understood as general philosophical problems. The benefits of addressing these philosophical issues feed back into philosophy too, because ESB provides excellent examples of scientific practice for the development of philosophy of science and philosophy of biology.

  20. Evolutionary models for insertions and deletions in a probabilistic modeling framework

    Directory of Open Access Journals (Sweden)

    Rivas Elena

    2005-03-01

    Full Text Available Abstract Background Probabilistic models for sequence comparison (such as hidden Markov models and pair hidden Markov models for proteins and mRNAs, or their context-free grammar counterparts for structural RNAs often assume a fixed degree of divergence. Ideally we would like these models to be conditional on evolutionary divergence time. Probabilistic models of substitution events are well established, but there has not been a completely satisfactory theoretical framework for modeling insertion and deletion events. Results I have developed a method for extending standard Markov substitution models to include gap characters, and another method for the evolution of state transition probabilities in a probabilistic model. These methods use instantaneous rate matrices in a way that is more general than those used for substitution processes, and are sufficient to provide time-dependent models for standard linear and affine gap penalties, respectively. Given a probabilistic model, we can make all of its emission probabilities (including gap characters and all its transition probabilities conditional on a chosen divergence time. To do this, we only need to know the parameters of the model at one particular divergence time instance, as well as the parameters of the model at the two extremes of zero and infinite divergence. I have implemented these methods in a new generation of the RNA genefinder QRNA (eQRNA. Conclusion These methods can be applied to incorporate evolutionary models of insertions and deletions into any hidden Markov model or stochastic context-free grammar, in a pair or profile form, for sequence modeling.

  1. Evolutionary modelling of the macro-economic impacts of catastrophic flood events

    NARCIS (Netherlands)

    Safarzynska, K.E.; Brouwer, R.; Hofkes, M.

    2013-01-01

    This paper examines the possible contribution of evolutionary economics to macro-economic modelling of flood impacts to provide guidance for future economic risk modelling. Most macro-economic models start from a neoclassical economic perspective and focus on equilibrium outcomes, either in a static

  2. Not just a theory--the utility of mathematical models in evolutionary biology.

    Directory of Open Access Journals (Sweden)

    Maria R Servedio

    2014-12-01

    Full Text Available Progress in science often begins with verbal hypotheses meant to explain why certain biological phenomena exist. An important purpose of mathematical models in evolutionary research, as in many other fields, is to act as “proof-of-concept” tests of the logic in verbal explanations, paralleling the way in which empirical data are used to test hypotheses. Because not all subfields of biology use mathematics for this purpose, misunderstandings of the function of proof-of-concept modeling are common. In the hope of facilitating communication, we discuss the role of proof-of-concept modeling in evolutionary biology.

  3. Not just a theory--the utility of mathematical models in evolutionary biology.

    Science.gov (United States)

    Servedio, Maria R; Brandvain, Yaniv; Dhole, Sumit; Fitzpatrick, Courtney L; Goldberg, Emma E; Stern, Caitlin A; Van Cleve, Jeremy; Yeh, D Justin

    2014-12-01

    Progress in science often begins with verbal hypotheses meant to explain why certain biological phenomena exist. An important purpose of mathematical models in evolutionary research, as in many other fields, is to act as “proof-of-concept” tests of the logic in verbal explanations, paralleling the way in which empirical data are used to test hypotheses. Because not all subfields of biology use mathematics for this purpose, misunderstandings of the function of proof-of-concept modeling are common. In the hope of facilitating communication, we discuss the role of proof-of-concept modeling in evolutionary biology.

  4. model synthetic studies towards palitantin total synthesis

    African Journals Online (AJOL)

    Synthesis of palitantin, 5-(1'E, 3'E-heptadienyl)~cis-2,3-dihydroxy-6-hydroxy- methylcyclohexan-l-oue (1), model ... envisioned a rctrosynthctic approach based on a one-pot Michael-Wittig reactions followed by standard .... the material may have been converted to the polyhydroxylated ester (21). The loss of regioselectivity ...

  5. Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination.

    Science.gov (United States)

    Mostowy, Rafal J; Croucher, Nicholas J; De Maio, Nicola; Chewapreecha, Claire; Salter, Susannah J; Turner, Paul; Aanensen, David M; Bentley, Stephen D; Didelot, Xavier; Fraser, Christophe

    2017-10-01

    Diversity of the polysaccharide capsule in Streptococcus pneumoniae-main surface antigen and the target of the currently used pneumococcal vaccines-constitutes a major obstacle in eliminating pneumococcal disease. Such diversity is genetically encoded by almost 100 variants of the capsule biosynthesis locus, cps. However, the evolutionary dynamics of the capsule remains not fully understood. Here, using genetic data from 4,519 bacterial isolates, we found cps to be an evolutionary hotspot with elevated substitution and recombination rates. These rates were a consequence of relaxed purifying selection and positive, diversifying selection acting at this locus, supporting the hypothesis that the capsule has an increased potential to generate novel diversity compared with the rest of the genome. Diversifying selection was particularly evident in the region of wzd/wze genes, which are known to regulate capsule expression and hence the bacterium's ability to cause disease. Using a novel, capsule-centered approach, we analyzed the evolutionary history of 12 major serogroups. Such analysis revealed their complex diversification scenarios, which were principally driven by recombination with other serogroups and other streptococci. Patterns of recombinational exchanges between serogroups could not be explained by serotype frequency alone, thus pointing to nonrandom associations between co-colonizing serotypes. Finally, we discovered a previously unobserved mosaic serotype 39X, which was confirmed to carry a viable and structurally novel capsule. Adding to previous discoveries of other mosaic capsules in densely sampled collections, these results emphasize the strong adaptive potential of the bacterium by its ability to generate novel antigenic diversity by recombination. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  6. Monogonont rotifers as model systems for the study of micro-evolutionary adaptation and its eco-evolutionary implications

    NARCIS (Netherlands)

    Declerck, S.A.J.; Papakostas, S.

    2017-01-01

    A better understanding of the ability of organisms to adapt to local selection conditions is essential for a better insight in their ecological dynamics. The study of micro-evolutionary adaptation and its eco-evolutionary consequences is challenging for many reasons and the choice of a suitable

  7. Pragmatic quality metrics for evolutionary software development models

    Science.gov (United States)

    Royce, Walker

    1990-01-01

    Due to the large number of product, project, and people parameters which impact large custom software development efforts, measurement of software product quality is a complex undertaking. Furthermore, the absolute perspective from which quality is measured (customer satisfaction) is intangible. While we probably can't say what the absolute quality of a software product is, we can determine the relative quality, the adequacy of this quality with respect to pragmatic considerations, and identify good and bad trends during development. While no two software engineers will ever agree on an optimum definition of software quality, they will agree that the most important perspective of software quality is its ease of change. We can call this flexibility, adaptability, or some other vague term, but the critical characteristic of software is that it is soft. The easier the product is to modify, the easier it is to achieve any other software quality perspective. This paper presents objective quality metrics derived from consistent lifecycle perspectives of rework which, when used in concert with an evolutionary development approach, can provide useful insight to produce better quality per unit cost/schedule or to achieve adequate quality more efficiently. The usefulness of these metrics is evaluated by applying them to a large, real world, Ada project.

  8. The expiry date of man: a synthesis of evolutionary biology and public health.

    Science.gov (United States)

    Bonneux, L; Barendregt, J J; Van der Maas, P J

    1998-10-01

    In industrialised countries, mortality and morbidity are dominated by age related chronic degenerative diseases. The health and health care needs of future populations will be heavily determined by these conditions of old age. Two opposite scenarios of future morbidity exist: morbidity might decrease ("compress"), because life span is limited, and the incidence of disease is postponed. Or morbidity might increase ("expand"), because death is delayed more than disease incidence. Optimality theory in evolutionary biology explains senescence as a by product of an optimised life history. The theory clarifies how senescence is timed by the competing needs for reproduction and survival, and why this leads to a generalised deterioration of many functions at many levels. As death and disease are not independent, future morbidity will depend on duration and severity of the process of senescence, partly determined by health care, palliating the disease severity but increasing the disease duration by postponing death. Even if morbidity might be compressed, health care needs will surely expand.

  9. Computational Modeling of Teaching and Learning through Application of Evolutionary Algorithms

    Directory of Open Access Journals (Sweden)

    Richard Lamb

    2015-09-01

    Full Text Available Within the mind, there are a myriad of ideas that make sense within the bounds of everyday experience, but are not reflective of how the world actually exists; this is particularly true in the domain of science. Classroom learning with teacher explanation are a bridge through which these naive understandings can be brought in line with scientific reality. The purpose of this paper is to examine how the application of a Multiobjective Evolutionary Algorithm (MOEA can work in concert with an existing computational-model to effectively model critical-thinking in the science classroom. An evolutionary algorithm is an algorithm that iteratively optimizes machine learning based computational models. The research question is, does the application of an evolutionary algorithm provide a means to optimize the Student Task and Cognition Model (STAC-M and does the optimized model sufficiently represent and predict teaching and learning outcomes in the science classroom? Within this computational study, the authors outline and simulate the effect of teaching on the ability of a “virtual” student to solve a Piagetian task. Using the Student Task and Cognition Model (STAC-M a computational model of student cognitive processing in science class developed in 2013, the authors complete a computational experiment which examines the role of cognitive retraining on student learning. Comparison of the STAC-M and the STAC-M with inclusion of the Multiobjective Evolutionary Algorithm shows greater success in solving the Piagetian science-tasks post cognitive retraining with the Multiobjective Evolutionary Algorithm. This illustrates the potential uses of cognitive and neuropsychological computational modeling in educational research. The authors also outline the limitations and assumptions of computational modeling.

  10. Genome-wide investigation reveals high evolutionary rates in annual model plants

    Directory of Open Access Journals (Sweden)

    Araki Hitoshi

    2010-11-01

    Full Text Available Abstract Background Rates of molecular evolution vary widely among species. While significant deviations from molecular clock have been found in many taxa, effects of life histories on molecular evolution are not fully understood. In plants, annual/perennial life history traits have long been suspected to influence the evolutionary rates at the molecular level. To date, however, the number of genes investigated on this subject is limited and the conclusions are mixed. To evaluate the possible heterogeneity in evolutionary rates between annual and perennial plants at the genomic level, we investigated 85 nuclear housekeeping genes, 10 non-housekeeping families, and 34 chloroplast genes using the genomic data from model plants including Arabidopsis thaliana and Medicago truncatula for annuals and grape (Vitis vinifera and popular (Populus trichocarpa for perennials. Results According to the cross-comparisons among the four species, 74-82% of the nuclear genes and 71-97% of the chloroplast genes suggested higher rates of molecular evolution in the two annuals than those in the two perennials. The significant heterogeneity in evolutionary rate between annuals and perennials was consistently found both in nonsynonymous sites and synonymous sites. While a linear correlation of evolutionary rates in orthologous genes between species was observed in nonsynonymous sites, the correlation was weak or invisible in synonymous sites. This tendency was clearer in nuclear genes than in chloroplast genes, in which the overall evolutionary rate was small. The slope of the regression line was consistently lower than unity, further confirming the higher evolutionary rate in annuals at the genomic level. Conclusions The higher evolutionary rate in annuals than in perennials appears to be a universal phenomenon both in nuclear and chloroplast genomes in the four dicot model plants we investigated. Therefore, such heterogeneity in evolutionary rate should result from

  11. Genetic Models in Evolutionary Game Theory: The Evolution of Altruism

    NARCIS (Netherlands)

    Rubin, Hannah

    2015-01-01

    While prior models of the evolution of altruism have assumed that organisms reproduce asexually, this paper presents a model of the evolution of altruism for sexually reproducing organisms using Hardy–Weinberg dynamics. In this model, the presence of reciprocal altruists allows the population to

  12. Evolutionary Stability of Minimal Mutation Rates in an Evo-epidemiological Model.

    Science.gov (United States)

    Birch, Michael; Bolker, Benjamin M

    2015-11-01

    We consider the evolution of mutation rate in a seasonally forced, deterministic, compartmental epidemiological model with a transmission-virulence trade-off. We model virulence as a quantitative genetic trait in a haploid population and mutation as continuous diffusion in the trait space. There is a mutation rate threshold above which the pathogen cannot invade a wholly susceptible population. The evolutionarily stable (ESS) mutation rate is the one which drives the lowest average density, over the course of one forcing period, of susceptible individuals at steady state. In contrast with earlier eco-evolutionary models in which higher mutation rates allow for better evolutionary tracking of a dynamic environment, numerical calculations suggest that in our model the minimum average susceptible population, and hence the ESS, is achieved by a pathogen strain with zero mutation. We discuss how this result arises within our model and how the model might be modified to obtain a nonzero optimum.

  13. An evolutionary model of energy transitions with interactive innovation-selection dynamics

    NARCIS (Netherlands)

    Safarzynska, K.E.; van den Bergh, J.C.J.M.

    2013-01-01

    We develop a stylized application of a new evolutionary model to study an energy transition in electricity production. The framework describes a population of boundedly rational electricity producers who decide each period on the allocation of profits among different energy technologies. They tend

  14. Gene duplication and an accelerated evolutionary rate in 11S globulin genes are associated with higher protein synthesis in dicots as compared to monocots

    Directory of Open Access Journals (Sweden)

    Li Chun

    2012-01-01

    Full Text Available Abstract Background Seed storage proteins are a major source of dietary protein, and the content of such proteins determines both the quantity and quality of crop yield. Significantly, examination of the protein content in the seeds of crop plants shows a distinct difference between monocots and dicots. Thus, it is expected that there are different evolutionary patterns in the genes underlying protein synthesis in the seeds of these two groups of plants. Results Gene duplication, evolutionary rate and positive selection of a major gene family of seed storage proteins (the 11S globulin genes, were compared in dicots and monocots. The results, obtained from five species in each group, show more gene duplications, a higher evolutionary rate and positive selections of this gene family in dicots, which are rich in 11S globulins, but not in the monocots. Conclusion Our findings provide evidence to support the suggestion that gene duplication and an accelerated evolutionary rate may be associated with higher protein synthesis in dicots as compared to monocots.

  15. Evaluation of models generated via hybrid evolutionary algorithms ...

    African Journals Online (AJOL)

    This model showed a square correlation coefficient (R2) of 0.90 when tested with the testing dataset (chosen by bootstrapping from the 2000–2009 input dataset) and a R2 of 0.53 when tested with the 3-year 'unseen' dataset from 2010–2012. Keywords: cyanobacteria, drinking water treatment works, prediction models, ...

  16. Models for cognition and emotion: Evolutionary and linguistic considerations.

    Science.gov (United States)

    Montemayor, Carlos

    2015-01-01

    A central claim in Luiz Pessoa's (2013) book is that the terms "emotion" and "cognition" can be useful in characterizing behaviors but will not be cleanly mapped into brain regions. In order to be verified, this claim requires models for the integration and interfacing of emotion and cognition; yet, such models remain problematic.

  17. Evolutionary ecology in silico: Does mathematical modelling help in ...

    Indian Academy of Sciences (India)

    Moreover, because of the availability of sufficiently fast computers, it has become possible to carry out detailed computer simulations of these models. For the sake of completeness and to put these recent developments in perspective, we begin with a brief summary of some older models of ecological phenomena and ...

  18. Seeding Evolutionary Thinking by Engaging Children in Modeling Its Foundations

    Science.gov (United States)

    Lehrer, Richard; Schauble, Leona

    2012-01-01

    Although the core work of science is oriented toward constructing, revising, applying, and defending models of the natural world, models appear only rarely in school science, and usually only as illustrations, rather than theory building tools. We describe the rationale and structure for a learning progression to understand the development of…

  19. Molecular genetic and molecular evolutionary studies on the bacteriochlorophyll synthesis genes of Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Burke-Agueero, Donald H. [Univ. of California, Berkeley, CA (United States)

    1992-08-01

    Rhodobacter capsulatus, purple bacterium capable of either aerobic or photosynthetic growth, has proven to be very useful in genetic studies of photosynthesis. Forty-four genes clustered together within a 46 kilobase region are required to establish photosynthetic ability in R. capsulatus. Approximately twenty of these genes are involved in bacteriochlorophyll synthesis of which eight ``bch`` genes are the subject of this thesis. Six of these genes were found to code for the two ring reductases. The first converts protochlorophyllide (PChlide) into a chlorin, the immediate precursor to chlorophyll a, and then into a bacteriochlorin. Each reductase is shown to be made up of three subunits. PChlide reductase is coded by the genes bchN, bchB, and bchL. Proteins with amino acid sequences markedly similar to those of bchN and bchL have been shown in other organisms to be required for chlorophyll synthesis; hence, their designation as chlN and chlB. A third chloroplast-encoded gene of heretofore unknown function shares amino acid identities with bchB and is probably the third subunit of the plant PChlide reductase. The bchA locus, which encodes the chlorin reductase, is found to be made up of three separate, translationally coupled genes, referred to as bchX, bchY, and bchZ. Amino acid similarities between bchX, bchL, and the nitrogenase reductase protein nifH suggest that all three classes of proteins share certain three-dimensional structural features, including elements that are central to the enzymatic mechanism of nifH. PChlide reductase and chlorin reductase are clearly derived from a common ancestor. Several lines of analysis suggests the ancestor of both enzyme systems reduced PChlide twice to produce bacteriochlorophyll supporting the concept bacteriochlorophyll as the ancestral reaction center pigment.

  20. Molecular genetic and molecular evolutionary studies on the bacteriochlorophyll synthesis genes of Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Burke-Agueero, D.H.

    1992-08-01

    Rhodobacter capsulatus, purple bacterium capable of either aerobic or photosynthetic growth, has proven to be very useful in genetic studies of photosynthesis. Forty-four genes clustered together within a 46 kilobase region are required to establish photosynthetic ability in R. capsulatus. Approximately twenty of these genes are involved in bacteriochlorophyll synthesis of which eight bch'' genes are the subject of this thesis. Six of these genes were found to code for the two ring reductases. The first converts protochlorophyllide (PChlide) into a chlorin, the immediate precursor to chlorophyll a, and then into a bacteriochlorin. Each reductase is shown to be made up of three subunits. PChlide reductase is coded by the genes bchN, bchB, and bchL. Proteins with amino acid sequences markedly similar to those of bchN and bchL have been shown in other organisms to be required for chlorophyll synthesis; hence, their designation as chlN and chlB. A third chloroplast-encoded gene of heretofore unknown function shares amino acid identities with bchB and is probably the third subunit of the plant PChlide reductase. The bchA locus, which encodes the chlorin reductase, is found to be made up of three separate, translationally coupled genes, referred to as bchX, bchY, and bchZ. Amino acid similarities between bchX, bchL, and the nitrogenase reductase protein nifH suggest that all three classes of proteins share certain three-dimensional structural features, including elements that are central to the enzymatic mechanism of nifH. PChlide reductase and chlorin reductase are clearly derived from a common ancestor. Several lines of analysis suggests the ancestor of both enzyme systems reduced PChlide twice to produce bacteriochlorophyll supporting the concept bacteriochlorophyll as the ancestral reaction center pigment.

  1. A dynamic eco-evolutionary model predicts slow response of alpine plants to climate warming.

    Science.gov (United States)

    Cotto, Olivier; Wessely, Johannes; Georges, Damien; Klonner, Günther; Schmid, Max; Dullinger, Stefan; Thuiller, Wilfried; Guillaume, Frédéric

    2017-05-05

    Withstanding extinction while facing rapid climate change depends on a species' ability to track its ecological niche or to evolve a new one. Current methods that predict climate-driven species' range shifts use ecological modelling without eco-evolutionary dynamics. Here we present an eco-evolutionary forecasting framework that combines niche modelling with individual-based demographic and genetic simulations. Applying our approach to four endemic perennial plant species of the Austrian Alps, we show that accounting for eco-evolutionary dynamics when predicting species' responses to climate change is crucial. Perennial species persist in unsuitable habitats longer than predicted by niche modelling, causing delayed range losses; however, their evolutionary responses are constrained because long-lived adults produce increasingly maladapted offspring. Decreasing population size due to maladaptation occurs faster than the contraction of the species range, especially for the most abundant species. Monitoring of species' local abundance rather than their range may likely better inform on species' extinction risks under climate change.

  2. Bipartite Graphs as Models of Population Structures in Evolutionary Multiplayer Games

    Science.gov (United States)

    Peña, Jorge; Rochat, Yannick

    2012-01-01

    By combining evolutionary game theory and graph theory, “games on graphs” study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner’s dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner’s dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures. PMID:22970237

  3. Bipartite graphs as models of population structures in evolutionary multiplayer games.

    Science.gov (United States)

    Peña, Jorge; Rochat, Yannick

    2012-01-01

    By combining evolutionary game theory and graph theory, "games on graphs" study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner's dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner's dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures.

  4. Bipartite graphs as models of population structures in evolutionary multiplayer games.

    Directory of Open Access Journals (Sweden)

    Jorge Peña

    Full Text Available By combining evolutionary game theory and graph theory, "games on graphs" study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner's dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner's dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures.

  5. A model for the evolutionary diversification of religions

    OpenAIRE

    Doebeli, Michael; Ispolatov, Iaroslav

    2008-01-01

    We address the problem of diversification in religions by studying selection on cultural memes that colonize humans hosts. In analogy to studying the evolution of pathogens or symbionts colonizing animal hosts, we use models for host-pathogen dynamics known from theoretical epidemiology. In these models, religious memes colonize individual humans. Rates of transmission of memes between humans, i.e., transmission of cultural content, and rates of loss of memes (loss of faith) are determined by...

  6. Evolutionary Schema of Modeling Based on Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Stacewicz Paweł

    2015-03-01

    Full Text Available In this paper, I propose a populational schema of modeling that consists of: (a a linear AFSV schema (with four basic stages of abstraction, formalization, simplification, and verification, and (b a higher-level schema employing the genetic algorithm (with partially random procedures of mutation, crossover, and selection. The basic ideas of the proposed solution are as follows: (1 whole populations of models are considered at subsequent stages of the modeling process, (2 successive populations are subjected to the activity of genetic operators and undergo selection procedures, (3 the basis for selection is the evaluation function of the genetic algorithm (this function corresponds to the model verification criterion and reflects the goal of the model. The schema can be applied to automate the modeling of the mind/brain by means of artificial neural networks: the structure of each network is modified by genetic operators, modified networks undergo a learning cycle, and successive populations of networks are verified during the selection procedure. The whole process can be automated only partially, because it is the researcher who defines the evaluation function of the genetic algorithm.

  7. Hypermedia Genes An Evolutionary Perspective on Concepts, Models, and Architectures

    CERN Document Server

    Guimarães, Nuno

    2009-01-01

    The design space of information services evolved from seminal works through a set of prototypical hypermedia systems and matured in open and widely accessible web-based systems. The original concepts of hypermedia systems are now expressed in different forms and shapes. The first works on hypertext invented the term itself, laid out the foundational concept of association or link, and highlighted navigation as the core paradigm for the future information systems. The first engineered systems demonstrated architectural requirements and models and fostered the emergence of the conceptual model r

  8. A Self-adaptive Dynamic Evaluation Model for Diabetes Mellitus, Based on Evolutionary Strategies

    Directory of Open Access Journals (Sweden)

    An-Jiang Lu

    2016-03-01

    Full Text Available In order to evaluate diabetes mellitus objectively and accurately, this paper builds a self-adaptive dynamic evaluation model for diabetes mellitus, based on evolutionary strategies. First of all, on the basis of a formalized description of the evolutionary process of diabetes syndromes, using a state transition function, it judges whether a disease is evolutionary, through an excitation parameter. It then, provides evidence for the rebuilding of the evaluation index system. After that, by abstracting and rebuilding the composition of evaluation indexes, it makes use of a heuristic algorithm to determine the composition of the evolved evaluation index set of diabetes mellitus, It then, calculates the weight of each index in the evolved evaluation index set of diabetes mellitus by building a dependency matrix and realizes the self-adaptive dynamic evaluation of diabetes mellitus under an evolutionary environment. Using this evaluation model, it is possible to, quantify all kinds of diagnoses and treatment experiences of diabetes and finally to adopt ideal diagnoses and treatment measures for different patients with diabetics.

  9. A test of genetic models for the evolutionary maintenance of same-sex sexual behaviour.

    Science.gov (United States)

    Hoskins, Jessica L; Ritchie, Michael G; Bailey, Nathan W

    2015-06-22

    The evolutionary maintenance of same-sex sexual behaviour (SSB) has received increasing attention because it is perceived to be an evolutionary paradox. The genetic basis of SSB is almost wholly unknown in non-human animals, though this is key to understanding its persistence. Recent theoretical work has yielded broadly applicable predictions centred on two genetic models for SSB: overdominance and sexual antagonism. Using Drosophila melanogaster, we assayed natural genetic variation for male SSB and empirically tested predictions about the mode of inheritance and fitness consequences of alleles influencing its expression. We screened 50 inbred lines derived from a wild population for male-male courtship and copulation behaviour, and examined crosses between the lines for evidence of overdominance and antagonistic fecundity selection. Consistent variation among lines revealed heritable genetic variation for SSB, but the nature of the genetic variation was complex. Phenotypic and fitness variation was consistent with expectations under overdominance, although predictions of the sexual antagonism model were also supported. We found an unexpected and strong paternal effect on the expression of SSB, suggesting possible Y-linkage of the trait. Our results inform evolutionary genetic mechanisms that might maintain low but persistently observed levels of male SSB in D. melanogaster, but highlight a need for broader taxonomic representation in studies of its evolutionary causes. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  10. 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.

  11. Evolutionary ecology in silico: Does mathematical modelling help in ...

    Indian Academy of Sciences (India)

    Unknown

    2004-05-02

    295. Drossel B and McKane A J 2003 Modelling food webs; in. Handbook of graphs and networks – From the genome to the internet (eds) S Bornholdt and H G Schuster (Weinheim: Wiley-VCH) p. 218. Drossel B, Higgs P G and ...

  12. An Agent-Based Model to study the epidemiological and evolutionary dynamics of Influenza viruses

    OpenAIRE

    Drake John M; Roche Benjamin; Rohani Pejman

    2011-01-01

    Abstract Background Influenza A viruses exhibit complex epidemiological patterns in a number of mammalian and avian hosts. Understanding transmission of these viruses necessitates taking into account their evolution, which represents a challenge for developing mathematical models. This is because the phrasing of multi-strain systems in terms of traditional compartmental ODE models either requires simplifying assumptions to be made that overlook important evolutionary processes, or leads to co...

  13. An evolutionary cascade model for sauropod dinosaur gigantism--overview, update and tests.

    Science.gov (United States)

    Sander, P Martin

    2013-01-01

    Sauropod dinosaurs are a group of herbivorous dinosaurs which exceeded all other terrestrial vertebrates in mean and maximal body size. Sauropod dinosaurs were also the most successful and long-lived herbivorous tetrapod clade, but no abiological factors such as global environmental parameters conducive to their gigantism can be identified. These facts justify major efforts by evolutionary biologists and paleontologists to understand sauropods as living animals and to explain their evolutionary success and uniquely gigantic body size. Contributions to this research program have come from many fields and can be synthesized into a biological evolutionary cascade model of sauropod dinosaur gigantism (sauropod gigantism ECM). This review focuses on the sauropod gigantism ECM, providing an updated version based on the contributions to the PLoS ONE sauropod gigantism collection and on other very recent published evidence. The model consist of five separate evolutionary cascades ("Reproduction", "Feeding", "Head and neck", "Avian-style lung", and "Metabolism"). Each cascade starts with observed or inferred basal traits that either may be plesiomorphic or derived at the level of Sauropoda. Each trait confers hypothetical selective advantages which permit the evolution of the next trait. Feedback loops in the ECM consist of selective advantages originating from traits higher in the cascades but affecting lower traits. All cascades end in the trait "Very high body mass". Each cascade is linked to at least one other cascade. Important plesiomorphic traits of sauropod dinosaurs that entered the model were ovipary as well as no mastication of food. Important evolutionary innovations (derived traits) were an avian-style respiratory system and an elevated basal metabolic rate. Comparison with other tetrapod lineages identifies factors limiting body size.

  14. An Evolutionary Cascade Model for Sauropod Dinosaur Gigantism - Overview, Update and Tests

    Science.gov (United States)

    Sander, P. Martin

    2013-01-01

    Sauropod dinosaurs are a group of herbivorous dinosaurs which exceeded all other terrestrial vertebrates in mean and maximal body size. Sauropod dinosaurs were also the most successful and long-lived herbivorous tetrapod clade, but no abiological factors such as global environmental parameters conducive to their gigantism can be identified. These facts justify major efforts by evolutionary biologists and paleontologists to understand sauropods as living animals and to explain their evolutionary success and uniquely gigantic body size. Contributions to this research program have come from many fields and can be synthesized into a biological evolutionary cascade model of sauropod dinosaur gigantism (sauropod gigantism ECM). This review focuses on the sauropod gigantism ECM, providing an updated version based on the contributions to the PLoS ONE sauropod gigantism collection and on other very recent published evidence. The model consist of five separate evolutionary cascades (“Reproduction”, “Feeding”, “Head and neck”, “Avian-style lung”, and “Metabolism”). Each cascade starts with observed or inferred basal traits that either may be plesiomorphic or derived at the level of Sauropoda. Each trait confers hypothetical selective advantages which permit the evolution of the next trait. Feedback loops in the ECM consist of selective advantages originating from traits higher in the cascades but affecting lower traits. All cascades end in the trait “Very high body mass”. Each cascade is linked to at least one other cascade. Important plesiomorphic traits of sauropod dinosaurs that entered the model were ovipary as well as no mastication of food. Important evolutionary innovations (derived traits) were an avian-style respiratory system and an elevated basal metabolic rate. Comparison with other tetrapod lineages identifies factors limiting body size. PMID:24205267

  15. An evolutionary cascade model for sauropod dinosaur gigantism--overview, update and tests.

    Directory of Open Access Journals (Sweden)

    P Martin Sander

    Full Text Available Sauropod dinosaurs are a group of herbivorous dinosaurs which exceeded all other terrestrial vertebrates in mean and maximal body size. Sauropod dinosaurs were also the most successful and long-lived herbivorous tetrapod clade, but no abiological factors such as global environmental parameters conducive to their gigantism can be identified. These facts justify major efforts by evolutionary biologists and paleontologists to understand sauropods as living animals and to explain their evolutionary success and uniquely gigantic body size. Contributions to this research program have come from many fields and can be synthesized into a biological evolutionary cascade model of sauropod dinosaur gigantism (sauropod gigantism ECM. This review focuses on the sauropod gigantism ECM, providing an updated version based on the contributions to the PLoS ONE sauropod gigantism collection and on other very recent published evidence. The model consist of five separate evolutionary cascades ("Reproduction", "Feeding", "Head and neck", "Avian-style lung", and "Metabolism". Each cascade starts with observed or inferred basal traits that either may be plesiomorphic or derived at the level of Sauropoda. Each trait confers hypothetical selective advantages which permit the evolution of the next trait. Feedback loops in the ECM consist of selective advantages originating from traits higher in the cascades but affecting lower traits. All cascades end in the trait "Very high body mass". Each cascade is linked to at least one other cascade. Important plesiomorphic traits of sauropod dinosaurs that entered the model were ovipary as well as no mastication of food. Important evolutionary innovations (derived traits were an avian-style respiratory system and an elevated basal metabolic rate. Comparison with other tetrapod lineages identifies factors limiting body size.

  16. Women's sexual working models: an evolutionary-attachment perspective.

    Science.gov (United States)

    Birnbaum, Gurit E; Reis, Harry T

    2006-11-01

    In three studies, we developed and validated a self-report measure of women's sexual working models. In a pilot study we created an initial version of the Women's Sexual Working Models Scale (WSWMS), administered it to an exploratory sample of 470 women, and identified its 5-factor structure. Study 1 confirmed the 5-factor structure in a new sample: (1) Fostering commitment; (2) Evaluating a sexual partner's suitability; (3) Promoting frequent sexual activity through positive affect; (4) Restricting sexuality through shamefulness; and (5) Negative emotions that signal incompatibility with relationship goals. In Study 2, 444 Israeli women completed the WSWMS. Confirmatory factor analysis provided cross-national evidence for the generalizability of the underlying factor structure of the WSWMS.

  17. Evolutionary Sequential Monte Carlo Samplers for Change-Point Models

    Directory of Open Access Journals (Sweden)

    Arnaud Dufays

    2016-03-01

    Full Text Available Sequential Monte Carlo (SMC methods are widely used for non-linear filtering purposes. However, the SMC scope encompasses wider applications such as estimating static model parameters so much that it is becoming a serious alternative to Markov-Chain Monte-Carlo (MCMC methods. Not only do SMC algorithms draw posterior distributions of static or dynamic parameters but additionally they provide an estimate of the marginal likelihood. The tempered and time (TNT algorithm, developed in this paper, combines (off-line tempered SMC inference with on-line SMC inference for drawing realizations from many sequential posterior distributions without experiencing a particle degeneracy problem. Furthermore, it introduces a new MCMC rejuvenation step that is generic, automated and well-suited for multi-modal distributions. As this update relies on the wide heuristic optimization literature, numerous extensions are readily available. The algorithm is notably appropriate for estimating change-point models. As an example, we compare several change-point GARCH models through their marginal log-likelihoods over time.

  18. Structural Equation Modeling: Applications in ecological and evolutionary biology research

    Science.gov (United States)

    Pugesek, Bruce H.; von Eye, Alexander; Tomer, Adrian

    2003-01-01

    This book presents an introduction to the methodology of structural equation modeling, illustrates its use, and goes on to argue that it has revolutionary implications for the study of natural systems. A major theme of this book is that we have, up to this point, attempted to study systems primarily using methods (such as the univariate model) that were designed only for considering individual processes. Understanding systems requires the capacity to examine simultaneous influences and responses. Structural equation modeling (SEM) has such capabilities. It also possesses many other traits that add strength to its utility as a means of making scientific progress. In light of the capabilities of SEM, it can be argued that much of ecological theory is currently locked in an immature state that impairs its relevance. It is further argued that the principles of SEM are capable of leading to the development and evaluation of multivariate theories of the sort vitally needed for the conservation of natural systems. Supplementary information can be found at the authors website, http://www.jamesbgrace.com/. • Details why multivariate analyses should be used to study ecological systems • Exposes unappreciated weakness in many current popular analyses • Emphasizes the future methodological developments needed to advance our understanding of ecological systems.

  19. Marine invertebrates, model organisms, and the modern synthesis: epistemic values, evo-devo, and exclusion.

    Science.gov (United States)

    Love, Alan C

    2009-03-01

    A central reason that undergirds the significance of evo-devo is the claim that development was left out of the Modern synthesis. This claim turns out to be quite complicated, both in terms of whether development was genuinely excluded and how to understand the different kinds of embryological research that might have contributed. The present paper reevaluates this central claim by focusing on the practice of model organism choice. Through a survey of examples utilized in the literature of the Modern synthesis, I identify a previously overlooked feature: exclusion of research on marine invertebrates. Understanding the import of this pattern requires interpreting it in terms of two epistemic values operating in biological research: theoretical generality and explanatory completeness. In tandem, these values clarify and enhance the significance of this exclusion. The absence of marine invertebrates implied both a lack of generality in the resulting theory and a lack of completeness with respect to particular evolutionary problems, such as evolvability and the origin of novelty. These problems were salient to embryological researchers aware of the variation and diversity of larval forms in marine invertebrates. In closing, I apply this analysis to model organism choice in evo-devo and discuss its relevance for an extended evolutionary synthesis.

  20. USING ECO-EVOLUTIONARY INDIVIDUAL-BASED MODELS TO INVESTIGATE SPATIALLY-DEPENDENT PROCESSES IN CONSERVATION GENETICS

    Science.gov (United States)

    Eco-evolutionary population simulation models are powerful new forecasting tools for exploring management strategies for climate change and other dynamic disturbance regimes. Additionally, eco-evo individual-based models (IBMs) are useful for investigating theoretical feedbacks ...

  1. EvoBuild: A Quickstart Toolkit for Programming Agent-Based Models of Evolutionary Processes

    Science.gov (United States)

    Wagh, Aditi; Wilensky, Uri

    2017-10-01

    Extensive research has shown that one of the benefits of programming to learn about scientific phenomena is that it facilitates learning about mechanisms underlying the phenomenon. However, using programming activities in classrooms is associated with costs such as requiring additional time to learn to program or students needing prior experience with programming. This paper presents a class of programming environments that we call quickstart: Environments with a negligible threshold for entry into programming and a modest ceiling. We posit that such environments can provide benefits of programming for learning without incurring associated costs for novice programmers. To make this claim, we present a design-based research study conducted to compare programming models of evolutionary processes with a quickstart toolkit with exploring pre-built models of the same processes. The study was conducted in six seventh grade science classes in two schools. Students in the programming condition used EvoBuild, a quickstart toolkit for programming agent-based models of evolutionary processes, to build their NetLogo models. Students in the exploration condition used pre-built NetLogo models. We demonstrate that although students came from a range of academic backgrounds without prior programming experience, and all students spent the same number of class periods on the activities including the time students took to learn programming in this environment, EvoBuild students showed greater learning about evolutionary mechanisms. We discuss the implications of this work for design research on programming environments in K-12 science education.

  2. The Tangled Nature Model of evolutionary dynamics reconsidered

    DEFF Research Database (Denmark)

    Andersen, Christian Walther; Sibani, Paolo

    2016-01-01

    The Tangled Nature Model of biological and cultural evolution features interacting agents which compete for limited resources and reproduce in an error prone fashion and at a rate depending on the `tangle' of interactions they maintain with others. The set of interactions linking a TNM individual...... all the interactions, while increasing $K$ up to the length of the genome ensures an increasing level of trait inheritance. We show that the distribution of the interactions generated by our rule is nearly independent of the value of $K$. Changing $K$ strengthens the core structure of the ecology......, leads to population abundance distributions which are better approximated by log-normal probability densities and increases the probability that a species extant at time $t_{\\rm w}$ is also extant at a later time $t$. In particular, survival probabilities are shown to decay as powers of the ratio $t...

  3. Noise-Optimized Speciation in a Simple Evolutionary Model

    Science.gov (United States)

    Dees, Nathan; Bahar, Sonya

    2009-03-01

    A simple computational model for Darwinian evolution is constructed based on three minimal requirements: inheritance, variability, and overpopulation. The fitness of organisms is based on their position in a two-dimensional fitness landscape which is changed periodically either by random fluctuations, or via a feedback mechanism based on the number of organisms in close proximity. The clustering of organisms in a morphospace overlaid on this landscape is considered an analog of speciation and is investigated as a function of the degree of variability, or ``noise'', allowed in the morphology of new (children) organisms with respect to their parents. We find that a maximum number of species are formed at an intermediate value of this noise parameter, suggesting a stochastic resonance-like effect. We also address the spread of inherited traits through the overall population, finding an ``all or none'' effect in which the properties of a traced organism either die out completely or percolate through the entire population, leading to what might be considered as ``homologous'' traits even in species widely separated in morphospace.

  4. THE APPLICATION OF AN EVOLUTIONARY ALGORITHM TO THE OPTIMIZATION OF A MESOSCALE METEOROLOGICAL MODEL

    Energy Technology Data Exchange (ETDEWEB)

    Werth, D.; O' Steen, L.

    2008-02-11

    We show that a simple evolutionary algorithm can optimize a set of mesoscale atmospheric model parameters with respect to agreement between the mesoscale simulation and a limited set of synthetic observations. This is illustrated using the Regional Atmospheric Modeling System (RAMS). A set of 23 RAMS parameters is optimized by minimizing a cost function based on the root mean square (rms) error between the RAMS simulation and synthetic data (observations derived from a separate RAMS simulation). We find that the optimization can be efficient with relatively modest computer resources, thus operational implementation is possible. The optimization efficiency, however, is found to depend strongly on the procedure used to perturb the 'child' parameters relative to their 'parents' within the evolutionary algorithm. In addition, the meteorological variables included in the rms error and their weighting are found to be an important factor with respect to finding the global optimum.

  5. Evolutionary demography of iteroparous plants: incorporating non-lethal costs of reproduction into integral projection models

    OpenAIRE

    Miller, Tom E. X.; Williams, Jennifer L.; Jongejans, Eelke; Brys, Rein; Jacquemyn, Hans

    2012-01-01

    Understanding the selective forces that shape reproductive strategies is a central goal of evolutionary ecology. Selection on the timing of reproduction is well studied in semelparous organisms because the cost of reproduction (death) can be easily incorporated into demographic models. Iteroparous organisms also exhibit delayed reproduction and experience reproductive costs, although these are not necessarily lethal. How non-lethal costs shape iteroparous life histories remains unresolved. We...

  6. Application of evolutionary algorithm-based symbolic regression to language assessment: Toward nonlinear modeling

    OpenAIRE

    Vahid Aryadoust

    2015-01-01

    This study applies evolutionary algorithm-based (EA-based) symbolic regression to assess the ability of metacognitive strategy use tested by the metacognitive awareness listening questionnaire (MALQ) and lexico-grammatical knowledge to predict listening comprehension proficiency among English learners. Initially, the psychometric validity of the MALQ subscales, the lexico-grammatical test, and the listening test was examined using the logistic Rasch model and the Rasch-Andrich rating scale mo...

  7. Linear and evolutionary polynomial regression models to forecast coastal dynamics: Comparison and reliability assessment

    Science.gov (United States)

    Bruno, Delia Evelina; Barca, Emanuele; Goncalves, Rodrigo Mikosz; de Araujo Queiroz, Heithor Alexandre; Berardi, Luigi; Passarella, Giuseppe

    2018-01-01

    In this paper, the Evolutionary Polynomial Regression data modelling strategy has been applied to study small scale, short-term coastal morphodynamics, given its capability for treating a wide database of known information, non-linearly. Simple linear and multilinear regression models were also applied to achieve a balance between the computational load and reliability of estimations of the three models. In fact, even though it is easy to imagine that the more complex the model, the more the prediction improves, sometimes a "slight" worsening of estimations can be accepted in exchange for the time saved in data organization and computational load. The models' outcomes were validated through a detailed statistical, error analysis, which revealed a slightly better estimation of the polynomial model with respect to the multilinear model, as expected. On the other hand, even though the data organization was identical for the two models, the multilinear one required a simpler simulation setting and a faster run time. Finally, the most reliable evolutionary polynomial regression model was used in order to make some conjecture about the uncertainty increase with the extension of extrapolation time of the estimation. The overlapping rate between the confidence band of the mean of the known coast position and the prediction band of the estimated position can be a good index of the weakness in producing reliable estimations when the extrapolation time increases too much. The proposed models and tests have been applied to a coastal sector located nearby Torre Colimena in the Apulia region, south Italy.

  8. Evolutionary Information Theory

    Directory of Open Access Journals (Sweden)

    Mark Burgin

    2013-04-01

    Full Text Available Evolutionary information theory is a constructive approach that studies information in the context of evolutionary processes, which are ubiquitous in nature and society. In this paper, we develop foundations of evolutionary information theory, building several measures of evolutionary information and obtaining their properties. These measures are based on mathematical models of evolutionary computations, machines and automata. To measure evolutionary information in an invariant form, we construct and study universal evolutionary machines and automata, which form the base for evolutionary information theory. The first class of measures introduced and studied in this paper is evolutionary information size of symbolic objects relative to classes of automata or machines. In particular, it is proved that there is an invariant and optimal evolutionary information size relative to different classes of evolutionary machines. As a rule, different classes of algorithms or automata determine different information size for the same object. The more powerful classes of algorithms or automata decrease the information size of an object in comparison with the information size of an object relative to weaker4 classes of algorithms or machines. The second class of measures for evolutionary information in symbolic objects is studied by introduction of the quantity of evolutionary information about symbolic objects relative to a class of automata or machines. To give an example of applications, we briefly describe a possibility of modeling physical evolution with evolutionary machines to demonstrate applicability of evolutionary information theory to all material processes. At the end of the paper, directions for future research are suggested.

  9. Numerical Simulation of Entropy Growth for a Nonlinear Evolutionary Model of Random Markets

    Directory of Open Access Journals (Sweden)

    Mahdi Keshtkar

    2016-01-01

    Full Text Available In this communication, the generalized continuous economic model for random markets is revisited. In this model for random markets, agents trade by pairs and exchange their money in a random and conservative way. They display the exponential wealth distribution as asymptotic equilibrium, independently of the effectiveness of the transactions and of the limitation of the total wealth. In the current work, entropy of mentioned model is defined and then some theorems on entropy growth of this evolutionary problem are given. Furthermore, the entropy increasing by simulation on some numerical examples is verified.

  10. Comprehensive Weighted Clique Degree Ranking Algorithms and Evolutionary Model of Complex Network

    Directory of Open Access Journals (Sweden)

    Xu Jie

    2016-01-01

    Full Text Available This paper analyses the degree ranking (DR algorithm, and proposes a new comprehensive weighted clique degree ranking (CWCDR algorithms for ranking importance of nodes in complex network. Simulation results show that CWCDR algorithms not only can overcome the limitation of degree ranking algorithm, but also can find important nodes in complex networks more precisely and effectively. To the shortage of small-world model and BA model, this paper proposes an evolutionary model of complex network based on CWCDR algorithms, named CWCDR model. Simulation results show that the CWCDR model accords with power-law distribution. And compare with the BA model, this model has better average shortest path length, and clustering coefficient. Therefore, the CWCDR model is more consistent with the real network.

  11. The evolutionary implications of epigenetic inheritance.

    Science.gov (United States)

    Jablonka, Eva

    2017-10-06

    The Modern Evolutionary Synthesis (MS) forged in the mid-twentieth century was built on a notion of heredity that excluded soft inheritance, the inheritance of the effects of developmental modifications. However, the discovery of molecular mechanisms that generate random and developmentally induced epigenetic variations is leading to a broadening of the notion of biological heredity that has consequences for ideas about evolution. After presenting some old challenges to the MS that were raised, among others, by Karl Popper, I discuss recent research on epigenetic inheritance, which provides experimental and theoretical support for these challenges. There is now good evidence that epigenetic inheritance is ubiquitous and is involved in adaptive evolution and macroevolution. I argue that the many evolutionary consequences of epigenetic inheritance open up new research areas and require the extension of the evolutionary synthesis beyond the current neo-Darwinian model.

  12. An Evolutionary Model of Cooperation, Fairness and Altruistic Punishment in Public Good Games

    Science.gov (United States)

    Hetzer, Moritz; Sornette, Didier

    2013-01-01

    We identify and explain the mechanisms that account for the emergence of fairness preferences and altruistic punishment in voluntary contribution mechanisms by combining an evolutionary perspective together with an expected utility model. We aim at filling a gap between the literature on the theory of evolution applied to cooperation and punishment, and the empirical findings from experimental economics. The approach is motivated by previous findings on other-regarding behavior, the co-evolution of culture, genes and social norms, as well as bounded rationality. Our first result reveals the emergence of two distinct evolutionary regimes that force agents to converge either to a defection state or to a state of coordination, depending on the predominant set of self- or other-regarding preferences. Our second result indicates that subjects in laboratory experiments of public goods games with punishment coordinate and punish defectors as a result of an aversion against disadvantageous inequitable outcomes. Our third finding identifies disadvantageous inequity aversion as evolutionary dominant and stable in a heterogeneous population of agents endowed initially only with purely self-regarding preferences. We validate our model using previously obtained results from three independently conducted experiments of public goods games with punishment. PMID:24260101

  13. Evolutionary contributions to solving the "matrilineal puzzle": a test of Holden, Sear, and Mace's model.

    Science.gov (United States)

    Mattison, Siobhán M

    2011-07-01

    Matriliny has long been debated by anthropologists positing either its primitive or its puzzling nature. More recently, evolutionary anthropologists have attempted to recast matriliny as an adaptive solution to modern social and ecological environments, tying together much of what was known to be associated with matriliny. This paper briefly reviews the major anthropological currents in studies of matriliny and discusses the contribution of evolutionary anthropology to this body of literature. It discusses the utility of an evolutionary framework in the context of the first independent test of Holden et al.'s 2003 model of matriliny as daughter-biased investment. It finds that historical daughter-biased transmission of land among the Mosuo is consistent with the model, whereas current income transmission is not. In both cases, resources had equivalent impacts on male and female reproduction, a result which predicts daughter-biased resource transmission given any nonzero level of paternity uncertainty. However, whereas land was transmitted traditionally to daughters, income today is invested in both sexes. Possible reasons for this discrepancy are discussed.

  14. Evolutionary Game Model Study of Construction Green Supply Chain Management under the Government Intervention

    Science.gov (United States)

    Xing, Yuanzhi; Deng, Xiaoyi

    2017-11-01

    The paper first has defined the concepts of green supply chain management and evolution game theory, and pointed out the characteristics of green supply chain management in construction. The main participants and key links of the construction green supply chain management are determined by constructing the organization framework. This paper established the evolutionary game model between construction enterprises and recycling enterprises for the green supply chain closed-loop structure. The waste recycling evolutionary stability equilibrium solution is obtained to explore the principle and effective scope of government policy intervention. This paper put forward the relevant countermeasures to the green supply chain management in construction recycling stage from the government point of view. The conclusion has reference value and guidance to the final product construction enterprises, recycling enterprises and the government during green supply chain.

  15. System-level synthesis of multi-ASIP platforms using an uncertainty model

    DEFF Research Database (Denmark)

    Micconi, Laura; Madsen, Jan; Pop, Paul

    2015-01-01

    In this paper we propose a system-level synthesis for MPSoCs that integrates multiple Application Specific Instruction Set Processors (ASIPs). Each ASIP is customized for a specific set of tasks. The system-level synthesis is responsible for assigning the tasks to the ASIPs, exploring different......-architecture can be derived only knowing the assignment of tasks to ASIP. To address this circular dependency, we propose an Uncertainty Model for the WCETs, which captures the performance of tasks running on a range of possible ASIP implementations. We propose a novel stochastic schedulability analysis...... to evaluate each multi-ASIP platform. We use an Evolutionary Algorithm-based approach to explore the design space of macro-architecture possibilities and we evaluate it using real case studies....

  16. A Study on Standard Competition with Network Effect Based on Evolutionary Game Model

    Science.gov (United States)

    Wang, Ye; Wang, Bingdong; Li, Kangning

    Owing to networks widespread in modern society, standard competition with network effect is now endowed with new connotation. This paper aims to study the impact of network effect on standard competition; it is organized in the mode of "introduction-model setup-equilibrium analysis-conclusion". Starting from a well-structured model of evolutionary game, it is then extended to a dynamic analysis. This article proves both theoretically and empirically that whether or not a standard can lead the market trends depends on the utility it would bring, and the author also discusses some advisable strategies revolving around the two factors of initial position and border break.

  17. Convolutional Pitch Target Approximation Model for Speech Synthesis

    OpenAIRE

    Na, Xingyu; Garner, Philip N.

    2013-01-01

    In this paper, we investigate pitch contour modelling in speech synthesis based on segmental units. A convolutional pitch target approximation model is proposed. This model allows jointly stochastic modelling of framewise pitch and pitch contour of longer units, of which the intuitive relations are revealed by a convolutional target approximation filter. The pitch contour is stylized by a linear representation called pitch target. In synthesis stage, the likelihood of the framewise model and ...

  18. The genetic architecture of normal variation in human pigmentation: an evolutionary perspective and model.

    Science.gov (United States)

    McEvoy, Brian; Beleza, Sandra; Shriver, Mark D

    2006-10-15

    Skin pigmentation varies substantially across human populations in a manner largely coincident with ultraviolet radiation intensity. This observation suggests that natural selection in response to sunlight is a major force in accounting for pigmentation variability. We review recent progress in identifying the genes controlling this variation with a particular focus on the trait's evolutionary past and the potential role of testing for signatures of selection in aiding the discovery of functionally important genes. We have analyzed SNP data from the International HapMap project in 77 pigmentation candidate genes for such signatures. On the basis of these results and other similar work, we provide a tentative three-population model (West Africa, East Asia and North Europe) of the evolutionary-genetic architecture of human pigmentation. These results suggest a complex evolutionary history, with selection acting on different gene targets at different times and places in the human past. Some candidate genes may have been selected in the ancestral human population, others in the 'out of Africa' proto European-Asian population, whereas most appear to have selectively evolved solely in either Europeans or East Asians separately despite the pigmentation similarities between these two populations. Selection signatures can provide important clues to aid gene discovery. However, these should be viewed as complements, rather than replacements of, functional studies including linkage and association analyses, which can directly refine our understanding of the trait.

  19. Articulatory speech synthesis and speech production modelling

    Science.gov (United States)

    Huang, Jun

    This dissertation addresses the problem of speech synthesis and speech production modelling based on the fundamental principles of human speech production. Unlike the conventional source-filter model, which assumes the independence of the excitation and the acoustic filter, we treat the entire vocal apparatus as one system consisting of a fluid dynamic aspect and a mechanical part. We model the vocal tract by a three-dimensional moving geometry. We also model the sound propagation inside the vocal apparatus as a three-dimensional nonplane-wave propagation inside a viscous fluid described by Navier-Stokes equations. In our work, we first propose a combined minimum energy and minimum jerk criterion to estimate the dynamic vocal tract movements during speech production. Both theoretical error bound analysis and experimental results show that this method can achieve very close match at the target points and avoid the abrupt change in articulatory trajectory at the same time. Second, a mechanical vocal fold model is used to compute the excitation signal of the vocal tract. The advantage of this model is that it is closely coupled with the vocal tract system based on fundamental aerodynamics. As a result, we can obtain an excitation signal with much more detail than the conventional parametric vocal fold excitation model. Furthermore, strong evidence of source-tract interaction is observed. Finally, we propose a computational model of the fricative and stop types of sounds based on the physical principles of speech production. The advantage of this model is that it uses an exogenous process to model the additional nonsteady and nonlinear effects due to the flow mode, which are ignored by the conventional source- filter speech production model. A recursive algorithm is used to estimate the model parameters. Experimental results show that this model is able to synthesize good quality fricative and stop types of sounds. Based on our dissertation work, we carefully argue

  20. General Methods for Evolutionary Quantitative Genetic Inference from Generalized Mixed Models.

    Science.gov (United States)

    de Villemereuil, Pierre; Schielzeth, Holger; Nakagawa, Shinichi; Morrissey, Michael

    2016-11-01

    Methods for inference and interpretation of evolutionary quantitative genetic parameters, and for prediction of the response to selection, are best developed for traits with normal distributions. Many traits of evolutionary interest, including many life history and behavioral traits, have inherently nonnormal distributions. The generalized linear mixed model (GLMM) framework has become a widely used tool for estimating quantitative genetic parameters for nonnormal traits. However, whereas GLMMs provide inference on a statistically convenient latent scale, it is often desirable to express quantitative genetic parameters on the scale upon which traits are measured. The parameters of fitted GLMMs, despite being on a latent scale, fully determine all quantities of potential interest on the scale on which traits are expressed. We provide expressions for deriving each of such quantities, including population means, phenotypic (co)variances, variance components including additive genetic (co)variances, and parameters such as heritability. We demonstrate that fixed effects have a strong impact on those parameters and show how to deal with this by averaging or integrating over fixed effects. The expressions require integration of quantities determined by the link function, over distributions of latent values. In general cases, the required integrals must be solved numerically, but efficient methods are available and we provide an implementation in an R package, QGglmm. We show that known formulas for quantities such as heritability of traits with binomial and Poisson distributions are special cases of our expressions. Additionally, we show how fitted GLMM can be incorporated into existing methods for predicting evolutionary trajectories. We demonstrate the accuracy of the resulting method for evolutionary prediction by simulation and apply our approach to data from a wild pedigreed vertebrate population. Copyright © 2016 de Villemereuil et al.

  1. Adaptive elastic segmentation of brain MRI via shape-model-guided evolutionary programming.

    Science.gov (United States)

    Pitiot, Alain; Toga, Arthur W; Thompson, Paul M

    2002-08-01

    This paper presents a fully automated segmentation method for medical images. The goal is to localize and parameterize a variety of types of structure in these images for subsequent quantitative analysis. We propose a new hybrid strategy that combines a general elastic template matching approach and an evolutionary heuristic. The evolutionary algorithm uses prior statistical information about the shape of the target structure to control the behavior of a number of deformable templates. Each template, modeled in the form of a B-spline, is warped in a potential field which is itself dynamically adapted. Such a hybrid scheme proves to be promising: by maintaining a population of templates, we cover a large domain of the solution space under the global guidance of the evolutionary heuristic, and thoroughly explore interesting areas. We address key issues of automated image segmentation systems. The potential fields are initially designed based on the spatial features of the edges in the input image, and are subjected to spatially adaptive diffusion to guarantee the deformation of the template. This also improves its global consistency and convergence speed. The deformation algorithm can modify the internal structure of the templates to allow a better match. We investigate in detail the preprocessing phase that the images undergo before they can be used more effectively in the iterative elastic matching procedure: a texture classifier, trained via linear discriminant analysis of a learning set, is used to enhance the contrast of the target structure with respect to surrounding tissues. We show how these techniques interact within a statistically driven evolutionary scheme to achieve a better tradeoff between template flexibility and sensitivity to noise and outliers. We focus on understanding the features of template matching that are most beneficial in terms of the achieved match. Examples from simulated and real image data are discussed, with considerations of

  2. Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology.

    Science.gov (United States)

    Morris, Dylan H; Gostic, Katelyn M; Pompei, Simone; Bedford, Trevor; Łuksza, Marta; Neher, Richard A; Grenfell, Bryan T; Lässig, Michael; McCauley, John W

    2017-10-30

    Seasonal influenza is controlled through vaccination campaigns. Evolution of influenza virus antigens means that vaccines must be updated to match novel strains, and vaccine effectiveness depends on the ability of scientists to predict nearly a year in advance which influenza variants will dominate in upcoming seasons. In this review, we highlight a promising new surveillance tool: predictive models. Developed through data-sharing and close collaboration between the World Health Organization and academic scientists, these models use surveillance data to make quantitative predictions regarding influenza evolution. Predictive models demonstrate the potential of applied evolutionary biology to improve public health and disease control. We review the state of influenza predictive modeling and discuss next steps and recommendations to ensure that these models deliver upon their considerable biomedical promise. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. On the validity of evolutionary models with site-specific parameters.

    Directory of Open Access Journals (Sweden)

    Konrad Scheffler

    Full Text Available Evolutionary models that make use of site-specific parameters have recently been criticized on the grounds that parameter estimates obtained under such models can be unreliable and lack theoretical guarantees of convergence. We present a simulation study providing empirical evidence that a simple version of the models in question does exhibit sensible convergence behavior and that additional taxa, despite not being independent of each other, lead to improved parameter estimates. Although it would be desirable to have theoretical guarantees of this, we argue that such guarantees would not be sufficient to justify the use of these models in practice. Instead, we emphasize the importance of taking the variance of parameter estimates into account rather than blindly trusting point estimates - this is standardly done by using the models to construct statistical hypothesis tests, which are then validated empirically via simulation studies.

  4. Spatial multiobjective optimization of agricultural conservation practices using a SWAT model and an evolutionary algorithm.

    Science.gov (United States)

    Rabotyagov, Sergey; Campbell, Todd; Valcu, Adriana; Gassman, Philip; Jha, Manoj; Schilling, Keith; Wolter, Calvin; Kling, Catherine

    2012-12-09

    Finding the cost-efficient (i.e., lowest-cost) ways of targeting conservation practice investments for the achievement of specific water quality goals across the landscape is of primary importance in watershed management. Traditional economics methods of finding the lowest-cost solution in the watershed context (e.g.,(5,12,20)) assume that off-site impacts can be accurately described as a proportion of on-site pollution generated. Such approaches are unlikely to be representative of the actual pollution process in a watershed, where the impacts of polluting sources are often determined by complex biophysical processes. The use of modern physically-based, spatially distributed hydrologic simulation models allows for a greater degree of realism in terms of process representation but requires a development of a simulation-optimization framework where the model becomes an integral part of optimization. Evolutionary algorithms appear to be a particularly useful optimization tool, able to deal with the combinatorial nature of a watershed simulation-optimization problem and allowing the use of the full water quality model. Evolutionary algorithms treat a particular spatial allocation of conservation practices in a watershed as a candidate solution and utilize sets (populations) of candidate solutions iteratively applying stochastic operators of selection, recombination, and mutation to find improvements with respect to the optimization objectives. The optimization objectives in this case are to minimize nonpoint-source pollution in the watershed, simultaneously minimizing the cost of conservation practices. A recent and expanding set of research is attempting to use similar methods and integrates water quality models with broadly defined evolutionary optimization methods(3,4,9,10,13-15,17-19,22,23,25). In this application, we demonstrate a program which follows Rabotyagov et al.'s approach and integrates a modern and commonly used SWAT water quality model(7) with a

  5. An IUR evolutionary game model on the patent cooperate of Shandong China

    Science.gov (United States)

    Liu, Mengmeng; Ma, Yinghong; Liu, Zhiyuan; You, Xuemei

    2017-06-01

    Organizations of industries and university & research institutes cooperate to meet their respective needs based on social contacts, trust and share complementary resources. From the perspective of complex network together with the patent data of Shandong province in China, a novel evolutionary game model on patent cooperation network is presented. Two sides in the game model are industries and universities & research institutes respectively. The cooperation is represented by a connection when a new patent is developed together by the two sides. The optimal strategy of the evolutionary game model is quantified by the average positive cooperation probability p ¯ and the average payoff U ¯ . The feasibility of this game model is simulated on the parameters such as the knowledge spillover, the punishment, the development cost and the distribution coefficient of the benefit. The numerical simulations show that the cooperative behaviors are affected by the variation of parameters. The knowledge spillover displays different behaviors when the punishment is larger than the development cost or less than it. Those results indicate that reasonable punishment would improve the positive cooperation. The appropriate punishment will be useful to enhance the big degree nodes positively cooperate with industries and universities & research institutes. And an equitable plan for the distribution of cooperative profits is half-and-half distribution strategy for the two sides in game.

  6. A mathematical model for metabolic tradeoffs, minimal requirements, and evolutionary transitions. (Invited)

    Science.gov (United States)

    Kempes, C.; Hoehler, T. M.; Follows, M. J.; Dutkiewicz, S.

    2013-12-01

    Understanding the minimal energy requirements for life is a difficult challenge because of the great variety of processes required for life. Our approach is to discover general trends applicable to diverse species in order to understand the average constraints faced by life. We then leverage these trends to predict minimal requirements for life. We have focused on broad trends in metabolism, growth, basic bioenergetics, and overall genomic structure and composition. We have developed a simple mathematical model of metabolic partitioning which is able to capture the growth of both single cells and populations of cells for diverse organisms spanning the three domains of life. This model also anticipates the observed interspecific trends in population growth rate and predicts the observed minimum size of a bacterium. Our model connects evolutionary limitations and transitions, including minimal life, to energetic constraints imposed by body architecture and the metabolism of a given species. This model can also be connected to genomic variation across species in order to describe the tradeoffs associated with various genes and their functionality. This forms the basis for a theory of the possibility space for minimal physiological function given evolutionary tradeoffs, general metabolic and biological architecture, and the energetic limitations of the environment.

  7. Differential Dynamic Evolutionary Model of Emergency Financial Service Supply Chain in Natural Disaster Risk Management

    Directory of Open Access Journals (Sweden)

    Shujian Ma

    2016-01-01

    Full Text Available A government-market-public partnership (GMPP could be a feasible arrangement for providing insurance coverage for natural disaster. Firstly, we put forward GMPP management mode. Secondly, the emergency financial service supply chain for natural disaster risk is built from the view of supply chain. Finally, the objective of this paper is to obtain insights into the cooperative and competitive relationship in GMPP system. We establish the cooperative and competitive differential dynamic evolutionary models and prove the existence of equilibrium solutions in order to solve the coordination problems. In conclusion, the equilibrium solutions can be achieved among the insurers, the operating governments, and the public.

  8. Limb, tooth, beak: Three modes of development and evolutionary ...

    Indian Academy of Sciences (India)

    The standard model of evolutionary change of form, deriving from Darwin's theory via the Modern Synthesis, assumes a gradualistic reshaping of anatomical structures, with major changes only occurring by many cycles of natural selection for marginal adaptive advantage. This model, with its assertion that a single ...

  9. An Agent-Based Model to study the epidemiological and evolutionary dynamics of Influenza viruses

    Directory of Open Access Journals (Sweden)

    Drake John M

    2011-03-01

    Full Text Available Abstract Background Influenza A viruses exhibit complex epidemiological patterns in a number of mammalian and avian hosts. Understanding transmission of these viruses necessitates taking into account their evolution, which represents a challenge for developing mathematical models. This is because the phrasing of multi-strain systems in terms of traditional compartmental ODE models either requires simplifying assumptions to be made that overlook important evolutionary processes, or leads to complex dynamical systems that are too cumbersome to analyse. Results Here, we develop an Individual-Based Model (IBM in order to address simultaneously the ecology, epidemiology and evolution of strain-polymorphic pathogens, using Influenza A viruses as an illustrative example. Conclusions We carry out careful validation of our IBM against comparable mathematical models to demonstrate the robustness of our algorithm and the sound basis for this novel framework. We discuss how this new approach can give critical insights in the study of influenza evolution.

  10. An agent-based model to study the epidemiological and evolutionary dynamics of Influenza viruses.

    Science.gov (United States)

    Roche, Benjamin; Drake, John M; Rohani, Pejman

    2011-03-30

    Influenza A viruses exhibit complex epidemiological patterns in a number of mammalian and avian hosts. Understanding transmission of these viruses necessitates taking into account their evolution, which represents a challenge for developing mathematical models. This is because the phrasing of multi-strain systems in terms of traditional compartmental ODE models either requires simplifying assumptions to be made that overlook important evolutionary processes, or leads to complex dynamical systems that are too cumbersome to analyse. Here, we develop an Individual-Based Model (IBM) in order to address simultaneously the ecology, epidemiology and evolution of strain-polymorphic pathogens, using Influenza A viruses as an illustrative example. We carry out careful validation of our IBM against comparable mathematical models to demonstrate the robustness of our algorithm and the sound basis for this novel framework. We discuss how this new approach can give critical insights in the study of influenza evolution.

  11. Research on Preference Polyhedron Model Based Evolutionary Multiobjective Optimization Method for Multilink Transmission Mechanism Conceptual Design

    Directory of Open Access Journals (Sweden)

    Haihua Zhu

    2016-01-01

    Full Text Available To make the optimal design of the multilink transmission mechanism applied in mechanical press, the intelligent optimization techniques are explored in this paper. A preference polyhedron model and new domination relationships evaluation methodology are proposed for the purpose of reaching balance among kinematic performance, dynamic performance, and other performances of the multilink transmission mechanism during the conceptual design phase. Based on the traditional evaluation index of single target of multicriteria design optimization, the robust metrics of the mechanism system and preference metrics of decision-maker are taken into consideration in this preference polyhedron model and reflected by geometrical characteristic of the model. At last, two optimized multilink transmission mechanisms are designed based on the proposed preference polyhedron model with different evolutionary algorithms, and the result verifies the validity of the proposed optimization method.

  12. Fractional-difference stochastic model of evolutionary substitutions in DNA sequences

    Science.gov (United States)

    West, Bruce J.; Bickel, David R.

    1999-05-01

    The number of molecular substitutions occurring in a DNA sequence over a given time is described by a fractional-difference random walk model. This is an empirically motivated stochastic model of molecular evolution and does not address the detailed evolutionary mechanisms that lead to the substitution of nucleotides. This fractal stochastic process yields a Fano Factor, the ratio of the variance to the mean in the number of molecular substitutions, that increases as a power law in time. This prediction agrees with the observed statistics across 49 different genes in mammals. The fractional-difference model of molecular evolution is episodic and can be made consistent with the punctuated equilibrium model of macroevolution.

  13. Synthesis of a naphthalene-hydroxynaphthalene polymer model compound

    Energy Technology Data Exchange (ETDEWEB)

    1991-10-02

    The objective of this project was the synthesis of one pound of a new naphthalene-hydroxynaphthalene polymer model compound for use in coal combustion studies. Since this compound was an unreported compound, this effort also required the development of a synthetic route to this compound (including routes to the unique and unreported intermediates leading to its synthesis).

  14. Evolutionary demography of iteroparous plants: incorporating non-lethal costs of reproduction into integral projection models.

    Science.gov (United States)

    Miller, Tom E X; Williams, Jennifer L; Jongejans, Eelke; Brys, Rein; Jacquemyn, Hans

    2012-07-22

    Understanding the selective forces that shape reproductive strategies is a central goal of evolutionary ecology. Selection on the timing of reproduction is well studied in semelparous organisms because the cost of reproduction (death) can be easily incorporated into demographic models. Iteroparous organisms also exhibit delayed reproduction and experience reproductive costs, although these are not necessarily lethal. How non-lethal costs shape iteroparous life histories remains unresolved. We analysed long-term demographic data for the iteroparous orchid Orchis purpurea from two habitat types (light and shade). In both the habitats, flowering plants had lower growth rates and this cost was greater for smaller plants. We detected an additional growth cost of fruit production in the light habitat. We incorporated these non-lethal costs into integral projection models to identify the flowering size that maximizes fitness. In both habitats, observed flowering sizes were well predicted by the models. We also estimated optimal parameters for size-dependent flowering effort, but found a strong mismatch with the observed flower production. Our study highlights the role of context-dependent non-lethal reproductive costs as selective forces in the evolution of iteroparous life histories, and provides a novel and broadly applicable approach to studying the evolutionary demography of iteroparous organisms.

  15. Evolutionary-Hierarchical Bases of the Formation of Cluster Model of Innovation Economic Development

    Directory of Open Access Journals (Sweden)

    Yuliya Vladimirovna Dubrovskaya

    2016-10-01

    Full Text Available The functioning of a modern economic system is based on the interaction of objects of different hierarchical levels. Thus, the problem of the study of innovation processes taking into account the mutual influence of the activities of these economic actors becomes important. The paper dwells evolutionary basis for the formation of models of innovation development on the basis of micro and macroeconomic analysis. Most of the concepts recognized that despite a big number of diverse models, the coordination of the relations between economic agents is of crucial importance for the successful innovation development. According to the results of the evolutionary-hierarchical analysis, the authors reveal key phases of the development of forms of business cooperation, science and government in the domestic economy. It has become the starting point of the conception of the characteristics of the interaction in the cluster models of innovation development of the economy. Considerable expectancies on improvement of the national innovative system are connected with the development of cluster and network structures. The main objective of government authorities is the formation of mechanisms and institutions that will foster cooperation between members of the clusters. The article explains that the clusters cannot become the factors in the growth of the national economy, not being an effective tool for interaction between the actors of the regional innovative systems.

  16. Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

    Directory of Open Access Journals (Sweden)

    Sofie Van Holle

    2017-05-01

    Full Text Available Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsis thaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica. The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST, hidden Markov models, and InterProScan analysis. Additionally, phylogenetic relationships were investigated by constructing maximum likelihood phylogenetic trees. The results demonstrate that the majority of the lectin families are present in each of the species under study. Domain organization analysis showed that most identified proteins are multi-domain proteins, owing to the modular rearrangement of protein domains during evolution. Most of these multi-domain proteins are widespread, while others display a lineage-specific distribution. Furthermore, the phylogenetic analyses reveal that some lectin families evolved to be similar to the phylogeny of the plant species, while others share a closer evolutionary history based on the corresponding protein domain architecture. Our results yield insights into the evolutionary relationships and functional divergence of plant lectins.

  17. The causal pie model: an epidemiological method applied to evolutionary biology and ecology.

    Science.gov (United States)

    Wensink, Maarten; Westendorp, Rudi G J; Baudisch, Annette

    2014-05-01

    A general concept for thinking about causality facilitates swift comprehension of results, and the vocabulary that belongs to the concept is instrumental in cross-disciplinary communication. The causal pie model has fulfilled this role in epidemiology and could be of similar value in evolutionary biology and ecology. In the causal pie model, outcomes result from sufficient causes. Each sufficient cause is made up of a "causal pie" of "component causes". Several different causal pies may exist for the same outcome. If and only if all component causes of a sufficient cause are present, that is, a causal pie is complete, does the outcome occur. The effect of a component cause hence depends on the presence of the other component causes that constitute some causal pie. Because all component causes are equally and fully causative for the outcome, the sum of causes for some outcome exceeds 100%. The causal pie model provides a way of thinking that maps into a number of recurrent themes in evolutionary biology and ecology: It charts when component causes have an effect and are subject to natural selection, and how component causes affect selection on other component causes; which partitions of outcomes with respect to causes are feasible and useful; and how to view the composition of a(n apparently homogeneous) population. The diversity of specific results that is directly understood from the causal pie model is a test for both the validity and the applicability of the model. The causal pie model provides a common language in which results across disciplines can be communicated and serves as a template along which future causal analyses can be made.

  18. Atomistic Modelling of Si Nanoparticles Synthesis

    Directory of Open Access Journals (Sweden)

    Giovanni Barcaro

    2017-02-01

    Full Text Available Silicon remains the most important material for electronic technology. Presently, some efforts are focused on the use of Si nanoparticles—not only for saving material, but also for improving the efficiency of optical and electronic devices, for instance, in the case of solar cells coated with a film of Si nanoparticles. The synthesis by a bottom-up approach based on condensation from low temperature plasma is a promising technique for the massive production of such nanoparticles, but the knowledge of the basic processes occurring at the atomistic level is still very limited. In this perspective, numerical simulations can provide fundamental information of the nucleation and growth mechanisms ruling the bottom-up formation of Si nanoclusters. We propose to model the low temperature plasma by classical molecular dynamics by using the reactive force field (ReaxFF proposed by van Duin, which can properly describe bond forming and breaking. In our approach, first-principles quantum calculations are used on a set of small Si clusters in order to collect all the necessary energetic and structural information to optimize the parameters of the reactive force-field for the present application. We describe in detail the procedure used for the determination of the force field and the following molecular dynamics simulations of model systems of Si gas at temperatures in the range 2000–3000 K. The results of the dynamics provide valuable information on nucleation rate, nanoparticle size distribution, and growth rate that are the basic quantities for developing a following mesoscale model.

  19. Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance

    Science.gov (United States)

    Ogbunugafor, C. Brandon; Wylie, C. Scott; Diakite, Ibrahim; Weinreich, Daniel M.; Hartl, Daniel L.

    2016-01-01

    The adaptive landscape analogy has found practical use in recent years, as many have explored how their understanding can inform therapeutic strategies that subvert the evolution of drug resistance. A major barrier to applications of these concepts is a lack of detail concerning how the environment affects adaptive landscape topography, and consequently, the outcome of drug treatment. Here we combine empirical data, evolutionary theory, and computer simulations towards dissecting adaptive landscape by environment interactions for the evolution of drug resistance in two dimensions—drug concentration and drug type. We do so by studying the resistance mediated by Plasmodium falciparum dihydrofolate reductase (DHFR) to two related inhibitors—pyrimethamine and cycloguanil—across a breadth of drug concentrations. We first examine whether the adaptive landscapes for the two drugs are consistent with common definitions of cross-resistance. We then reconstruct all accessible pathways across the landscape, observing how their structure changes with drug environment. We offer a mechanism for non-linearity in the topography of accessible pathways by calculating of the interaction between mutation effects and drug environment, which reveals rampant patterns of epistasis. We then simulate evolution in several different drug environments to observe how these individual mutation effects (and patterns of epistasis) influence paths taken at evolutionary “forks in the road” that dictate adaptive dynamics in silico. In doing so, we reveal how classic metrics like the IC50 and minimal inhibitory concentration (MIC) are dubious proxies for understanding how evolution will occur across drug environments. We also consider how the findings reveal ambiguities in the cross-resistance concept, as subtle differences in adaptive landscape topography between otherwise equivalent drugs can drive drastically different evolutionary outcomes. Summarizing, we discuss the results with

  20. Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment.

    Science.gov (United States)

    Großkopf, Tobias; Consuegra, Jessika; Gaffé, Joël; Willison, John C; Lenski, Richard E; Soyer, Orkun S; Schneider, Dominique

    2016-08-20

    Predicting adaptive trajectories is a major goal of evolutionary biology and useful for practical applications. Systems biology has enabled the development of genome-scale metabolic models. However, analysing these models via flux balance analysis (FBA) cannot predict many evolutionary outcomes including adaptive diversification, whereby an ancestral lineage diverges to fill multiple niches. Here we combine in silico evolution with FBA and apply this modelling framework, evoFBA, to a long-term evolution experiment with Escherichia coli. Simulations predicted the adaptive diversification that occurred in one experimental population and generated hypotheses about the mechanisms that promoted coexistence of the diverged lineages. We experimentally tested and, on balance, verified these mechanisms, showing that diversification involved niche construction and character displacement through differential nutrient uptake and altered metabolic regulation. The evoFBA framework represents a promising new way to model biochemical evolution, one that can generate testable predictions about evolutionary and ecosystem-level outcomes.

  1. How effective and efficient are multiobjective evolutionary algorithms at hydrologic model calibration?

    Directory of Open Access Journals (Sweden)

    Y. Tang

    2006-01-01

    Full Text Available This study provides a comprehensive assessment of state-of-the-art evolutionary multiobjective optimization (EMO tools' relative effectiveness in calibrating hydrologic models. The relative computational efficiency, accuracy, and ease-of-use of the following EMO algorithms are tested: Epsilon Dominance Nondominated Sorted Genetic Algorithm-II (ε-NSGAII, the Multiobjective Shuffled Complex Evolution Metropolis algorithm (MOSCEM-UA, and the Strength Pareto Evolutionary Algorithm 2 (SPEA2. This study uses three test cases to compare the algorithms' performances: (1 a standardized test function suite from the computer science literature, (2 a benchmark hydrologic calibration test case for the Leaf River near Collins, Mississippi, and (3 a computationally intensive integrated surface-subsurface model application in the Shale Hills watershed in Pennsylvania. One challenge and contribution of this work is the development of a methodology for comprehensively comparing EMO algorithms that have different search operators and randomization techniques. Overall, SPEA2 attained competitive to superior results for most of the problems tested in this study. The primary strengths of the SPEA2 algorithm lie in its search reliability and its diversity preservation operator. The biggest challenge in maximizing the performance of SPEA2 lies in specifying an effective archive size without a priori knowledge of the Pareto set. In practice, this would require significant trial-and-error analysis, which is problematic for more complex, computationally intensive calibration applications. ε-NSGAII appears to be superior to MOSCEM-UA and competitive with SPEA2 for hydrologic model calibration. ε-NSGAII's primary strength lies in its ease-of-use due to its dynamic population sizing and archiving which lead to rapid convergence to very high quality solutions with minimal user input. MOSCEM-UA is best suited for hydrologic model calibration applications that have small

  2. Evolutionary dynamics in the two-locus two-allele model with weak selection.

    Science.gov (United States)

    Pontz, Martin; Hofbauer, Josef; Bürger, Reinhard

    2018-01-01

    Two-locus two-allele models are among the most studied models in population genetics. The reason is that they are the simplest models to explore the role of epistasis for a variety of important evolutionary problems, including the maintenance of polymorphism and the evolution of genetic incompatibilities. Many specific types of models have been explored. However, due to the mathematical complexity arising from the fact that epistasis generates linkage disequilibrium, few general insights have emerged. Here, we study a simpler problem by assuming that linkage disequilibrium can be ignored. This is a valid approximation if selection is sufficiently weak relative to recombination. The goal of our paper is to characterize all possible equilibrium structures, or more precisely and general, all robust phase portraits or evolutionary flows arising from this weak-selection dynamics. For general fitness matrices, we have not fully accomplished this goal, because some cases remain undecided. However, for many specific classes of fitness schemes, including additive fitnesses, purely additive-by-additive epistasis, haploid selection, multilinear epistasis, marginal overdominance or underdominance, and the symmetric viability model, we obtain complete characterizations of the possible equilibrium structures and, in several cases, even of all possible phase portraits. A central point in our analysis is the inference of the number and stability of fully polymorphic equilibria from the boundary flow, i.e., from the dynamics at the four marginal single-locus subsystems. The key mathematical ingredient for this is index theory. The specific form of epistasis has both a big influence on the possible boundary flows as well as on the internal equilibrium structure admitted by a given boundary flow.

  3. GrayStarServer: Stellar atmospheric modeling and spectrum synthesis

    Science.gov (United States)

    Short, C. Ian

    2017-01-01

    GrayStarServer is a stellar atmospheric modeling and spectrum synthesis code of pedagogical accuracy that is accessible in any web browser on commonplace computational devices and that runs on a timescale of a few seconds.

  4. Comparative Studies of Population Synthesis Models in the ...

    Indian Academy of Sciences (India)

    Evolutionary models form a vital part of stellar population research in understanding their evolution, but despite their long history of development, they are often misrepresented and the properties of stellar population observed through broadband and spectroscopic measurements are also misinterpreted. With growing ...

  5. An evolutionary model for protein-coding regions with conserved RNA structure

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Forsberg, Roald; Meyer, Irmtraud Margret

    2004-01-01

    components of traditional phylogenetic models. We applied this to a data set of full-genome sequences from the hepatitis C virus where five RNA structures are mapped within the coding region. This allowed us to partition the effects of selection on different structural elements and to test various hypotheses...... concerning the relation of these effects. Of particular interest, we found evidence of a functional role of loop and bulge regions, as these were shown to evolve according to a different and more constrained selective regime than the nonpairing regions outside the RNA structures. Other potential applications......Here we present a model of nucleotide substitution in protein-coding regions that also encode the formation of conserved RNA structures. In such regions, apparent evolutionary context dependencies exist, both between nucleotides occupying the same codon and between nucleotides forming a base pair...

  6. Environmental Quality, Developmental Plasticity and the Thrifty Phenotype: A Review of Evolutionary Models

    Directory of Open Access Journals (Sweden)

    Jonathan CK Wells

    2007-01-01

    Full Text Available The concept of the thrifty phenotype, first proposed by Hales and Barker, is now widely used in medical research, often in contrast to the thrifty genotype model, to interpret associations between early-life experience and adult health status. Several evolutionary models of the thrifty phenotype, which refers to developmental plasticity, have been presented. These include (A the weather forecast model of Bateson, (B the maternal fi tness model of Wells, (C the intergenerational phenotypic inertia model of Kuzawa, and (D the predictive adaptive response model of Gluckman and Hanson. These models are compared and contrasted, in order to assess their relative utility for understanding human ontogenetic development. The most broadly applicable model is model A, which proposes that developing organisms respond to cues of environmental quality, and that mismatches between this forecast and subsequent reality generate significant adverse effects in adult phenotype. The remaining models all address in greater detail what kind of information is provided by such a forecast. Whereas both models B and C emphasise the adaptive benefits of exploiting information about the past, encapsulated in maternal phenotype, model D assumes that the fetus uses cues about the present external environment to predict its probable adult environment. I argue that for humans, with a disproportionately long period between the closing of sensitive windows of plasticity and the attainment of reproductive maturity, backward-looking models B and C represent a better approach, and indicate that the developing offspring aligns itself with stable cues of maternal phenotype so as to match its energy demand with maternal capacity to supply. In contrast, the predictive adaptive response model D over-estimates the capacity of the offspring to predict the future, and also fails to address the long-term parent-offspring dynamics of human development. Differences between models have

  7. Hybrid evolutionary computing model for mobile agents of wireless Internet multimedia

    Science.gov (United States)

    Hortos, William S.

    2001-03-01

    The ecosystem is used as an evolutionary paradigm of natural laws for the distributed information retrieval via mobile agents to allow the computational load to be added to server nodes of wireless networks, while reducing the traffic on communication links. Based on the Food Web model, a set of computational rules of natural balance form the outer stage to control the evolution of mobile agents providing multimedia services with a wireless Internet protocol WIP. The evolutionary model shows how mobile agents should behave with the WIP, in particular, how mobile agents can cooperate, compete and learn from each other, based on an underlying competition for radio network resources to establish the wireless connections to support the quality of service QoS of user requests. Mobile agents are also allowed to clone themselves, propagate and communicate with other agents. A two-layer model is proposed for agent evolution: the outer layer is based on the law of natural balancing, the inner layer is based on a discrete version of a Kohonen self-organizing feature map SOFM to distribute network resources to meet QoS requirements. The former is embedded in the higher OSI layers of the WIP, while the latter is used in the resource management procedures of Layer 2 and 3 of the protocol. Algorithms for the distributed computation of mobile agent evolutionary behavior are developed by adding a learning state to the agent evolution state diagram. When an agent is in an indeterminate state, it can communicate to other agents. Computing models can be replicated from other agents. Then the agents transitions to the mutating state to wait for a new information-retrieval goal. When a wireless terminal or station lacks a network resource, an agent in the suspending state can change its policy to submit to the environment before it transitions to the searching state. The agents learn the facts of agent state information entered into an external database. In the cloning process, two

  8. Utilizing evolutionary information and gene expression data for estimating gene networks with bayesian network models.

    Science.gov (United States)

    Tamada, Yoshinori; Bannai, Hideo; Imoto, Seiya; Katayama, Toshiaki; Kanehisa, Minoru; Miyano, Satoru

    2005-12-01

    Since microarray gene expression data do not contain sufficient information for estimating accurate gene networks, other biological information has been considered to improve the estimated networks. Recent studies have revealed that highly conserved proteins that exhibit similar expression patterns in different organisms, have almost the same function in each organism. Such conserved proteins are also known to play similar roles in terms of the regulation of genes. Therefore, this evolutionary information can be used to refine regulatory relationships among genes, which are estimated from gene expression data. We propose a statistical method for estimating gene networks from gene expression data by utilizing evolutionarily conserved relationships between genes. Our method simultaneously estimates two gene networks of two distinct organisms, with a Bayesian network model utilizing the evolutionary information so that gene expression data of one organism helps to estimate the gene network of the other. We show the effectiveness of the method through the analysis on Saccharomyces cerevisiae and Homo sapiens cell cycle gene expression data. Our method was successful in estimating gene networks that capture many known relationships as well as several unknown relationships which are likely to be novel. Supplementary information is available at http://bonsai.ims.u-tokyo.ac.jp/~tamada/bayesnet/.

  9. Evolutionary responses to a constructed niche: ancient Mesoamericans as a model of gene-culture coevolution.

    Directory of Open Access Journals (Sweden)

    Tábita Hünemeier

    Full Text Available Culture and genetics rely on two distinct but not isolated transmission systems. Cultural processes may change the human selective environment and thereby affect which individuals survive and reproduce. Here, we evaluated whether the modes of subsistence in Native American populations and the frequencies of the ABCA1*Arg230Cys polymorphism were correlated. Further, we examined whether the evolutionary consequences of the agriculturally constructed niche in Mesoamerica could be considered as a gene-culture coevolution model. For this purpose, we genotyped 229 individuals affiliated with 19 Native American populations and added data for 41 other Native American groups (n = 1905 to the analysis. In combination with the SNP cluster of a neutral region, this dataset was then used to unravel the scenario involved in 230Cys evolutionary history. The estimated age of 230Cys is compatible with its origin occurring in the American continent. The correlation of its frequencies with the archeological data on Zea pollen in Mesoamerica/Central America, the neutral coalescent simulations, and the F(ST-based natural selection analysis suggest that maize domestication was the driving force in the increase in the frequencies of 230Cys in this region. These results may represent the first example of a gene-culture coevolution involving an autochthonous American allele.

  10. Evolutionary Responses to a Constructed Niche: Ancient Mesoamericans as a Model of Gene-Culture Coevolution

    Science.gov (United States)

    Hünemeier, Tábita; Amorim, Carlos Eduardo Guerra; Azevedo, Soledad; Contini, Veronica; Acuña-Alonzo, Víctor; Rothhammer, Francisco; Dugoujon, Jean-Michel; Mazières, Stephane; Barrantes, Ramiro; Villarreal-Molina, María Teresa; Paixão-Côrtes, Vanessa Rodrigues; Salzano, Francisco M.; Canizales-Quinteros, Samuel; Ruiz-Linares, Andres; Bortolini, Maria Cátira

    2012-01-01

    Culture and genetics rely on two distinct but not isolated transmission systems. Cultural processes may change the human selective environment and thereby affect which individuals survive and reproduce. Here, we evaluated whether the modes of subsistence in Native American populations and the frequencies of the ABCA1*Arg230Cys polymorphism were correlated. Further, we examined whether the evolutionary consequences of the agriculturally constructed niche in Mesoamerica could be considered as a gene-culture coevolution model. For this purpose, we genotyped 229 individuals affiliated with 19 Native American populations and added data for 41 other Native American groups (n = 1905) to the analysis. In combination with the SNP cluster of a neutral region, this dataset was then used to unravel the scenario involved in 230Cys evolutionary history. The estimated age of 230Cys is compatible with its origin occurring in the American continent. The correlation of its frequencies with the archeological data on Zea pollen in Mesoamerica/Central America, the neutral coalescent simulations, and the FST-based natural selection analysis suggest that maize domestication was the driving force in the increase in the frequencies of 230Cys in this region. These results may represent the first example of a gene-culture coevolution involving an autochthonous American allele. PMID:22768049

  11. Evolutionary responses to a constructed niche: ancient Mesoamericans as a model of gene-culture coevolution.

    Science.gov (United States)

    Hünemeier, Tábita; Amorim, Carlos Eduardo Guerra; Azevedo, Soledad; Contini, Veronica; Acuña-Alonzo, Víctor; Rothhammer, Francisco; Dugoujon, Jean-Michel; Mazières, Stephane; Barrantes, Ramiro; Villarreal-Molina, María Teresa; Paixão-Côrtes, Vanessa Rodrigues; Salzano, Francisco M; Canizales-Quinteros, Samuel; Ruiz-Linares, Andres; Bortolini, Maria Cátira

    2012-01-01

    Culture and genetics rely on two distinct but not isolated transmission systems. Cultural processes may change the human selective environment and thereby affect which individuals survive and reproduce. Here, we evaluated whether the modes of subsistence in Native American populations and the frequencies of the ABCA1*Arg230Cys polymorphism were correlated. Further, we examined whether the evolutionary consequences of the agriculturally constructed niche in Mesoamerica could be considered as a gene-culture coevolution model. For this purpose, we genotyped 229 individuals affiliated with 19 Native American populations and added data for 41 other Native American groups (n = 1905) to the analysis. In combination with the SNP cluster of a neutral region, this dataset was then used to unravel the scenario involved in 230Cys evolutionary history. The estimated age of 230Cys is compatible with its origin occurring in the American continent. The correlation of its frequencies with the archeological data on Zea pollen in Mesoamerica/Central America, the neutral coalescent simulations, and the F(ST)-based natural selection analysis suggest that maize domestication was the driving force in the increase in the frequencies of 230Cys in this region. These results may represent the first example of a gene-culture coevolution involving an autochthonous American allele.

  12. Evolutionary Game Theory-Based Collaborative Sensing Model in Emergency CRAHNs

    Directory of Open Access Journals (Sweden)

    Sasirekha GVK

    2012-01-01

    Full Text Available Game theory has been a tool of choice for modeling dynamic interactions between autonomous systems. Cognitive radio ad hoc networks (CRAHNs constituted of autonomous wireless nodes are a natural fit for game theory-based modeling. The game theory-based model is particularly suitable for “collaborative spectrum sensing” where each cognitive radio senses the spectrum and shares the results with other nodes such that the targeted sensing accuracy is achieved. Spectrum sensing in CRAHNs, especially when used in emergency scenarios such as disaster management and military applications, needs to be not only accurate and resource efficient, but also adaptive to the changing number of users as well as signal-to-noise ratios. In addition, spectrum sensing mechanism must also be proactive, fair, and tolerant to security attacks. Existing work in collaborative spectrum sensing has mostly been confined to resource efficiency in static systems using request-based reactive sensing resulting in high latencies. In this paper, evolutionary game theory (EGT is used to model the behavior of the emergency CRAHNS, providing an efficient model for collaborative spectrum sensing. The resulting implementation model is adaptive to the changes in its environment such as signal-to-noise ratio and number of users in the network. The analytical and simulation models presented validate the system design and the desired performance.

  13. Selection of relevant input variables in storm water quality modeling by multiobjective evolutionary polynomial regression paradigm

    Science.gov (United States)

    Creaco, E.; Berardi, L.; Sun, Siao; Giustolisi, O.; Savic, D.

    2016-04-01

    The growing availability of field data, from information and communication technologies (ICTs) in "smart" urban infrastructures, allows data modeling to understand complex phenomena and to support management decisions. Among the analyzed phenomena, those related to storm water quality modeling have recently been gaining interest in the scientific literature. Nonetheless, the large amount of available data poses the problem of selecting relevant variables to describe a phenomenon and enable robust data modeling. This paper presents a procedure for the selection of relevant input variables using the multiobjective evolutionary polynomial regression (EPR-MOGA) paradigm. The procedure is based on scrutinizing the explanatory variables that appear inside the set of EPR-MOGA symbolic model expressions of increasing complexity and goodness of fit to target output. The strategy also enables the selection to be validated by engineering judgement. In such context, the multiple case study extension of EPR-MOGA, called MCS-EPR-MOGA, is adopted. The application of the proposed procedure to modeling storm water quality parameters in two French catchments shows that it was able to significantly reduce the number of explanatory variables for successive analyses. Finally, the EPR-MOGA models obtained after the input selection are compared with those obtained by using the same technique without benefitting from input selection and with those obtained in previous works where other data-modeling techniques were used on the same data. The comparison highlights the effectiveness of both EPR-MOGA and the input selection procedure.

  14. The comet assay in higher terrestrial plant model: Review and evolutionary trends.

    Science.gov (United States)

    Lanier, Caroline; Manier, Nicolas; Cuny, Damien; Deram, Annabelle

    2015-12-01

    The comet assay is a sensitive technique for the measurement of DNA damage in individual cells. Although it has been primarily applied to animal cells, its adaptation to higher plant tissues significantly extends the utility of plants for environmental genotoxicity research. The present review focuses on 101 key publications and discusses protocols and evolutionary trends specific to higher plants. General consensus validates the use of the percentage of DNA found in the tail, the alkaline version of the test and root study. The comet protocol has proved its effectiveness and its adaptability for cultivated plant models. Its transposition in wild plants thus appears as a logical evolution. However, certain aspects of the protocol can be improved, namely through the systematic use of positive controls and increasing the number of nuclei read. These optimizations will permit the increase in the performance of this test, namely when interpreting mechanistic and physiological phenomena. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Evolutionary Neural Gas (ENG): A Model of Self Organizing Network from Input Categorization

    CERN Document Server

    Licata, Ignazio

    2010-01-01

    Despite their claimed biological plausibility, most self organizing networks have strict topological constraints and consequently they cannot take into account a wide range of external stimuli. Furthermore their evolution is conditioned by deterministic laws which often are not correlated with the structural parameters and the global status of the network, as it should happen in a real biological system. In nature the environmental inputs are noise affected and fuzzy. Which thing sets the problem to investigate the possibility of emergent behaviour in a not strictly constrained net and subjected to different inputs. It is here presented a new model of Evolutionary Neural Gas (ENG) with any topological constraints, trained by probabilistic laws depending on the local distortion errors and the network dimension. The network is considered as a population of nodes that coexist in an ecosystem sharing local and global resources. Those particular features allow the network to quickly adapt to the environment, accor...

  16. 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.

  17. Comparative Studies of Population Synthesis Models in the Framework of Modified Strömgren Filters

    Science.gov (United States)

    Sreedhar, Yuvraj Harsha; Rakos, Karl; Hensler, Gerhard

    2014-03-01

    Evolutionary models form a vital part of stellar population research in understanding their evolution, but despite their long history of development, they are often misrepresented and the properties of stellar population observed through broadband and spectroscopic measurements are also misinterpreted. With growing numbers of these synthesis models, model comparison becomes an important analysis to choose a suitable model for understanding stellar populations and model up-gradation. Along with model comparison, we reinvestigate the technique of modified Strömgren photometry to measure reliable parameter-sensitive colours and estimate precise model ages and metallicities. The assessment of Rakos/Schulz models with GALEV and Worthey's Lick/IDS model find smaller colour variation: Δ( uz - vz) ≤ 0.056, Δ( bz - yz) ≤ -0.05 and Δ( vz - yz) ≤ 0.061. The study conveys a good agreement of GALEV models with modified Strömgren colours but with poor UV model predictions and observed globular cluster data, while the spectroscopic models perform badly because of outdated isochrone and stellar spectral libraries with inaccurate/insufficient knowledge of various stellar phases and their treatment. Overall, the assessment finds modified Strömgren photometry well suited to study different types stellar populations by mitigating the effects of age-metallicity degeneracy.

  18. Improving evolutionary models for mitochondrial protein data with site-class specific amino acid exchangeability matrices.

    Directory of Open Access Journals (Sweden)

    Katherine A Dunn

    Full Text Available Adequate modeling of mitochondrial sequence evolution is an essential component of mitochondrial phylogenomics (comparative mitogenomics. There is wide recognition within the field that lineage-specific aspects of mitochondrial evolution should be accommodated through lineage-specific amino-acid exchangeability matrices (e.g., mtMam for mammalian data. However, such a matrix must be applied to all sites and this implies that all sites are subject to the same, or largely similar, evolutionary constraints. This assumption is unjustified. Indeed, substantial differences are expected to arise from three-dimensional structures that impose different physiochemical environments on individual amino acid residues. The objectives of this paper are (1 to investigate the extent to which amino acid evolution varies among sites of mitochondrial proteins, and (2 to assess the potential benefits of explicitly modeling such variability. To achieve this, we developed a novel method for partitioning sites based on amino acid physiochemical properties. We apply this method to two datasets derived from complete mitochondrial genomes of mammals and fish, and use maximum likelihood to estimate amino acid exchangeabilities for the different groups of sites. Using this approach we identified large groups of sites evolving under unique physiochemical constraints. Estimates of amino acid exchangeabilities differed significantly among such groups. Moreover, we found that joint estimates of amino acid exchangeabilities do not adequately represent the natural variability in evolutionary processes among sites of mitochondrial proteins. Significant improvements in likelihood are obtained when the new matrices are employed. We also find that maximum likelihood estimates of branch lengths can be strongly impacted. We provide sets of matrices suitable for groups of sites subject to similar physiochemical constraints, and discuss how they might be used to analyze real data. We

  19. Improving Evolutionary Models for Mitochondrial Protein Data with Site-Class Specific Amino Acid Exchangeability Matrices

    Science.gov (United States)

    Dunn, Katherine A.; Jiang, Wenyi; Field, Christopher; Bielawski, Joseph P.

    2013-01-01

    Adequate modeling of mitochondrial sequence evolution is an essential component of mitochondrial phylogenomics (comparative mitogenomics). There is wide recognition within the field that lineage-specific aspects of mitochondrial evolution should be accommodated through lineage-specific amino-acid exchangeability matrices (e.g., mtMam for mammalian data). However, such a matrix must be applied to all sites and this implies that all sites are subject to the same, or largely similar, evolutionary constraints. This assumption is unjustified. Indeed, substantial differences are expected to arise from three-dimensional structures that impose different physiochemical environments on individual amino acid residues. The objectives of this paper are (1) to investigate the extent to which amino acid evolution varies among sites of mitochondrial proteins, and (2) to assess the potential benefits of explicitly modeling such variability. To achieve this, we developed a novel method for partitioning sites based on amino acid physiochemical properties. We apply this method to two datasets derived from complete mitochondrial genomes of mammals and fish, and use maximum likelihood to estimate amino acid exchangeabilities for the different groups of sites. Using this approach we identified large groups of sites evolving under unique physiochemical constraints. Estimates of amino acid exchangeabilities differed significantly among such groups. Moreover, we found that joint estimates of amino acid exchangeabilities do not adequately represent the natural variability in evolutionary processes among sites of mitochondrial proteins. Significant improvements in likelihood are obtained when the new matrices are employed. We also find that maximum likelihood estimates of branch lengths can be strongly impacted. We provide sets of matrices suitable for groups of sites subject to similar physiochemical constraints, and discuss how they might be used to analyze real data. We also discuss how

  20. Combining Interactive Infrastructure Modeling and Evolutionary Algorithm Optimization for Sustainable Water Resources Design

    Science.gov (United States)

    Smith, R.; Kasprzyk, J. R.; Zagona, E. A.

    2013-12-01

    Population growth and climate change, combined with difficulties in building new infrastructure, motivate portfolio-based solutions to ensuring sufficient water supply. Powerful simulation models with graphical user interfaces (GUI) are often used to evaluate infrastructure portfolios; these GUI based models require manual modification of the system parameters, such as reservoir operation rules, water transfer schemes, or system capacities. Multiobjective evolutionary algorithm (MOEA) based optimization can be employed to balance multiple objectives and automatically suggest designs for infrastructure systems, but MOEA based decision support typically uses a fixed problem formulation (i.e., a single set of objectives, decisions, and constraints). This presentation suggests a dynamic framework for linking GUI-based infrastructure models with MOEA search. The framework begins with an initial formulation which is solved using a MOEA. Then, stakeholders can interact with candidate solutions, viewing their properties in the GUI model. This is followed by changes in the formulation which represent users' evolving understanding of exigent system properties. Our case study is built using RiverWare, an object-oriented, data-centered model that facilitates the representation of a diverse array of water resources systems. Results suggest that assumptions within the initial MOEA search are violated after investigating tradeoffs and reveal how formulations should be modified to better capture stakeholders' preferences.

  1. Evolutionary models of hot subdwarf B stars with radiative levitation of iron

    Science.gov (United States)

    Anilmis, Nurdan

    2012-01-01

    A B type hot subdwarf star is a very blue horizontal branch star which has a core mass around 0.5 solar mass; and a very thin inert hydrogen envelope. It has colors corresponding to those of a B star in which the Balmer lines are abnormally broad for the color as compared to population I main sequence B stars. SdB stars are puzzling in a number of ways; the theories about their origin and evolution have difficulty explaining the large amount of mass that has to be lost prior to or at the start of core He-burning to attain a very thin envelope. Their peculiar surface abundances are not yet explained by any diffusion processes. First discovered in a Palomar survey undertaken in 1947, B type hot subdwarfs got attention after the discovery of their short period p-mode and long period g-mode oscillations. The potential of asteroseismology gives hope to put the pieces of the sdB puzzle together. The pulsations are explained by a Z-bump mechanism due to enhancement of heavy elements in the location in the star where driving of the pulsations occur. Therefore, it is important to make models of heavy metal abundance profiles during the sdB phase to determine the pulsation modes accurately. Fe is believed to be the major contributor to opacity in the driving zone. In this thesis, we present the results from our evolutionary calculations which take into account radiative levitation of Fe in addition to gravitational settling, thermal and elemental diffusion. Our method is an advance on previous calculations that are non-evolutionary static models in which equilibrium Fe profiles are determined by assuming a balance between gravity and the radiative force, ignoring other diffusive processes. In our work, we also incorporate mass loss and thermohaline convection which reduce the effectiveness of radiative levitation in enhancing the Fe abundance. Our model has a mass of 0.47 solar mass and with T eff = 27 000 K and log g = 5.6. It is derived from an evolutionary sequence that

  2. The photometric evolution of dissolving star clusters. II. Realistic models. Colours and M/L ratios

    NARCIS (Netherlands)

    Anders, P.|info:eu-repo/dai/nl/304833967; Lamers, H.J.G.L.M.|info:eu-repo/dai/nl/072834870; BAumgardt, H.

    2009-01-01

    Evolutionary synthesis models are the primary means of constructing spectrophotometric models of stellar populations, and deriving physical parameters from observations compared with these models. One of the basic assumptions of evolutionary synthesis models has been the time-independence of the

  3. The Hypothesis that the Genetic Code Originated in Coupled Synthesis of Proteins and the Evolutionary Predecessors of Nucleic Acids in Primitive Cells

    Directory of Open Access Journals (Sweden)

    Brian R. Francis

    2015-02-01

    Full Text Available Although analysis of the genetic code has allowed explanations for its evolution to be proposed, little evidence exists in biochemistry and molecular biology to offer an explanation for the origin of the genetic code. In particular, two features of biology make the origin of the genetic code difficult to understand. First, nucleic acids are highly complicated polymers requiring numerous enzymes for biosynthesis. Secondly, proteins have a simple backbone with a set of 20 different amino acid side chains synthesized by a highly complicated ribosomal process in which mRNA sequences are read in triplets. Apparently, both nucleic acid and protein syntheses have extensive evolutionary histories. Supporting these processes is a complex metabolism and at the hub of metabolism are the carboxylic acid cycles. This paper advances the hypothesis that the earliest predecessor of the nucleic acids was a β-linked polyester made from malic acid, a highly conserved metabolite in the carboxylic acid cycles. In the β-linked polyester, the side chains are carboxylic acid groups capable of forming interstrand double hydrogen bonds. Evolution of the nucleic acids involved changes to the backbone and side chain of poly(β-d-malic acid. Conversion of the side chain carboxylic acid into a carboxamide or a longer side chain bearing a carboxamide group, allowed information polymers to form amide pairs between polyester chains. Aminoacylation of the hydroxyl groups of malic acid and its derivatives with simple amino acids such as glycine and alanine allowed coupling of polyester synthesis and protein synthesis. Use of polypeptides containing glycine and l-alanine for activation of two different monomers with either glycine or l-alanine allowed simple coded autocatalytic synthesis of polyesters and polypeptides and established the first genetic code. A primitive cell capable of supporting electron transport, thioester synthesis, reduction reactions, and synthesis of

  4. An evolutionary model of cooperation, fairness and altruistic punishment in public good games

    National Research Council Canada - National Science Library

    Hetzer, Moritz; Sornette, Didier

    2013-01-01

    We identify and explain the mechanisms that account for the emergence of fairness preferences and altruistic punishment in voluntary contribution mechanisms by combining an evolutionary perspective...

  5. Evolutionary Theory under Fire.

    Science.gov (United States)

    Lewin, Roger

    1980-01-01

    Summarizes events of a conference on evolutionary biology in Chicago entitled: "Macroevolution." Reviews the theory of modern synthesis, a term used to explain Darwinism in terms of population biology and genetics. Issues presented at the conference are discussed in detail. (CS)

  6. An Evolutionary Algorithm for Multiobjective Fuzzy Portfolio Selection Models with Transaction Cost and Liquidity

    Directory of Open Access Journals (Sweden)

    Wei Yue

    2015-01-01

    Full Text Available The major issues for mean-variance-skewness models are the errors in estimations that cause corner solutions and low diversity in the portfolio. In this paper, a multiobjective fuzzy portfolio selection model with transaction cost and liquidity is proposed to maintain the diversity of portfolio. In addition, we have designed a multiobjective evolutionary algorithm based on decomposition of the objective space to maintain the diversity of obtained solutions. The algorithm is used to obtain a set of Pareto-optimal portfolios with good diversity and convergence. To demonstrate the effectiveness of the proposed model and algorithm, the performance of the proposed algorithm is compared with the classic MOEA/D and NSGA-II through some numerical examples based on the data of the Shanghai Stock Exchange Market. Simulation results show that our proposed algorithm is able to obtain better diversity and more evenly distributed Pareto front than the other two algorithms and the proposed model can maintain quite well the diversity of portfolio. The purpose of this paper is to deal with portfolio problems in the weighted possibilistic mean-variance-skewness (MVS and possibilistic mean-variance-skewness-entropy (MVS-E frameworks with transaction cost and liquidity and to provide different Pareto-optimal investment strategies as diversified as possible for investors at a time, rather than one strategy for investors at a time.

  7. Firms' Decision Making Process in an Evolutionary Model of Industrial Dynamics

    Science.gov (United States)

    Kwasnicki, Witold

    Evolutionary model of industrial dynamics, presented in this paper, can be classified as Schumpeterian one. The model describes the behaviour of a number of competing firms producing functionally equivalent products. Each firm tries to improve its position in the industry and in the market by introducing innovations in order to minimize the unit costs of production, maximize the productivity of capital, and maximize the competitiveness of its products on the market. The problem how decisions are made seems to be crucial for relevant modelling of socio-economic processes. The main aim of the simulations presented in the second part of the paper is to show how fluctuations and discontinuities occurs in economic processes due to boundedly rational decisions of competing firms. It is shown how fluctuation of 3-6 years and of 10 years periodicity can occur in an industry development because of firms' bounded rationality. Long waves of development of 50-60 years period (Kondratieff cycles) occur in the model because of radical innovation emergence at the maturity phase of an `old' technology.

  8. BIRDS AS A MODEL TO STUDY ADULT NEUROGENESIS: BRIDGING EVOLUTIONARY, COMPARATIVE AND NEUROETHOLOGICAL APPROCHES

    Science.gov (United States)

    BARNEA, ANAT; PRAVOSUDOV, VLADIMIR

    2011-01-01

    During the last few decades evidence has demonstrated that adult neurogenesis is a well-preserved feature throughout the animal kingdom. In birds, ongoing neuronal addition occurs rather broadly, to a number of brain regions. This review describes adult avian neurogenesis and neuronal recruitment, discusses factors that regulate these processes, and touches upon the question of their genetic control. Several attributes make birds an extremely advantageous model to study neurogenesis. First, song learning exhibits seasonal variation that is associated with seasonal variation in neuronal turnover in some song control brain nuclei, which seems to be regulated via adult neurogenesis. Second, food-caching birds naturally use memory-dependent behavior in learning locations of thousands of food caches scattered over their home ranges. In comparison with other birds, food-caching species have relatively enlarged hippocampi with more neurons and intense neurogenesis, which appears to be related to spatial learning. Finally, migratory behavior and naturally occurring social systems in birds also provide opportunities to investigate neurogenesis. Such diversity of naturally-occurring memory-based behaviors, combined with the fact that birds can be studied both in the wild and in the laboratory, make them ideal for investigation of neural processes underlying learning. This can be done by using various approaches, from evolutionary and comparative to neuroethological and molecular. Finally, we connect the avian arena to a broader view by providing a brief comparative and evolutionary overview of adult neurogenesis and by discussing the possible functional role of the new neurons. We conclude by indicating future directions and possible medical applications. PMID:21929623

  9. Combining optimal defense theory and the evolutionary dilemma model to refine predictions regarding plant invasion.

    Science.gov (United States)

    Alba, Christina; Bowers, M Deane; Hufbauer, Ruth

    2012-08-01

    Optimal defense theory posits that plants with limited resources deploy chemical defenses based on the fitness value of different tissues and their probability of attack. However, what constitutes optimal defense depends on the identity of the herbivores involved in the interaction. Generalists, which are not tightly coevolved with their many host plants, are typically deterred by chemical defenses, while coevolved specialists are often attracted to these same chemicals. This imposes an "evolutionary dilemma" in which generalists and specialists exert opposing selection on plant investment in defense, thereby stabilizing defenses at intermediate levels. We used the natural shift in herbivore community composition that typifies many plant invasions to test a novel, combined prediction of optimal defense theory and the evolutionary dilemma model: that the within-plant distribution of defenses reflects both the value of different tissues (i.e., young vs. old leaves) and the relative importance of specialist and generalist herbivores in the community. Using populations of Verbascum thapsus exposed to ambient herbivory in its native range (where specialist and generalist chewing herbivores are prevalent) and its introduced range (where only generalist chewing herbivores are prevalent), we illustrate significant differences in the way iridoid glycosides are distributed among young and old leaves. Importantly, high-quality young leaves are 6.5x more highly defended than old leaves in the introduced range, but only 2x more highly defended in the native range. Additionally, defense levels are tracked by patterns of chewing damage, with damage restricted mostly to low-quality old leaves in the introduced range, but not the native range. Given that whole-plant investment in defense does not differ between ranges, introduced mullein may achieve increased fitness simply by optimizing its within-plant distribution of defense in the absence of certain specialist herbivores.

  10. Eco-evolutionary feedbacks, adaptive dynamics and evolutionary rescue theory.

    Science.gov (United States)

    Ferriere, Regis; Legendre, Stéphane

    2013-01-19

    Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause 'evolutionary suicide'. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called 'evolutionary trapping'. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps.

  11. Teachers' Views on Understanding Evolutionary Theory: A PCK-Study in the Framework of the ERTE-Model

    Science.gov (United States)

    van Dijk, Esther M.

    2009-01-01

    The study of Pedagogical Content Knowledge (PCK) that is presented in this paper aims to obtain an impression of teachers' knowledge and beliefs concerning teaching evolutionary theory. The starting point of this project was the development of the Educational Reconstruction for Teacher Education model (ERTE). The PCK-study shows that teachers'…

  12. Use of genome-scale metabolic models in evolutionary systems biology.

    NARCIS (Netherlands)

    Papp, B.; Szappanos, B.; Notebaart, R.A.

    2011-01-01

    One of the major aims of the nascent field of evolutionary systems biology is to test evolutionary hypotheses that are not only realistic from a population genetic point of view but also detailed in terms of molecular biology mechanisms. By providing a mapping between genotype and phenotype for

  13. Grand challenges in evolutionary and population genetics: The importance of integrating epigenetics, genomics, modeling, and experimentation

    Science.gov (United States)

    Samuel A. Cushman

    2014-01-01

    This is a time of explosive growth in the fields of evolutionary and population genetics, with whole genome sequencing and bioinformatics driving a transformative paradigm shift (Morozova and Marra, 2008). At the same time, advances in epigenetics are thoroughly transforming our understanding of evolutionary processes and their implications for populations, species and...

  14. Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.

    Directory of Open Access Journals (Sweden)

    Sanzo Miyazawa

    Full Text Available BACKGROUND: A mechanistic codon substitution model, in which each codon substitution rate is proportional to the product of a codon mutation rate and the average fixation probability depending on the type of amino acid replacement, has advantages over nucleotide, amino acid, and empirical codon substitution models in evolutionary analysis of protein-coding sequences. It can approximate a wide range of codon substitution processes. If no selection pressure on amino acids is taken into account, it will become equivalent to a nucleotide substitution model. If mutation rates are assumed not to depend on the codon type, then it will become essentially equivalent to an amino acid substitution model. Mutation at the nucleotide level and selection at the amino acid level can be separately evaluated. RESULTS: The present scheme for single nucleotide mutations is equivalent to the general time-reversible model, but multiple nucleotide changes in infinitesimal time are allowed. Selective constraints on the respective types of amino acid replacements are tailored to each gene in a linear function of a given estimate of selective constraints. Their good estimates are those calculated by maximizing the respective likelihoods of empirical amino acid or codon substitution frequency matrices. Akaike and Bayesian information criteria indicate that the present model performs far better than the other substitution models for all five phylogenetic trees of highly-divergent to highly-homologous sequences of chloroplast, mitochondrial, and nuclear genes. It is also shown that multiple nucleotide changes in infinitesimal time are significant in long branches, although they may be caused by compensatory substitutions or other mechanisms. The variation of selective constraint over sites fits the datasets significantly better than variable mutation rates, except for 10 slow-evolving nuclear genes of 10 mammals. An critical finding for phylogenetic analysis is that

  15. Evolutionary transition from biological to social systems via generation of reflexive models of externality.

    Science.gov (United States)

    Igamberdiev, Abir U

    2017-12-01

    Evolutionary transition from biological to social systems corresponds to the emergence of the structure of subject that incorporates the internal image of the external world. This structure, established on the basis of referral of the subject (self) to its symbolic image, acquires a potential to rationally describe the external world through the semiotic structure of human language. It has been modelled in reflexive psychology using the algebra of simple relations (Lefebvre, V.A., J. Soc. Biol. Struct. 10, 129-175, 1987). The model introduces a substantial opposition of the two basic complementary types of reflexion defined as Western (W) and Eastern (E). These types generate opposite models of behavior and opposite organizations of societies. Development of human societies involves the interactions of W and E types not only between the societies but also within one society underlying its homeostasis and dynamics. Invention of new ideas and implementation of new technologies shift the probability pattern of reflexive choices, appearing as internal assessments of the individual agents within a society, and direct changes in the preference of reflexive types. The dynamics of societies and of interactions between societies is based on the interference of opposite reflexive structures and on the establishment of different patterns during such interference. At different times in the history of human civilization these changing patterns resulted in the formation and splitting of large empires, the development and spreading of new technologies, the consecutive periods of wellness and decline. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Unsupervised Primary Object Discovery in Videos Based on Evolutionary Primary Object Modeling With Reliable Object Proposals.

    Science.gov (United States)

    Koh, Yeong Jun; Kim, Chang-Su

    2017-11-01

    A novel primary object discovery (POD) algorithm, which uses reliable object proposals while exploiting the recurrence property of a primary object in a video sequence, is proposed in this paper. First, we generate both color-based and motion-based object proposals in each frame, and extract the feature of each proposal using the random walk with restart simulation. Next, we estimate the foreground confidence for each proposal to remove unreliable proposals. By superposing the features of the remaining reliable proposals, we construct the primary object models. To this end, we develop the evolutionary primary object modeling technique, which exploits the recurrence property of the primary object. Then, using the primary object models, we choose the main proposal in each frame and find the location of the primary object by merging the main proposal with candidate proposals selectively. Finally, we refine the discovered bounding boxes by exploiting temporal correlations of the recurring primary object. Extensive experimental results demonstrate that the proposed POD algorithm significantly outperforms conventional algorithms.

  17. Subject-specific planning of femoroplasty: a combined evolutionary optimization and particle diffusion model approach.

    Science.gov (United States)

    Basafa, Ehsan; Armand, Mehran

    2014-07-18

    A potential effective treatment for prevention of osteoporotic hip fractures is augmentation of the mechanical properties of the femur by injecting it with agents such as (PMMA) bone cement - femoroplasty. The operation, however, is only in research stage and can benefit substantially from computer planning and optimization. We report the results of computational planning and optimization of the procedure for biomechanical evaluation. An evolutionary optimization method was used to optimally place the cement in finite element (FE) models of seven osteoporotic bone specimens. The optimization, with some inter-specimen variations, suggested that areas close to the cortex in the superior and inferior of the neck and supero-lateral aspect of the greater trochanter will benefit from augmentation. We then used a particle-based model for bone cement diffusion simulation to match the optimized pattern, taking into account the limitations of the actual surgery, including limited volume of injection to prevent thermal necrosis. Simulations showed that the yield load can be significantly increased by more than 30%, using only 9 ml of bone cement. This increase is comparable to previous literature reports where gross filling of the bone was employed instead, using more than 40 ml of cement. These findings, along with the differences in the optimized plans between specimens, emphasize the need for subject-specific models for effective planning of femoral augmentation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. SIS evolutionary game model and multi-agent simulation of an infectious disease emergency.

    Science.gov (United States)

    Yang, Fan; Yang, Qing; Liu, Xingxing; Wang, Pan

    2015-01-01

    Susceptible-Infected-Susceptible (SIS) infectious disease outbreaks are hazardous events. However, if governments sectors do not adequately supervise such outbreaks, these infectious diseases could spread significantly, resulting in large economic losses and social issues. In this paper, an evolutionary game and simulation model based on the interactions between strategies and states was proposed, and the game between the public and government sectors and its impact on epidemic situations was discussed. Replicator dynamics equations and the multi-agent model simulation were used for analysis. According to replicator dynamics equations as well as the multi-agent model simulation, the public all eventually adopted the mobility strategy. In addition, the supervision strength of the governmental sectors was equal to 0 after the strength fluctuated at a low level under the trigger strategy. Ultimately, the entire public shifted to the S state throughout the course of the emergency. Social order was maintained and social loss was controlled to a certain extent in the final analysis.

  19. A molecular phylogeny of nephilid spiders: evolutionary history of a model lineage.

    Science.gov (United States)

    Kuntner, Matjaž; Arnedo, Miquel A; Trontelj, Peter; Lokovšek, Tjaša; Agnarsson, Ingi

    2013-12-01

    The pantropical orb web spider family Nephilidae is known for the most extreme sexual size dimorphism among terrestrial animals. Numerous studies have made Nephilidae, particularly Nephila, a model lineage in evolutionary research. However, a poorly understood phylogeny of this lineage, relying only on morphology, has prevented thorough evolutionary syntheses of nephilid biology. We here use three nuclear and five mitochondrial genes for 28 out of 40 nephilid species to provide a more robust nephilid phylogeny and infer clade ages in a fossil-calibrated Bayesian framework. We complement the molecular analyses with total evidence analysis including morphology. All analyses find strong support for nephilid monophyly and exclusivity and the monophyly of the genera Herennia and Clitaetra. The inferred phylogenetic structure within Nephilidae is novel and conflicts with morphological phylogeny and traditional taxonomy. Nephilengys species fall into two clades, one with Australasian species (true Nephilengys) as sister to Herennia, and another with Afrotropical species (Nephilingis Kuntner new genus) as sister to a clade containing Clitaetra plus most currently described Nephila. Surprisingly, Nephila is also diphyletic, with true Nephila containing N. pilipes+N. constricta, and the second clade with all other species sister to Clitaetra; this "Nephila" clade is further split into an Australasian clade that also contains the South American N. sexpunctata and the Eurasian N. clavata, and an African clade that also contains the Panamerican N. clavipes. An approximately unbiased test constraining the monophyly of Nephilengys, Nephila, and Nephilinae (Nephila, Nephilengys, Herennia), respectively, rejected Nephilengys monophyly, but not that of Nephila and Nephilinae. Further data are therefore necessary to robustly test these two new, but inconclusive findings, and also to further test the precise placement of Nephilidae within the Araneoidea. For divergence date estimation

  20. AN EVOLUTIONARY MODEL FOR COLLAPSING MOLECULAR CLOUDS AND THEIR STAR FORMATION ACTIVITY

    Energy Technology Data Exchange (ETDEWEB)

    Zamora-Aviles, Manuel; Vazquez-Semadeni, Enrique; Colin, Pedro [Centro de Radioastronomia y Astrofisica, Universidad Nacional Autonoma de Mexico, Apdo. Postal 3-72, Morelia, Michoacan, 58089 (Mexico)

    2012-05-20

    We present an idealized, semi-empirical model for the evolution of gravitationally contracting molecular clouds (MCs) and their star formation rate (SFR) and efficiency (SFE). The model assumes that the instantaneous SFR is given by the mass above a certain density threshold divided by its free-fall time. The instantaneous number of massive stars is computed assuming a Kroupa initial mass function. These stars feed back on the cloud through ionizing radiation, eroding it. The main controlling parameter of the evolution turns out to be the maximum cloud mass, M{sub max}. This allows us to compare various properties of the model clouds against their observational counterparts. A giant molecular cloud (GMC) model (M{sub max} {approx} 10{sup 5} M{sub Sun }) adheres very well to the evolutionary scenario recently inferred by Kawamura et al. for GMCs in the Large Magellanic Cloud. A model cloud with M{sub max} Almost-Equal-To 2000 M{sub Sun} evolves in the Kennicutt-Schmidt diagram, first passing through the locus of typical low-to-intermediate-mass star-forming clouds, and then moving toward the locus of high-mass star-forming ones over the course of {approx}10 Myr. Also, the stellar age histograms for this cloud a few Myr before its destruction agree very well with those observed in the {rho}-Oph stellar association, whose parent cloud has a similar mass, and imply that the SFR of the clouds increases with time. Our model thus agrees well with various observed properties of star-forming MCs, suggesting that the scenario of gravitationally collapsing MCs, with their SFR regulated by stellar feedback, is entirely feasible and in agreement with key observed properties of MCs.

  1. Evolutionary optimization of life-history traits in the sea beet Beta vulgaris subsp. maritima: Comparing model to data

    Science.gov (United States)

    Hautekèete, N.-C.; Van Dijk, H.; Piquot, Y.; Teriokhin, A.

    2009-01-01

    At evolutionary equilibrium, ecological factors will determine the optimal combination of life-history trait values of an organism. This optimum can be assessed by assuming that the species maximizes some criterion of fitness such as the Malthusian coefficient or lifetime reproductive success depending on the degree of density-dependence. We investigated the impact of the amount of resources and habitat stability on a plant's age at maturity and life span by using an evolutionary optimization model in combination with empirical data. We conducted this study on sea beet, Beta vulgaris subsp. maritima, because of its large variation in life span and age at first reproduction along a latitudinal gradient including considerable ecological variation. We also compared the consequence in our evolutionary model of maximizing either the Malthusian coefficient or the lifetime reproductive success. Both the data analysis and the results of evolutionary modeling pointed to habitat disturbance and resources like length of the growing season as factors negatively related to life span and age at maturity in sea beet. Resource availability had a negative theoretical influence with the Malthusian coefficient as the chosen optimality criterion, while there was no influence in the case of lifetime reproductive success. As suggested by previous theoretical work the final conclusion on what criterion is more adequate depends on the assumptions of how in reality density-dependence restrains population growth. In our case of sea beet data R0 seems to be less appropriate than λ.

  2. Synthesis analysis of regression models with a continuous outcome.

    Science.gov (United States)

    Zhou, Xiao-Hua; Hu, Nan; Hu, Guizhou; Root, Martin

    2009-05-15

    To estimate the multivariate regression model from multiple individual studies, it would be challenging to obtain results if the input from individual studies only provide univariate or incomplete multivariate regression information. Samsa et al. (J. Biomed. Biotechnol. 2005; 2:113-123) proposed a simple method to combine coefficients from univariate linear regression models into a multivariate linear regression model, a method known as synthesis analysis. However, the validity of this method relies on the normality assumption of the data, and it does not provide variance estimates. In this paper we propose a new synthesis method that improves on the existing synthesis method by eliminating the normality assumption, reducing bias, and allowing for the variance estimation of the estimated parameters. (c) 2009 John Wiley & Sons, Ltd.

  3. Genome-scale modeling of the evolutionary path to C4 photosynthesis

    Science.gov (United States)

    Myers, Christopher R.; Bogart, Eli

    In C4 photosynthesis, plants maintain a high carbon dioxide level in specialized bundle sheath cells surrounding leaf veins and restrict CO2 assimilation to those cells, favoring CO2 over O2 in competition for Rubisco active sites. In C3 plants, which do not possess such a carbon concentrating mechanism, CO2 fixation is reduced due to this competition. Despite the complexity of the C4 system, it has evolved convergently from more than 60 independent origins in diverse families of plants around the world over the last 30 million years. We study the evolution of the C4 system in a genome-scale model of plant metabolism that describes interacting mesophyll and bundle sheath cells and enforces key nonlinear kinetic relationships. Adapting the zero-temperature string method for simulating transition paths in physics and chemistry, we find the highest-fitness paths connecting C3 and C4 positions in the model's high-dimensional parameter space, and show that they reproduce known aspects of the C3-C4 transition while making additional predictions about metabolic changes along the path. We explore the relationship between evolutionary history and C4 biochemical subtype, and the effects of atmospheric carbon dioxide levels.

  4. A shape-guided deformable model with evolutionary algorithm initialization for 3D soft tissue segmentation.

    Science.gov (United States)

    Heimann, Tobias; Münzing, Sascha; Meinzer, Hans-Peter; Wolf, Ivo

    2007-01-01

    We present a novel method for the segmentation of volumetric images, which is especially suitable for highly variable soft tissue structures. Core of the algorithm is a statistical shape model (SSM) of the structure of interest. A global search with an evolutionary algorithm is employed to detect suitable initial parameters for the model, which are subsequently optimized by a local search similar to the Active Shape mechanism. After that, a deformable mesh with the same topology as the SSM is used for the final segmentation: While external forces strive to maximize the posterior probability of the mesh given the local appearance around the boundary, internal forces governed by tension and rigidity terms keep the shape similar to the underlying SSM. To prevent outliers and increase robustness, we determine the applied external forces by an algorithm for optimal surface detection with smoothness constraints. The approach is evaluated on 54 CT images of the liver and reaches an average surface distance of 1.6 +/- 0.5 mm in comparison to manual reference segmentations.

  5. A unified model of Hymenopteran preadaptations that trigger the evolutionary transition to eusociality

    Science.gov (United States)

    Quiñones, Andrés E.; Pen, Ido

    2017-01-01

    Explaining the origin of eusociality, with strict division of labour between workers and reproductives, remains one of evolutionary biology’s greatest challenges. Specific combinations of genetic, behavioural and demographic traits in Hymenoptera are thought to explain their relatively high frequency of eusociality, but quantitative models integrating such preadaptations are lacking. Here we use mathematical models to show that the joint evolution of helping behaviour and maternal sex ratio adjustment can synergistically trigger both a behavioural change from solitary to eusocial breeding, and a demographic change from a life cycle with two reproductive broods to a life cycle in which an unmated cohort of female workers precedes a final generation of dispersing reproductives. Specific suits of preadaptations are particularly favourable to the evolution of eusociality: lifetime monogamy, bivoltinism with male generation overlap, hibernation of mated females and haplodiploidy with maternal sex ratio adjustment. The joint effects of these preadaptations may explain the abundance of eusociality in the Hymenoptera and its virtual absence in other haplodiploid lineages. PMID:28643786

  6. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.

    Science.gov (United States)

    Biasini, Marco; Bienert, Stefan; Waterhouse, Andrew; Arnold, Konstantin; Studer, Gabriel; Schmidt, Tobias; Kiefer, Florian; Gallo Cassarino, Tiziano; Bertoni, Martino; Bordoli, Lorenza; Schwede, Torsten

    2014-07-01

    Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces generate reliable models without the need for complex software packages or downloading large databases. Here, we describe the latest version of the SWISS-MODEL expert system for protein structure modelling. The SWISS-MODEL template library provides annotation of quaternary structure and essential ligands and co-factors to allow for building of complete structural models, including their oligomeric structure. The improved SWISS-MODEL pipeline makes extensive use of model quality estimation for selection of the most suitable templates and provides estimates of the expected accuracy of the resulting models. The accuracy of the models generated by SWISS-MODEL is continuously evaluated by the CAMEO system. The new web site allows users to interactively search for templates, cluster them by sequence similarity, structurally compare alternative templates and select the ones to be used for model building. In cases where multiple alternative template structures are available for a protein of interest, a user-guided template selection step allows building models in different functional states. SWISS-MODEL is available at http://swissmodel.expasy.org/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Direct Test of the Brown Dwarf Evolutionary Models Through Secondary Eclipse Spectroscopy of LHS 6343

    Science.gov (United States)

    Albert, Loic

    2015-10-01

    As the number of field Brown Dwarfs counts in the thousands, interpreting their physical parameters (mass, temperature, radius, luminosity, age, metallicity) relies as heavily as ever on atmosphere and evolutionary models. Fortunately, models are largely successful in explaining observations (colors, spectral types, luminosity), so they appear well calibrated in a relative sense. However, an absolute model-independent calibration is still lacking. Eclipsing BDs systems are a unique laboratory in this respect but until recently only one such system was known, 2M0535-05 - a very young (Brown Dwarfs showing a peculiar temperature reversal (Stassun et al. 2006). Due to its young age, 2M0535-05 is an ill-suited test for Gyr-old field Brown Dwarfs whose population is by far the most common in the solar neighborhood. Recently, a second system - an evolved BD (>1 Gyr) - was identified (62.1+/-1.2 MJup, 0.783+/-0.011 RJup) transiting LHS6343 with a 12.7-day period. We propose to use WFC3 in drift scan mode and 5 HST orbits to determine the spectral type (a proxy for temperature) as well as the near-infrared luminosity of this brown dwarf. We conducted simulations that predict a signal-to-noise ratio ranging between 10 and 30 per resolution element in the peaks of the spectrum. These measurements, coupled with existing luminosity measurements with Spitzer at 3.6 and 4.5 microns, will allow us to trace the spectral energy distribution of the Brown Dwarf and directly calculate its blackbody temperature. It will be the first field Brown Dwarfs with simultaneous measurements of its radius, mass, luminosity and temperature all measured independently of models.

  8. Computational Models of Financial Price Prediction: A Survey of Neural Networks, Kernel Machines and Evolutionary Computation Approaches

    Directory of Open Access Journals (Sweden)

    Javier Sandoval

    2011-12-01

    Full Text Available A review of the representative models of machine learning research applied to the foreign exchange rate and stock price prediction problem is conducted.  The article is organized as follows: The first section provides a context on the definitions and importance of foreign exchange rate and stock markets.  The second section reviews machine learning models for financial prediction focusing on neural networks, SVM and evolutionary methods. Lastly, the third section draws some conclusions.

  9. Diversity arrays technology (DArT for pan-genomic evolutionary studies of non-model organisms.

    Directory of Open Access Journals (Sweden)

    Karen E James

    Full Text Available BACKGROUND: High-throughput tools for pan-genomic study, especially the DNA microarray platform, have sparked a remarkable increase in data production and enabled a shift in the scale at which biological investigation is possible. The use of microarrays to examine evolutionary relationships and processes, however, is predominantly restricted to model or near-model organisms. METHODOLOGY/PRINCIPAL FINDINGS: This study explores the utility of Diversity Arrays Technology (DArT in evolutionary studies of non-model organisms. DArT is a hybridization-based genotyping method that uses microarray technology to identify and type DNA polymorphism. Theoretically applicable to any organism (even one for which no prior genetic data are available, DArT has not yet been explored in exclusively wild sample sets, nor extensively examined in a phylogenetic framework. DArT recovered 1349 markers of largely low copy-number loci in two lineages of seed-free land plants: the diploid fern Asplenium viride and the haploid moss Garovaglia elegans. Direct sequencing of 148 of these DArT markers identified 30 putative loci including four routinely sequenced for evolutionary studies in plants. Phylogenetic analyses of DArT genotypes reveal phylogeographic and substrate specificity patterns in A. viride, a lack of phylogeographic pattern in Australian G. elegans, and additive variation in hybrid or mixed samples. CONCLUSIONS/SIGNIFICANCE: These results enable methodological recommendations including procedures for detecting and analysing DArT markers tailored specifically to evolutionary investigations and practical factors informing the decision to use DArT, and raise evolutionary hypotheses concerning substrate specificity and biogeographic patterns. Thus DArT is a demonstrably valuable addition to the set of existing molecular approaches used to infer biological phenomena such as adaptive radiations, population dynamics, hybridization, introgression, ecological

  10. An Evolutionary Game Theory Model of Revision-Resistant Motivations and Strategic Reasoning

    National Research Council Canada - National Science Library

    DeLancey, Craig

    2008-01-01

    Strong reciprocity and other forms of cooperation with non-kin in large groups and in one-time social interactions is difficult to explain with traditional economic or with simple evolutionary accounts...

  11. Asteroseismological study of massive ZZ Ceti stars with fully evolutionary models

    Energy Technology Data Exchange (ETDEWEB)

    Romero, A. D.; Kepler, S. O. [Departamento de Astronomia, Universidade Federal do Rio Grande do Sul, Av. Bento Goncalves 9500, Porto Alegre 91501-970, RS (Brazil); Córsico, A. H.; Althaus, L. G. [Facultad de Ciencias Astronómicas y Geofísicas, Universidad Nacional de La Plata, Paseo del Bosque s/n, (1900) La Plata (Argentina); Fraga, L., E-mail: alejandra.romero@ufrgs.br [Southern Observatory for Astrophysical Research, Casilla 603, La Serena (Chile)

    2013-12-10

    We present the first asteroseismological study for 42 massive ZZ Ceti stars based on a large set of fully evolutionary carbon-oxygen core DA white dwarf models characterized by a detailed and consistent chemical inner profile for the core and the envelope. Our sample comprises all of the ZZ Ceti stars with spectroscopic stellar masses between 0.72 and 1.05 M {sub ☉} known to date. The asteroseismological analysis of a set of 42 stars enables study of the ensemble properties of the massive, pulsating white dwarf stars with carbon-oxygen cores, in particular the thickness of the hydrogen envelope and the stellar mass. A significant fraction of stars in our sample have stellar mass that is high enough to crystallize at the effective temperatures of the ZZ Ceti instability strip, which enables us to study the effects of crystallization on the pulsation properties of these stars. Our results show that the phase diagram presented in Horowitz et al. seems to be a good representation of the crystallization process inside white dwarf stars, in agreement with the results from white dwarf luminosity function in globular clusters.

  12. Probing the Structure of Kepler ZZ Ceti Stars with Full Evolutionary Models-based Asteroseismology

    Science.gov (United States)

    Romero, Alejandra D.; Córsico, A. H.; Castanheira, B. G.; De Gerónimo, F. C.; Kepler, S. O.; Koester, D.; Kawka, A.; Althaus, L. G.; Hermes, J. J.; Bonato, C.; Gianninas, A.

    2017-12-01

    We present an asteroseismological analysis of four ZZ Ceti stars observed with the Kepler spacecraft: GD 1212, SDSS J113655.17+040952.6, KIC 11911480, and KIC 4552982, based on a grid of full evolutionary models of DA white dwarf (WD) stars. We employ a grid of carbon–oxygen core models, characterized by a detailed and consistent chemical inner profile for the core and the envelope. In addition to the observed periods, we take into account other information from the observational data, such as amplitudes, rotational splittings, and period spacing, as well as photometry and spectroscopy. For each star, we present an asteroseismological model that closely reproduces their observed properties. The asteroseismological stellar mass and effective temperature of the target stars are (0.632+/- 0.027 {M}ȯ , 10737 ± 73 K) for GD 1212, (0.745+/- 0.007 {M}ȯ , 11110 ± 69 K) for KIC 4552982, (0.5480+/- 0.01 {M}ȯ , 12,721 ± 228 K) for KIC11911480, and (0.570+/- 0.01 {M}ȯ , 12,060 ± 300 K) for SDSS J113655.17+040952.6. In general, the asteroseismological values are in good agreement with the spectroscopy. For KIC 11911480 and SDSS J113655.17+040952.6 we derive a similar seismological mass, but the hydrogen envelope is an order of magnitude thinner for SDSS J113655.17+040952.6, which is part of a binary system and went through a common envelope phase.

  13. Comparative and Evolutionary Analysis of Grass Pollen Allergens Using Brachypodium distachyon as a Model System

    Science.gov (United States)

    Sharma, Akanksha; Sharma, Niharika; Bhalla, Prem; Singh, Mohan

    2017-01-01

    Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses. Combining genomic data with the anther RNA-Seq dataset revealed 24 pollen allergen genes belonging to eight allergen groups mapping on the five chromosomes in B. distachyon. High levels of anther-specific expression profiles were observed for the 24 identified putative allergen-encoding genes in Brachypodium. The genomic evidence suggests that gene encoding the group 5 allergen, the most potent trigger of hay fever and allergic asthma originated as a pollen specific orphan gene in a common grass ancestor of Brachypodium and Triticiae clades. Gene structure analysis showed that the putative allergen-encoding genes in Brachypodium either lack or contain reduced number of introns. Promoter analysis of the identified Brachypodium genes revealed the presence of specific cis-regulatory sequences likely responsible for high anther/pollen-specific expression. With the identification of putative allergen-encoding genes in Brachypodium, this study has also described some important plant gene families (e.g. expansin superfamily, EF-Hand family, profilins etc) for the first time in the model plant Brachypodium. Altogether, the present study provides new insights into structural characterization and evolution of pollen allergens and will further serve as a base for their functional

  14. Comparative and Evolutionary Analysis of Grass Pollen Allergens Using Brachypodium distachyon as a Model System.

    Directory of Open Access Journals (Sweden)

    Akanksha Sharma

    Full Text Available Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses. Combining genomic data with the anther RNA-Seq dataset revealed 24 pollen allergen genes belonging to eight allergen groups mapping on the five chromosomes in B. distachyon. High levels of anther-specific expression profiles were observed for the 24 identified putative allergen-encoding genes in Brachypodium. The genomic evidence suggests that gene encoding the group 5 allergen, the most potent trigger of hay fever and allergic asthma originated as a pollen specific orphan gene in a common grass ancestor of Brachypodium and Triticiae clades. Gene structure analysis showed that the putative allergen-encoding genes in Brachypodium either lack or contain reduced number of introns. Promoter analysis of the identified Brachypodium genes revealed the presence of specific cis-regulatory sequences likely responsible for high anther/pollen-specific expression. With the identification of putative allergen-encoding genes in Brachypodium, this study has also described some important plant gene families (e.g. expansin superfamily, EF-Hand family, profilins etc for the first time in the model plant Brachypodium. Altogether, the present study provides new insights into structural characterization and evolution of pollen allergens and will further serve as a base for their

  15. Towards a Generic Model of Smart Synthesis Tools

    NARCIS (Netherlands)

    Schotborgh, W.O.; Tragter, Hendrik; Kokkeler, Frans; van Houten, Frederikus J.A.M.; Tomiyama, T.; Krause, Frank-Lothar

    2007-01-01

    Software support for the solution generation phase of the design process did not yet have the same industrial acceptance as e.g. 3D modellers and finite element analysis. The “smart synthesis tools” research project aims to bridge part of this gap between academic research and industrial

  16. 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

  17. Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes.

    Science.gov (United States)

    Nakatani, Yoichiro; McLysaght, Aoife

    2017-07-15

    It has been argued that whole-genome duplication (WGD) exerted a profound influence on the course of evolution. For the purpose of fully understanding the impact of WGD, several formal algorithms have been developed for reconstructing pre-WGD gene order in yeast and plant. However, to the best of our knowledge, those algorithms have never been successfully applied to WGD events in teleost and vertebrate, impeded by extensive gene shuffling and gene losses. Here, we present a probabilistic model of macrosynteny (i.e. conserved linkage or chromosome-scale distribution of orthologs), develop a variational Bayes algorithm for inferring the structure of pre-WGD genomes, and study estimation accuracy by simulation. Then, by applying the method to the teleost WGD, we demonstrate effectiveness of the algorithm in a situation where gene-order reconstruction algorithms perform relatively poorly due to a high rate of rearrangement and extensive gene losses. Our high-resolution reconstruction reveals previously overlooked small-scale rearrangements, necessitating a revision to previous views on genome structure evolution in teleost and vertebrate. We have reconstructed the structure of a pre-WGD genome by employing a variational Bayes approach that was originally developed for inferring topics from millions of text documents. Interestingly, comparison of the macrosynteny and topic model algorithms suggests that macrosynteny can be regarded as documents on ancestral genome structure. From this perspective, the present study would seem to provide a textbook example of the prevalent metaphor that genomes are documents of evolutionary history. The analysis data are available for download at http://www.gen.tcd.ie/molevol/supp_data/MacrosyntenyTGD.zip , and the software written in Java is available upon request. yoichiro.nakatani@tcd.ie or aoife.mclysaght@tcd.ie. Supplementary data are available at Bioinformatics online.

  18. Intention recognition, commitment and their roles in the evolution of cooperation from artificial intelligence techniques to evolutionary game theory models

    CERN Document Server

    Han, The Anh

    2013-01-01

    This original and timely monograph describes a unique self-contained excursion that reveals to the readers the roles of two basic cognitive abilities, i.e. intention recognition and arranging commitments, in the evolution of cooperative behavior. This book analyses intention recognition, an important ability that helps agents predict others’ behavior, in its artificial intelligence and evolutionary computational modeling aspects, and proposes a novel intention recognition method. Furthermore, the book presents a new framework for intention-based decision making and illustrates several ways in which an ability to recognize intentions of others can enhance a decision making process. By employing the new intention recognition method and the tools of evolutionary game theory, this book introduces computational models demonstrating that intention recognition promotes the emergence of cooperation within populations of self-regarding agents. Finally, the book describes how commitment provides a pathway to the evol...

  19. Stylistic gait synthesis based on hidden Markov models

    Science.gov (United States)

    Tilmanne, Joëlle; Moinet, Alexis; Dutoit, Thierry

    2012-12-01

    In this work we present an expressive gait synthesis system based on hidden Markov models (HMMs), following and modifying a procedure originally developed for speaking style adaptation, in speech synthesis. A large database of neutral motion capture walk sequences was used to train an HMM of average walk. The model was then used for automatic adaptation to a particular style of walk using only a small amount of training data from the target style. The open source toolkit that we adapted for motion modeling also enabled us to take into account the dynamics of the data and to model accurately the duration of each HMM state. We also address the assessment issue and propose a procedure for qualitative user evaluation of the synthesized sequences. Our tests show that the style of these sequences can easily be recognized and look natural to the evaluators.

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

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    In recent years, optimization algorithms have received increasing attention by the research community as well as the industry. In the area of evolutionary computation (EC), inspiration for optimization algorithms originates in Darwin’s ideas of evolution and survival of the fittest. Such algorithms...... 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...... optimization. In addition to general investigations in these areas, I introduce a number of algorithms and demonstrate their potential on real-world problems in system identification and control. Furthermore, I investigate dynamic optimization problems in the context of the three fundamental areas as well...

  1. Obscured Supermassive Black Hole Growth - Connections to Host Galaxies and Evolutionary Models

    Science.gov (United States)

    DiPompeo, Michael A.; Hickox, Ryan C.; Myers, Adam D.

    2017-08-01

    A large fraction of the supermassive black hole growth in the Universe is hidden from view behind thick columns of dust. The most heavily obscured quasars can be challenging to detect even with current high energy X-ray observatories such as NuSTAR - however with infrared observations that can detect the hot nuclear dust in even the most enshrouded systems, we are now beginning to characterize large populations of these hidden monsters.With roughly half-a-million quasars selected with WISE, we have found via clustering and CMB lensing cross-correlation measurements that obscured quasars reside in dark matter halos 0.5 dex more massive than unobscured quasars. This implies that obscuration is directly linked to host galaxy properties, and not simply the dust geometry around the quasar. Using cross-correlations we accurately characterize the redshift distribution of the obscured quasar population, confirming that it peaks at z = 1, and using long-wavelength bands find that it has a similar bolometric luminosity distribution as unobscured quasars as well. Finally, using a simple model based on empirical relationships between halo, stellar, and black hole masses, we show that an evolutionary sequence from obscured to unobscured quasar, combined with a flux limit, can predict the observed halo mass differences.Studies of the most obscured quasars provide valuable insights on the rapid growth of the most massive black holes in the Universe, and motivates future work with the next generation high energy observatories such as eROSITA, Athena, and Lynx.

  2. RF building block modeling: optimization and synthesis

    NARCIS (Netherlands)

    Cheng, W.

    2012-01-01

    For circuit designers it is desirable to have relatively simple RF circuit models that do give decent estimation accuracy and provide sufficient understanding of circuits. Chapter 2 in this thesis shows a general weak nonlinearity model that meets these demands. Using a method that is related to

  3. 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.

  4. Evolutionary modeling and correcting for observation error support a 3/5 brain-body allometry for primates.

    Science.gov (United States)

    Grabowski, Mark; Voje, Kjetil L; Hansen, Thomas F

    2016-05-01

    The tight brain-body allometry across mammals and primates has motivated and informed many hypotheses about brain evolution in humans and other taxa. While a 2/3 or a 3/4 scaling is often at the core of such research, such exponents are derived from estimates based on particular statistical and evolutionary assumptions without careful consideration of how either may influence findings. Here we quantify primate brain-body allometry using phylogenetic comparative methods based on models of both adaptive and constrained evolution, and estimate and account for observational error in both response and predictor variables. Our results supported an evolutionary model in which brain size is directly constrained to evolve in unison with body size, rather than adapting to changes in the latter. The effects of controlling for phylogeny and observation error were substantial, and our analysis yielded a novel 3/5 scaling exponent for primate brain-body evolutionary allometry. Using this exponent with the latest brain- and body-size estimates to calculate new encephalization quotients for apes, humans, and fossil hominins, we found early hominins were substantially more encephalized than previously thought. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. An Evolutionary Robotics Approach to the Control of Plant Growth and Motion: Modeling Plants and Crossing the Reality Gap

    DEFF Research Database (Denmark)

    Wahby, Mostafa; Hofstadler, Daniel Nicolas; Heinrich, Mary Katherine

    2016-01-01

    The self-organizing bio-hybrid collaboration of robots and natural plants allows for a variety of interesting applications. As an example we investigate how robots can be used to control the growth and motion of a natural plant, using LEDs to provide stimuli. We follow an evolutionary robotics ap......, for a model of the plant stem dynamics. Future work will extend to two-axes image sampling for a 3-d approach.......The self-organizing bio-hybrid collaboration of robots and natural plants allows for a variety of interesting applications. As an example we investigate how robots can be used to control the growth and motion of a natural plant, using LEDs to provide stimuli. We follow an evolutionary robotics...

  6. Towards an Extended Evolutionary Game Theory with Survival Analysis and Agreement Algorithms for Modeling Uncertainty, Vulnerability, and Deception

    Science.gov (United States)

    Ma, Zhanshan (Sam)

    Competition, cooperation and communication are the three fundamental relationships upon which natural selection acts in the evolution of life. Evolutionary game theory (EGT) is a 'marriage' between game theory and Darwin's evolution theory; it gains additional modeling power and flexibility by adopting population dynamics theory. In EGT, natural selection acts as optimization agents and produces inherent strategies, which eliminates some essential assumptions in traditional game theory such as rationality and allows more realistic modeling of many problems. Prisoner's Dilemma (PD) and Sir Philip Sidney (SPS) games are two well-known examples of EGT, which are formulated to study cooperation and communication, respectively. Despite its huge success, EGT exposes a certain degree of weakness in dealing with time-, space- and covariate-dependent (i.e., dynamic) uncertainty, vulnerability and deception. In this paper, I propose to extend EGT in two ways to overcome the weakness. First, I introduce survival analysis modeling to describe the lifetime or fitness of game players. This extension allows more flexible and powerful modeling of the dynamic uncertainty and vulnerability (collectively equivalent to the dynamic frailty in survival analysis). Secondly, I introduce agreement algorithms, which can be the Agreement algorithms in distributed computing (e.g., Byzantine Generals Problem [6][8], Dynamic Hybrid Fault Models [12]) or any algorithms that set and enforce the rules for players to determine their consensus. The second extension is particularly useful for modeling dynamic deception (e.g., asymmetric faults in fault tolerance and deception in animal communication). From a computational perspective, the extended evolutionary game theory (EEGT) modeling, when implemented in simulation, is equivalent to an optimization methodology that is similar to evolutionary computing approaches such as Genetic algorithms with dynamic populations [15][17].

  7. Equilibrium selection in alternating-offers bargaining models: the evolutionary computing approach

    NARCIS (Netherlands)

    D.D.B. van Bragt; E.H. Gerding (Enrico); J.A. La Poutré (Han)

    2000-01-01

    textabstractA systematic validation of evolutionary techniques in the field of bargaining is presented. For this purpose, the dynamic and equilibrium-selecting behavior of a multi-agent system consisting of adaptive bargaining agents is investigated. The agents' bargaining strategies are updated by

  8. Assessing variation in life-history tactics within a population using mixture regression models: a practical guide for evolutionary ecologists.

    Science.gov (United States)

    Hamel, Sandra; Yoccoz, Nigel G; Gaillard, Jean-Michel

    2017-05-01

    Mixed models are now well-established methods in ecology and evolution because they allow accounting for and quantifying within- and between-individual variation. However, the required normal distribution of the random effects can often be violated by the presence of clusters among subjects, which leads to multi-modal distributions. In such cases, using what is known as mixture regression models might offer a more appropriate approach. These models are widely used in psychology, sociology, and medicine to describe the diversity of trajectories occurring within a population over time (e.g. psychological development, growth). In ecology and evolution, however, these models are seldom used even though understanding changes in individual trajectories is an active area of research in life-history studies. Our aim is to demonstrate the value of using mixture models to describe variation in individual life-history tactics within a population, and hence to promote the use of these models by ecologists and evolutionary ecologists. We first ran a set of simulations to determine whether and when a mixture model allows teasing apart latent clustering, and to contrast the precision and accuracy of estimates obtained from mixture models versus mixed models under a wide range of ecological contexts. We then used empirical data from long-term studies of large mammals to illustrate the potential of using mixture models for assessing within-population variation in life-history tactics. Mixture models performed well in most cases, except for variables following a Bernoulli distribution and when sample size was small. The four selection criteria we evaluated [Akaike information criterion (AIC), Bayesian information criterion (BIC), and two bootstrap methods] performed similarly well, selecting the right number of clusters in most ecological situations. We then showed that the normality of random effects implicitly assumed by evolutionary ecologists when using mixed models was often

  9. A system dynamics model based on evolutionary game theory for green supply chain management diffusion among Chinese manufacturers

    DEFF Research Database (Denmark)

    Tian, Yihui; Govindan, Kannan; Zhu, Qinghua

    2014-01-01

    In this study, a system dynamics (SD) model is developed to guide the subsidy policies to promote the diffusion of green supply chain management (GSCM) in China. The relationships of stakeholders such as government, enterprises and consumers are analyzed through evolutionary game theory. Finally......, the GSCM diffusion process is simulated by the model with a case study on Chinese automotive manufacturing industry. The results show that the subsidies for manufacturers are better than that for consumers to promote GSCM diffusion, and the environmental awareness is another influential key factor....

  10. Restart Operator Meta-heuristics for a Problem-Oriented Evolutionary Strategies Algorithm in Inverse Mathematical MISO Modelling Problem Solving

    Science.gov (United States)

    Ryzhikov, I. S.; Semenkin, E. S.

    2017-02-01

    This study is focused on solving an inverse mathematical modelling problem for dynamical systems based on observation data and control inputs. The mathematical model is being searched in the form of a linear differential equation, which determines the system with multiple inputs and a single output, and a vector of the initial point coordinates. The described problem is complex and multimodal and for this reason the proposed evolutionary-based optimization technique, which is oriented on a dynamical system identification problem, was applied. To improve its performance an algorithm restart operator was implemented.

  11. Sound Synthesis of Objects Swinging through Air Using Physical Models

    Directory of Open Access Journals (Sweden)

    Rod Selfridge

    2017-11-01

    Full Text Available A real-time physically-derived sound synthesis model is presented that replicates the sounds generated as an object swings through the air. Equations obtained from fluid dynamics are used to determine the sounds generated while exposing practical parameters for a user or game engine to vary. Listening tests reveal that for the majority of objects modelled, participants rated the sounds from our model as plausible as actual recordings. The sword sound effect performed worse than others, and it is speculated that one cause may be linked to the difference between expectations of a sound and the actual sound for a given object.

  12. PRE-FORK SYNTHESIS: A MODEL FOR DNA REPLICATION*

    Science.gov (United States)

    Haskell, Edwin H.; Davern, Cedric I.

    1969-01-01

    A model of DNA replication is presented in which DNA synthesis is continuously initiated from parental strand nicks and occurs, with conservation of helix winding number, ahead of the so-called replicating fork. The fork in this model is the locus of unwinding of already replicated, but presumably unstable, DNA. The model, involving Okazaki's notion of multiple initiation, is based upon the properties of Kornberg's DNA polymerase and accounts for the presence of single-stranded nascent DNA fragments in cell lysates. In addition to acting as sites of initiation, the parental strand nicks are implicated as sites of free rotation allowing unwinding of the replicated DNA. PMID:5264136

  13. Paleoanthropology and evolutionary theory.

    Science.gov (United States)

    Tattersall, Ian

    2012-01-01

    Paleoanthropologists of the first half of the twentieth century were little concerned either with evolutionary theory or with the technicalities and broader implications of zoological nomenclature. In consequence, the paleoanthropological literature of the period consisted largely of a series of descriptions accompanied by authoritative pronouncements, together with a huge excess of hominid genera and species. Given the intellectual flimsiness of the resulting paleoanthropological framework, it is hardly surprising that in 1950 the ornithologist Ernst Mayr met little resistance when he urged the new postwar generation of paleoanthropologists to accept not only the elegant reductionism of the Evolutionary Synthesis but a vast oversimplification of hominid phylogenetic history and nomenclature. Indeed, the impact of Mayr's onslaught was so great that even when developments in evolutionary biology during the last quarter of the century brought other paleontologists to the realization that much more has been involved in evolutionary histories than the simple action of natural selection within gradually transforming lineages, paleoanthropologists proved highly reluctant to follow. Even today, paleoanthropologists are struggling to reconcile an intuitive realization that the burgeoning hominid fossil record harbors a substantial diversity of species (bringing hominid evolutionary patterns into line with that of other successful mammalian families), with the desire to cram a huge variety of morphologies into an unrealistically minimalist systematic framework. As long as this theoretical ambivalence persists, our perception of events in hominid phylogeny will continue to be distorted.

  14. The psychological synthesis evaluated by the interactive model

    OpenAIRE

    Giavoni,Adriana; Tamayo,Álvaro

    2010-01-01

    The purpose of this article was to elaborate a model to evaluate the synthesis process resulting from the interaction which is established between opposing constructs, like gender schemas. In social psychology, the existence of opposites is possible to be detecting in contemporary theories, such as individualism versus collectivism and masculinity versus femininity. In all these themes, opposites assume both an oppositional and complementary attitude, but little relevance has been given to th...

  15. Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories.

    Science.gov (United States)

    Guthrie, Violeta Beleva; Allen, Jennifer; Camps, Manel; Karchin, Rachel

    2011-09-01

    Understanding how novel functions evolve (genetic adaptation) is a critical goal of evolutionary biology. Among asexual organisms, genetic adaptation involves multiple mutations that frequently interact in a non-linear fashion (epistasis). Non-linear interactions pose a formidable challenge for the computational prediction of mutation effects. Here we use the recent evolution of β-lactamase under antibiotic selection as a model for genetic adaptation. We build a network of coevolving residues (possible functional interactions), in which nodes are mutant residue positions and links represent two positions found mutated together in the same sequence. Most often these pairs occur in the setting of more complex mutants. Focusing on extended-spectrum resistant sequences, we use network-theoretical tools to identify triple mutant trajectories of likely special significance for adaptation. We extrapolate evolutionary paths (n = 3) that increase resistance and that are longer than the units used to build the network (n = 2). These paths consist of a limited number of residue positions and are enriched for known triple mutant combinations that increase cefotaxime resistance. We find that the pairs of residues used to build the network frequently decrease resistance compared to their corresponding singlets. This is a surprising result, given that their coevolution suggests a selective advantage. Thus, β-lactamase adaptation is highly epistatic. Our method can identify triplets that increase resistance despite the underlying rugged fitness landscape and has the unique ability to make predictions by placing each mutant residue position in its functional context. Our approach requires only sequence information, sufficient genetic diversity, and discrete selective pressures. Thus, it can be used to analyze recent evolutionary events, where coevolution analysis methods that use phylogeny or statistical coupling are not possible. Improving our ability to assess

  16. Mathematical Model of Synthesis Catalyst with Local Reaction Centers

    Directory of Open Access Journals (Sweden)

    I. V. Derevich

    2017-01-01

    Full Text Available The article considers a catalyst granule with a porous ceramic passive substrate and point active centers on which an exothermic synthesis reaction occurs. A rate of the chemical reaction depends on the temperature according to the Arrhenius law. Heat is removed from the pellet surface in products of synthesis due to heat transfer. In our work we first proposed a model for calculating the steady-state temperature of a catalyst pellet with local reaction centers. Calculation of active centers temperature is based on the idea of self-consistent field (mean-field theory. At first, it is considered that powers of the reaction heat release at the centers are known. On the basis of the found analytical solution, which describes temperature distribution inside the granule, the average temperature of the reaction centers is calculated, which then is inserted in the formula for heat release. The resulting system of transcendental algebraic equations is transformed into a system of ordinary differential equations of relaxation type and solved numerically to achieve a steady-state value. As a practical application, the article considers a Fischer-Tropsch synthesis catalyst granule with active cobalt metallic micro-particles. Cobalt micro-particles are the centers of the exothermic reaction of hydrocarbons macromolecular synthesis. Synthesis occurs as a result of absorption of the components of the synthesis gas on metallic cobalt. The temperature distribution inside the granule for a single local center and reaction centers located on the same granule diameter is found. It was found that there is a critical temperature of reactor exceeding of which leads to significant local overheating of the centers - thermal explosion. The temperature distribution with the local reaction centers is qualitatively different from the granule temperature, calculated in the homogeneous approximation. It is shown that, in contrast to the homogeneous approximation, the

  17. The Simulation and Analysis of an Evolutionary Model of Deoxyribonucleic Acid (DNA).

    Science.gov (United States)

    1983-09-01

    Academy of Science: 3311-3315, December 1977. 155. and Edward D. Rothman . "Indirect Estimates of Mutation Rates in Tribal Amerindians," Proceedings Qf...1974. 189. Rothman , Edward D. and Julian Adams. "Estimation of Expected Number of Rare Alleles of a Locus and Calculation of Mutation Rate," P of the...34 " --.. . . . . . .. . . . . . . . . . ." -. ’- - - . - -" . . " ." .- i 230. Van den Berg, Johan , et al. "Comparison of cloned Rabbit and Mouse B-Globin Genes Showing Strong Evolutionary

  18. Citizen science reveals unexpected continental-scale evolutionary change in a model organism.

    Directory of Open Access Journals (Sweden)

    Jonathan Silvertown

    Full Text Available Organisms provide some of the most sensitive indicators of climate change and evolutionary responses are becoming apparent in species with short generation times. Large datasets on genetic polymorphism that can provide an historical benchmark against which to test for recent evolutionary responses are very rare, but an exception is found in the brown-lipped banded snail (Cepaea nemoralis. This species is sensitive to its thermal environment and exhibits several polymorphisms of shell colour and banding pattern affecting shell albedo in the majority of populations within its native range in Europe. We tested for evolutionary changes in shell albedo that might have been driven by the warming of the climate in Europe over the last half century by compiling an historical dataset for 6,515 native populations of C. nemoralis and comparing this with new data on nearly 3,000 populations. The new data were sampled mainly in 2009 through the Evolution MegaLab, a citizen science project that engaged thousands of volunteers in 15 countries throughout Europe in the biggest such exercise ever undertaken. A known geographic cline in the frequency of the colour phenotype with the highest albedo (yellow was shown to have persisted and a difference in colour frequency between woodland and more open habitats was confirmed, but there was no general increase in the frequency of yellow shells. This may have been because snails adapted to a warming climate through behavioural thermoregulation. By contrast, we detected an unexpected decrease in the frequency of Unbanded shells and an increase in the Mid-banded morph. Neither of these evolutionary changes appears to be a direct response to climate change, indicating that the influence of other selective agents, possibly related to changing predation pressure and habitat change with effects on micro-climate.

  19. Citizen Science Reveals Unexpected Continental-Scale Evolutionary Change in a Model Organism

    Science.gov (United States)

    Silvertown, Jonathan; Cook, Laurence; Cameron, Robert; Dodd, Mike; McConway, Kevin; Worthington, Jenny; Skelton, Peter; Anton, Christian; Bossdorf, Oliver; Baur, Bruno; Schilthuizen, Menno; Fontaine, Benoît; Sattmann, Helmut; Bertorelle, Giorgio; Correia, Maria; Oliveira, Cristina; Pokryszko, Beata; Ożgo, Małgorzata; Stalažs, Arturs; Gill, Eoin; Rammul, Üllar; Sólymos, Péter; Féher, Zoltan; Juan, Xavier

    2011-01-01

    Organisms provide some of the most sensitive indicators of climate change and evolutionary responses are becoming apparent in species with short generation times. Large datasets on genetic polymorphism that can provide an historical benchmark against which to test for recent evolutionary responses are very rare, but an exception is found in the brown-lipped banded snail (Cepaea nemoralis). This species is sensitive to its thermal environment and exhibits several polymorphisms of shell colour and banding pattern affecting shell albedo in the majority of populations within its native range in Europe. We tested for evolutionary changes in shell albedo that might have been driven by the warming of the climate in Europe over the last half century by compiling an historical dataset for 6,515 native populations of C. nemoralis and comparing this with new data on nearly 3,000 populations. The new data were sampled mainly in 2009 through the Evolution MegaLab, a citizen science project that engaged thousands of volunteers in 15 countries throughout Europe in the biggest such exercise ever undertaken. A known geographic cline in the frequency of the colour phenotype with the highest albedo (yellow) was shown to have persisted and a difference in colour frequency between woodland and more open habitats was confirmed, but there was no general increase in the frequency of yellow shells. This may have been because snails adapted to a warming climate through behavioural thermoregulation. By contrast, we detected an unexpected decrease in the frequency of Unbanded shells and an increase in the Mid-banded morph. Neither of these evolutionary changes appears to be a direct response to climate change, indicating that the influence of other selective agents, possibly related to changing predation pressure and habitat change with effects on micro-climate. PMID:21556137

  20. Turbopump Performance Improved by Evolutionary Algorithms

    Science.gov (United States)

    Oyama, Akira; Liou, Meng-Sing

    2002-01-01

    The development of design optimization technology for turbomachinery has been initiated using the multiobjective evolutionary algorithm under NASA's Intelligent Synthesis Environment and Revolutionary Aeropropulsion Concepts programs. As an alternative to the traditional gradient-based methods, evolutionary algorithms (EA's) are emergent design-optimization algorithms modeled after the mechanisms found in natural evolution. EA's search from multiple points, instead of moving from a single point. In addition, they require no derivatives or gradients of the objective function, leading to robustness and simplicity in coupling any evaluation codes. Parallel efficiency also becomes very high by using a simple master-slave concept for function evaluations, since such evaluations often consume the most CPU time, such as computational fluid dynamics. Application of EA's to multiobjective design problems is also straightforward because EA's maintain a population of design candidates in parallel. Because of these advantages, EA's are a unique and attractive approach to real-world design optimization problems.

  1. A New Model of the Early Paleozoic Tectonics and Evolutionary History in the Northern Qinling, China

    Science.gov (United States)

    Dong, Yunpeng; Zhang, Guowei; Yang, Zhao; Qu, Hongjun; Liu, Xiaoming

    2010-05-01

    The Qinling Orogenic Belt extends from the Qinling Mountains in the west to the Dabie Mountains in the east. It lies between the North China and South China Blocks, and is bounded on the north by the Lushan fault and on the south by the Mianlue-Bashan-Xiangguang fault (Zhang et al., 2000). The Qinling Orogenic Belt itself is divided into the North and South Qinling Terranes by the Shangdan suture zone. Although the Shangdan zone is thought to represent the major suture separating the two blocks, there still exists debate about the timing and mechanism of convergence between these two blocks. For instance, some authors suggested an Early Paleozoic collision between the North China Block and South China Block (Ren et al., 1991; Kroner et al., 1993; Zhai et al., 1998). Others postulated left-lateral strike-slip faulting along the Shangdan suture at ca. 315 Ma and inferred a pre-Devonian collision between the two blocks (Mattauer et al., 1985; Xu et al., 1988). Geochemistry of fine-grained sediments in the Qinling Mountains was used to argue for a Silurian-Devonian collision (Gao et al., 1995). A Late Triassic collision has also been proposed (Sengor, 1985; Hsu et al., 1987; Wang et al., 1989), based on the formation of ultrahigh-pressure metamorphic rocks in the easternmost part of the Qinling Orogenic Belt at ~230 Ma (e.g., Li et al., 1993; Ames et al., 1996). Paleomagnetic data favor a Late Triassic-Middle Jurassic amalgamation of the North China and South China Blocks (Zhao and Coe, 1987; Enkin et al., 1992). It is clear that most authors thought that the Qinling Mountains are a collisional orogen, even they have different methods about the timing of the orogeny. Based on new detailed investigations, we propose a new model of the Early Paleozoic Tectonics and Evolutionary History between the North China and South China Blocks along the Shangdan Suture. The Shangdan suture is marked by a great number of ophiolites, island-arc volcanic rocks and other related rock

  2. Evolutionary systems biology: what it is and why it matters.

    Science.gov (United States)

    Soyer, Orkun S; O'Malley, Maureen A

    2013-08-01

    Evolutionary systems biology (ESB) is a rapidly growing integrative approach that has the core aim of generating mechanistic and evolutionary understanding of genotype-phenotype relationships at multiple levels. ESB's more specific objectives include extending knowledge gained from model organisms to non-model organisms, predicting the effects of mutations, and defining the core network structures and dynamics that have evolved to cause particular intracellular and intercellular responses. By combining mathematical, molecular, and cellular approaches to evolution, ESB adds new insights and methods to the modern evolutionary synthesis, and offers ways in which to enhance its explanatory and predictive capacities. This combination of prediction and explanation marks ESB out as a research manifesto that goes further than its two contributing fields. Here, we summarize ESB via an analysis of characteristic research examples and exploratory questions, while also making a case for why these integrative efforts are worth pursuing. © 2013 WILEY Periodicals, Inc.

  3. Modeling consonant-vowel coarticulation for articulatory speech synthesis.

    Directory of Open Access Journals (Sweden)

    Peter Birkholz

    Full Text Available A central challenge for articulatory speech synthesis is the simulation of realistic articulatory movements, which is critical for the generation of highly natural and intelligible speech. This includes modeling coarticulation, i.e., the context-dependent variation of the articulatory and acoustic realization of phonemes, especially of consonants. Here we propose a method to simulate the context-sensitive articulation of consonants in consonant-vowel syllables. To achieve this, the vocal tract target shape of a consonant in the context of a given vowel is derived as the weighted average of three measured and acoustically-optimized reference vocal tract shapes for that consonant in the context of the corner vowels /a/, /i/, and /u/. The weights are determined by mapping the target shape of the given context vowel into the vowel subspace spanned by the corner vowels. The model was applied for the synthesis of consonant-vowel syllables with the consonants /b/, /d/, /g/, /l/, /r/, /m/, /n/ in all combinations with the eight long German vowels. In a perception test, the mean recognition rate for the consonants in the isolated syllables was 82.4%. This demonstrates the potential of the approach for highly intelligible articulatory speech synthesis.

  4. Mathematical Modelling of the Synthesis of New Materials

    Directory of Open Access Journals (Sweden)

    Antonov Valery

    2017-01-01

    Full Text Available The paper focuses primarily on a magnetohydrodynamical approach to solving the numerical problems arising in studying the high energy input technologies of the synthesis of new materials. The underlining mathematical model combines the description of both electromagnetic and hydrodynamic phenomena for the metals and surrounding media in supercritical conditions. A detailed specification of this model is provided. The crucial role of the correct choice of equation of state is outlined. The results section includes the latest finding regarding the numerical simulation of underwater electrical explosion.

  5. 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.

  6. An Evolutionary Robotics Approach to the Control of Plant Growth and Motion: Modeling Plants and Crossing the Reality Gap

    DEFF Research Database (Denmark)

    Wahby, Mostafa; Hofstadler, Daniel Nicolas; Heinrich, Mary Katherine

    2016-01-01

    The self-organizing bio-hybrid collaboration of robots and natural plants allows for a variety of interesting applications. As an example we investigate how robots can be used to control the growth and motion of a natural plant, using LEDs to provide stimuli. We follow an evolutionary robotics...... approach where task performance is determined by monitoring the plant's reaction. First, we do initial plant experiments with simple, predetermined controllers. Then we use image sampling data as a model of the dynamics of the plant tip xy position. Second, we use this approach to evolve robot controllers...

  7. Evolutionary profiling reveals the heterogeneous origins of classes of human disease genes: implications for modeling disease genetics in animals.

    Science.gov (United States)

    Maxwell, Evan K; Schnitzler, Christine E; Havlak, Paul; Putnam, Nicholas H; Nguyen, Anh-Dao; Moreland, R Travis; Baxevanis, Andreas D

    2014-10-04

    The recent expansion of whole-genome sequence data available from diverse animal lineages provides an opportunity to investigate the evolutionary origins of specific classes of human disease genes. Previous studies have observed that human disease genes are of particularly ancient origin. While this suggests that many animal species have the potential to serve as feasible models for research on genes responsible for human disease, it is unclear whether this pattern has meaningful implications and whether it prevails for every class of human disease. We used a comparative genomics approach encompassing a broad phylogenetic range of animals with sequenced genomes to determine the evolutionary patterns exhibited by human genes associated with different classes of disease. Our results support previous claims that most human disease genes are of ancient origin but, more importantly, we also demonstrate that several specific disease classes have a significantly large proportion of genes that emerged relatively recently within the metazoans and/or vertebrates. An independent assessment of the synonymous to non-synonymous substitution rates of human disease genes found in mammals reveals that disease classes that arose more recently also display unexpected rates of purifying selection between their mammalian and human counterparts. Our results reveal the heterogeneity underlying the evolutionary origins of (and selective pressures on) different classes of human disease genes. For example, some disease gene classes appear to be of uncommonly recent (i.e., vertebrate-specific) origin and, as a whole, have been evolving at a faster rate within mammals than the majority of disease classes having more ancient origins. The novel patterns that we have identified may provide new insight into cases where studies using traditional animal models were unable to produce results that translated to humans. Conversely, we note that the larger set of disease classes do have ancient origins

  8. An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope.

    Directory of Open Access Journals (Sweden)

    Art F Y Poon

    2007-11-01

    Full Text Available The third variable loop (V3 of the human immunodeficiency virus type 1 (HIV-1 envelope is a principal determinant of antibody neutralization and progression to AIDS. Although it is undoubtedly an important target for vaccine research, extensive genetic variation in V3 remains an obstacle to the development of an effective vaccine. Comparative methods that exploit the abundance of sequence data can detect interactions between residues of rapidly evolving proteins such as the HIV-1 envelope, revealing biological constraints on their variability. However, previous studies have relied implicitly on two biologically unrealistic assumptions: (1 that founder effects in the evolutionary history of the sequences can be ignored, and; (2 that statistical associations between residues occur exclusively in pairs. We show that comparative methods that neglect the evolutionary history of extant sequences are susceptible to a high rate of false positives (20%-40%. Therefore, we propose a new method to detect interactions that relaxes both of these assumptions. First, we reconstruct the evolutionary history of extant sequences by maximum likelihood, shifting focus from extant sequence variation to the underlying substitution events. Second, we analyze the joint distribution of substitution events among positions in the sequence as a Bayesian graphical model, in which each branch in the phylogeny is a unit of observation. We perform extensive validation of our models using both simulations and a control case of known interactions in HIV-1 protease, and apply this method to detect interactions within V3 from a sample of 1,154 HIV-1 envelope sequences. Our method greatly reduces the number of false positives due to founder effects, while capturing several higher-order interactions among V3 residues. By mapping these interactions to a structural model of the V3 loop, we find that the loop is stratified into distinct evolutionary clusters. We extend our model to

  9. Population Synthesis Models for Normal Galaxies with Dusty Disks

    Directory of Open Access Journals (Sweden)

    Kyung-Won Suh

    2003-09-01

    Full Text Available To investigate the SEDs of galaxies considering the dust extinction processes in the galactic disks, we present the population synthesis models for normal galaxies with dusty disks. We use PEGASE (Fioc & Rocca-Volmerange 1997 to model them with standard input parameters for stars and new dust parameters. We find that the model results are strongly dependent on the dust parameters as well as other parameters (e.g. star formation history. We compare the model results with the observations and discuss about the possible explanations. We find that the dust opacity functions derived from studies of asymptotic giant branch stars are useful for modeling a galaxy with a dusty disk.

  10. 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.

  11. An introduction to evolutionary developmental psychology.

    Science.gov (United States)

    Machluf, Karin; Liddle, James R; Bjorklund, David F

    2014-04-29

    Evolutionary developmental psychology represents a synthesis of modern evolutionary theory and developmental psychology. Here we introduce the special issue on evolutionary developmental psychology by briefly discussing the history of this field and then summarizing the variety of topics that are covered. In this special issue, leading researchers provide a collection of theoretical and empirical articles that highlight recent findings and propose promising areas for future research.

  12. An Introduction to Evolutionary Developmental Psychology

    OpenAIRE

    Karin Machluf; James R. Liddle; David F. Bjorklund

    2014-01-01

    Evolutionary developmental psychology represents a synthesis of modern evolutionary theory and developmental psychology. Here we introduce the special issue on evolutionary developmental psychology by briefly discussing the history of this field and then summarizing the variety of topics that are covered. In this special issue, leading researchers provide a collection of theoretical and empirical articles that highlight recent findings and propose promising areas for future research.

  13. An Introduction to Evolutionary Developmental Psychology

    Directory of Open Access Journals (Sweden)

    Karin Machluf

    2014-04-01

    Full Text Available Evolutionary developmental psychology represents a synthesis of modern evolutionary theory and developmental psychology. Here we introduce the special issue on evolutionary developmental psychology by briefly discussing the history of this field and then summarizing the variety of topics that are covered. In this special issue, leading researchers provide a collection of theoretical and empirical articles that highlight recent findings and propose promising areas for future research.

  14. Modeling of environmental and genetic interactions with AMBROSIA, an information-theoretic model synthesis method.

    Science.gov (United States)

    Chanda, P; Zhang, A; Ramanathan, M

    2011-10-01

    To develop a model synthesis method for parsimoniously modeling gene-environmental interactions (GEI) associated with clinical outcomes and phenotypes. The AMBROSIA model synthesis approach utilizes the k-way interaction information (KWII), an information-theoretic metric capable of identifying variable combinations associated with GEI. For model synthesis, AMBROSIA considers relevance of combinations to the phenotype, it precludes entry of combinations with redundant information, and penalizes for unjustifiable complexity; each step is KWII based. The performance and power of AMBROSIA were evaluated with simulations and Genetic Association Workshop 15 (GAW15) data sets of rheumatoid arthritis (RA). AMBROSIA identified parsimonious models in data sets containing multiple interactions with linkage disequilibrium present. For the GAW15 data set containing 9187 single-nucleotide polymorphisms, the parsimonious AMBROSIA model identified nine RA-associated combinations with power >90%. AMBROSIA was compared with multifactor dimensionality reduction across several diverse models and had satisfactory power. Software source code is available from http://www.cse.buffalo.edu/DBGROUP/bioinformatics/resources.html. AMBROSIA is a promising method for GEI model synthesis.

  15. Modeling of exothermic synthesis of composite with oxide inclusions

    Directory of Open Access Journals (Sweden)

    Knyazeva Anna

    2017-01-01

    Full Text Available The model is suggested for composite synthesis on the base of metallic matrix with inclusions of aluminum oxide at the conditions close to thermal explosion. Chemical reactions are described with the help of two summary stages. The melting, the dependence of reaction rates on pressure and reaction retardation by the product layer are taken into account. It was shown that during reactions proceeding in any regime the formation of final composition of the matrix does not occur. It agrees with known experimental data.

  16. Synthesis, model and stability of helically coiled carbon nanotubes

    DEFF Research Database (Denmark)

    Fejes, Dora; Raffai, Manuella; Hernadi, Klara

    2013-01-01

    . Our experiments focused on the production and development of catalysts for the synthesis of helically coiled CNTs (carbon nanotubes). The catalysts were tested in the decomposition of acetylene by CCVD (Catalytic Chemical Vapor Deposition) method. The carbon deposit was imaged by TEM (Transmission......Structural model of helically coiled carbon nanotubes is proposed. It is constructed by means of topological coordinate method. Relaxation and cohesive energy calculation are performed by molecular mechanics, using second-generation bond order potential for hydrocarbons introduced by D. W. Brenner...

  17. A probabilistic model for component-based shape synthesis

    KAUST Repository

    Kalogerakis, Evangelos

    2012-07-01

    We present an approach to synthesizing shapes from complex domains, by identifying new plausible combinations of components from existing shapes. Our primary contribution is a new generative model of component-based shape structure. The model represents probabilistic relationships between properties of shape components, and relates them to learned underlying causes of structural variability within the domain. These causes are treated as latent variables, leading to a compact representation that can be effectively learned without supervision from a set of compatibly segmented shapes. We evaluate the model on a number of shape datasets with complex structural variability and demonstrate its application to amplification of shape databases and to interactive shape synthesis. © 2012 ACM 0730-0301/2012/08-ART55.

  18. Analysis of Urban Car Owners Commute Mode Choice Based on Evolutionary Game Model

    Directory of Open Access Journals (Sweden)

    Huawei Gong

    2015-01-01

    Full Text Available With the aggravation of the traffic congestion in the city, car owners will have to give up commuting with private cars and take the public transportation instead. The paper uses the replication dynamic mechanism to simulate the learning and adjustment mechanism of the automobile owners commuting mode selection. The evolutionary stable strategy is used to describe the long-term evolution of competition game trend. Finally we simulate equilibrium and stability of an evolution of the game under a payoff imbalance situation. The research shows that a certain proportion of car owners will choose public transit under the pressure of public transport development and heavy traffic, and the proportion will be closely related to the initial conditions and urban transportation development policy.

  19. 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.

  20. Evolutionary macroecology

    Directory of Open Access Journals (Sweden)

    José Alexandre F. Diniz-Filho

    2013-10-01

    Full Text Available Macroecology focuses on ecological questions at broad spatial and temporal scales, providing a statistical description of patterns in species abundance, distribution and diversity. More recently, historical components of these patterns have begun to be investigated more deeply. We tentatively refer to the practice of explicitly taking species history into account, both analytically and conceptually, as ‘evolutionary macroecology’. We discuss how the evolutionary dimension can be incorporated into macroecology through two orthogonal and complementary data types: fossils and phylogenies. Research traditions dealing with these data have developed more‐or‐less independently over the last 20–30 years, but merging them will help elucidate the historical components of diversity gradients and the evolutionary dynamics of species’ traits. Here we highlight conceptual and methodological advances in merging these two research traditions and review the viewpoints and toolboxes that can, in combination, help address patterns and unveil processes at temporal and spatial macro‐scales.

  1. Evolutionary Expectations

    DEFF Research Database (Denmark)

    Nash, Ulrik William

    2014-01-01

    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......, 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......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...

  2. [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.

  3. Evolutionary aspects of non-cell-autonomous regulation in vascular plants: structural background and models to study

    Directory of Open Access Journals (Sweden)

    Anastasiia I. Evkaikina

    2014-02-01

    Full Text Available Plasmodesmata (PD serve for the exchange of information in form of miRNA, proteins and mRNA between adjacent cells in the course of plant development. This fundamental role of PD is well established in angiosperms but has not yet been traced back to the evolutionary ancient plant taxa where functional studies lag behind studies of PD structure and ontogenetic origin. There is convincing evidence that the ability to form secondary (post-cytokinesis PD, which can connect any adjacent cells, contrary to primary PD which form during cytokinesis and link only cells of the same lineage, appeared in the evolution of higher plants at least twice: in seed plants and in some representatives of the Lycopodiophyta. The (inability to form secondary PD is manifested in the symplastic organization of the shoot apical meristem (SAM which in most taxa of seedless vascular plants differs dramatically from that in seed plants. Lycopodiophyta appear to be suitable models to analyze the transport of developmental regulators via PD in SAMs with symplastic organization both different from, as well as analogous to, that in angiosperms, and to understand the evolutionary aspects of the role of this transport in the morphogenesis of vascular plant taxa.

  4. The mathematical model for synthesis process management of the carbon nanostructures

    Science.gov (United States)

    Chistyakova, T. B.; Petrov, D. N.

    2017-01-01

    In this article, key difficulties of management process for carbon nanostructure synthesis are described. Tasks of optimum control of the carbon nanostructure synthesis process and management in case of emergency situations are formulated. The mathematical model of carbon nanostructure synthesis is offered. The equations for calculation of quantitative, qualitative indexes, indicators of safety and operability of engineering procedure are provided. The necessity of mathematical model use for carbon nanostructure synthesis is caused by improvement of the quality, the quantity, a decrease in the cost value of carbon nanostructures and an increase in safety of the engineering procedure of their obtaining. Testing and approbation of the mathematical model for carbon nanostructure synthesis are executed on a fullerene industrial production line. Suitability of the mathematical model of carbon nanostructure synthesis for production control in the mode of optimum control and management in case of emergency situations is confirmed. The obtained solution is recommended for implementation on the enterprises of a similar purpose.

  5. Estimation of the elastic parameters of human liver biomechanical models by means of medical images and evolutionary computation.

    Science.gov (United States)

    Martínez-Martínez, F; Rupérez, M J; Martín-Guerrero, J D; Monserrat, C; Lago, M A; Pareja, E; Brugger, S; López-Andújar, R

    2013-09-01

    This paper presents a method to computationally estimate the elastic parameters of two biomechanical models proposed for the human liver. The method is aimed at avoiding the invasive measurement of its mechanical response. The chosen models are a second order Mooney-Rivlin model and an Ogden model. A novel error function, the geometric similarity function (GSF), is formulated using similarity coefficients widely applied in the field of medical imaging (Jaccard coefficient and Hausdorff coefficient). This function is used to compare two 3D images. One of them corresponds to a reference deformation carried out over a finite element (FE) mesh of a human liver from a computer tomography image, whilst the other one corresponds to the FE simulation of that deformation in which variations in the values of the model parameters are introduced. Several search strategies, based on GSF as cost function, are developed to accurately find the elastics parameters of the models, namely: two evolutionary algorithms (scatter search and genetic algorithm) and an iterative local optimization. The results show that GSF is a very appropriate function to estimate the elastic parameters of the biomechanical models since the mean of the relative mean absolute errors committed by the three algorithms is lower than 4%. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  6. Modelling, Synthesis, and Configuration of Networks-on-Chips

    DEFF Research Database (Denmark)

    Stuart, Matthias Bo

    This thesis presents three contributions in two different areas of network-on-chip and system-on-chip research: Application modelling and identifying and solving different optimization problems related to two specific network-on-chip architectures. The contribution related to application modelling...... is an analytical method for deriving the worst-case traffic pattern caused by an application and the cache-coherence protocol in a cache-coherent shared-memory system. The contributions related to network-on-chip optimization problems consist of two parts: The development and evaluation of six heuristics...... for solving the network synthesis problem in the MANGO network-on-chip, and the identification and formalization of the ReNoC configuration problem together with three heuristics for solving it....

  7. Kinetic model of ammonia synthesis in the solar nebula

    Science.gov (United States)

    Norris, T. L.

    1980-03-01

    Kinetic model of ammonia formation by iron catalysis in the primordial solar nebula is developed. The maximum time to reach equilibrium concentration is determined for various temperatures between 1000 and 200 K on the basis of reaction rates derived from industrial data on iron catalysts for ammonia. Application of the method for calculating the equilibrium time to an arbitrary nebula cooling model which maximizes the time available for ammonia synthesis results in an upper limit of 3% of the equilibrium value to the proportion of nitrogen in the form of ammonia at the time of planetary accretion, with ammonia abundance decreasing with distance from the sun. It is concluded that kinetic rather than equilibrium considerations control the abundance of ammonia in the solar nebula, and implications of the dominance of nitrogen for the evolution of the atmospheres of the terrestrial and Jovian planets and the composition of comets are indicated.

  8. Evolutionary relationships of Aurora kinases: Implications for model organism studies and the development of anti-cancer drugs

    Directory of Open Access Journals (Sweden)

    Patrick Denis R

    2004-10-01

    Full Text Available Abstract Background As key regulators of mitotic chromosome segregation, the Aurora family of serine/threonine kinases play an important role in cell division. Abnormalities in Aurora kinases have been strongly linked with cancer, which has lead to the recent development of new classes of anti-cancer drugs that specifically target the ATP-binding domain of these kinases. From an evolutionary perspective, the species distribution of the Aurora kinase family is complex. Mammals uniquely have three Aurora kinases, Aurora-A, Aurora-B, and Aurora-C, while for other metazoans, including the frog, fruitfly and nematode, only Aurora-A and Aurora-B kinases are known. The fungi have a single Aurora-like homolog. Based on the tacit assumption of orthology to human counterparts, model organism studies have been central to the functional characterization of Aurora kinases. However, the ortholog and paralog relationships of these kinases across various species have not been rigorously examined. Here, we present comprehensive evolutionary analyses of the Aurora kinase family. Results Phylogenetic trees suggest that all three vertebrate Auroras evolved from a single urochordate ancestor. Specifically, Aurora-A is an orthologous lineage in cold-blooded vertebrates and mammals, while structurally similar Aurora-B and Aurora-C evolved more recently in mammals from a duplication of an ancestral Aurora-B/C gene found in cold-blooded vertebrates. All so-called Aurora-A and Aurora-B kinases of non-chordates are ancestral to the clade of chordate Auroras and, therefore, are not strictly orthologous to vertebrate counterparts. Comparisons of human Aurora-B and Aurora-C sequences to the resolved 3D structure of human Aurora-A lends further support to the evolutionary scenario that vertebrate Aurora-B and Aurora-C are closely related paralogs. Of the 26 residues lining the ATP-binding active site, only three were variant and all were specific to Aurora-A. Conclusions In

  9. Modelling of the enzymatic kinetically controlled synthesis of cephalexin

    NARCIS (Netherlands)

    Schroën, C.G.P.H.; Fretz, C.B.; Bruin, de V.H.; Berendsen, W.; Moody, H.M.; Roos, E.C.; Roon, van J.L.; Kroon, P.J.; Strubel, M.; Janssen, A.E.M.; Tramper, J.

    2002-01-01

    In this study the influence of diffusion limitation on enzymatic kinetically controlled cephalexin synthesis from phenylglycine amide and 7-aminodeacetoxycephalosporinic acid (7-ADCA) was investigated systematically. It was found that if diffusion limitation occurred, both the synthesis/hydrolysis

  10. Metabolic modeling of synthesis gas fermentation in bubble column reactors.

    Science.gov (United States)

    Chen, Jin; Gomez, Jose A; Höffner, Kai; Barton, Paul I; Henson, Michael A

    2015-01-01

    A promising route to renewable liquid fuels and chemicals is the fermentation of synthesis gas (syngas) streams to synthesize desired products such as ethanol and 2,3-butanediol. While commercial development of syngas fermentation technology is underway, an unmet need is the development of integrated metabolic and transport models for industrially relevant syngas bubble column reactors. We developed and evaluated a spatiotemporal metabolic model for bubble column reactors with the syngas fermenting bacterium Clostridium ljungdahlii as the microbial catalyst. Our modeling approach involved combining a genome-scale reconstruction of C. ljungdahlii metabolism with multiphase transport equations that govern convective and dispersive processes within the spatially varying column. The reactor model was spatially discretized to yield a large set of ordinary differential equations (ODEs) in time with embedded linear programs (LPs) and solved using the MATLAB based code DFBAlab. Simulations were performed to analyze the effects of important process and cellular parameters on key measures of reactor performance including ethanol titer, ethanol-to-acetate ratio, and CO and H2 conversions. Our computational study demonstrated that mathematical modeling provides a complementary tool to experimentation for understanding, predicting, and optimizing syngas fermentation reactors. These model predictions could guide future cellular and process engineering efforts aimed at alleviating bottlenecks to biochemical production in syngas bubble column reactors.

  11. Strategies for Partitioning Clock Models in Phylogenomic Dating: Application to the Angiosperm Evolutionary Timescale

    Science.gov (United States)

    Ho, Simon Y.W.

    2017-01-01

    Abstract Evolutionary timescales can be inferred from molecular sequence data using a Bayesian phylogenetic approach. In these methods, the molecular clock is often calibrated using fossil data. The uncertainty in these fossil calibrations is important because it determines the limiting posterior distribution for divergence-time estimates as the sequence length tends to infinity. Here, we investigate how the accuracy and precision of Bayesian divergence-time estimates improve with the increased clock-partitioning of genome-scale data into clock-subsets. We focus on a data set comprising plastome-scale sequences of 52 angiosperm taxa. There was little difference among the Bayesian date estimates whether we chose clock-subsets based on patterns of among-lineage rate heterogeneity or relative rates across genes, or by random assignment. Increasing the degree of clock-partitioning usually led to an improvement in the precision of divergence-time estimates, but this increase was asymptotic to a limit presumably imposed by fossil calibrations. Our clock-partitioning approaches yielded highly precise age estimates for several key nodes in the angiosperm phylogeny. For example, when partitioning the data into 20 clock-subsets based on patterns of among-lineage rate heterogeneity, we inferred crown angiosperms to have arisen 198–178 Ma. This demonstrates that judicious clock-partitioning can improve the precision of molecular dating based on phylogenomic data, but the meaning of this increased precision should be considered critically. PMID:29036288

  12. Soft tissue freezing process. Identification of the dual-phase lag model parameters using the evolutionary algorithm

    Science.gov (United States)

    Mochnacki, Bohdan; Majchrzak, Ewa; Paruch, Marek

    2018-01-01

    In the paper the soft tissue freezing process is considered. The tissue sub-domain is subjected to the action of cylindrical cryoprobe. Thermal processes proceeding in the domain considered are described using the dual-phase lag equation (DPLE) supplemented by the appropriate boundary and initial conditions. DPLE results from the generalization of the Fourier law in which two lag times are introduced (relaxation and thermalization times). The aim of research is the identification of these parameters on the basis of measured cooling curves at the set of points selected from the tissue domain. To solve the problem the evolutionary algorithms are used. The paper contains the mathematical model of the tissue freezing process, the very short information concerning the numerical solution of the basic problem, the description of the inverse problem solution and the results of computations.

  13. Multivariate dynamic linear models for estimating the effect of experimental interventions in an evolutionary operations setup in dairy herds

    DEFF Research Database (Denmark)

    Stygar, Anna Helena; Krogh, Mogens Agerbo; Kristensen, Troels

    2017-01-01

    Evolutionary operations is a method to exploit the association of often small changes in process variables, planned during systematic experimentation and occurring during the normal production flow, to production characteristics to find a way to alter the production process to be more efficient...... from a herd, and an intervention effect on a given day. The model was constructed to handle any number of cows, experimental interventions, different data sources, or presence of control groups. In this study, data from 2 commercial Danish herds were used. In herd 1, data on 98,046 and 12,133 milkings......,471) were used. In herd 1, the manager wanted to explore the possibility of reducing the amount of concentrate provided to the cows in an AMS. In herd 2, the manager wanted to know if the milk yield could be increased by elevating the energy level provided to the cows in a total mixed ration. The experiment...

  14. Improved Hidden Markov Model training for multiple sequence alignment by a particle swarm optimization-evolutionary algorithm hybrid.

    Science.gov (United States)

    Rasmussen, Thomas Kiel; Krink, Thiemo

    2003-11-01

    Multiple sequence alignment (MSA) is one of the basic problems in computational biology. Realistic problem instances of MSA are computationally intractable for exact algorithms. One way to tackle MSA is to use Hidden Markov Models (HMMs), which are known to be very powerful in the related problem domain of speech recognition. However, the training of HMMs is computationally hard and there is no known exact method that can guarantee optimal training within reasonable computing time. Perhaps the most powerful training method is the Baum-Welch algorithm, which is fast, but bears the problem of stagnation at local optima. In the study reported in this paper, we used a hybrid algorithm combining particle swarm optimization with evolutionary algorithms to train HMMs for the alignment of protein sequences. Our experiments show that our approach yields better alignments for a set of benchmark protein sequences than the most commonly applied HMM training methods, such as Baum-Welch and Simulated Annealing.

  15. [Construction of high-effective symbiotic bacteria: evolutionary models and genetic approaches].

    Science.gov (United States)

    Provorov, N A; Onishchuk, O P; Iurgel', S N; Kurchak, O N; Chizhevskaia, E P; Vorob'ev, N I; Zatovskaia, T V; Simarov, B V

    2014-11-01

    Using the example of N2-fixing legume-rhizobial symbiosis, we demonstrated that the origin and evolution of bacteria symbiotic for plants involve the following: 1) the formation of novel sym gene systems based on reorganizations of the bacterial genomes and on the gene transfer from the distant organisms; 2) the loss of genes encoding for functions that are required for autonomous performance but interfere with symbiotic functions (negative regulators of symbiosis). Therefore, the construction of effective rhizobia strains should involve improvement of sym genes activities (for instance, nif, fix, and dct genes, encoding for nitrogenase synthesis or for the energy supply of N2 fixation), as well as the inactivation of negative regulators of symbiosis identified in our lab (eff genes encoding for the transport of sugars, and the production of polysaccharides, and storage compounds, as well as for oxidative-reductive processes).

  16. Mitochondrial glutamate carriers from Drosophila melanogaster: biochemical, evolutionary and modeling studies.

    Science.gov (United States)

    Lunetti, Paola; Cappello, Anna Rita; Marsano, René Massimiliano; Pierri, Ciro Leonardo; Carrisi, Chiara; Martello, Emanuela; Caggese, Corrado; Dolce, Vincenza; Capobianco, Loredana

    2013-10-01

    The mitochondrial carriers are members of a family of transport proteins that mediate solute transport across the inner mitochondrial membrane. Two isoforms of the glutamate carriers, GC1 and GC2 (encoded by the SLC25A22 and SLC25A18 genes, respectively), have been identified in humans. Two independent mutations in SLC25A22 are associated with severe epileptic encephalopathy. In the present study we show that two genes (CG18347 and CG12201) phylogenetically related to the human GC encoding genes are present in the D. melanogaster genome. We have functionally characterized the proteins encoded by CG18347 and CG12201, designated as DmGC1p and DmGC2p respectively, by overexpression in Escherichia coli and reconstitution into liposomes. Their transport properties demonstrate that DmGC1p and DmGC2p both catalyze the transport of glutamate across the inner mitochondrial membrane. Computational approaches have been used in order to highlight residues of DmGC1p and DmGC2p involved in substrate binding. Furthermore, gene expression analysis during development and in various adult tissues reveals that CG18347 is ubiquitously expressed in all examined D. melanogaster tissues, while the expression of CG12201 is strongly testis-biased. Finally, we identified mitochondrial glutamate carrier orthologs in 49 eukaryotic species in order to attempt the reconstruction of the evolutionary history of the glutamate carrier function. Comparison of the exon/intron structure and other key features of the analyzed orthologs suggests that eukaryotic glutamate carrier genes descend from an intron-rich ancestral gene already present in the common ancestor of lineages that diverged as early as bilateria and radiata. © 2013.

  17. Spectral modeling, analysis, and synthesis of musical sounds

    Science.gov (United States)

    Marchand, Sylvain; Desainte-Catherine, Myriam

    2002-11-01

    Spectral models provide general representations for sound well-suited for expressive musical transformations. These models allow us to extract and modify perceptually-relevant parameters such as amplitude, frequency, and spectrum. Thus, they are of great interest for the classification of musical sounds. A new analysis method was proposed to accurately extract the spectral parameters for the model from existing sounds. This method extends the classic short-time Fourier analysis by also considering the derivatives of the sound signal, and it can work with very short analysis windows. Although originally designed for stationary sounds with no noise, this method shows excellent results in the presence of noise and it is currently being extended in order to handle nonstationary sounds as well. A very efficient synthesis algorithm, based on a recursive description of the sine function, is able to reproduce sound in real time from the model parameters. This algorithm allows an extremely fine control of the partials of the sounds while avoiding signal discontinuities as well as numerical imprecision, and with a nearly optimal number of operations per partial. Psychoacoustic phenomena such as masking are considered in order to reduce on the fly the number of partials to be synthesized.

  18. An Evolutionary, Agent-Based Model to Aid in Computer Intrusion Detection and Prevention

    National Research Council Canada - National Science Library

    Shargel, Ben; Bonabeau, Eric; Budynek, Julien; Gaudiano, Paolo

    2005-01-01

    We have developed a realistic agent-based simulation model of hacker behavior. In the model, hacker scripts are generated using a simple but powerful hacker grammar that has the potential to cover all possible hacker scripts...

  19. Evolutionary mysteries in meiosis

    NARCIS (Netherlands)

    Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E.; Wijnker, Erik; Haag, Christoph R.

    2016-01-01

    Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these

  20. Solution of classical evolutionary models in the limit when the diffusion approximation breaks down

    Science.gov (United States)

    Saakian, David B.; Hu, Chin-Kun

    2016-10-01

    The discrete time mathematical models of evolution (the discrete time Eigen model, the Moran model, and the Wright-Fisher model) have many applications in complex biological systems. The discrete time Eigen model rather realistically describes the serial passage experiments in biology. Nevertheless, the dynamics of the discrete time Eigen model is solved in this paper. The 90% of results in population genetics are connected with the diffusion approximation of the Wright-Fisher and Moran models. We considered the discrete time Eigen model of asexual virus evolution and the Wright-Fisher model from population genetics. We look at the logarithm of probabilities and apply the Hamilton-Jacobi equation for the models. We define exact dynamics for the population distribution for the discrete time Eigen model. For the Wright-Fisher model, we express the exact steady state solution and fixation probability via the solution of some nonlocal equation then give the series expansion of the solution via degrees of selection and mutation rates. The diffusion theories result in the zeroth order approximation in our approach. The numeric confirms that our method works in the case of strong selection, whereas the diffusion method fails there. Although the diffusion method is exact for the mean first arrival time, it provides incorrect approximation for the dynamics of the tail of distribution.

  1. Prediction of cyclosporine blood levels in heart transplantation patients using a pharmacokinetic model identified by evolutionary algorithms.

    Science.gov (United States)

    Hoda, M Raschid; Grimm, Michael; Laufer, Guenther

    2005-11-01

    Artificial intelligence (AI)-based computation methods have been recently shown to be applicable in several clinical diagnostic fields. The purpose of this study was to introduce a novel AI method called evolutionary algorithms (EAs) to clinical predictions. The technique was used to create a pharmacokinetic model for the prediction of whole blood levels of cyclosporine (CyA). One hundred one adult cardiac transplant recipients were randomly selected and included in this study. All patients had been receiving oral cyclosporine twice daily, and the trough levels in whole blood were measured by monoclonal-specific radioimmunoassay. An evolutionary algorithm (EA)-based software tool was trained with pre- and post-operative variables from 64 patients. The results of this process were then tested on data sets from 37 patients. The mean value of the predicted CyA level throughout the measurement period for the test data was 175 +/- 27 ng/ml, which compared well with the mean observed CyA level of 180 +/- 31 ng/ml. The system bias expressed as the mean percent error (MPE) for the training and test data sets were 7.1 +/- 5.4% (0.1% to 26.7%) and 8.0 +/- 6.7% (0.8% to 28.8%), respectively. The prediction accuracy ranged from 80% to 90%. The correlation coefficient between predicted and observed CyA concentration for the training data were 0.93 (p cyclosporine whole blood levels in heart transplant recipients. This and other similar technologies should be considered as future clinical tools to reduce costs in our health systems.

  2. 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.

  3. Evolutionary developmental biology its roots and characteristics.

    Science.gov (United States)

    Morange, Michel

    2011-09-01

    The rise of evolutionary developmental biology was not the progressive isolation and characterization of developmental genes and gene networks. Many obstacles had to be overcome: the idea that all genes were more or less involved in development; the evidence that developmental processes in insects had nothing in common with those of vertebrates. Different lines of research converged toward the creation of evolutionary developmental biology, giving this field of research its present heterogeneity. This does not prevent all those working in the field from sharing the conviction that a precise characterization of evolutionary variations is required to fully understand the evolutionary process. Some evolutionary developmental biologists directly challenge the Modern Synthesis. I propose some ways to reconcile these apparently opposed visions of evolution. The turbulence seen in evolutionary developmental biology reflects the present entry of history into biology. Copyright © 2011 Elsevier Inc. All rights reserved.

  4. The Zebrafish Models to Explore Genetic and Epigenetic Impacts on Evolutionary Developmental Origins of Aging

    Science.gov (United States)

    Kishi, Shuji

    2014-01-01

    hand, unexpected senescence-related genes might also be involved in the early developmental process and its regulation. The ease of manipulation using the zebrafish system allows us to conduct an exhaustive exploration of novel genes/genotypes and epigenotype that can be linked to the senescence phenotype, and thereby facilitates searching for the evolutionary and developmental origins of aging in vertebrates. PMID:24239812

  5. Modeling methodology for supply chain synthesis and disruption analysis

    Science.gov (United States)

    Wu, Teresa; Blackhurst, Jennifer

    2004-11-01

    The concept of an integrated or synthesized supply chain is a strategy for managing today's globalized and customer driven supply chains in order to better meet customer demands. Synthesizing individual entities into an integrated supply chain can be a challenging task due to a variety of factors including conflicting objectives, mismatched incentives and constraints of the individual entities. Furthermore, understanding the effects of disruptions occurring at any point in the system is difficult when working toward synthesizing supply chain operations. Therefore, the goal of this research is to present a modeling methodology to manage the synthesis of a supply chain by linking hierarchical levels of the system and to model and analyze disruptions in the integrated supply chain. The contribution of this research is threefold: (1) supply chain systems can be modeled hierarchically (2) the performance of synthesized supply chain system can be evaluated quantitatively (3) reachability analysis is used to evaluate the system performance and verify whether a specific state is reachable, allowing the user to understand the extent of effects of a disruption.

  6. Evolutionary considerations on complex emotions and music-induced emotions. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

    Science.gov (United States)

    Gingras, Bruno; Marin, Manuela M.

    2015-06-01

    Recent efforts to uncover the neural underpinnings of emotional experiences have provided a foundation for novel neurophysiological theories of emotions, adding to the existing body of psychophysiological, motivational, and evolutionary theories. Besides explicitly modeling human-specific emotions and considering the interactions between emotions and language, Koelsch et al.'s original contribution to this challenging endeavor is to identify four brain areas as distinct "affect systems" which differ in terms of emotional qualia and evolutionary pathways [1]. Here, we comment on some features of this promising Quartet Theory of Emotions, focusing particularly on evolutionary and biological aspects related to the four affect systems and their relation to prevailing emotion theories, as well as on the role of music-induced emotions.

  7. Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics.

    Science.gov (United States)

    Noel, Jeffrey K; Morcos, Faruck; Onuchic, Jose N

    2016-01-01

    Experimentally derived structural constraints have been crucial to the implementation of computational models of biomolecular dynamics. For example, not only does crystallography provide essential starting points for molecular simulations but also high-resolution structures permit for parameterization of simplified models. Since the energy landscapes for proteins and other biomolecules have been shown to be minimally frustrated and therefore funneled, these structure-based models have played a major role in understanding the mechanisms governing folding and many functions of these systems. Structural information, however, may be limited in many interesting cases. Recently, the statistical analysis of residue co-evolution in families of protein sequences has provided a complementary method of discovering residue-residue contact interactions involved in functional configurations. These functional configurations are often transient and difficult to capture experimentally. Thus, co-evolutionary information can be merged with that available for experimentally characterized low free-energy structures, in order to more fully capture the true underlying biomolecular energy landscape.

  8. Confirming Time-reversal Symmetry of a Directed Percolation Phase Transition in a Model of Neutral Evolutionary Dynamics

    Science.gov (United States)

    Ordway, Stephen; King, Dawn; Bahar, Sonya

    Reaction-diffusion processes, such as branching-coalescing random walks, can be used to describe the underlying dynamics of nonequilibrium phase transitions. In an agent-based, neutral model of evolutionary dynamics, we have previously shown that our system undergoes a continuous, nonequilibrium phase transition, from extinction to survival, as various system parameters were tuned. This model was shown to belong to the directed percolation (DP) universality class, by measuring the critical exponents corresponding to correlation length ξ⊥, correlation time ξ| |, and particle density β. The fourth critical exponent that defines the DP universality class is β', which measures the survival probability of growth from a single seed organism. Since DP universality is theorized to have time-reversal symmetry, it is assumed that β = β '. In order to confirm the existence of time-reversal symmetry in our model, we evaluate the system growth from a single asexually reproducing organism. Importantly, the critical exponent β' could be useful for comparison to experimental studies of phase transitions in biological systems, since observing growth of microbial populations is significantly easier than observing death. This research was supported by funding from the James S. McDonnell Foundation.

  9. Social traits, social networks and evolutionary biology.

    Science.gov (United States)

    Fisher, D N; McAdam, A G

    2017-12-01

    The social environment is both an important agent of selection for most organisms, and an emergent property of their interactions. As an aggregation of interactions among members of a population, the social environment is a product of many sets of relationships and so can be represented as a network or matrix. Social network analysis in animals has focused on why these networks possess the structure they do, and whether individuals' network traits, representing some aspect of their social phenotype, relate to their fitness. Meanwhile, quantitative geneticists have demonstrated that traits expressed in a social context can depend on the phenotypes and genotypes of interacting partners, leading to influences of the social environment on the traits and fitness of individuals and the evolutionary trajectories of populations. Therefore, both fields are investigating similar topics, yet have arrived at these points relatively independently. We review how these approaches are diverged, and yet how they retain clear parallelism and so strong potential for complementarity. This demonstrates that, despite separate bodies of theory, advances in one might inform the other. Techniques in network analysis for quantifying social phenotypes, and for identifying community structure, should be useful for those studying the relationship between individual behaviour and group-level phenotypes. Entering social association matrices into quantitative genetic models may also reduce bias in heritability estimates, and allow the estimation of the influence of social connectedness on trait expression. Current methods for measuring natural selection in a social context explicitly account for the fact that a trait is not necessarily the property of a single individual, something the network approaches have not yet considered when relating network metrics to individual fitness. Harnessing evolutionary models that consider traits affected by genes in other individuals (i.e. indirect genetic

  10. Testability of evolutionary game dynamics models based on experimental economics data

    CERN Document Server

    Wang, Yijia; Wang, Zhijian

    2016-01-01

    In order to better understand the dynamic processes of a real game system, we need an appropriate dynamics model, so to evaluate the validity of a model is not a trivial task. Here, we demonstrate an approach, considering the dynamic patterns of angular momentum and speed as the measurement variables, for evaluating the validity of various dynamics models. Using the data in real time Rock-Paper-Scissors (RPS) games experiments, we obtain the experimental patterns, and then derive the related theoretical patterns from a series of typical dynamics models respectively. By testing the goodness-of-fit between the experimental and theoretical patterns, the validity of the models can be evaluated. One of the results is that, among all the non-parametric models tested, the best-known Replicator dynamics model performs almost worst, while the Projection dynamics model performs best. Besides providing new empirical patterns of social dynamics, we demonstrate that the approach can be an effective and rigorous method to ...

  11. A Simple Model to Think about the Evolutionary Rate in Macroevolution.

    Science.gov (United States)

    Marco, Oscar Barbera

    1993-01-01

    Presents a simple model that can help students think about evolution and better understand the gradualist and punctuationist macroevolution approaches. The model also improves instruction for concepts of mutation, selection, fitness, extinction, and origin of life. Describes an IBM computer program for instruction in these areas. (PR)

  12. Restructuring of workflows to minimise errors via stochastic model checking: An automated evolutionary approach

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Hansen, Zaza Nadja Lee

    2016-01-01

    This article presents a framework for the automated restructuring of stochastic workflows to reduce the impact of faults. The framework allows for the modelling of workflows by means of a formalised subset of the BPMN workflow language. We extend this modelling formalism to describe faults...

  13. A hybrid evolutionary data driven model for river water quality early warning.

    Science.gov (United States)

    Burchard-Levine, Alejandra; Liu, Shuming; Vince, Francois; Li, Mingming; Ostfeld, Avi

    2014-10-01

    China's fast pace industrialization and growing population has led to several accidental surface water pollution events in the last decades. The government of China, after the 2005 Songhua River incident, has pushed for the development of early warning systems (EWS) for drinking water source protection. However, there are still many weaknesses in EWS in China such as the lack of pollution monitoring and advanced water quality prediction models. The application of Data Driven Models (DDM) such as Artificial Neural Networks (ANN) has acquired recent attention as an alternative to physical models. For a case study in a south industrial city in China, a DDM based on genetic algorithm (GA) and ANN was tested to increase the response time of the city's EWS. The GA-ANN model was used to predict NH3-N, CODmn and TOC variables at station B 2 h ahead of time while showing the most sensitive input variables available at station A, 12 km upstream. For NH3-N, the most sensitive input variables were TOC, CODmn, TP, NH3-N and Turbidity with model performance giving a mean square error (MSE) of 0.0033, mean percent error (MPE) of 6% and regression (R) of 92%. For COD, the most sensitive input variables were Turbidity and CODmn with model performance giving a MSE of 0.201, MPE of 5% and R of 0.87. For TOC, the most sensitive input variables were Turbidity and CODmn with model performance giving a MSE of 0.101, MPE of 2% and R of 0.94. In addition, the GA-ANN model performed better for 8 h ahead of time. For future studies, the use of a GA-ANN modelling technique can be very useful for water quality prediction in Chinese monitoring stations which already measure and have immediately available water quality data. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Application of crowd-sourced data to multi-scale evolutionary exposure and vulnerability models

    Science.gov (United States)

    Pittore, Massimiliano

    2016-04-01

    Seismic exposure, defined as the assets (population, buildings, infrastructure) exposed to earthquake hazard and susceptible to damage, is a critical -but often neglected- component of seismic risk assessment. This partly stems from the burden associated with the compilation of a useful and reliable model over wide spatial areas. While detailed engineering data have still to be collected in order to constrain exposure and vulnerability models, the availability of increasingly large crowd-sourced datasets (e. g. OpenStreetMap) opens up the exciting possibility to generate incrementally evolving models. Integrating crowd-sourced and authoritative data using statistical learning methodologies can reduce models uncertainties and also provide additional drive and motivation to volunteered geoinformation collection. A case study in Central Asia will be presented and discussed.

  15. Why do we like to stay with our friends? Modelling the evolutionary dynamics of interpersonal commitment

    NARCIS (Netherlands)

    Back, I.; Flache, A.; Takahashi, S; Scallach, D; Rouchier, J

    2007-01-01

    Why are people inclined to build friendships and maintain durable, nonreproductive relationships? Previous computational modeling work on the evolution of commitment in repeated exchange showed that being largely unconditionally cooperative in committed relationships is more viable than conditional

  16. An evolutionary approach for determining hidden Markov model for medical image analysis

    OpenAIRE

    Goh, J.; Tang, HL; Peto, T.; Saleh, G.

    2012-01-01

    Hidden Markov Model (HMM) is a technique highly capable of modelling the structure of an observation sequence. In this paper, HMM is used to provide the contextual information for detecting clinical signs present in diabetic retinopathy screen images. However, there is a need to determine a feature set that best represents the complexity of the data as well as determine an optimal HMM. This paper addresses these problems by automatically selecting the best feature set while evolving the struc...

  17. From the Schumpeterian entrepreneur toward modern evolutionary economics

    DEFF Research Database (Denmark)

    Andersen, Esben Sloth

    This paper argues that Schumpeter’s core books are organised in three groups. The first of them is the programmatic duology that consists of his two early German books. The second is the evolutionary economic duology that consists of The Theory of Economic Development and Business Cycles. The third...... is the socioeconomic synthesis that is found in parts of Capitalism, Socialism and Democracy. The paper considers the internal logic of and the interconnections between these groups of works. This analysis is supported by the distinction between Schumpeter’s three different models of evolutionary processes...... and by the distinction between microevolution and macroevolution. The Mark I model describes economic evolution as the outcome of the interaction between individual innovative entrepreneurs and routine-based incumbent firms.Mark II describes economic evolution as the outcome of the innovative oligopolistic competition...

  18. Application of evolutionary algorithms to optimize the model parameters of casting cooling process

    Directory of Open Access Journals (Sweden)

    S. Kluska-Nawarecka

    2010-10-01

    Full Text Available One of the most commonly used methods of numerical simulation is the finite element method (FEM. Its popularity is reflected in thenumber of tools supporting the preparation of simulation models. However, despite its usefulness, FEM is often very troublesome in use;the problem is the selection of the finite element mesh or shape function. In addition, MES assumes a complete knowledge of thesimulated process and of the parameters describing the investigated phenomena, including model geometry, boundary conditions, physicalparameters, and mathematical model describing these phenomena. A comparison of the data obtained from physical experiments andsimulations indicates an inaccuracy, which may result from the incorrectly chosen shape of element or geometry of the grid. Theapplication of computational intelligence methods, combined with knowledge of the manufacturing technology of metal products, shouldallow an efficient selection of parameters of the mathematical models and, as a consequence, more precise control of the process of thecasting solidification and cooling to ensure the required quality. The designed system has been integrated with the existing simulationenvironment, which will significantly facilitate the preparation and implementation of calculations of this type. Moreover, the use of adistributed model will significantly reduce the time complexity of calculations, requiring multiple repetition of complex simulations toestimate the quality of the different sets of parameters.

  19. Um modelo evolucionário Norte-Sul A North-South evolutionary model

    Directory of Open Access Journals (Sweden)

    André Luiz Fernandes

    2007-12-01

    Full Text Available This work expands the classical Nelson and Winter model of Schumpeterian competition by including two sectors and a North-South dynamics, with a view to analyzing how different institutions and technological regimes affect the processes of convergence and divergence in the international economy. The results suggest that convergence may emerge out of the efforts for imitation in the South when the technological regime is cumulative. But when the regime is science-based, imitation is not enough for a successful catching-up. In this case convergence requires the South to invest in innovation as well. The work also analyses the robustness of the model results using Montecarlo techniques.

  20. 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.

  1. The Evolutionary Role of Interorganizational Communication: Modeling Social Capital in Disaster Contexts

    Science.gov (United States)

    Doerfel, Marya L.; Lai, Chih-Hui; Chewning, Lisa V.

    2010-01-01

    Employing a community ecology perspective, this study examines how interorganizational (IO) communication and social capital (SC) facilitated organizational recovery after Hurricane Katrina. In-depth interviews with 56 New Orleans organizations enabled longitudinal analysis and a grounded theory model that illustrates how communication…

  2. Bayesian Analysis of Evolutionary Divergence with Genomic Data under Diverse Demographic Models.

    Science.gov (United States)

    Chung, Yujin; Hey, Jody

    2017-06-01

    We present a new Bayesian method for estimating demographic and phylogenetic history using population genomic data. Several key innovations are introduced that allow the study of diverse models within an Isolation-with-Migration framework. The new method implements a 2-step analysis, with an initial Markov chain Monte Carlo (MCMC) phase that samples simple coalescent trees, followed by the calculation of the joint posterior density for the parameters of a demographic model. In step 1, the MCMC sampling phase, the method uses a reduced state space, consisting of coalescent trees without migration paths, and a simple importance sampling distribution without the demography of interest. Once obtained, a single sample of trees can be used in step 2 to calculate the joint posterior density for model parameters under multiple diverse demographic models, without having to repeat MCMC runs. Because migration paths are not included in the state space of the MCMC phase, but rather are handled by analytic integration in step 2 of the analysis, the method is scalable to a large number of loci with excellent MCMC mixing properties. With an implementation of the new method in the computer program MIST, we demonstrate the method's accuracy, scalability, and other advantages using simulated data and DNA sequences of two common chimpanzee subspecies: Pan troglodytes (P. t.) troglodytes and P. t. verus. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. A Process Model of Locational Change in Entrepreneurial Firms: An Evolutionary Perspective

    NARCIS (Netherlands)

    F.C. Stam (Erik)

    2006-01-01

    textabstractHow do changes in the spatial organization of entrepreneurial firms come about? This paper provides a conceptualisation of the process of locational change. A process model of locational change is constructed on the basis of an empirical study of 109 locational events during the life

  4. Evolutionary View Planning for Optimized UAV Terrain Modeling in a Simulated Environment

    Directory of Open Access Journals (Sweden)

    Ronald A. Martin

    2015-12-01

    Full Text Available This work demonstrates the use of genetic algorithms in optimized view planning for 3D reconstruction applications using small unmanned aerial vehicles (UAVs. The quality of UAV site models is currently highly dependent on manual pilot operations or grid-based automation solutions. When applied to 3D structures, these approaches can result in gaps in the total coverage or inconsistency in final model resolution. Genetic algorithms can effectively explore the search space to locate image positions that produce high quality models in terms of coverage and accuracy. A fitness function is defined, and optimization parameters are selected through semi-exhaustive search. A novel simulation environment for evaluating view plans is demonstrated using terrain generation software. The view planning algorithm is tested in two separate simulation cases: a water drainage structure and a reservoir levee, as representative samples of infrastructure monitoring. The optimized flight plan is compared against three alternate flight plans in each case. The optimized view plan is found to yield terrain models with up to 43% greater accuracy than a standard grid flight pattern, while maintaining comparable coverage and completeness.

  5. The triple-helix model of smart cities: a neo-evolutionary perspective

    NARCIS (Netherlands)

    Leydesdorff, L.; Deakin, M.

    2011-01-01

    This paper sets out to demonstrate how the triple-helix model enables us to study the knowledge base of an urban economy in terms of its civil society's support for the evolution of the city as a key component of an innovation system. It argues that cities can be considered as densities in networks

  6. Automated evolutionary restructuring of workflows to minimise errors via stochastic model checking

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Hansen, Zaza Nadja Lee; Jacobsen, Peter

    2014-01-01

    by means of a case study from the food industry. Through this case study we explore the extent to which the risk of production faults can be reduced and the impact of these can be minimised, primarily through restructuring of the production workflows. This approach is fully automated and only the modelling...

  7. Polarisation Spectral Synthesis For Type Ia Supernova Explosion Models

    Science.gov (United States)

    Bulla, Mattia

    2017-02-01

    provide a clear distinction. In particular, we find that one model is too strongly asymmetric and produces polarisation levels that are too high and clearly inconsistent with those detected for the bulk of Type Ia supernovae. Polarisation signals - and their time evolution - extracted for the remaining two models are instead in good agreement with the currently available spectropolarimetry data. Providing a powerful way to connect hydrodynamic explosion models to observed data, the study presented in this thesis is an important step towards a better understanding of Type Ia supernovae from a synthesis of theory and observations.

  8. Hydrologic Predictions in the Anthropocene: Exploration with Co-evolutionary Socio-hydrologic Models

    Science.gov (United States)

    Sivapalan, Murugesu; Tian, Fuqiang; Liu, Dengfeng

    2013-04-01

    Socio-hydrology studies the co-evolution and self-organization of humans in the hydrologic landscape, which requires a thorough understanding of the complex interactions between humans and water. On the one hand, the nature of water availability greatly impacts the development of society. On the other hand, humans can significantly alter the spatio-temporal distribution of water and in this way provide feedback to the society itself. The human-water system functions underlying such complex human-water interactions are not well understood. Exploratory models with the appropriate level of simplification in any given area can be valuable to understand these functions and the self-organization associated with socio-hydrology. In this study, a simple coupled modeling framework for socio-hydrology co-evolution is developed, and is used to illustrate the explanatory power of such models. In the Tarim River, humans depend heavily on agricultural production (other industries can be ignored for a start), and the social processes can be described principally by two variables, i.e., irrigated-area and human population. The eco-hydrological processes are expressed in terms of area under natural vegetation and stream discharge. The study area is the middle and the lower reaches of the Tarim River, which is divided into two modeling units, i.e. middle reach and lower reach. In each modeling unit, four ordinary differential equations are used to simulate the dynamics of the hydrological system represented by stream discharge, ecological system represented by area under natural vegetation, the economic system represented by irrigated area under agriculture and social system represented by human population. The four dominant variables are coupled together by several internal variables. For example, the stream discharge is coupled to irrigated area by the colonization rate and mortality rate of the irrigated area in the middle reach and the irrigated area is coupled to stream

  9. AstraZeneca and Covance Laboratories Clinical Bioanalysis Alliance: an evolutionary outsourcing model.

    Science.gov (United States)

    Arfvidsson, Cecilia; Severin, Paul; Holmes, Victoria; Mitchell, Richard; Bailey, Christopher; Cape, Stephanie; Li, Yan; Harter, Tammy

    2017-08-01

    The AstraZeneca and Covance Laboratories Clinical Bioanalysis Alliance (CBioA) was launched in 2011 after a period of global economic recession. In this challenging environment, AstraZeneca elected to move to a full and centralized outsourcing model that could optimize the number of people supporting bioanalytical work and reduce the analytical cost. This paper describes the key aspects of CBioA, the innovative operational model implemented, and our ways of ensuring this was much more than simply a cost reduction exercise. As we have recently passed the first 5-year cycle, this paper also summarizes some of the concluding benefits, wins and lessons learned, and how we now plan to extend and develop the relationship even further moving into a new clinical laboratory partnership.

  10. Evolutionary Implications of Mechanistic Models of TE-Mediated Hybrid Incompatibility

    Science.gov (United States)

    Castillo, Dean M.; Moyle, Leonie C.

    2012-01-01

    New models of TE repression in plants (specifically Arabidopsis) have suggested specific mechanisms by which TE misregulation in hybrids might result in the expression of hybrid inviability. If true, these models suggest as yet undescribed consequences for (1) mechanistic connections between hybrid problems expressed at different postzygotic stages (e.g., inviability versus sterility), (2) the predicted strength, stage, and direction of isolation between diverging lineages that differ in TE activity, and (3) the association between species attributes that influence TE dynamics (e.g., mode of reproduction, geographical structure) and the rate at which they could accumulate incompatibilities. In this paper, we explore these implications and outline future empirical directions for generating data necessary to evaluate them. PMID:22518335

  11. Evolutionary stability and resistance to cheating in an indirect reciprocity model based on reputation

    CERN Document Server

    Martinez-Vaquero, Luis A

    2013-01-01

    Indirect reciprocity is one of the main mechanisms to explain the emergence and sustainment of altruism in societies. The standard approach to indirect reciprocity are reputation models. These are games in which players base their decisions on their opponent's reputation gained in past interactions with other players (moral assessment). The combination of actions and moral assessment leads to a large diversity of strategies, thus determining the stability of any of them against invasions by all the others is a difficult task. We use a variant of a previously introduced reputation-based model that let us systematically analyze all these invasions and determine which ones are successful. Accordingly we are able to identify the third-order strategies (those which, apart from the action, judge considering both the reputation of the donor and that of the recipient) that are evolutionarily stable. Our results reveal that if a strategy resists the invasion of any other one sharing its same moral assessment, it can r...

  12. Using rules to adapt applications for business models with high evolutionary rates

    Directory of Open Access Journals (Sweden)

    Juan Fuente, A. A

    2013-06-01

    Full Text Available Nowadays, business models are in permanent evolution since the requirements belongs to a rapidly evolving world. In a context where communications all around the world travel so fast the business models need to be adapted permanently to the information the managers receive. In such world, traditional software development, needed for adapting software to changes, do not work properly since business changes need to be in exploitation in shorter times. In that situation, it is needed to go quicker from the business idea to the exploitation environment. This issue can be solved accelerating the development speed: from the expert to the customer, with no –or few, technical intervention. This paper proposes an approach to empower domain experts in developing adaptability solutions by using automated sets of production rules in a friendly way. Furthermore, a use case that implements this kind of development was used in a real problem prototype.

  13. Social Defense: An Evolutionary-Developmental Model of Children's Strategies for Coping with Threat in the Peer Group

    National Research Council Canada - National Science Library

    Martin, Meredith J; Davies, Patrick T; MacNeill, Leigha A

    2014-01-01

    ... challenges of establishing a social niche. To address this gap, we utilize the ethological reformulation of the emotional security theory as a guide to developing an evolutionary framework for advancing an understanding of the defense...

  14. Modeling the Integration of Open Systems and Evolutionary Acquisition in DoD Programs

    Science.gov (United States)

    2009-08-19

    Integration Production Readiness, LRIP & IOT &E Full Rate Production & Deployment 80% Solution FRP 80% Solution LRIP System Development...Demonstration System Demonstration System Integration Full Rate Production & Deployment Production & Deployment Production Readiness, LRIP & IOT ...3 A3 B3 DRR3 C3 FRP3 Time Periods Figure 4. Information Flows in a Three-block Acquisition Project - 15 - A Formal Simulation Model of an

  15. An evolutionary model explaining the Neolithic transition from egalitarianism to leadership and despotism.

    Science.gov (United States)

    Powers, Simon T; Lehmann, Laurent

    2014-09-22

    The Neolithic was marked by a transition from small and relatively egalitarian groups to much larger groups with increased stratification. But, the dynamics of this remain poorly understood. It is hard to see how despotism can arise without coercion, yet coercion could not easily have occurred in an egalitarian setting. Using a quantitative model of evolution in a patch-structured population, we demonstrate that the interaction between demographic and ecological factors can overcome this conundrum. We model the coevolution of individual preferences for hierarchy alongside the degree of despotism of leaders, and the dispersal preferences of followers. We show that voluntary leadership without coercion can evolve in small groups, when leaders help to solve coordination problems related to resource production. An example is coordinating construction of an irrigation system. Our model predicts that the transition to larger despotic groups will then occur when: (i) surplus resources lead to demographic expansion of groups, removing the viability of an acephalous niche in the same area and so locking individuals into hierarchy; (ii) high dispersal costs limit followers' ability to escape a despot. Empirical evidence suggests that these conditions were probably met, for the first time, during the subsistence intensification of the Neolithic. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  16. An evolutionary model explaining the Neolithic transition from egalitarianism to leadership and despotism

    Science.gov (United States)

    Powers, Simon T.; Lehmann, Laurent

    2014-01-01

    The Neolithic was marked by a transition from small and relatively egalitarian groups to much larger groups with increased stratification. But, the dynamics of this remain poorly understood. It is hard to see how despotism can arise without coercion, yet coercion could not easily have occurred in an egalitarian setting. Using a quantitative model of evolution in a patch-structured population, we demonstrate that the interaction between demographic and ecological factors can overcome this conundrum. We model the coevolution of individual preferences for hierarchy alongside the degree of despotism of leaders, and the dispersal preferences of followers. We show that voluntary leadership without coercion can evolve in small groups, when leaders help to solve coordination problems related to resource production. An example is coordinating construction of an irrigation system. Our model predicts that the transition to larger despotic groups will then occur when: (i) surplus resources lead to demographic expansion of groups, removing the viability of an acephalous niche in the same area and so locking individuals into hierarchy; (ii) high dispersal costs limit followers' ability to escape a despot. Empirical evidence suggests that these conditions were probably met, for the first time, during the subsistence intensification of the Neolithic. PMID:25100704

  17. A Behavioral Handwriting Model for Static and Dynamic Signature Synthesis.

    Science.gov (United States)

    Ferrer, Miguel A; Diaz, Moises; Carmona-Duarte, Cristina; Morales, Aythami

    2017-06-01

    The synthetic generation of static handwritten signatures based on motor equivalence theory has been recently proposed for biometric applications. Motor equivalence divides the human handwriting action into an effector dependent cognitive level and an effector independent motor level. The first level has been suggested by others as an engram, generated through a spatial grid, and the second has been emulated with kinematic filters. Our paper proposes a development of this methodology in which we generate dynamic information and provide a unified comprehensive synthesizer for both static and dynamic signature synthesis. The dynamics are calculated by lognormal sampling of the 8-connected continuous signature trajectory, which includes, as a novelty, the pen-ups. The forgery generation imitates a signature by extracting the most perceptually relevant points of the given genuine signature and interpolating them. The capacity to synthesize both static and dynamic signatures using a unique model is evaluated according to its ability to adapt to the static and dynamic signature inter- and intra-personal variability. Our highly promising results suggest the possibility of using the synthesizer in different areas beyond the generation of unlimited databases for biometric training.

  18. Parametric Hidden Markov Models for Recognition and Synthesis of Movements

    DEFF Research Database (Denmark)

    Herzog, Dennis; Krüger, Volker; Grest, Daniel

    2008-01-01

    . For understanding the whole meaning of a movement of a human, the recognition of its type, likewise its parameterization are important. Only both together convey the whole meaning. Vice versa, for mimicry, the synthesis of movements for the motor control of a robot needs to be parameterized, e.g., by the relative......) to represent parametric movements. As HMMs are generative, they are well suited for synthesis as well as for recognition. Synthesis and recognition are carried out through interpolation of exemplar movements to generalize over the parameterization of a movement class. In the evaluation of the approach we...

  19. Method for determining the duration of construction basing on evolutionary modeling taking into account random organizational expectations

    Directory of Open Access Journals (Sweden)

    Alekseytsev Anatoliy Viktorovich

    2016-10-01

    Full Text Available One of the problems of construction planning is failure to meet time constraints and increase of workflow duration. In the recent years informational technologies are efficiently used to solve the problem of estimation of construction period. The issue of optimal estimate of the duration of construction, taking into account the possible organizational expectations is considered in the article. In order to solve this problem the iteration scheme of evolutionary modeling, in which random values of organizational expectations are used as variable parameters is developed. Adjustable genetic operators are used to improve the efficiency of the search for solutions. The reliability of the proposed approach is illustrated by an example of formation of construction schedules of monolithic foundations for buildings, taking into account possible disruptions of supply of concrete and reinforcement cages. Application of the presented methodology enables automated acquisition of several alternative scheduling of construction in accordance with standard or directive duration. Application of this computational procedure has the prospects of taking into account of construction downtime due to weather, accidents related to construction machinery breakdowns or local emergency collapses of the structures being erected.

  20. Managing uncertainty, ambiguity and ignorance in impact assessment by embedding evolutionary resilience, participatory modelling and adaptive management.

    Science.gov (United States)

    Bond, Alan; Morrison-Saunders, Angus; Gunn, Jill A E; Pope, Jenny; Retief, Francois

    2015-03-15

    In the context of continuing uncertainty, ambiguity and ignorance in impact assessment (IA) prediction, the case is made that existing IA processes are based on false 'normal' assumptions that science can solve problems and transfer knowledge into policy. Instead, a 'post-normal science' approach is needed that acknowledges the limits of current levels of scientific understanding. We argue that this can be achieved through embedding evolutionary resilience into IA; using participatory workshops; and emphasising adaptive management. The goal is an IA process capable of informing policy choices in the face of uncertain influences acting on socio-ecological systems. We propose a specific set of process steps to operationalise this post-normal science approach which draws on work undertaken by the Resilience Alliance. This process differs significantly from current models of IA, as it has a far greater focus on avoidance of, or adaptation to (through incorporating adaptive management subsequent to decisions), unwanted future scenarios rather than a focus on the identification of the implications of a single preferred vision. Implementing such a process would represent a culture change in IA practice as a lack of knowledge is assumed and explicit, and forms the basis of future planning activity, rather than being ignored. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model.

    Science.gov (United States)

    Kühnert, Denise; Stadler, Tanja; Vaughan, Timothy G; Drummond, Alexei J

    2014-05-06

    The evolution of RNA viruses, such as human immunodeficiency virus (HIV), hepatitis C virus and influenza virus, occurs so rapidly that the viruses' genomes contain information on past ecological dynamics. Hence, we develop a phylodynamic method that enables the joint estimation of epidemiological parameters and phylogenetic history. Based on a compartmental susceptible-infected-removed (SIR) model, this method provides separate information on incidence and prevalence of infections. Detailed information on the interaction of host population dynamics and evolutionary history can inform decisions on how to contain or entirely avoid disease outbreaks. We apply our birth-death SIR method to two viral datasets. First, five HIV type 1 clusters sampled in the UK between 1999 and 2003 are analysed. The estimated basic reproduction ratios range from 1.9 to 3.2 among the clusters. All clusters show a decline in the growth rate of the local epidemic in the middle or end of the 1990s. The analysis of a hepatitis C virus genotype 2c dataset shows that the local epidemic in the Córdoban city Cruz del Eje originated around 1906 (median), coinciding with an immigration wave from Europe to central Argentina that dates from 1880 to 1920. The estimated time of epidemic peak is around 1970.

  2. Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model

    Science.gov (United States)

    Kühnert, Denise; Stadler, Tanja; Vaughan, Timothy G.; Drummond, Alexei J.

    2014-01-01

    The evolution of RNA viruses, such as human immunodeficiency virus (HIV), hepatitis C virus and influenza virus, occurs so rapidly that the viruses' genomes contain information on past ecological dynamics. Hence, we develop a phylodynamic method that enables the joint estimation of epidemiological parameters and phylogenetic history. Based on a compartmental susceptible–infected–removed (SIR) model, this method provides separate information on incidence and prevalence of infections. Detailed information on the interaction of host population dynamics and evolutionary history can inform decisions on how to contain or entirely avoid disease outbreaks. We apply our birth–death SIR method to two viral datasets. First, five HIV type 1 clusters sampled in the UK between 1999 and 2003 are analysed. The estimated basic reproduction ratios range from 1.9 to 3.2 among the clusters. All clusters show a decline in the growth rate of the local epidemic in the middle or end of the 1990s. The analysis of a hepatitis C virus genotype 2c dataset shows that the local epidemic in the Córdoban city Cruz del Eje originated around 1906 (median), coinciding with an immigration wave from Europe to central Argentina that dates from 1880 to 1920. The estimated time of epidemic peak is around 1970. PMID:24573331

  3. Prediction of putative protein interactions through evolutionary analysis of osmotic stress response in the model yeast Saccharomyces cerevisae.

    Science.gov (United States)

    Thorne, Thomas W; Ho, Hsueh-Lui; Huvet, Maxime; Haynes, Ken; Stumpf, Michael P H

    2011-05-01

    The osmotic stress response signalling pathway of the model yeast Saccharomyces cerevisae is crucial for the survival of cells under osmotic stress, and is preserved to varying degrees in other related fungal species. We apply a method for inference of ancestral states of characteristics over a phylogeny to 17 fungal species to infer the maximum likelihood estimate of presence or absence in ancestral genomes of genes involved in osmotic stress response. The same method allows us furthermore to perform a statistical test for correlated evolution between genes. Where such correlations exist within the osmotic stress response pathway of S. cerevisae, we have used this in order to predict and subsequently test for the presence of physical protein-protein interactions in an attempt to detect novel interactions. Finally we assess the relevance of observed evolutionary correlations in predicting protein interactions in light of the experimental results. We do find that correlated evolution provides some useful information for the prediction of protein-protein interactions, but that these alone are not sufficient to explain detectable patterns of correlated evolution. Copyright © 2010 Elsevier Inc. All rights reserved.

  4. Wind Farm Layout Optimization through a Crossover-Elitist Evolutionary Algorithm performed over a High Performing Analytical Wake Model

    Science.gov (United States)

    Kirchner-Bossi, Nicolas; Porté-Agel, Fernando

    2017-04-01

    Wind turbine wakes can significantly disrupt the performance of further downstream turbines in a wind farm, thus seriously limiting the overall wind farm power output. Such effect makes the layout design of a wind farm to play a crucial role on the whole performance of the project. An accurate definition of the wake interactions added to a computationally compromised layout optimization strategy can result in an efficient resource when addressing the problem. This work presents a novel soft-computing approach to optimize the wind farm layout by minimizing the overall wake effects that the installed turbines exert on one another. An evolutionary algorithm with an elitist sub-optimization crossover routine and an unconstrained (continuous) turbine positioning set up is developed and tested over an 80-turbine offshore wind farm over the North Sea off Denmark (Horns Rev I). Within every generation of the evolution, the wind power output (cost function) is computed through a recently developed and validated analytical wake model with a Gaussian profile velocity deficit [1], which has shown to outperform the traditionally employed wake models through different LES simulations and wind tunnel experiments. Two schemes with slightly different perimeter constraint conditions (full or partial) are tested. Results show, compared to the baseline, gridded layout, a wind power output increase between 5.5% and 7.7%. In addition, it is observed that the electric cable length at the facilities is reduced by up to 21%. [1] Bastankhah, Majid, and Fernando Porté-Agel. "A new analytical model for wind-turbine wakes." Renewable Energy 70 (2014): 116-123.

  5. A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility.

    Science.gov (United States)

    Huang, Tsun-Tsao; del Valle Marcos, María Laura; Hwang, Jenn-Kang; Echave, Julian

    2014-04-09

    Protein sites evolve at different rates due to functional and biophysical constraints. It is usually considered that the main structural determinant of a site's rate of evolution is its Relative Solvent Accessibility (RSA). However, a recent comparative study has shown that the main structural determinant is the site's Local Packing Density (LPD). LPD is related with dynamical flexibility, which has also been shown to correlate with sequence variability. Our purpose is to investigate the mechanism that connects a site's LPD with its rate of evolution. We consider two models: an empirical Flexibility Model and a mechanistic Stress Model. The Flexibility Model postulates a linear increase of site-specific rate of evolution with dynamical flexibility. The Stress Model, introduced here, models mutations as random perturbations of the protein's potential energy landscape, for which we use simple Elastic Network Models (ENMs). To account for natural selection we assume a single active conformation and use basic statistical physics to derive a linear relationship between site-specific evolutionary rates and the local stress of the mutant's active conformation.We compare both models on a large and diverse dataset of enzymes. In a protein-by-protein study we found that the Stress Model outperforms the Flexibility Model for most proteins. Pooling all proteins together we show that the Stress Model is strongly supported by the total weight of evidence. Moreover, it accounts for the observed nonlinear dependence of sequence variability on flexibility. Finally, when mutational stress is controlled for, there is very little remaining correlation between sequence variability and dynamical flexibility. We developed a mechanistic Stress Model of evolution according to which the rate of evolution of a site is predicted to depend linearly on the local mutational stress of the active conformation. Such local stress is proportional to LPD, so that this model explains the relationship

  6. Galactic cold cores. VIII. Filament formation and evolution: Filament properties in context with evolutionary models

    Science.gov (United States)

    Rivera-Ingraham, A.; Ristorcelli, I.; Juvela, M.; Montillaud, J.; Men'shchikov, A.; Malinen, J.; Pelkonen, V.-M.; Marston, A.; Martin, P. G.; Pagani, L.; Paladini, R.; Paradis, D.; Ysard, N.; Ward-Thompson, D.; Bernard, J.-P.; Marshall, D. J.; Montier, L.; Tóth, L. V.

    2017-05-01

    Context. The onset of star formation is intimately linked with the presence of massive unstable filamentary structures. These filaments are therefore key for theoretical models that aim to reproduce the observed characteristics of the star formation process in the Galaxy. Aims: As part of the filament study carried out by the Herschel Galactic Cold Cores Key Programme, here we study and discuss the filament properties presented in GCC VII (Paper I) in context with theoretical models of filament formation and evolution. Methods: A conservatively selected sample of filaments located at a distance Dextracted from the GCC fields with the getfilaments algorithm. The physical structure of the filaments was quantified according to two main components: the central (Gaussian) region of the filament (core component), and the power-law-like region dominating the filament column density profile at larger radii (wing component). The properties and behaviour of these components relative to the total linear mass density of the filament and the column density of its environment were compared with the predictions from theoretical models describing the evolution of filaments under gravity-dominated conditions. Results: The feasibility of a transition from a subcritical to supercritical state by accretion at any given time is dependent on the combined effect of filament intrinsic properties and environmental conditions. Reasonably self-gravitating (high Mline,core) filaments in dense environments (AV≳ 3 mag) can become supercritical on timescales of t 1 Myr by accreting mass at constant or decreasing width. The trend of increasing Mline,tot (Mline,core and Mline,wing) and ridge AV with background for the filament population also indicates that the precursors of star-forming filaments evolve coevally with their environment. The simultaneous increase of environment and filament AV explains the observed association between dense environments and high Mline,core values, and it argues

  7. Electronic design automation of analog ICs combining gradient models with multi-objective evolutionary algorithms

    CERN Document Server

    Rocha, Frederico AE; Lourenço, Nuno CC; Horta, Nuno CG

    2013-01-01

    This book applies to the scientific area of electronic design automation (EDA) and addresses the automatic sizing of analog integrated circuits (ICs). Particularly, this book presents an approach to enhance a state-of-the-art layout-aware circuit-level optimizer (GENOM-POF), by embedding statistical knowledge from an automatically generated gradient model into the multi-objective multi-constraint optimization kernel based on the NSGA-II algorithm. The results showed allow the designer to explore the different trade-offs of the solution space, both through the achieved device sizes, or the resp

  8. Lovastatin corrects excess protein synthesis and prevents epileptogenesis in a mouse model of fragile X syndrome

    National Research Council Canada - National Science Library

    Osterweil, Emily K; Chuang, Shih-Chieh; Chubykin, Alexander A; Sidorov, Michael; Bianchi, Riccardo; Wong, Robert K S; Bear, Mark F

    2013-01-01

    .... We discovered that lovastatin, a drug that is widely prescribed for the treatment of high cholesterol, can correct excess hippocampal protein synthesis in the mouse model of FXS and can prevent one...

  9. Evolutionary stability and resistance to cheating in an indirect reciprocity model based on reputation

    Science.gov (United States)

    Martinez-Vaquero, Luis A.; Cuesta, José A.

    2013-05-01

    Indirect reciprocity is one of the main mechanisms to explain the emergence and sustainment of altruism in societies. The standard approach to indirect reciprocity is reputation models. These are games in which players base their decisions on their opponent's reputation gained in past interactions with other players (moral assessment). The combination of actions and moral assessment leads to a large diversity of strategies; thus determining the stability of any of them against invasions by all the others is a difficult task. We use a variant of a previously introduced reputation-based model that let us systematically analyze all these invasions and determine which ones are successful. Accordingly, we are able to identify the third-order strategies (those which, apart from the action, judge considering both the reputation of the donor and that of the recipient) that are evolutionarily stable. Our results reveal that if a strategy resists the invasion of any other one sharing its same moral assessment, it can resist the invasion of any other strategy. However, if actions are not always witnessed, cheaters (i.e., individuals with a probability of defecting regardless of the opponent's reputation) have a chance to defeat the stable strategies for some choices of the probabilities of cheating and of being witnessed. Remarkably, by analyzing this issue with adaptive dynamics we find that whether an honest population resists the invasion of cheaters is determined by a Hamilton-like rule, with the probability that the cheat is discovered playing the role of the relatedness parameter.

  10. Evolutionary modeling and prediction of non-coding RNAs in Drosophila.

    Directory of Open Access Journals (Sweden)

    Robert K Bradley

    2009-08-01

    Full Text Available We performed benchmarks of phylogenetic grammar-based ncRNA gene prediction, experimenting with eight different models of structural evolution and two different programs for genome alignment. We evaluated our models using alignments of twelve Drosophila genomes. We find that ncRNA prediction performance can vary greatly between different gene predictors and subfamilies of ncRNA gene. Our estimates for false positive rates are based on simulations which preserve local islands of conservation; using these simulations, we predict a higher rate of false positives than previous computational ncRNA screens have reported. Using one of the tested prediction grammars, we provide an updated set of ncRNA predictions for D. melanogaster and compare them to previously-published predictions and experimental data. Many of our predictions show correlations with protein-coding genes. We found significant depletion of intergenic predictions near the 3' end of coding regions and furthermore depletion of predictions in the first intron of protein-coding genes. Some of our predictions are colocated with larger putative unannotated genes: for example, 17 of our predictions showing homology to the RFAM family snoR28 appear in a tandem array on the X chromosome; the 4.5 Kbp spanned by the predicted tandem array is contained within a FlyBase-annotated cDNA.

  11. Creating wavelet-based models for real-time synthesis of perceptually convincing environmental sounds

    Science.gov (United States)

    Miner, Nadine Elizabeth

    1998-09-01

    This dissertation presents a new wavelet-based method for synthesizing perceptually convincing, dynamic sounds using parameterized sound models. The sound synthesis method is applicable to a variety of applications including Virtual Reality (VR), multi-media, entertainment, and the World Wide Web (WWW). A unique contribution of this research is the modeling of the stochastic, or non-pitched, sound components. This stochastic-based modeling approach leads to perceptually compelling sound synthesis. Two preliminary studies conducted provide data on multi-sensory interaction and audio-visual synchronization timing. These results contributed to the design of the new sound synthesis method. The method uses a four-phase development process, including analysis, parameterization, synthesis and validation, to create the wavelet-based sound models. A patent is pending for this dynamic sound synthesis method, which provides perceptually-realistic, real-time sound generation. This dissertation also presents a battery of perceptual experiments developed to verify the sound synthesis results. These experiments are applicable for validation of any sound synthesis technique.

  12. Modeling and computer simulation of ion beam synthesis of nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Strobel, M.

    1999-11-01

    The following topics were dealt with: ion beam synthesis of nanoclusters, kinetic three dimensional lattice Monte Carlo method, Ostwald ripening, redistribution of implanted impurities, buried layer formation, comparisation to experimental results.

  13. Extinction phase transitions in a model of ecological and evolutionary dynamics

    Science.gov (United States)

    Barghathi, Hatem; Tackkett, Skye; Vojta, Thomas

    2017-07-01

    We study the non-equilibrium phase transition between survival and extinction of spatially extended biological populations using an agent-based model. We especially focus on the effects of global temporal fluctuations of the environmental conditions, i.e., temporal disorder. Using large-scale Monte-Carlo simulations of up to 3 × 107 organisms and 105 generations, we find the extinction transition in time-independent environments to be in the well-known directed percolation universality class. In contrast, temporal disorder leads to a highly unusual extinction transition characterized by logarithmically slow population decay and enormous fluctuations even for large populations. The simulations provide strong evidence for this transition to be of exotic infinite-noise type, as recently predicted by a renormalization group theory. The transition is accompanied by temporal Griffiths phases featuring a power-law dependence of the life time on the population size.

  14. Large extinctions in an evolutionary model: The role of innovation and keystone species

    Science.gov (United States)

    Jain, Sanjay; Krishna, Sandeep

    2002-02-01

    The causes of major and rapid transitions observed in biological macroevolution as well as in the evolution of social systems are a subject of much debate. Here we identify the proximate causes of crashes and recoveries that arise dynamically in a model system in which populations of (molecular) species coevolve with their network of chemical interactions. Crashes are events that involve the rapid extinction of many species, and recoveries the assimilation of new ones. These are analyzed and classified in terms of the structural properties of the network. We find that in the absence of large external perturbation, "innovation" is a major cause of large extinctions and the prime cause of recoveries. Another major cause of crashes is the extinction of a "keystone species." Different classes of causes produce crashes of different characteristic sizes.

  15. Hydraulic Modeling and Evolutionary Optimization for Enhanced Real-Time Decision Support of Combined Sewer Overflows

    Science.gov (United States)

    Zimmer, A. L.; Minsker, B. S.; Schmidt, A. R.; Ostfeld, A.

    2011-12-01

    Real-time mitigation of combined sewer overflows (CSOs) requires evaluation of multiple operational strategies during rapidly changing rainfall events. Simulation models for hydraulically complex systems can effectively provide decision support for short time intervals when coupled with efficient optimization. This work seeks to reduce CSOs for a test case roughly based on the North Branch of the Chicago Tunnel and Reservoir Plan (TARP), which is operated by the Metropolitan Water Reclamation District of Greater Chicago (MWRDGC). The North Branch tunnel flows to a junction with the main TARP system. The Chicago combined sewer system alleviates potential CSOs by directing high interceptor flows through sluice gates and dropshafts to a deep tunnel. Decision variables to control CSOs consist of sluice gate positions that control water flow to the tunnel as well as a treatment plant pumping rate that lowers interceptor water levels. A physics-based numerical model is used to simulate the hydraulic effects of changes in the decision variables. The numerical model is step-wise steady and conserves water mass and momentum at each time step by iterating through a series of look-up tables. The look-up tables are constructed offline to avoid extensive real-time calculations, and describe conduit storage and water elevations as a function of flow. A genetic algorithm (GA) is used to minimize CSOs at each time interval within a moving horizon framework. Decision variables are coded at 15-minute increments and GA solutions are two hours in duration. At each 15-minute interval, the algorithm identifies a good solution for a two-hour rainfall forecast. Three GA modifications help reduce optimization time. The first adjustment reduces the search alphabet by eliminating sluice gate positions that do not influence overflow volume. The second GA retains knowledge of the best decision at the previous interval by shifting the genes in the best previous sequence to initialize search at

  16. Application of Differential Evolutionary Optimization Methodology for Parameter Structure Identification in Groundwater Modeling

    Science.gov (United States)

    Chiu, Y.; Nishikawa, T.

    2013-12-01

    With the increasing complexity of parameter-structure identification (PSI) in groundwater modeling, there is a need for robust, fast, and accurate optimizers in the groundwater-hydrology field. For this work, PSI is defined as identifying parameter dimension, structure, and value. In this study, Voronoi tessellation and differential evolution (DE) are used to solve the optimal PSI problem. Voronoi tessellation is used for automatic parameterization, whereby stepwise regression and the error covariance matrix are used to determine the optimal parameter dimension. DE is a novel global optimizer that can be used to solve nonlinear, nondifferentiable, and multimodal optimization problems. It can be viewed as an improved version of genetic algorithms and employs a simple cycle of mutation, crossover, and selection operations. DE is used to estimate the optimal parameter structure and its associated values. A synthetic numerical experiment of continuous hydraulic conductivity distribution was conducted to demonstrate the proposed methodology. The results indicate that DE can identify the global optimum effectively and efficiently. A sensitivity analysis of the control parameters (i.e., the population size, mutation scaling factor, crossover rate, and mutation schemes) was performed to examine their influence on the objective function. The proposed DE was then applied to solve a complex parameter-estimation problem for a small desert groundwater basin in Southern California. Hydraulic conductivity, specific yield, specific storage, fault conductance, and recharge components were estimated simultaneously. Comparison of DE and a traditional gradient-based approach (PEST) shows DE to be more robust and efficient. The results of this work not only provide an alternative for PSI in groundwater models, but also extend DE applications towards solving complex, regional-scale water management optimization problems.

  17. Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology.

    Science.gov (United States)

    Briskine, Roman V; Paape, Timothy; Shimizu-Inatsugi, Rie; Nishiyama, Tomoaki; Akama, Satoru; Sese, Jun; Shimizu, Kentaro K

    2017-09-01

    The self-incompatible species Arabidopsis halleri is a close relative of the self-compatible model plant Arabidopsis thaliana. The broad European and Asian distribution and heavy metal hyperaccumulation ability make A. halleri a useful model for ecological genomics studies. We used long-insert mate-pair libraries to improve the genome assembly of the A. halleri ssp. gemmifera Tada mine genotype (W302) collected from a site with high contamination by heavy metals in Japan. After five rounds of forced selfing, heterozygosity was reduced to 0.04%, which facilitated subsequent genome assembly. Our assembly now covers 196 Mb or 78% of the estimated genome size and achieved scaffold N50 length of 712 kb. To validate assembly and annotation, we used synteny of A. halleri Tada mine with a previously published high-quality reference assembly of a closely related species, Arabidopsis lyrata. Further validation of the assembly quality comes from synteny and phylogenetic analysis of the HEAVY METAL ATPASE4 (HMA4) and METAL TOLERANCE PROTEIN1 (MTP1) regions using published sequences from European A. halleri for comparison. Three tandemly duplicated copies of HMA4, key gene involved in cadmium and zinc hyperaccumulation, were assembled on a single scaffold. The assembly will enhance the genomewide studies of A. halleri as well as the allopolyploid Arabidopsis kamchatica derived from A. lyrata and A. halleri. © 2016 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

  18. Femininity and Kin-Directed Altruism in Androphilic Men: A Test of an Evolutionary Developmental Model.

    Science.gov (United States)

    VanderLaan, Doug P; Petterson, Lanna J; Vasey, Paul L

    2016-04-01

    Androphilia refers to sexual attraction and arousal toward males whereas gynephilia refers to sexual attraction and arousal toward females. This study tested the adaptive feminine phenotype model of the evolution of male androphilia via kin selection, which posits that the development of an evolved disposition toward elevated kin-directed altruism among androphilic males is contingent on the behavioral expression of femininity. Gynephilic men, androphilic women, and androphilic men (N = 387) completed measures of childhood and adulthood gender expression and concern for kin's well-being. Adulthood femininity correlated positively with uncle/aunt-like tendencies among androphilic men and women. Although androphilic women reported greater willingness to invest in nieces and nephews than gynephilic and androphilic men, mediation analyses indicated that adult femininity completely mediated these group differences. In addition, changes in the expression of femininity between childhood and adulthood were associated with parallel changes in concern for the well-being of kin among androphilic men. Thus, these findings suggest that femininity is key to the expression of kin-directed altruism among androphilic males and may have been important in the evolution of male androphilia.

  19. Tracing hepatitis B virus (HBV) genotype B5 (formerly B6) evolutionary history in the circumpolar Arctic through phylogeographic modelling.

    Science.gov (United States)

    Bouckaert, Remco; Simons, Brenna C; Krarup, Henrik; Friesen, T Max; Osiowy, Carla

    2017-01-01

    Indigenous populations of the circumpolar Arctic are considered to be endemically infected (>2% prevalence) with hepatitis B virus (HBV), with subgenotype B5 (formerly B6) unique to these populations. The distinctive properties of HBV/B5, including high nucleotide diversity yet no significant liver disease, suggest virus adaptation through long-term host-pathogen association. To investigate the origin and evolutionary spread of HBV/B5 into the circumpolar Arctic, fifty-seven partial and full genome sequences from Alaska, Canada and Greenland, having known location and sampling dates spanning 40 years, were phylogeographically investigated by Bayesian analysis (BEAST 2) using a reversible-jump-based substitution model and a clock rate estimated at 4.1 × 10(-5) substitutions/site/year. Following an initial divergence from an Asian viral ancestor approximately 1954 years before present (YBP; 95% highest probability density interval [1188, 2901]), HBV/B5 coalescence occurred almost 1000 years later. Surprisingly, the HBV/B5 ancestor appears to locate first to Greenland in a rapid coastal route progression based on the landscape aware geographic model, with subsequent B5 evolution and spread westward. Bayesian skyline plot analysis demonstrated an HBV/B5 population expansion occurring approximately 400 YBP, coinciding with the disruption of the Neo-Eskimo Thule culture into more heterogeneous and regionally distinct Inuit populations throughout the North American Arctic. HBV/B5 origin and spread appears to occur coincident with the movement of Neo-Eskimo (Inuit) populations within the past 1000 years, further supporting the hypothesis of HBV/host co-expansion, and illustrating the concept of host-pathogen adaptation and balance.

  20. Tracing hepatitis B virus (HBV genotype B5 (formerly B6 evolutionary history in the circumpolar Arctic through phylogeographic modelling

    Directory of Open Access Journals (Sweden)

    Remco Bouckaert

    2017-08-01

    Full Text Available Background Indigenous populations of the circumpolar Arctic are considered to be endemically infected (>2% prevalence with hepatitis B virus (HBV, with subgenotype B5 (formerly B6 unique to these populations. The distinctive properties of HBV/B5, including high nucleotide diversity yet no significant liver disease, suggest virus adaptation through long-term host-pathogen association. Methods To investigate the origin and evolutionary spread of HBV/B5 into the circumpolar Arctic, fifty-seven partial and full genome sequences from Alaska, Canada and Greenland, having known location and sampling dates spanning 40 years, were phylogeographically investigated by Bayesian analysis (BEAST 2 using a reversible-jump-based substitution model and a clock rate estimated at 4.1 × 10−5 substitutions/site/year. Results Following an initial divergence from an Asian viral ancestor approximately 1954 years before present (YBP; 95% highest probability density interval [1188, 2901], HBV/B5 coalescence occurred almost 1000 years later. Surprisingly, the HBV/B5 ancestor appears to locate first to Greenland in a rapid coastal route progression based on the landscape aware geographic model, with subsequent B5 evolution and spread westward. Bayesian skyline plot analysis demonstrated an HBV/B5 population expansion occurring approximately 400 YBP, coinciding with the disruption of the Neo-Eskimo Thule culture into more heterogeneous and regionally distinct Inuit populations throughout the North American Arctic. Discussion HBV/B5 origin and spread appears to occur coincident with the movement of Neo-Eskimo (Inuit populations within the past 1000 years, further supporting the hypothesis of HBV/host co-expansion, and illustrating the concept of host-pathogen adaptation and balance.

  1. Modeling Temporal Variation in Social Network: An Evolutionary Web Graph Approach

    Science.gov (United States)

    Mitra, Susanta; Bagchi, Aditya

    A social network is a social structure between actors (individuals, organization or other social entities) and indicates the ways in which they are connected through various social relationships like friendships, kinships, professional, academic etc. Usually, a social network represents a social community, like a club and its members or a city and its citizens etc. or a research group communicating over Internet. In seventies Leinhardt [1] first proposed the idea of representing a social community by a digraph. Later, this idea became popular among other research workers like, network designers, web-service application developers and e-learning modelers. It gave rise to a rapid proliferation of research work in the area of social network analysis. Some of the notable structural properties of a social network are connectedness between actors, reachability between a source and a target actor, reciprocity or pair-wise connection between actors with bi-directional links, centrality of actors or the important actors having high degree or more connections and finally the division of actors into sub-structures or cliques or strongly-connected components. The cycles present in a social network may even be nested [2, 3]. The formal definition of these structural properties will be provided in Sect. 8.2.1. The division of actors into cliques or sub-groups can be a very important factor for understanding a social structure, particularly the degree of cohesiveness in a community. The number, size, and connections among the sub-groups in a network are useful in understanding how the network, as a whole, is likely to behave.

  2. From Mimicry to Language: A Neuroanatomically Based Evolutionary Model of the Emergence of Vocal Language

    Science.gov (United States)

    Poliva, Oren

    2016-01-01

    The auditory cortex communicates with the frontal lobe via the middle temporal gyrus (auditory ventral stream; AVS) or the inferior parietal lobule (auditory dorsal stream; ADS). Whereas the AVS is ascribed only with sound recognition, the ADS is ascribed with sound localization, voice detection, prosodic perception/production, lip-speech integration, phoneme discrimination, articulation, repetition, phonological long-term memory and working memory. Previously, I interpreted the juxtaposition of sound localization, voice detection, audio-visual integration and prosodic analysis, as evidence that the behavioral precursor to human speech is the exchange of contact calls in non-human primates. Herein, I interpret the remaining ADS functions as evidence of additional stages in language evolution. According to this model, the role of the ADS in vocal control enabled early Homo (Hominans) to name objects using monosyllabic calls, and allowed children to learn their parents' calls by imitating their lip movements. Initially, the calls were forgotten quickly but gradually were remembered for longer periods. Once the representations of the calls became permanent, mimicry was limited to infancy, and older individuals encoded in the ADS a lexicon for the names of objects (phonological lexicon). Consequently, sound recognition in the AVS was sufficient for activating the phonological representations in the ADS and mimicry became independent of lip-reading. Later, by developing inhibitory connections between acoustic-syllabic representations in the AVS and phonological representations of subsequent syllables in the ADS, Hominans became capable of concatenating the monosyllabic calls for repeating polysyllabic words (i.e., developed working memory). Finally, due to strengthening of connections between phonological representations in the ADS, Hominans became capable of encoding several syllables as a single representation (chunking). Consequently, Hominans began vocalizing and

  3. Evolutionary approaches to cultural and linguistic diversity.

    Science.gov (United States)

    Steele, James; Jordan, Peter; Cochrane, Ethan

    2010-12-12

    Evolutionary approaches to cultural change are increasingly influential, and many scientists believe that a 'grand synthesis' is now in sight. The papers in this Theme Issue, which derives from a symposium held by the AHRC Centre for the Evolution of Cultural Diversity (University College London) in December 2008, focus on how the phylogenetic tree-building and network-based techniques used to estimate descent relationships in biology can be adapted to reconstruct cultural histories, where some degree of inter-societal diffusion will almost inevitably be superimposed on any deeper signal of a historical branching process. The disciplines represented include the three most purely 'cultural' fields from the four-field model of anthropology (cultural anthropology, archaeology and linguistic anthropology). In this short introduction, some context is provided from the history of anthropology, and key issues raised by the papers are highlighted.

  4. Microfluidic very large scale integration (VLSI) modeling, simulation, testing, compilation and physical synthesis

    CERN Document Server

    Pop, Paul; Madsen, Jan

    2016-01-01

    This book presents the state-of-the-art techniques for the modeling, simulation, testing, compilation and physical synthesis of mVLSI biochips. The authors describe a top-down modeling and synthesis methodology for the mVLSI biochips, inspired by microelectronics VLSI methodologies. They introduce a modeling framework for the components and the biochip architecture, and a high-level microfluidic protocol language. Coverage includes a topology graph-based model for the biochip architecture, and a sequencing graph to model for biochemical application, showing how the application model can be obtained from the protocol language. The techniques described facilitate programmability and automation, enabling developers in the emerging, large biochip market. · Presents the current models used for the research on compilation and synthesis techniques of mVLSI biochips in a tutorial fashion; · Includes a set of "benchmarks", that are presented in great detail and includes the source code of several of the techniques p...

  5. 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

  6. Model-Based Synthesis of Visual Speech Movements from 3D Video

    Directory of Open Access Journals (Sweden)

    Edge JamesD

    2009-01-01

    Full Text Available We describe a method for the synthesis of visual speech movements using a hybrid unit selection/model-based approach. Speech lip movements are captured using a 3D stereo face capture system and split up into phonetic units. A dynamic parameterisation of this data is constructed which maintains the relationship between lip shapes and velocities; within this parameterisation a model of how lips move is built and is used in the animation of visual speech movements from speech audio input. The mapping from audio parameters to lip movements is disambiguated by selecting only the most similar stored phonetic units to the target utterance during synthesis. By combining properties of model-based synthesis (e.g., HMMs, neural nets with unit selection we improve the quality of our speech synthesis.

  7. Asymmetric Evolutionary Games.

    Directory of Open Access Journals (Sweden)

    Alex McAvoy

    2015-08-01

    Full Text Available 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.

  8. Asymmetric Evolutionary Games.

    Science.gov (United States)

    McAvoy, Alex; Hauert, Christoph

    2015-08-01

    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.

  9. Evolutionary developmental psychology

    National Research Council Canada - National Science Library

    King, Ashley C; Bjorklund, David F

    2010-01-01

    The field of evolutionary developmental psychology can potentially broaden the horizons of mainstream evolutionary psychology by combining the principles of Darwinian evolution by natural selection...

  10. Social defense: an evolutionary-developmental model of children's strategies for coping with threat in the peer group.

    Science.gov (United States)

    Martin, Meredith J; Davies, Patrick T; MacNeill, Leigha A

    2014-04-29

    Navigating the ubiquitous conflict, competition, and complex group dynamics of the peer group is a pivotal developmental task of childhood. Difficulty negotiating these challenges represents a substantial source of risk for psychopathology. Evolutionary developmental psychology offers a unique perspective with the potential to reorganize the way we think about the role of peer relationships in shaping how children cope with the everyday challenges of establishing a social niche. To address this gap, we utilize the ethological reformulation of the emotional security theory as a guide to developing an evolutionary framework for advancing an understanding of the defense strategies children use to manage antagonistic peer relationships and protect themselves from interpersonal threat (Davies and Sturge-Apple, 2007). In this way, we hope to illustrate the value of an evolutionary developmental lens in generating unique theoretical insight and novel research directions into the role of peer relationships in the development of psychopathology.

  11. Evolutionary history of the grey-faced Sengi, Rhynchocyon udzungwensis, from Tanzania: a molecular and species distribution modelling approach.

    Directory of Open Access Journals (Sweden)

    Lucinda P Lawson

    Full Text Available Rhynchocyon udzungwensis is a recently described and poorly understood sengi (giant elephant-shrew endemic to two small montane forests in Southern Tanzania, and surrounded in lower forests by R. cirnei reichardi. In this study, we investigate the molecular genetic relationship between R. udzungwensis and R. c. reichardi, and the possible role that shifting species distributions in response to climate fluctuations may have played in shaping their evolutionary history. Rhynchocyon udzungwensis and R. c. reichardi individuals were sampled from five localities for genetic analyses. Three mitochondrial and two nuclear loci were used to construct species trees for delimitation and to determine whether introgression was detectable either from ancient or ongoing hybridization. All species-tree results show R. udzungwensis and R. c. reichardi as distinct lineages, though mtDNA shows evidence of introgression in some populations. Nuclear loci of each species were monophyletic, implying introgression is exclusively historical. Because we found evidence of introgression, we used distribution data and species distribution modelling for present, glacial, and interglacial climate cycles to predict how shifting species distributions may have facilitated hybridization in some populations. Though interpretations are affected by the limited range of these species, a likely scenario is that the mtDNA introgression found in eastern mid-elevation populations was facilitated by low numbers of R. udzungwensis that expanded into lowland heavily occupied R. c. reichardi areas during interglacial climate cycles. These results imply that relationships within the genus Rhynchocyon may be confounded by porous species boundaries and introgression, even if species are not currently sympatric.

  12. Evolutionary History of Wild Barley (Hordeum vulgare subsp. spontaneum) Analyzed Using Multilocus Sequence Data and Paleodistribution Modeling

    Science.gov (United States)

    Jakob, Sabine S.; Rödder, Dennis; Engler, Jan O.; Shaaf, Salar; Özkan, Hakan; Blattner, Frank R.; Kilian, Benjamin

    2014-01-01

    Studies of Hordeum vulgare subsp. spontaneum, the wild progenitor of cultivated barley, have mostly relied on materials collected decades ago and maintained since then ex situ in germplasm repositories. We analyzed spatial genetic variation in wild barley populations collected rather recently, exploring sequence variations at seven single-copy nuclear loci, and inferred the relationships among these populations and toward the genepool of the crop. The wild barley collection covers the whole natural distribution area from the Mediterranean to Middle Asia. In contrast to earlier studies, Bayesian assignment analyses revealed three population clusters, in the Levant, Turkey, and east of Turkey, respectively. Genetic diversity was exceptionally high in the Levant, while eastern populations were depleted of private alleles. Species distribution modeling based on climate parameters and extant occurrence points of the taxon inferred suitable habitat conditions during the ice-age, particularly in the Levant and Turkey. Together with the ecologically wide range of habitats, they might contribute to structured but long-term stable populations in this region and their high genetic diversity. For recently collected individuals, Bayesian assignment to geographic clusters was generally unambiguous, but materials from genebanks often showed accessions that were not placed according to their assumed geographic origin or showed traces of introgression from cultivated barley. We assign this to gene flow among accessions during ex situ maintenance. Evolutionary studies based on such materials might therefore result in wrong conclusions regarding the history of the species or the origin and mode of domestication of the crop, depending on the accessions included. PMID:24586028

  13. An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1.

    Directory of Open Access Journals (Sweden)

    Sergei L Kosakovsky Pond

    2009-11-01

    Full Text Available Genetically diverse pathogens (such as Human Immunodeficiency virus type 1, HIV-1 are frequently stratified into phylogenetically or immunologically defined subtypes for classification purposes. Computational identification of such subtypes is helpful in surveillance, epidemiological analysis and detection of novel variants, e.g., circulating recombinant forms in HIV-1. A number of conceptually and technically different techniques have been proposed for determining the subtype of a query sequence, but there is not a universally optimal approach. We present a model-based phylogenetic method for automatically subtyping an HIV-1 (or other viral or bacterial sequence, mapping the location of breakpoints and assigning parental sequences in recombinant strains as well as computing confidence levels for the inferred quantities. Our Subtype Classification Using Evolutionary ALgorithms (SCUEAL procedure is shown to perform very well in a variety of simulation scenarios, runs in parallel when multiple sequences are being screened, and matches or exceeds the performance of existing approaches on typical empirical cases. We applied SCUEAL to all available polymerase (pol sequences from two large databases, the Stanford Drug Resistance database and the UK HIV Drug Resistance Database. Comparing with subtypes which had previously been assigned revealed that a minor but substantial (approximately 5% fraction of pure subtype sequences may in fact be within- or inter-subtype recombinants. A free implementation of SCUEAL is provided as a module for the HyPhy package and the Datamonkey web server. Our method is especially useful when an accurate automatic classification of an unknown strain is desired, and is positioned to complement and extend faster but less accurate methods. Given the increasingly frequent use of HIV subtype information in studies focusing on the effect of subtype on treatment, clinical outcome, pathogenicity and vaccine design, the importance

  14. Finite-Element Model-Based Design Synthesis of Axial Flux PMBLDC Motors

    DEFF Research Database (Denmark)

    Fasil, Muhammed; Mijatovic, Nenad; Jensen, Bogi Bech

    2016-01-01

    This paper discusses design synthesis of a permanent magnet brushless DC (PMBLDC) machine using a finite element (FE) model. This work differentiates itself from the past studies by following a synthesis approach, in which many designs that satisfy performance criteria are considered instead...... of a unique solution. The designer can later select a design, based on comparing parameters of the designs, which are critical to the application that the motor will be used. The presented approach makes it easier to define constraints for a design synthesis problem. A detailed description of the setting up...... is demonstrated by designing a segmented axial torus PMBLDC motor for an electric two-wheeler....

  15. Systematic identification and evolutionary analysis of catalytically versatile cytochrome p450 monooxygenase families enriched in model basidiomycete fungi.

    Science.gov (United States)

    Syed, Khajamohiddin; Shale, Karabo; Pagadala, Nataraj Sekhar; Tuszynski, Jack

    2014-01-01

    knowledge, this is the first report on the identification and comparative-evolutionary analysis of P450 families enriched in model basidiomycetes.

  16. Systematic identification and evolutionary analysis of catalytically versatile cytochrome p450 monooxygenase families enriched in model basidiomycete fungi.

    Directory of Open Access Journals (Sweden)

    Khajamohiddin Syed

    material. To our knowledge, this is the first report on the identification and comparative-evolutionary analysis of P450 families enriched in model basidiomycetes.

  17. Automatic synthesis of mathematical models using graph theory for optimisation of thermal energy systems

    Energy Technology Data Exchange (ETDEWEB)

    Grekas, Denis N.; Frangopoulos, Christos A. [National Technical University of Athens, Zografou (Greece). Department of Naval Architecture and Marine Engineering

    2007-11-15

    During the synthesis optimisation of an energy system, the configuration changes and there is need to adapt properly the mathematical model of the system. A method is presented here for the automatic synthesis of the model itself of the energy system, which is based on the graph theory. The topology of the graph is stored in the computer memory and the computer model of the respective system is constructed automatically by Object Oriented Programming. The modelling diagram of the system is introduced by an Application Programming Interface. A combined-cycle system serves as an application example. The method has been proved efficient and convenient. (author)

  18. Sources for Imanishi Kinji's views of sociality and evolutionary ...

    Indian Academy of Sciences (India)

    2007-05-10

    May 10, 2007 ... Prior to the contribution of genetics or the modern evolutionary synthesis (MES) to natural selection theory, social ecologists searched for factors in addition to natural selection that could influence species change. The idea that sociality, not just biology, was important in determining evolutionary outcomes ...

  19. Evolutionary theory and teleology.

    Science.gov (United States)

    O'Grady, R T

    1984-04-21

    The order within and among living systems can be explained rationally by postulating a process of descent with modification, effected by factors which are extrinsic or intrinsic to the organisms. Because at the time Darwin proposed his theory of evolution there was no concept of intrinsic factors which could evolve, he postulated a process of extrinsic effects--natural selection. Biological order was thus seen as an imposed, rather than an emergent, property. Evolutionary change was seen as being determined by the functional efficiency (adaptedness) of the organism in its environment, rather than by spontaneous changes in intrinsically generated organizing factors. The initial incompleteness of Darwin's explanatory model, and the axiomatization of its postulates in neo-Darwinism, has resulted in a theory of functionalism, rather than structuralism. As such, it introduces an unnecessary teleology which confounds evolutionary studies and reduces the usefulness of the theory. This problem cannot be detected from within the neo-Darwinian paradigm because the different levels of end-directed activity--teleomatic, teleonomic, and teleological--are not recognized. They are, in fact, considered to influence one another. The theory of nonequilibrium evolution avoids these problems by returning to the basic principles of biological order and developing a structuralist explanation of intrinsically generated change. Extrinsic factors may affect the resultant evolutionary pattern, but they are neither necessary nor sufficient for evolution to occur.

  20. Evolutionary mysteries in meiosis.

    Science.gov (United States)

    Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E; Wijnker, Erik; Haag, Christoph R

    2016-10-19

    Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these often 'weird' features. We discuss the origin of meiosis (origin of ploidy reduction and recombination, two-step meiosis), its secondary modifications (in polyploids or asexuals, inverted meiosis), its importance in punctuating life cycles (meiotic arrests, epigenetic resetting, meiotic asymmetry, meiotic fairness) and features associated with recombination (disjunction constraints, heterochiasmy, crossover interference and hotspots). We present the various evolutionary scenarios and selective pressures that have been proposed to account for these features, and we highlight that their evolutionary significance often remains largely mysterious. Resolving these mysteries will likely provide decisive steps towards understanding why sex and recombination are found in the majority of eukaryotes.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'. © 2016 The Author(s).

  1. CCS Site Optimization by Applying a Multi-objective Evolutionary Algorithm to Semi-Analytical Leakage Models

    Science.gov (United States)

    Cody, B. M.; Gonzalez-Nicolas, A.; Bau, D. A.

    2011-12-01

    Carbon capture and storage (CCS) has been proposed as a method of reducing global carbon dioxide (CO2) emissions. Although CCS has the potential to greatly retard greenhouse gas loading to the atmosphere while cleaner, more sustainable energy solutions are developed, there is a possibility that sequestered CO2 may leak and intrude into and adversely affect groundwater resources. It has been reported [1] that, while CO2 intrusion typically does not directly threaten underground drinking water resources, it may cause secondary effects, such as the mobilization of hazardous inorganic constituents present in aquifer minerals and changes in pH values. These risks must be fully understood and minimized before CCS project implementation. Combined management of project resources and leakage risk is crucial for the implementation of CCS. In this work, we present a method of: (a) minimizing the total CCS cost, the summation of major project costs with the cost associated with CO2 leakage; and (b) maximizing the mass of injected CO2, for a given proposed sequestration site. Optimization decision variables include the number of CO2 injection wells, injection rates, and injection well locations. The capital and operational costs of injection wells are directly related to injection well depth, location, injection flow rate, and injection duration. The cost of leakage is directly related to the mass of CO2 leaked through weak areas, such as abandoned oil wells, in the cap rock layers overlying the injected formation. Additional constraints on fluid overpressure caused by CO2 injection are imposed to maintain predefined effective stress levels that prevent cap rock fracturing. Here, both mass leakage and fluid overpressure are estimated using two semi-analytical models based upon work by [2,3]. A multi-objective evolutionary algorithm coupled with these semi-analytical leakage flow models is used to determine Pareto-optimal trade-off sets giving minimum total cost vs. maximum mass

  2. Sound Synthesis of the Harpsichord Using a Computationally Efficient Physical Model

    OpenAIRE

    Knif Jonte; Laurson Mikael; Välimäki Vesa; Penttinen Henri; Erkut Cumhur

    2004-01-01

    A sound synthesis algorithm for the harpsichord has been developed by applying the principles of digital waveguide modeling. A modification to the loss filter of the string model is introduced that allows more flexible control of decay rates of partials than is possible with a one-pole digital filter, which is a usual choice for the loss filter. A version of the commuted waveguide synthesis approach is used, where each tone is generated with a parallel combination of the string model and a s...

  3. 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...... material. In this way, the computer becomes a creative tool that is integrated into the artistic process. Several implementations of these ideas are presented, based on interactive evolution, genetic algorithms and artificial life models. A number of different representations of music and sound...... are discussed, with a focus on parameterized sound synthesis and the representation of scores as recursively described trees. The dynamic behavior of a class of sound synthesis engines, consisting of networks of modulating oscillators, is also investigated. Finally, a number of compositions that have been...

  4. On the Evolutionary Bases of Consumer Reinforcement

    Science.gov (United States)

    Nicholson, Michael; Xiao, Sarah Hong

    2010-01-01

    This article locates consumer behavior analysis within the modern neo-Darwinian synthesis, seeking to establish an interface between the ultimate-level theorizing of human evolutionary psychology and the proximate level of inquiry typically favored by operant learning theorists. Following an initial overview of the central tenets of neo-Darwinism,…

  5. Integrating fossils, phylogenies, and niche models into biogeography to reveal ancient evolutionary history: the case of Hypericum (hypericaceae).

    Science.gov (United States)

    Meseguer, Andrea S; Lobo, Jorge M; Ree, Richard; Beerling, David J; Sanmartín, Isabel

    2015-03-01

    In disciplines such as macroevolution that are not amenable to experimentation, scientists usually rely on current observations to test hypotheses about historical events, assuming that "the present is the key to the past." Biogeographers, for example, used this assumption to reconstruct ancestral ranges from the distribution of extant species. Yet, under scenarios of high extinction rates, the biodiversity we observe today might not be representative of the historical diversity and this could result in incorrect biogeographic reconstructions. Here, we introduce a new approach to incorporate into biogeographic inference the temporal, spatial, and environmental information provided by the fossil record, as a direct evidence of the extinct biodiversity fraction. First, inferences of ancestral ranges for those nodes in the phylogeny calibrated with the fossil record are constrained to include the geographic distribution of the fossil. Second, we use fossil distribution and past climate data to reconstruct the climatic preferences and potential distribution of ancestral lineages over time, and use this information to build a biogeographic model that takes into account "ecological connectivity" through time. To show the power of this approach, we reconstruct the biogeographic history of the large angiosperm genus Hypericum, which has a fossil record extending back to the Early Cenozoic. Unlike previous reconstructions based on extant species distributions, our results reveal that Hypericum stem lineages were already distributed in the Holarctic before diversification of its crown-group, and that the geographic distribution of the genus has been relatively stable throughout the climatic oscillations of the Cenozoic. Geographical movement was mediated by the existence of climatic corridors, like Beringia, whereas the equatorial tropical belt acted as a climatic barrier, preventing Hypericum lineages to reach the southern temperate regions. Our study shows that an

  6. Functional and Evolutionary Characterization of a UDP-Xylose Synthase Gene from the Plant Pathogen Xylella fastidiosa, Involved in the Synthesis of Bacterial Lipopolysaccharide.

    Science.gov (United States)

    Alencar, Valquíria Campos; Jabes, Daniela Leite; Menegidio, Fabiano Bezerra; Sassaki, Guilherme Lanzi; de Souza, Lucas Rodrigo; Puzer, Luciano; Meneghetti, Maria Cecília Zorél; Lima, Marcelo Andrade; Tersariol, Ivarne Luis Dos Santos; de Oliveira, Regina Costa; Nunes, Luiz R

    2017-02-07

    Xylella fastidiosa is a plant-infecting bacillus, responsible for many important crop diseases, such as Pierce's disease of vineyards, citrus variegated chlorosis, and coffee leaf scorch (CLS), among others. Recent genomic comparisons involving two CLS-related strains, belonging to X. fastidiosa subsp. pauca, revealed that one of them carries a frameshift mutation that inactivates a gene encoding an oxidoreductase of the short-chain dehydrogenase/reductase (SDR) superfamily, which may play important roles in determining structural variations in bacterial glycans and glycoconjugates. However, the exact nature of this SDR has been a matter of controversy, as different annotations of X. fastidiosa genomes have implicated it in distinct reactions. To confirm the nature of this mutated SDR, a comparative analysis was initially performed, suggesting that it belongs to a subgroup of SDR decarboxylases, representing a UDP-xylose synthase (Uxs). Functional assays, using a recombinant derivative of this enzyme, confirmed its nature as XfUxs, and carbohydrate composition analyses, performed with lipopolysaccharide (LPS) molecules obtained from different strains, indicate that inactivation of the X. fastidiosa uxs gene affects the LPS structure among CLS-related X. fastidiosa strains. Finally, a comparative sequence analysis suggests that this mutation is likely to result in a morphological and evolutionary hallmark that differentiates two subgroups of CLS-related strains, which may influence interactions between these bacteria and their plant and/or insect hosts.

  7. Models of Sexual and Relational Orientation: A Critical Review and Synthesis

    Science.gov (United States)

    Moe, Jeffry L.; Reicherzer, Stacee; Dupuy, Paula J.

    2011-01-01

    Many frameworks exist to explain and describe the phenomenon of same-sex sexuality as it applies to human development. This conceptual article provides a critical overview and synthesis of previous models to serve as a theoretical bridge for the suggested multiple continua model of sexual and relational orientations. Recommendations for how…

  8. A Best-Evidence Synthesis of Research on Orientation and Mobility Involving Tactile Maps and Models

    Science.gov (United States)

    Wright, Tessa; Harris, Beth; Sticken, Eric

    2010-01-01

    A review of the literature from 1965 to 2008 on tactile maps and models in orientation and mobility yielded four pre-experimental and three experimental articles. The articles were analyzed via best-evidence synthesis--a combined narrative and statistical approach--allowing for recommendations for the most effective use of tactile maps and models.…

  9. Uncertainty and Sensitivity Analysis for an Ibuprofen Synthesis Model Based on Hoechst Path

    DEFF Research Database (Denmark)

    da Conceicao Do Carmo Montes, Frederico; Gernaey, Krist V.; Sin, Gürkan

    2017-01-01

    . To this end, we integrated different models in this work to obtain a comprehensive synthesis model for ibuprofen, in a MATLAB /Simulink modelinterface. The process flowsheet is based on the Hoechst path, starting from the Friedel-Craftsacetylation of isobutylbenzene to 4-isobutylphenylacetophenone, its...

  10. Synthesis

    NARCIS (Netherlands)

    Hettelingh, J.P.; Vries, de W.; Posch, M.

    2015-01-01

    This chapter first presents an overview of findings described in this book. This includes a summary of the combined use of empirical and model-based approaches, main results of these analyses, and their relevance in view of impacts on ecosystem health, human health and effects on ecosystem services.

  11. Bupivacaine decreases cell viability and matrix protein synthesis in an intervertebral disc organ model system.

    Science.gov (United States)

    Wang, Dong; Vo, Nam V; Sowa, Gwendolyn A; Hartman, Robert A; Ngo, Kevin; Choe, So Ra; Witt, William T; Dong, Qing; Lee, Joon Y; Niedernhofer, Laura J; Kang, James D

    2011-02-01

    Bupivacaine is a local anesthetic commonly used for back pain management in interventional procedures. Cytotoxic effects of bupivacaine have been reported in articular cartilage and, recently, in intervertebral disc cell culture. However, the relevance of these effects to discs in vivo remains unclear. This study examines the effect of bupivacaine on disc cell metabolism using an organotypic culture model system that mimics the in vivo environment. To assess the effect of bupivacaine on disc cell viability and matrix protein synthesis using an organotypic model system and to determine whether this anesthetic has toxic effects. Mouse intervertebral discs were isolated and maintained ex vivo in an organotypic culture then exposed to clinically relevant concentrations of bupivacaine, and the impact on disc cell viability and matrix proteoglycan (PG) and collagen syntheses were measured in the presence and absence of the drug. Mouse functional spine units (FSUs) were isolated from the lumbar spines of 10-week-old mice. Cell viability was assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Total PG and collagen syntheses were determined by measuring the incorporation of radioactive (35)S-sulfate and (3)H-l-proline into PG and collagen, respectively. Organotypic cultures of mouse FSUs were exposed to different concentrations (0%-0.5%) of bupivacaine for variable amounts of time (0-2 hours). Cell viability within disc tissue was quantified by MTT staining and histologic assay. Matrix protein synthesis was measured by incorporation of radioactive (35)S-sulfate (for PG synthesis) and (3)H-l-proline (for collagen synthesis). Untreated mouse disc organs were maintained in culture for up to 1 month with minimal changes in tissue histology, cell viability, and matrix protein synthesis. Exposure to bupivacaine decreased cell viability in a dose- and time-dependent manner. Exposure to bupivacaine at concentrations less than or equal to 0.25% did

  12. Ancestor of the new archetypal biology: Goethe's dynamic typology as a model for contemporary evolutionary developmental biology.

    Science.gov (United States)

    Riegner, Mark F

    2013-12-01

    As understood historically, typological thinking has no place in evolutionary biology since its conceptual framework is viewed as incompatible with population thinking. In this article, I propose that what I describe as dynamic typological thinking has been confused with, and has been overshadowed by, a static form of typological thinking. This conflation results from an inability to grasp dynamic typological thinking due to the overlooked requirement to engage our cognitive activity in an unfamiliar way. Thus, analytical thinking alone is unsuited to comprehend the nature of dynamic typological thinking. Over 200 years ago, J. W. von Goethe, in his Metamorphosis of Plants (1790) and other writings, introduced a dynamic form of typological thinking that has been traditionally misunderstood and misrepresented. I describe in detail Goethe's phenomenological methodology and its contemporary value in understanding morphological patterns in living organisms. Furthermore, contrary to the implications of static typological thinking, dynamic typological thinking is perfectly compatible with evolutionary dynamics and, if rightly understood, can contribute significantly to the still emerging field of evolutionary developmental biology (evo-devo). Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Parameter Estimation of a Plucked String Synthesis Model Using a Genetic Algorithm with Perceptual Fitness Calculation

    Directory of Open Access Journals (Sweden)

    Riionheimo Janne

    2003-01-01

    Full Text Available We describe a technique for estimating control parameters for a plucked string synthesis model using a genetic algorithm. The model has been intensively used for sound synthesis of various string instruments but the fine tuning of the parameters has been carried out with a semiautomatic method that requires some hand adjustment with human listening. An automated method for extracting the parameters from recorded tones is described in this paper. The calculation of the fitness function utilizes knowledge of the properties of human hearing.

  14. Mathematical model of Fischer-Tropsch catalyst pellet with pointed centers of synthesis

    Science.gov (United States)

    Derevich, I. V.; Fokina, A. Yu

    2017-11-01

    The productivity of Fischer-Tropsch reactors is determined by the efficiency of heat and mass transfer processes inside the catalyst pellets. To reduce the diffusion resistance, the pellet base is made porous. The porous structure of the granules causes a discrete arrangement of cobalt metallic microparticles whose size can reach tens of microns. The distance between these active centres significantly exceeds their characteristic size and the homogeneous catalyst model is incorrect. A mathematical model of heat and mass transfer processes inside a porous spherical pellet with localised active centres is proposed. The heat of the exothermic synthesis reaction is removed from the surface of the granule to the synthesis gas stream washing the catalyst pellet by heat transfer. The components of the synthesis gas enter the granule surface as a result of mass transfer. On the basis of the self-consistent field method, the values of the temperature and concentration of the synthesis gas components at the active centres were determined. It is shown that there is a critical temperature of the synthesis gas washing the granule, exceeding critical temperature leads to a substantial overheating of the active centres. In this case, the surface of the catalyst pellet is superheated slightly. The principal difference between the homogeneous and heterogeneous models in catalytic reactions is discussed.

  15. Synthesis of model compounds for coal liquefaction research

    Energy Technology Data Exchange (ETDEWEB)

    Hirschon, A.S.; Asaro, M.; Bottaro, J.

    1990-11-02

    The objectives of this project are to develop feasible synthetic routes to produce (1) 4(4{prime}- hydroxy- 5{prime},6{prime},7{prime},8{prime}- tetrahydro-1{prime}- naphthylmethyl)- 6-methyl dibenzothiophene, and (2) a 1-hydroxy naphthalene- dibenzothiophene polymer. These compounds are thought to be representative of sulfur containing molecules in coal. The program is divided into three tasks, the first of which is a project work plan that we have already submitted. Our experimental work during this quarter concentrated on Task 2: Synthesis of 4(4{prime}- hydroxy- 5{prime},6{prime},7{prime},8{prime}- tetrahydro-1{prime}- naphthylmethyl)- 6-methyldibenzothiophene. 11 refs.

  16. A constraint-based evolutionary learning approach to the expectation maximization for optimal estimation of the hidden Markov model for speech signal modeling.

    Science.gov (United States)

    Huda, Shamsul; Yearwood, John; Togneri, Roberto

    2009-02-01

    This paper attempts to overcome the tendency of the expectation-maximization (EM) algorithm to locate a local rather than global maximum when applied to estimate the hidden Markov model (HMM) parameters in speech signal modeling. We propose a hybrid algorithm for estimation of the HMM in automatic speech recognition (ASR) using a constraint-based evolutionary algorithm (EA) and EM, the CEL-EM. The novelty of our hybrid algorithm (CEL-EM) is that it is applicable for estimation of the constraint-based models with many constraints and large numbers of parameters (which use EM) like HMM. Two constraint-based versions of the CEL-EM with different fusion strategies have been proposed using a constraint-based EA and the EM for better estimation of HMM in ASR. The first one uses a traditional constraint-handling mechanism of EA. The other version transforms a constrained optimization problem into an unconstrained problem using Lagrange multipliers. Fusion strategies for the CEL-EM use a staged-fusion approach where EM has been plugged with the EA periodically after the execution of EA for a specific period of time to maintain the global sampling capabilities of EA in the hybrid algorithm. A variable initialization approach (VIA) has been proposed using a variable segmentation to provide a better initialization for EA in the CEL-EM. Experimental results on the TIMIT speech corpus show that CEL-EM obtains higher recognition accuracies than the traditional EM algorithm as well as a top-standard EM (VIA-EM, constructed by applying the VIA to EM).

  17. Evolutionary status of Polaris

    Science.gov (United States)

    Fadeyev, Yu. A.

    2015-05-01

    Hydrodynamic models of short-period Cepheids were computed to determine the pulsation period as a function of evolutionary time during the first and third crossings of the instability strip. The equations of radiation hydrodynamics and turbulent convection for radial stellar pulsations were solved with the initial conditions obtained from the evolutionary models of Population I stars (X = 0.7, Z = 0.02) with masses from 5.2 to 6.5 M⊙ and the convective core overshooting parameter 0.1 ≤ αov ≤ 0.3. In Cepheids with period of 4 d the rate of pulsation period change during the first crossing of the instability strip is over 50 times larger than that during the third crossing. Polaris is shown to cross the instability strip for the first time and to be the fundamental mode pulsator. The best agreement between the predicted and observed rates of period change was obtained for the model with mass of 5.4 M⊙ and the overshooting parameter αov = 0.25. The bolometric luminosity and radius are L = 1.26 × 103 L⊙ and R = 37.5 R⊙, respectively. In the HR diagram, Polaris is located at the red edge of the instability strip.

  18. Improving the Accuracy of Fitted Atomic Models in Cryo-EM Density Maps of Protein Assemblies Using Evolutionary Information from Aligned Homologous Proteins.

    Science.gov (United States)

    Rakesh, Ramachandran; Srinivasan, Narayanaswamy

    2016-01-01

    Cryo-Electron Microscopy (cryo-EM) has become an important technique to obtain structural insights into large macromolecular assemblies. However the resolution of the density maps do not allow for its interpretation at atomic level. Hence they are combined with high resolution structures along with information from other experimental or bioinformatics techniques to obtain pseudo-atomic models. Here, we describe the use of evolutionary conservation of residues as obtained from protein structures and alignments of homologous proteins to detect errors in the fitting of atomic structures as well as improve accuracy of the protein-protein interfacial regions in the cryo-EM density maps.

  19. Synthesis

    Directory of Open Access Journals (Sweden)

    Akshay Kumar

    2013-12-01

    Full Text Available Driven by the increased demand of pyrazolines exhibiting biological activities like antioxidant, anti-inflammatory, antidepressant, antimicrobial, antitumor, and antitubercular drug activity as a stable fragment in biological moieties, lead us to synthesize 2-pyrazolines by the condensation of various substituted chalcones and hydrazine hydrate in the presence of ethanol. The structure of the synthesized molecules was confirmed on the basis of physical data and extensive spectral studies. All the 13 compounds have been screened for antioxidant activity using DPPH radical scavenging method, NO scavenging assay, superoxide radical scavenging assay and hydrogen peroxide radical scavenging assay. All the compounds showed good free radical scavenging activity which is comparable to that of the standard ascorbic acid, out of which ATP-1, ATP-2 and ATP-3 come out to be the best molecules with an IC50 less than 40 mcg/ml. The results indicated that 2-pyrazolines could be the potential candidates eliciting antioxidant activity, and further studies can be conducted using molecular modeling tools for designing 2-pyrazolines having better activity.

  20. Task-Level Data Model for Hardware Synthesis Based on Concurrent Collections

    Directory of Open Access Journals (Sweden)

    Jason Cong

    2012-01-01

    Full Text Available The ever-increasing design complexity of modern digital systems makes it necessary to develop electronic system-level (ESL methodologies with automation and optimization in the higher abstraction level. How the concurrency is modeled in the application specification plays a significant role in ESL design frameworks. The state-of-art concurrent specification models are not suitable for modeling task-level concurrent behavior for the hardware synthesis design flow. Based on the concurrent collection (CnC model, which provides the maximum freedom of task rescheduling, we propose task-level data model (TLDM, targeted at the task-level optimization in hardware synthesis for data processing applications. Polyhedral models are embedded in TLDM for concise expression of task instances, array accesses, and dependencies. Examples are shown to illustrate the advantages of our TLDM specification compared to other widely used concurrency specifications.

  1. Thermodynamic models to predict gas-liquid solubilities in the methanol synthesis, the methanol-higher alcohol synthesis, and the Fischer-Tropsch synthesis via gas-slurry processes

    NARCIS (Netherlands)

    Breman, B.B; Beenackers, A.A C M

    1996-01-01

    Various thermodynamic models were tested concerning their applicability to predict gas-liquid solubilities, relevant for synthesis gas conversion to methanol, higher alcohols, and hydrocarbons via gas-slurry processes. Without any parameter optimization the group contribution equation of state

  2. Model-Based Learning: A Synthesis of Theory and Research

    Science.gov (United States)

    Seel, Norbert M.

    2017-01-01

    This article provides a review of theoretical approaches to model-based learning and related research. In accordance with the definition of model-based learning as an acquisition and utilization of mental models by learners, the first section centers on mental model theory. In accordance with epistemology of modeling the issues of semantics,…

  3. Molecular modeling of directed self-assembly of block copolymers: Fundamental studies of processing conditions and evolutionary pattern design

    Science.gov (United States)

    Khaira, Gurdaman Singh

    Rapid progress in the semi-conductor industry has pushed for smaller feature sizes on integrated electronic circuits. Current photo-lithographic techniques for nanofabrication have reached their technical limit and are problematic when printing features small enough to meet future industrial requirements. "Bottom-up'' techniques, such as the directed self-assembly (DSA) of block copolymers (BCP), are the primary contenders to compliment current "top-down'' photo-lithography ones. For industrial requirements, the defect density from DSA needs to be less than 1 defect per 10 cm by 10 cm. Knowledge of both material synthesis and the thermodynamics of the self-assembly process are required before optimal operating conditions can be found to produce results adequate for industry. The work present in this thesis is divided into three chapters, each discussing various aspects of DSA as studied via a molecular model that contains the essential physics of BCP self-assembly. Though there are various types of guiding fields that can be used to direct BCPs over large wafer areas with minimum defects, this study focuses only on chemically patterned substrates. The first chapter addresses optimal pattern design by describing a framework where molecular simulations of various complexities are coupled with an advanced optimization technique to find a pattern that directs a target morphology. It demonstrates the first ever study where BCP self-assembly on a patterned substrate is optimized using a three-dimensional description of the block-copolymers. For problems pertaining to DSA, the methodology is shown to converge much faster than the traditional random search approach. The second chapter discusses the metrology of BCP thin films using TEM tomography and X-ray scattering techniques, such as CDSAXS and GISAXS. X-ray scattering has the advantage of being able to quickly probe the average structure of BCP morphologies over large wafer areas; however, deducing the BCP morphology

  4. Discovery of Antibiotics-derived Polymers for Gene Delivery using Combinatorial Synthesis and Cheminformatics Modeling

    Science.gov (United States)

    Potta, Thrimoorthy; Zhen, Zhuo; Grandhi, Taraka Sai Pavan; Christensen, Matthew D.; Ramos, James; Breneman, Curt M.; Rege, Kaushal

    2014-01-01

    We describe the combinatorial synthesis and cheminformatics modeling of aminoglycoside antibiotics-derived polymers for transgene delivery and expression. Fifty-six polymers were synthesized by polymerizing aminoglycosides with diglycidyl ether cross-linkers. Parallel screening resulted in identification of several lead polymers that resulted in high transgene expression levels in cells. The role of polymer physicochemical properties in determining efficacy of transgene expression was investigated using Quantitative Structure-Activity Relationship (QSAR) cheminformatics models based on Support Vector Regression (SVR) and ‘building block’ polymer structures. The QSAR model exhibited high predictive ability, and investigation of descriptors in the model, using molecular visualization and correlation plots, indicated that physicochemical attributes related to both, aminoglycosides and diglycidyl ethers facilitated transgene expression. This work synergistically combines combinatorial synthesis and parallel screening with cheminformatics-based QSAR models for discovery and physicochemical elucidation of effective antibiotics-derived polymers for transgene delivery in medicine and biotechnology. PMID:24331709

  5. A discourse model of affect for text-to-speech synthesis

    CSIR Research Space (South Africa)

    Schlunz, GI

    2013-12-01

    Full Text Available This paper introduces a model of affect to improve prosody in text-to-speech synthesis. It operates on the discourse level of text to predict the underlying linguistic factors that contribute towards emotional appraisal, rather than any particular...

  6. Absorption tuning of the green fluorescent protein chromophore: synthesis and studies of model compounds

    DEFF Research Database (Denmark)

    Brøndsted Nielsen, Mogens; Andersen, Lars Henrik; Rinza, Tomás Rocha

    2011-01-01

    The green fluorescent protein (GFP) chromophore is a heterocyclic compound containing a p-hydroxybenzylidine attached to an imidazol-5(4H)-one ring. This review covers the synthesis of a variety of model systems for elucidating the intrinsic optical properties of the chromophore in the gas phase...

  7. Synthesis of semantic modelling and risk analysis methodology applied to animal welfare

    NARCIS (Netherlands)

    Bracke, M.B.M.; Edwards, S.A.; Metz, J.H.M.; Noordhuizen, J.P.T.M.; Algers, B.

    2008-01-01

    Decision-making on animal welfare issues requires a synthesis of information. For the assessment of farm animal welfare based on scientific information collected in a database, a methodology called `semantic modelling¿ has been developed. To date, however, this methodology has not been generally

  8. Combined model- and rule-based controller synthesis with application to helicopter flight

    Science.gov (United States)

    Jiang, Tian-Yue

    This thesis deals with synthesis of combined (nonlinear) model-based and (fuzzy logic) rule-based controllers, along with their applications to helicopter flight control problem. The synthesis involves superimposing two control techniques in order to meet both stability and performance objectives. One is model-based control technique, which is based on inversion of an approximate model of the real system. The other is rule-based control technique that adaptively cancels the inversion errors caused by the approximate model inversion. There are two major aspects of the research effort in this thesis. The first is the development of the adaptive rule-based (fuzzy logic) controllers. The linguistic rule weights and defuzzification output weights in the controllers are adapted for ultimate boundedness of the tracking errors. Numerical results from a helicopter flight control problem indicate improvement and demonstrate effectiveness of the control technique. The second aspect of this research work is the extension of the synthesis to account for control limits. In this thesis, a control saturation related rule-bank in conjunction with the adaptive fuzzy logic controller is designed to trade-off system performance for closed-loop stability when the tendency towards control amplitude and/or rate saturation is detected. Simulation results from both a fixed-wing aircraft trajectory control problem and a helicopter flight control problem show the effectiveness of the synthesis method and the resulting controller in avoiding control saturations.

  9. MATHEMATICAL MODELING OF PROCESSES IN THE ELECTRIC ARC SYNTHESIS OF CARBON NANOTUBES

    Directory of Open Access Journals (Sweden)

    G. V. Abramov

    2013-01-01

    Full Text Available In this work the mathematical model of heat transfer at synthesis of CNTs considering heat removal from a zone evaporation of the anode are synthesized. Influence of parameters of the heat-removing element on the width of a zone of formation of CNTs is researched.

  10. Quality of Early Family Relationships and Individual Differences in the Timing of Pubertal Maturation in Girls: A Longitudinal Test of an Evolutionary Model

    Science.gov (United States)

    Ellis, Bruce J.; McFadyen-Ketchum, Steven; Dodge, Kenneth A.; Pettit, Gregory S.; Bates, John E.

    2009-01-01

    In an 8-year prospective study of 173 girls and their families, the authors tested predictions from J. Belsky, L. Steinberg, and P. Draper's (1991) evolutionary model of individual differences in pubertal timing. This model suggests that more negative–coercive (or less positive–harmonious) family relationships in early childhood provoke earlier reproductive development in adolescence. Consistent with the model, fathers' presence in the home, more time spent by fathers in child care, greater supportiveness in the parental dyad, more father–daughter affection, and more mother–daughter affection, as assessed prior to kindergarten, each predicted later pubertal timing by daughters in 7th grade, The positive dimension of family relationships, rather than the negative dimension, accounted for these relations. In total, the quality of fathers' investment in the family emerged as the most important feature of the proximal family environment relative to daughters' pubertal timing. PMID:10474213

  11. Democratizing evolutionary biology, lessons from insects

    DEFF Research Database (Denmark)

    Dunn, Robert Roberdeau; Beasley, DeAnna E.

    2016-01-01

    The engagement of the public in the scientific process is an old practice. Yet with recent advances in technology, the role of the citizen scientist in studying evolutionary processes has increased. Insects provide ideal models for understanding these evolutionary processes at large scales. This ...

  12. Evolutionary perspectives on learning: conceptual and methodological issues in the study of adaptive specializations.

    Science.gov (United States)

    Krause, Mark A

    2015-07-01

    Inquiry into evolutionary adaptations has flourished since the modern synthesis of evolutionary biology. Comparative methods, genetic techniques, and various experimental and modeling approaches are used to test adaptive hypotheses. In psychology, the concept of adaptation is broadly applied and is central to comparative psychology and cognition. The concept of an adaptive specialization of learning is a proposed account for exceptions to general learning processes, as seen in studies of Pavlovian conditioning of taste aversions, sexual responses, and fear. The evidence generally consists of selective associations forming between biologically relevant conditioned and unconditioned stimuli, with conditioned responses differing in magnitude, persistence, or other measures relative to non-biologically relevant stimuli. Selective associations for biologically relevant stimuli may suggest adaptive specializations of learning, but do not necessarily confirm adaptive hypotheses as conceived of in evolutionary biology. Exceptions to general learning processes do not necessarily default to an adaptive specialization explanation, even if experimental results "make biological sense". This paper examines the degree to which hypotheses of adaptive specializations of learning in sexual and fear response systems have been tested using methodologies developed in evolutionary biology (e.g., comparative methods, quantitative and molecular genetics, survival experiments). A broader aim is to offer perspectives from evolutionary biology for testing adaptive hypotheses in psychological science.

  13. Exponential Expansion in Evolutionary Economics

    DEFF Research Database (Denmark)

    Frederiksen, Peter; Jagtfelt, Tue

    2013-01-01

    of Thomas Kuhn’s notion of scientific paradigms and criteria for a good theory (1977, 1996). The paper thus aims to augment and assimilate the fragmented and scattered body of concepts presently residing within the field of evolutionary economics, by presenting an intuitive framework, applicable within...... concepts are described in detail. Taken together it provides the rudimentary aspects of an economic system within an analytical perspective. It is argued that the main dynamic processes of the evolutionary perspective can be reduced to these four concepts. The model and concepts are evaluated in the light...

  14. Evolutionary Dynamics of Biological Games

    Science.gov (United States)

    Nowak, Martin A.; Sigmund, Karl

    2004-02-01

    Darwinian dynamics based on mutation and selection form the core of mathematical models for adaptation and coevolution of biological populations. The evolutionary outcome is often not a fitness-maximizing equilibrium but can include oscillations and chaos. For studying frequency-dependent selection, game-theoretic arguments are more appropriate than optimization algorithms. Replicator and adaptive dynamics describe short- and long-term evolution in phenotype space and have found applications ranging from animal behavior and ecology to speciation, macroevolution, and human language. Evolutionary game theory is an essential component of a mathematical and computational approach to biology.

  15. Ammonia synthesis and decomposition on a Ru-based catalyst modeled by first-principles

    Science.gov (United States)

    Hellman, A.; Honkala, K.; Remediakis, I. N.; Logadóttir, Á.; Carlsson, A.; Dahl, S.; Christensen, C. H.; Nørskov, J. K.

    2009-06-01

    A recently published first-principles model for the ammonia synthesis on an unpromoted Ru-based catalyst is extended to also describe ammonia decomposition. In addition, further analysis concerning trends in ammonia productivity, surface conditions during the reaction, and macro-properties, such as apparent activation energies and reaction orders are provided. All observed trends in activity are captured by the model and the absolute value of ammonia synthesis/decomposition productivity is predicted to within a factor of 1-100 depending on the experimental conditions. Moreover it is shown: (i) that small changes in the relative adsorption potential energies are sufficient to get a quantitative agreement between theory and experiment ( Appendix A) and (ii) that it is possible to reproduce results from the first-principles model by a simple micro-kinetic model ( Appendix B).

  16. Ammonia synthesis and decomposition on a Ru-based catalyst modeled by first-principles

    DEFF Research Database (Denmark)

    Hellman, A.; Honkala, Johanna Karoliina; Remediakis, Ioannis

    2009-01-01

    A recently published first-principles model for the ammonia synthesis on an unpromoted Ru-based catalyst is extended to also describe ammonia decomposition. In addition, further analysis concerning trends in ammonia productivity, surface conditions during the reaction, and macro......-properties, such as apparent activation energies and reaction orders are provided. All observed trends in activity are captured by the model and the absolute value of ammonia synthesis/decomposition productivity is predicted to within a factor of 1-100 depending on the experimental conditions. Moreover it is shown: (i......) that small changes in the relative adsorption potential energies are sufficient to get a quantitative agreement between theory and experiment (Appendix A) and (ii) that it is possible to reproduce results from the first-principles model by a simple micro-kinetic model (Appendix B)....

  17. Integrating evolutionary game theory into an agent-based model of ductal carcinoma in situ: Role of gap junctions in cancer progression.

    Science.gov (United States)

    Malekian, Negin; Habibi, Jafar; Zangooei, Mohammad Hossein; Aghakhani, Hojjat

    2016-11-01

    There are many cells with various phenotypic behaviors in cancer interacting with each other. For example, an apoptotic cell may induce apoptosis in adjacent cells. A living cell can also protect cells from undergoing apoptosis and necrosis. These survival and death signals are propagated through interaction pathways between adjacent cells called gap junctions. The function of these signals depends on the cellular context of the cell receiving them. For instance, a receiver cell experiencing a low level of oxygen may interpret a received survival signal as an apoptosis signal. In this study, we examine the effect of these signals on tumor growth. We make an evolutionary game theory component in order to model the signal propagation through gap junctions. The game payoffs are defined as a function of cellular context. Then, the game theory component is integrated into an agent-based model of tumor growth. After that, the integrated model is applied to ductal carcinoma in situ, a type of early stage breast cancer. Different scenarios are explored to observe the impact of the gap junction communication and parameters of the game theory component on cancer progression. We compare these scenarios by using the Wilcoxon signed-rank test. The Wilcoxon signed-rank test succeeds in proving a significant difference between the tumor growth of the model before and after considering the gap junction communication. The Wilcoxon signed-rank test also proves that the tumor growth significantly depends on the oxygen threshold of turning survival signals into apoptosis. In this study, the gap junction communication is modeled by using evolutionary game theory to illustrate its role at early stage cancers such as ductal carcinoma in situ. This work indicates that the gap junction communication and the oxygen threshold of turning survival signals into apoptosis can notably affect cancer progression. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  18. A Multi-Valued Diagnostic Model Synthesis Based on Descrete Wavelet Transform

    Directory of Open Access Journals (Sweden)

    Borowczyk Henryk

    2015-01-01

    Full Text Available The method of a multi-valued diagnostic model synthesis using discrete wavelet transform is presented. The method's algorithm consists of three stages: (1 - signal decomposition into low- and high frequency parts - approximations and details, (2 - approximations and details parameterization, (3 - multi-valued encoding parameters obtained in stage 2. The method is illustrated with vibroacoustic signal in real life experiment. The multi-valued diagnostic model is the final result.

  19. Analysis and synthesis for interval type-2 fuzzy-model-based systems

    CERN Document Server

    Li, Hongyi; Lam, Hak-Keung; Gao, Yabin

    2016-01-01

    This book develops a set of reference methods capable of modeling uncertainties existing in membership functions, and analyzing and synthesizing the interval type-2 fuzzy systems with desired performances. It also provides numerous simulation results for various examples, which fill certain gaps in this area of research and may serve as benchmark solutions for the readers. Interval type-2 T-S fuzzy models provide a convenient and flexible method for analysis and synthesis of complex nonlinear systems with uncertainties.

  20. Cascading failures and the emergence of cooperation in evolutionary-game based models of social and economical networks.

    Science.gov (United States)

    Wang, Wen-Xu; Lai, Ying-Cheng; Armbruster, Dieter

    2011-09-01

    We study catastrophic behaviors in large networked systems in the paradigm of evolutionary games by incorporating a realistic "death" or "bankruptcy" mechanism. We find that a cascading bankruptcy process can arise when defection strategies exist and individuals are vulnerable to deficit. Strikingly, we observe that, after the catastrophic cascading process terminates, cooperators are the sole survivors, regardless of the game types and of the connection patterns among individuals as determined by the topology of the underlying network. It is necessary that individuals cooperate with each other to survive the catastrophic failures. Cooperation thus becomes the optimal strategy and absolutely outperforms defection in the game evolution with respect to the "death" mechanism. Our results can be useful for understanding large-scale catastrophe in real-world systems and in particular, they may yield insights into significant social and economical phenomena such as large-scale failures of financial institutions and corporations during an economic recession.

  1. 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.

  2. Multivariable frequency weighted model order reduction for control synthesis

    Science.gov (United States)

    Schmidt, David K.

    1989-01-01

    Quantitative criteria are presented for model simplification, or order reduction, such that the reduced order model may be used to synthesize and evaluate a control law, and the stability robustness obtained using the reduced order model will be preserved when controlling the full-order system. The error introduced due to model simplification is treated as modeling uncertainty, and some of the results from multivariate robustness theory are brought to bear on the model simplification problem. A numerical procedure developed previously is shown to lead to results that meet the necessary criteria. The procedure is applied to reduce the model of a flexible aircraft. Also, the importance of the control law itself, in meeting the modeling criteria, is underscored. An example is included that demonstrates that an apparently robust control law actually amplifies modest modeling errors in the critical frequency region, and leads to undesirable results. The cause of this problem is associated with the canceling of lightly damped transmission zeroes in the plant. An attempt is made to expand on some of the earlier results and to further clarify the theoretical basis behind the proposed methodology.

  3. Synthesis of a naphthalene-hydroxynaphthalene polymer model compound. Final report, June 13, 1990--September 12, 1991

    Energy Technology Data Exchange (ETDEWEB)

    1991-10-02

    The objective of this project was the synthesis of one pound of a new naphthalene-hydroxynaphthalene polymer model compound for use in coal combustion studies. Since this compound was an unreported compound, this effort also required the development of a synthetic route to this compound (including routes to the unique and unreported intermediates leading to its synthesis).

  4. Modelling of flame temperature of solution combustion synthesis of ...

    Indian Academy of Sciences (India)

    A regression model has also been developed to correlate the input parameters, viz. batch size, diluents, fuel to oxidizer ratio and initial furnace temperature, with flame temperature of the solution combustion reaction. The adequacy of the developed model has been checked using analysis of variance technique.

  5. Change detection in the dynamics of an intracellular protein synthesis model using nonlinear Kalman filtering.

    Science.gov (United States)

    Rigatos, Gerasimos G; Rigatou, Efthymia G; Djida, Jean Daniel

    2015-10-01

    A method for early diagnosis of parametric changes in intracellular protein synthesis models (e.g. the p53 protein - mdm2 inhibitor model) is developed with the use of a nonlinear Kalman Filtering approach (Derivative-free nonlinear Kalman Filter) and of statistical change detection methods. The intracellular protein synthesis dynamic model is described by a set of coupled nonlinear differential equations. It is shown that such a dynamical system satisfies differential flatness properties and this allows to transform it, through a change of variables (diffeomorphism), to the so-called linear canonical form. For the linearized equivalent of the dynamical system, state estimation can be performed using the Kalman Filter recursion. Moreover, by applying an inverse transformation based on the previous diffeomorphism it becomes also possible to obtain estimates of the state variables of the initial nonlinear model. By comparing the output of the Kalman Filter (which is assumed to correspond to the undistorted dynamical model) with measurements obtained from the monitored protein synthesis system, a sequence of differences (residuals) is obtained. The statistical processing of the residuals with the use of x2 change detection tests, can provide indication within specific confidence intervals about parametric changes in the considered biological system and consequently indications about the appearance of specific diseases (e.g. malignancies).

  6. Modeling the two-locus architecture of divergent pollinator adaptation: how variation in SAD paralogs affects fitness and evolutionary divergence in sexually deceptive orchids.

    Science.gov (United States)

    Xu, Shuqing; Schlüter, Philipp M

    2015-01-01

    Divergent selection by pollinators can bring about strong reproductive isolation via changes at few genes of large effect. This has recently been demonstrated in sexually deceptive orchids, where studies (1) quantified the strength of reproductive isolation in the field; (2) identified genes that appear to be causal for reproductive isolation; and (3) demonstrated selection by analysis of natural variation in gene sequence and expression. In a group of closely related Ophrys orchids, specific floral scent components, namely n-alkenes, are the key floral traits that control specific pollinator attraction by chemical mimicry of insect sex pheromones. The genetic basis of species-specific differences in alkene production mainly lies in two biosynthetic genes encoding stearoyl-acyl carrier protein desaturases (SAD) that are associated with floral scent variation and reproductive isolation between closely related species, and evolve under pollinator-mediated selection. However, the implications of this genetic architecture of key floral traits on the evolutionary processes of pollinator adaptation and speciation in this plant group remain unclear. Here, we expand on these recent findings to model scenarios of adaptive evolutionary change at SAD2 and SAD5, their effects on plant fitness (i.e., offspring number), and the dynamics of speciation. Our model suggests that the two-locus architecture of reproductive isolation allows for rapid sympatric speciation by pollinator shift; however, the likelihood of such pollinator-mediated speciation is asymmetric between the two orchid species O. sphegodes and O. exaltata due to different fitness effects of their predominant SAD2 and SAD5 alleles. Our study not only provides insight into pollinator adaptation and speciation mechanisms of sexually deceptive orchids but also demonstrates the power of applying a modeling approach to the study of pollinator-driven ecological speciation.

  7. Shape Synthesis from Sketches via Procedural Models and Convolutional Networks.

    Science.gov (United States)

    Huang, Haibin; Kalogerakis, Evangelos; Yumer, Ersin; Mech, Radomir

    2017-08-01

    Procedural modeling techniques can produce high quality visual content through complex rule sets. However, controlling the outputs of these techniques for design purposes is often notoriously difficult for users due to the large number of parameters involved in these rule sets and also their non-linear relationship to the resulting content. To circumvent this problem, we present a sketch-based approach to procedural modeling. Given an approximate and abstract hand-drawn 2D sketch provided by a user, our algorithm automatically computes a set of procedural model parameters, which in turn yield multiple, detailed output shapes that resemble the user's input sketch. The user can then select an output shape, or further modify the sketch to explore alternative ones. At the heart of our approach is a deep Convolutional Neural Network (CNN) that is trained to map sketches to procedural model parameters. The network is trained by large amounts of automatically generated synthetic line drawings. By using an intuitive medium, i.e., freehand sketching as input, users are set free from manually adjusting procedural model parameters, yet they are still able to create high quality content. We demonstrate the accuracy and efficacy of our method in a variety of procedural modeling scenarios including design of man-made and organic shapes.

  8. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  9. Bourbaki's structure theory in the problem of complex systems simulation models synthesis and model-oriented programming

    Science.gov (United States)

    Brodsky, Yu. I.

    2015-01-01

    The work is devoted to the application of Bourbaki's structure theory to substantiate the synthesis of simulation models of complex multicomponent systems, where every component may be a complex system itself. An application of the Bourbaki's structure theory offers a new approach to the design and computer implementation of simulation models of complex multicomponent systems—model synthesis and model-oriented programming. It differs from the traditional object-oriented approach. The central concept of this new approach and at the same time, the basic building block for the construction of more complex structures is the concept of models-components. A model-component endowed with a more complicated structure than, for example, the object in the object-oriented analysis. This structure provides to the model-component an independent behavior-the ability of standard responds to standard requests of its internal and external environment. At the same time, the computer implementation of model-component's behavior is invariant under the integration of models-components into complexes. This fact allows one firstly to construct fractal models of any complexity, and secondly to implement a computational process of such constructions uniformly-by a single universal program. In addition, the proposed paradigm allows one to exclude imperative programming and to generate computer code with a high degree of parallelism.

  10. Realistic camera noise modeling with application to improved HDR synthesis

    Science.gov (United States)

    Goossens, Bart; Luong, Hiêp; Aelterman, Jan; Pižurica, Aleksandra; Philips, Wilfried

    2012-12-01

    Due to the ongoing miniaturization of digital camera sensors and the steady increase of the "number of megapixels", individual sensor elements of the camera become more sensitive to noise, even deteriorating the final image quality. To go around this problem, sophisticated processing algorithms in the devices, can help to maximally exploit the knowledge on the sensor characteristics (e.g., in terms of noise), and offer a better image reconstruction. Although a lot of research focuses on rather simplistic noise models, such as stationary additive white Gaussian noise, only limited attention has gone to more realistic digital camera noise models. In this article, we first present a digital camera noise model that takes several processing steps in the camera into account, such as sensor signal amplification, clipping, post-processing,.. We then apply this noise model to the reconstruction problem of high dynamic range (HDR) images from a small set of low dynamic range (LDR) exposures of a static scene. In literature, HDR reconstruction is mostly performed by computing a weighted average, in which the weights are directly related to the observer pixel intensities of the LDR image. In this work, we derive a Bayesian probabilistic formulation of a weighting function that is near-optimal in the MSE sense (or SNR sense) of the reconstructed HDR image, by assuming exponentially distributed irradiance values. We define the weighting function as the probability that the observed pixel intensity is approximately unbiased. The weighting function can be directly computed based on the noise model parameters, which gives rise to different symmetric and asymmetric shapes when electronic noise or photon noise is dominant. We also explain how to deal with the case that some of the noise model parameters are unknown and explain how the camera response function can be estimated using the presented noise model. Finally, experimental results are provided to support our findings.

  11. Binders for Energetics - Modelling and Synthesis in Harmony

    Science.gov (United States)

    Dossi, Licia; Cleaver, Doug; Gould, Peter; Dunnett, Jim; Cavaye, Hamish; Ellison, Laurence; Luppi, Federico; Hollands, Ron; Bradley, Mark

    The Binders by Design UK programme develop new polymeric materials for energetic applications that can overcome problems related to chemico-physical properties, aging, additives, environmental and performance of energetic compositions. Combined multi-scale modelling and experiment is used for the development of a new modelling tool and with the aim to produce novel materials with great confidence and fast turnaround. New synthesised binders with attractive properties for energetic applications used to provide a high level of confidence in the results of developed models. Molecular dynamics simulations investigate the thermal behaviour and the results directly feed into a Group Interaction Model (GIM). A viscoelastic constitutive model has been developed examining stress development in energetic/binder configurations. GIM data has been used as the basis for developing hydrocode equations of state, which then applied in run-to-detonation type investigations to examine the effect of the shock properties of a binder on the reactivity of a typical Polymer Bonded Explosive in a high-velocity impact type scenario. The Binders by Design UK programme is funded through the Weapons Science and Technology Centre by DSTL.

  12. Computational model for analyzing the evolutionary patterns of the neuraminidase gene of influenza A/H1N1.

    Science.gov (United States)

    Ahn, Insung; Son, Hyeon Seok

    2012-02-01

    In this study, we performed computer simulations to evaluate the changes of selection potentials of codons in influenza A/H1N1 from 1999 to 2009. We artificially generated the sequences by using the transition matrices of positively selected codons over time, and their similarities against the database of influenzavirus A genus were determined by BLAST search. This is the first approach to predict the evolutionary direction of influenza A virus (H1N1) by simulating the codon substitutions over time. We observed that the BLAST results showed the high similarities with pandemic influenza A/H1N1 in 2009, suggesting that the classical human-origin influenza A/H1N1 isolated before 2009 might contain some selection potentials of swine-origin viruses. Computer simulations using the time series codon substitution patterns resulted dramatic changes of BLAST results in influenza A/H1N1, providing a possibility of developing a method for predicting the viral evolution in silico. Copyright © 2011 Elsevier Ltd. All rights reserved.

  13. Characterization of a 3D multi-mechanism SMA material model for the prediction of the cyclic "evolutionary" response of NiTi for use in actuations

    Science.gov (United States)

    Dhakal, Binod

    The intermetallic NiTi-based alloys are known as Shape Memory material. They exhibit unique ability to remember a shape after large deformation. They are desirable in various engineering applications, such as actuators, biomedical devices, vibration damping, etc, as they can absorb and dissipate mechanical/thermal energies by undergoing a reversible hysteretic shape change under the applied mechanical/thermal cyclic loadings. This reflects the effect of micro-structural changes occurring during phase transformation between Austenite(A) and Martensite(M), as well as differently-oriented M-variants. As typically utilized in applications, a particular shape memory alloy (SMA) device or component operates under a large number of thermo-mechanical cycles, hence, the importance of accounting for the cyclic behavior characteristics in modeling and characterization of these systems. A detailed study of the multi-mechanism-based, comprehensive, thus complex modeling framework (by Saleeb et al) and the determination of its material parameters responsible for the physical significance of the shape memory effect are made. This formulation utilizes multiple, inelastic mechanisms to regulate the partitioning of energy dissipation and storage governing the evolutionary thermo-mechanical behavior. Equipped with the understanding of the physical significance of the model parameters and utilizing the SMA modeling strategy effectively, a comprehensive characterization of the evolutionary, cyclic response of the complex real SMA, known as 55NiTi (Ni49.9Ti50.1) is carried out. The detailed comparisons between the SMA model and experimental results provided the necessary validation of the modeling capabilities of the framework to calibrate the complex alloys like 55NiTi. In addition, the details of interplays between the internal mechanisms to describe the material behavior within all the important response characteristic regions provides a convenient means to compliment the theoretical

  14. 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.

  15. Eluding the Physical Constraints in a Nonlinear Interaction Sound Synthesis Model for Gesture Guidance

    Directory of Open Access Journals (Sweden)

    Etienne Thoret

    2016-06-01

    Full Text Available In this paper, a flexible control strategy for a synthesis model dedicated to nonlinear friction phenomena is proposed. This model enables to synthesize different types of sound sources, such as creaky doors, singing glasses, squeaking wet plates or bowed strings. Based on the perceptual stance that a sound is perceived as the result of an action on an object we propose a genuine source/filter synthesis approach that enables to elude physical constraints induced by the coupling between the interacting objects. This approach makes it possible to independently control and freely combine the action and the object. Different implementations and applications related to computer animation, gesture learning for rehabilitation and expert gestures are presented at the end of this paper.

  16. MATHEMATICAL AND COMPUTATIONAL MODELLING OF RIBOSOMAL MOVEMENT AND PROTEIN SYNTHESIS: AN OVERVIEW

    Directory of Open Access Journals (Sweden)

    Tobias von der Haar

    2012-04-01

    Full Text Available Translation or protein synthesis consists of a complex system of chemical reactions, which ultimately result in decoding of the mRNA and the production of a protein. The complexity of this reaction system makes it difficult to quantitatively connect its input parameters (such as translation factor or ribosome concentrations, codon composition of the mRNA, or energy availability to output parameters (such as protein synthesis rates or ribosome densities on mRNAs. Mathematical and computational models of translation have now been used for nearly five decades to investigate translation, and to shed light on the relationship between the different reactions in the system. This review gives an overview over the principal approaches used in the modelling efforts, and summarises some of the major findings that were made.

  17. Complex evolutionary systems in behavioral finance

    NARCIS (Netherlands)

    Hommes, C.; Wagener, F.

    2008-01-01

    Traditional finance is built on the rationality paradigm. This chapter discusses simple models from an alternative approach in which financial markets are viewed as complex evolutionary systems. Agents are boundedly rational and base their investment decisions upon market forecasting heuristics.

  18. Investigating Evolutionary Dynamics of RHA1 Operons.

    Science.gov (United States)

    Chen, Yong; Geng, Dandan; Ehrhardt, Kristina; Zhang, Shaoqiang

    2016-01-01

    Grouping genes as operons is an important genomic feature of prokaryotic organisms. The comprehensive understanding of the operon organizations would be helpful to decipher transcriptional mechanisms, cellular pathways, and the evolutionary landscape of prokaryotic genomes. Although thousands of prokaryotes have been sequenced, genome-wide investigation of the evolutionary dynamics (division and recombination) of operons among these genomes remains unexplored. Here, we systematically analyzed the operon dynamics of Rhodococcus jostii RHA1 (RHA1), an oleaginous bacterium with high potential applications in biofuel, by comparing 340 prokaryotic genomes that were carefully selected from different genera. Interestingly, 99% of RHA1 operons were observed to exhibit evolutionary events of division and recombination among the 340 compared genomes. An operon that encodes all enzymes related to histidine biosynthesis in RHA1 (His-operon) was found to be segmented into smaller gene groups (sub-operons) in diverse genomes. These sub-operons were further reorganized with different functional genes as novel operons that are related to different biochemical processes. Comparatively, the operons involved in the functional categories of lipid transport and metabolism are relatively conserved among the 340 compared genomes. At the pathway level, RHA1 operons found to be significantly conserved were involved in ribosome synthesis, oxidative phosphorylation, and fatty acid synthesis. These analyses provide evolutionary insights of operon organization and the dynamic associations of various biochemical pathways in different prokaryotes.

  19. Comparative Studies of Population Synthesis Models in the ...

    Indian Academy of Sciences (India)

    2014-01-08

    Jan 8, 2014 ... Infra Red (NIR) colours. Models by Gunn et al. (1981), which included empirical. RGB, Asymptotic Giant Branch (AGB), lower-Main Sequence (MS) phases and isochrones with uncalibrated mixing length of different stellar phases, badly failed to reproduce the MS stars of the galactic Globular Clusters (GCs) ...

  20. Application of Model-Checking Technology to Controller Synthesis

    DEFF Research Database (Denmark)

    David, Alexandre; Grunnet, Jacob Deleuran; Jessen, Jan Jacob

    2011-01-01

    its continuous environment, which is modelled and taken care of in our frameworks. Our first technique does it by using Matlab to discretise the problem and then Uppaal-tiga to solve the obtained timed game. This is implemented as a toolbox. The second technique relies on the user defining a timed...

  1. Synthesis and Analytical Centrifugation of Magnetic Model Colloids

    NARCIS (Netherlands)

    Luigjes, B.|info:eu-repo/dai/nl/31412330X

    2012-01-01

    This thesis is a study of the preparation and thermodynamic properties of magnetic colloids. First, two types of magnetic model colloids are investigated: composite colloids and single-domain nanoparticles. Thermodynamics of magnetic colloids is studied using analytical centrifugation, including a

  2. Synthesis, Characterization, and Modeling of Nanotube Materials with Variable Stiffness Tethers

    Science.gov (United States)

    Frankland, S. J. V.; Herzog, M. N.; Odegard, G. M.; Gates, T. S.; Fay, C. C.

    2004-01-01

    Synthesis, mechanical testing, and modeling have been performed for carbon nanotube based materials. Tests using nanoindentation indicated a six-fold enhancement in the storage modulus when comparing the base material (no nanotubes) to the composite that contained 5.3 wt% of nanotubes. To understand how crosslinking the nanotubes may further alter the stiffness, a model of the system was constructed using nanotubes crosslinked with a variable stiffness tether (VST). The model predicted that for a composite with 5 wt% nanotubes at random orientations, crosslinked with the VST, the bulk Young's modulus was reduced by 30% compared to the noncrosslinked equivalent.

  3. A green chemistry-based classification model for the synthesis of silver nanoparticles

    OpenAIRE

    Cinelli, Marco; Coles, Stuart R.; Nadagouda, M. (Mallikarjuna); Blaszczynski, Jerzy; Slowinski, Roman; Rajender S. Varma; Kirwan, Kerry

    2015-01-01

    The assessment of the implementation of green chemistry principles in the syntheses of nanomaterials is a complex decision-making problem that necessitates the integration of several evaluation criteria. Multiple Criteria Decision Aiding (MCDA) provides support for such a challenge. One of its methods – Dominance-based Rough Set Approach (DRSA) – was used in this research to develop a model for the green chemistry-based classification of silver nanoparticle synthesis protocols into preference...

  4. Robustness in Escherichia coli Glutamate and Glutamine Synthesis Studied by a Kinetic Model

    OpenAIRE

    Lodeiro, Aníbal; Melgarejo, Augusto

    2008-01-01

    Metabolic control of glutamine and glutamate synthesis from ammonia and oxoglutarate in Escherichia coli is tight and complex. In this work, the role of glutamine synthetase (GS) and glutamate dehydrogenase (GDH) regulation in this control was studied. Both enzymes form a linear pathway, which can also have a cyclic topology if glutamate–oxoglutarate amino transferase (GOGAT) activity is included. We modelled the metabolic pathways in the linear or cyclic topologies using a coupled nonlinear...

  5. Revised enzyme synthesis rate expression in cybernetic models of bacterial growth.

    Science.gov (United States)

    Turner, B G; Ramkrishna, D

    1988-01-01

    A revised enzyme synthesis rate expression for cybernetic models of bacterial growth is presented. The rate expression, which is comprised of inducible and constitutive contributions, provides for a basal enzyme level that is necessary to predict certain types of commonly observed continuous culture transients. The response of a continuous culture to a step change in feed stream composition is simulated using both the old and new formulations, and the ramifications for the "matching-law" formulation are discussed.

  6. Evolutionary Trees can be Learned in Polynomial-Time in the Two-State General Markov Model

    DEFF Research Database (Denmark)

    Cryan, Mary; Goldberg, Leslie Ann; Goldberg, Paul Wilfred

    2001-01-01

    The j-state general Markov model of evolution (due to Steel) is a stochastic model concerned with the evolution of strings over an alphabet of size j. In particular, the two-state general Markov model of evolution generalizes the well-known Cavender-Farris-Neyman model of evolution by removing...

  7. AERIS - applications for the environment : real-time information synthesis : eco-lanes operational scenario modeling report.

    Science.gov (United States)

    2014-12-01

    This report constitutes the detailed modeling and evaluation results of the Eco-Lanes Operational Scenario : defined by the Applications for the Environment: Real-Time Information Synthesis (AERIS) Program. The : Operational Scenario constitutes six ...

  8. Inhibiting corticosterone synthesis during fear memory formation exacerbates cued fear extinction memory deficits within the single prolonged stress model.

    Science.gov (United States)

    Keller, Samantha M; Schreiber, William B; Stanfield, Briana R; Knox, Dayan

    2015-01-01

    Using the single prolonged stress (SPS) animal model of post-traumatic stress disorder (PTSD), previous studies suggest that enhanced glucocorticoid receptor (GR) expression leads to cued fear extinction retention deficits. However, it is unknown how the endogenous ligand of GRs, corticosterone (CORT), may contribute to extinction retention deficits in the SPS model. Given that CORT synthesis during fear learning is critical for fear memory consolidation and SPS enhances GR expression, CORT synthesis during fear memory formation could strengthen fear memory in SPS rats by enhancing GR activation during fear learning. In turn, this could lead to cued fear extinction retention deficits. We tested the hypothesis that CORT synthesis during fear learning leads to cued fear extinction retention deficits in SPS rats by administering the CORT synthesis inhibitor metyrapone to SPS and control rats prior to fear conditioning, and observed the effect this had on extinction memory. Inhibiting CORT synthesis during fear memory formation in control rats tended to decrease cued freezing, though this effect never reached statistical significance. Contrary to our hypothesis, inhibiting CORT synthesis during fear memory formation disrupted extinction retention in SPS rats. This finding suggests that even though SPS exposure leads to cued fear extinction memory deficits, CORT synthesis during fear memory formation enhances extinction retention in SPS rats. This suggests that stress-induced CORT synthesis in previously stressed rats can be beneficial. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Synthesis and Analytical Centrifugation of Magnetic Model Colloids

    OpenAIRE

    Luigjes, B.

    2012-01-01

    This thesis is a study of the preparation and thermodynamic properties of magnetic colloids. First, two types of magnetic model colloids are investigated: composite colloids and single-domain nanoparticles. Thermodynamics of magnetic colloids is studied using analytical centrifugation, including a specially adapted centrifuge for measuring heavy and strongly light absorbing colloids. Magnetic composite colloids can be prepared from thermodynamically stable Pickering emulsions of 3-methacrylox...

  10. Model synthesis in frequency analysis of Missouri floods

    Science.gov (United States)

    Hauth, Leland D.

    1974-01-01

    Synthetic flood records for 43 small-stream sites aided in definition of techniques for estimating the magnitude and frequency of floods in Missouri. The long-term synthetic flood records were generated by use of a digital computer model of the rainfall-runoff process. A relatively short period of concurrent rainfall and runoff data observed at each of the 43 sites was used to calibrate the model, and rainfall records covering from 66 to 78 years for four Missouri sites and pan-evaporation data were used to generate the synthetic records. Flood magnitude and frequency characteristics of both the synthetic records and observed long-term flood records available for 109 large-stream sites were used in a multiple-regression analysis to define relations for estimating future flood characteristics at ungaged sites. That analysis indicated that drainage basin size and slope were the most useful estimating variables. It also indicated that a more complex regression model than the commonly used log-linear one was needed for the range of drainage basin sizes available in this study.

  11. 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.

  12. An Evolutionary Framework for Understanding the Origin of Eukaryotes

    OpenAIRE

    Neil W Blackstone

    2016-01-01

    Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major fea...

  13. Synthesis and intracellular localization of chick acid alpha-glucosidase in chick erythrocyte-human fibroblast heterokaryons. A model system for the study of lysosomal enzyme synthesis.

    Science.gov (United States)

    Sips, H J; Reuser, A J; van der Veer, E

    1986-02-01

    The synthesis and localization of chick acid alpha-glucosidase has been studied in chick erythrocyte-human fibroblast heterokaryons. Monospecific antibodies raised against purified chick liver acid alpha-glucosidase were used. It was found that the acid alpha-glucosidase in the heterokaryons is of chick origin, and is localized in the same lysosomes as the human lysosomal enzymes. It is concluded that chick erythrocyte-human fibroblast heterokaryons provide a useful model system for the study of lysosomal enzyme synthesis and routing.

  14. Intelligent control of HVAC systems. Part I: Modeling and synthesis

    Directory of Open Access Journals (Sweden)

    Adrian TOADER

    2013-03-01

    Full Text Available This is the first part of a work on intelligent type control of Heating, Ventilating and Air-Conditioning (HVAC systems. The study is performed from the perspective of giving a unitary control method to ensure high energy efficiency and air quality improving. To illustrate the proposed HVAC control technique, in this first part it is considered as benchmark problem a single thermal space HVAC system. The construction of the mathematical model is performed only with a view to obtain a framework of HVAC intelligent control validation by numerical simulations. The latter will be reported in a second part of the study.

  15. Evaluation of water resources system vulnerability based on co-operative co-evolutionary genetic algorithm and projection pursuit model under the DPSIR framework

    Science.gov (United States)

    Zhao, Y.; Su, X. H.; Wang, M. H.; Li, Z. Y.; Li, E. K.; Xu, X.

    2017-08-01

    Water resources vulnerability control management is essential because it is related to the benign evolution of socio-economic, environmental and water resources system. Research on water resources system vulnerability is helpful to realization of water resources sustainable utilization. In this study, the DPSIR framework of driving forces-pressure-state-impact-response was adopted to construct the evaluation index system of water resources system vulnerability. Then the co-evolutionary genetic algorithm and projection pursuit were used to establish evaluation model of water resources system vulnerability. Tengzhou City in Shandong Province was selected as a study area. The system vulnerability was analyzed in terms of driving forces, pressure, state, impact and response on the basis of the projection value calculated by the model. The results show that the five components all belong to vulnerability Grade II, the vulnerability degree of impact and state were higher than other components due to the fierce imbalance in supply-demand and the unsatisfied condition of water resources utilization. It is indicated that the influence of high speed socio-economic development and the overuse of the pesticides have already disturbed the benign development of water environment to some extents. While the indexes in response represented lower vulnerability degree than the other components. The results of the evaluation model are coincident with the status of water resources system in the study area, which indicates that the model is feasible and effective.

  16. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 7; Issue 11. Evolutionary Biology Today - The Domain of Evolutionary Biology. Amitabh Joshi. Series Article Volume 7 Issue 11 November 2002 pp 8-17. Fulltext. Click here to view fulltext PDF. Permanent link:

  17. Part E: Evolutionary Computation

    DEFF Research Database (Denmark)

    2015-01-01

    evolutionary algorithms, such as memetic algorithms, which have emerged as a very promising tool for solving many real-world problems in a multitude of areas of science and technology. Moreover, parallel evolutionary combinatorial optimization has been presented. Search operators, which are crucial in all...

  18. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Amitabh Joshi studies and teaches evolutionary ' genetics and population ecology at the Jawaharlal. Nehru Centre for Advanced. Scientific Research,. Bangalore. His current research interests are in life- history, evolution, the evolutionary genetics of biological clocks, the evolution of ecological specialization dynamics. He.

  19. Evolutionary humanoid robotics

    CERN Document Server

    Eaton, Malachy

    2015-01-01

    This book examines how two distinct strands of research on autonomous robots, evolutionary robotics and humanoid robot research, are converging. The book will be valuable for researchers and postgraduate students working in the areas of evolutionary robotics and bio-inspired computing.

  20. Evolutionary Biology Today

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 8; Issue 2. Evolutionary Biology Today - What do Evolutionary Biologists do? Amitabh Joshi. Series Article Volume 8 Issue 2 February 2003 pp 6-18. Fulltext. Click here to view fulltext PDF. Permanent link:

  1. Applying evolutionary anthropology

    OpenAIRE

    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 h...

  2. Cellular Hyperproliferation and Cancer as Evolutionary Variables

    Science.gov (United States)

    Alvarado, Alejandro Sánchez

    2012-01-01

    Technological advances in biology have begun to dramatically change the way we think about evolution, development, health and disease. The ability to sequence the genomes of many individuals within a population, and across multiple species, has opened the door to the possibility of answering some long-standing and perplexing questions about our own genetic heritage. One such question revolves around the nature of cellular hyperproliferation. This cellular behavior is used to effect wound healing in most animals, as well as, in some animals, the regeneration of lost body parts. Yet at the same time, cellular hyperproliferation is the fundamental pathological condition responsible for cancers in humans. Here, I will discuss why microevolution, macroevolution and developmental biology all have to be taken into consideration when interpreting studies of both normal and malignant hyperproliferation. I will also illustrate how a synthesis of evolutionary sciences and developmental biology through the study of diverse model organisms can inform our understanding of both health and disease. PMID:22975008

  3. Soft context clustering for F0 modeling in HMM-based speech synthesis

    Science.gov (United States)

    Khorram, Soheil; Sameti, Hossein; King, Simon

    2015-12-01

    This paper proposes the use of a new binary decision tree, which we call a soft decision tree, to improve generalization performance compared to the conventional `hard' decision tree method that is used to cluster context-dependent model parameters in statistical parametric speech synthesis. We apply the method to improve the modeling of fundamental frequency, which is an important factor in synthesizing natural-sounding high-quality speech. Conventionally, hard decision tree-clustered hidden Markov models (HMMs) are used, in which each model parameter is assigned to a single leaf node. However, this `divide-and-conquer' approach leads to data sparsity, with the consequence that it suffers from poor generalization, meaning that it is unable to accurately predict parameters for models of unseen contexts: the hard decision tree is a weak function approximator. To alleviate this, we propose the soft decision tree, which is a binary decision tree with soft decisions at the internal nodes. In this soft clustering method, internal nodes select both their children with certain membership degrees; therefore, each node can be viewed as a fuzzy set with a context-dependent membership function. The soft decision tree improves model generalization and provides a superior function approximator because it is able to assign each context to several overlapped leaves. In order to use such a soft decision tree to predict the parameters of the HMM output probability distribution, we derive the smoothest (maximum entropy) distribution which captures all partial first-order moments and a global second-order moment of the training samples. Employing such a soft decision tree architecture with maximum entropy distributions, a novel speech synthesis system is trained using maximum likelihood (ML) parameter re-estimation and synthesis is achieved via maximum output probability parameter generation. In addition, a soft decision tree construction algorithm optimizing a log-likelihood measure

  4. Real-Time Gesture-Controlled Physical Modelling Music Synthesis with Tactile Feedback

    Directory of Open Access Journals (Sweden)

    David M. Howard

    2004-06-01

    Full Text Available Electronic sound synthesis continues to offer huge potential possibilities for the creation of new musical instruments. The traditional approach is, however, seriously limited in that it incorporates only auditory feedback and it will typically make use of a sound synthesis model (e.g., additive, subtractive, wavetable, and sampling that is inherently limited and very often nonintuitive to the musician. In a direct attempt to challenge these issues, this paper describes a system that provides tactile as well as acoustic feedback, with real-time synthesis that invokes a more intuitive response from players since it is based upon mass-spring physical modelling. Virtual instruments are set up via a graphical user interface in terms of the physical properties of basic well-understood sounding objects such as strings, membranes, and solids. These can be interconnected to form complex integrated structures. Acoustic excitation can be applied at any point mass via virtual bowing, plucking, striking, specified waveform, or from any external sound source. Virtual microphones can be placed at any point masses to deliver the acoustic output. These aspects of the instrument are described along with the nature of the resulting acoustic output.

  5. Green Synthesis of Ultraviolet Absorber 2-Ethylhexyl Salicylate: Experimental Design and Artificial Neural Network Modeling

    Directory of Open Access Journals (Sweden)

    Shang-Ming Huang

    2017-11-01

    Full Text Available 2-Ethylhexyl salicylate, an ultraviolet filter, is widely used to protect skin against sunlight-induced harmful effects in the cosmetic industry. In this study, the green synthesis of 2-ethylhexyl salicylate using immobilized lipase through a solvent-free and reduced pressure evaporation system was investigated. A Box–Behnken design was employed to develop an artificial neural network (ANN model. The parameters for an optimal architecture of an ANN were set out: a quick propagation algorithm, a hyperbolic tangent transfer function, 10,000 iterations, and six nodes within the hidden layer. The best-fitting performance of the ANN was determined by the coefficient of determination and the root-mean-square error between the correlation of predicted and experimental data, indicating that the ANN displayed excellent data-fitting properties. Finally, the experimental conditions of synthesis were well established with the optimal parameters to obtain a high conversion of 2-ethylhexyl salicylate. In conclusion, this study efficiently replaces the traditional solvents with a green process for the synthesis of 2-ethylhexyl salicylate to avoid environmental contamination, and this process is well-modeled by a methodological ANN for optimization, which might be a benefit for industrial production.

  6. Physically Inspired Models for the Synthesis of Stiff Strings with Dispersive Waveguides

    Directory of Open Access Journals (Sweden)

    Testa I

    2004-01-01

    Full Text Available We review the derivation and design of digital waveguides from physical models of stiff systems, useful for the synthesis of sounds from strings, rods, and similar objects. A transform method approach is proposed to solve the classic fourth-order equations of stiff systems in order to reduce it to two second-order equations. By introducing scattering boundary matrices, the eigenfrequencies are determined and their dependency is discussed for the clamped, hinged, and intermediate cases. On the basis of the frequency-domain physical model, the numerical discretization is carried out, showing how the insertion of an all-pass delay line generalizes the Karplus-Strong algorithm for the synthesis of ideally flexible vibrating strings. Knowing the physical parameters, the synthesis can proceed using the generalized structure. Another point of view is offered by Laguerre expansions and frequency warping, which are introduced in order to show that a stiff system can be treated as a nonstiff one, provided that the solutions are warped. A method to compute the all-pass chain coefficients and the optimum warping curves from sound samples is discussed. Once the optimum warping characteristic is found, the length of the dispersive delay line to be employed in the simulation is simply determined from the requirement of matching the desired fundamental frequency. The regularization of the dispersion curves by means of optimum unwarping is experimentally evaluated.

  7. Coping with complexity: machine learning optimization of cell-free protein synthesis.

    Science.gov (United States)

    Caschera, Filippo; Bedau, Mark A; Buchanan, Andrew; Cawse, James; de Lucrezia, Davide; Gazzola, Gianluca; Hanczyc, Martin M; Packard, Norman H

    2011-09-01

    Biological systems contain complex metabolic pathways with many nonlinearities and synergies that make them difficult to predict from first principles. Protein synthesis is a canonical example of such a pathway. Here we show how cell-free protein synthesis may be improved through a series of iterated high-throughput experiments guided by a machine-learning algorithm implementing a form of evolutionary design of experiments (Evo-DoE). The algorithm predicts fruitful experiments from statistical models of the previous experimental results, combined with stochastic exploration of the experimental space. The desired experimental response, or evolutionary fitness, was defined as the yield of the target product, and new experimental conditions were discovered to have ∼ 350% greater yield than the standard. An analysis of the best experimental conditions discovered indicates that there are two distinct classes of kinetics, thus showing how our evolutionary design of experiments is capable of significant innovation, as well as gradual improvement. Copyright © 2011 Wiley Periodicals, Inc.

  8. System-Level Modeling and Synthesis of Flow-Based Microfluidic Biochips

    DEFF Research Database (Denmark)

    Minhass, Wajid Hassan; Pop, Paul; Madsen, Jan

    2011-01-01

    Microfluidic biochips are replacing the conventional biochemical analyzers and are able to integrate the necessary functions for biochemical analysis on-chip. There are several types of microfluidic biochips, each having its advantages and limitations. In this paper we are interested in flow......-based biochips, in which the flow of liquid is manipulated using integrated microvalves. By combining several microvalves, more complex units, such as micropumps, switches, mixers, and multiplexers, can be built. Although researchers have proposed significant work on the system-level synthesis of droplet......-based biochips, which manipulate droplets on a two-dimensional array of electrodes, no research on system-level synthesis of flow-based biochips has been reported so far. The focus has been on application modeling and component-level simulation. Therefore, for the first time to our knowledge, we propose a system-level...

  9. Encryption in TECB Mode: Modeling, Simulation and Synthesis

    Science.gov (United States)

    Reaz, M. B. I.; Ibrahimy, M. I.; Mohd-Yasin, F.; Wei, C. S.; Kamada, M.

    The growth of the Internet as a vehicle for secure communication has resulted in Data Encryption Standard (DES) no longer capable of providing high-level security for data protection. Triple Data Encryption Standard (3DES) is a symmetric block cipher with 192 bits key proposed to further enhance DES. Many applications crave for the speed of a hardware encryption implementation while trying to preserve the flexibility and low cost of a software implementation. This project used single core module to implement encryption in Triple DES Electronic Code Book (TECB) mode, which was modeled using hardware description language VHDL. The architecture was mapped in Altera EPF10K100EFC484-1 and EP20K200EFC672-1X for performance investigations and resulted in achieving encryption rate of 102.56 Mbps, area utilization of 2111 logic cells (25%) and a higher maximum operating frequency of 78.59 MHz by implementing on the larger FPGA device EP20K200EFC672-1X. It also suggested that 3DES hardware was 2.4 times faster than its software counterpart.

  10. Facial Sketch Synthesis Using 2D Direct Combined Model-Based Face-Specific Markov Network.

    Science.gov (United States)

    Tu, Ching-Ting; Chan, Yu-Hsien; Chen, Yi-Chung

    2016-08-01

    A facial sketch synthesis system is proposed, featuring a 2D direct combined model (2DDCM)-based face-specific Markov network. In contrast to the existing facial sketch synthesis systems, the proposed scheme aims to synthesize sketches, which reproduce the unique drawing style of a particular artist, where this drawing style is learned from a data set consisting of a large number of image/sketch pairwise training samples. The synthesis system comprises three modules, namely, a global module, a local module, and an enhancement module. The global module applies a 2DDCM approach to synthesize the global facial geometry and texture of the input image. The detailed texture is then added to the synthesized sketch in a local patch-based manner using a parametric 2DDCM model and a non-parametric Markov random field (MRF) network. Notably, the MRF approach gives the synthesized results an appearance more consistent with the drawing style of the training samples, while the 2DDCM approach enables the synthesis of outcomes with a more derivative style. As a result, the similarity between the synthesized sketches and the input images is greatly improved. Finally, a post-processing operation is performed to enhance the shadowed regions of the synthesized image by adding strong lines or curves to emphasize the lighting conditions. The experimental results confirm that the synthesized facial images are in good qualitative and quantitative agreement with the input images as well as the ground-truth sketches provided by the same artist. The representing power of the proposed framework is demonstrated by synthesizing facial sketches from input images with a wide variety of facial poses, lighting conditions, and races even when such images are not included in the training data set. Moreover, the practical applicability of the proposed framework is demonstrated by means of automatic facial recognition tests.

  11. Exploring phylogenetic hypotheses via Gibbs sampling on evolutionary networks

    OpenAIRE

    Yu, Yun; Jermaine, Christopher; Nakhleh, Luay

    2016-01-01

    Abstract Background Phylogenetic networks are leaf-labeled graphs used to model and display complex evolutionary relationships that do not fit a single tree. There are two classes of phylogenetic networks: Data-display networks and evolutionary networks. While data-display networks are very commonly used to explore data, they are not amenable to incorporating probabilistic models of gene and genome evolution. Evolutionary networks, on the other hand, can accommodate such probabilistic models,...

  12. Synthesis of cocoa butter triacylglycerols using a model acidolysis system

    Directory of Open Access Journals (Sweden)

    Göǧüş, Fahrettin

    2008-12-01

    Full Text Available The effects of reaction parameters such as substrate mole ratio, reaction temperature, enzyme load, water content and reaction time were studied in a model enzymatic acidolysis system. Palmitic and stearic acids were incorporated into triolein (OOO under the catalysis of sn-1,3 specific lipase to produce the three major triacylglycerols (TAGs in cocoa butter (CB, namely, 1,3-dipalmitoyl-2-oleoyl--glycerol (POP, 1(3-palmitoyl-3(1-stearoyl-2-oleoyl-glycerol (POS and 1,3distearoyl-2-oleoyl-glycerol (SOS. TAG contents of the reaction products were analyzed by High Performance Liquid Chromatograph (HPLC.The best results (15.2% POP, 30.4% POS, 15.2 % SOS were obtained at 1:3:3 (OOO:palmitic acid:stearic acid substrate mole ratio and reaction parameters: time 10 h, temperature 45 oC, enzyme load 20 %, water content 5 %. The results obtained in this model system might be used for the optimization and application of lipase catalyzed acidolysis reactions in natural systems to produce cocoa butter equivalents (CBEs.El efecto de parámetros de reacción como el ratio molar de sustratos, carga de enzima, contenido de agua o temperatura de reacción fueron estudiados en un sistema modelo de acidolisis para la síntesis de triglicéridos disaturados. Los ácidos grasos palmítico y esteárico se incorporaron a la molécula de trioleína (OOO mediante la catálisis con una li-pasa sn-1,3 específica para producir los tres triglicéridos (TAGs mayoritarios de la manteca de cacao (CB: 1,3-dipalmitil-2-oleoil glicerol (POP, 1(3-palmitil-3(1-estearil-2glicerol (POS and 1,3-diestearil-2-oleoil glicerol (SOS. Los TAGs producidos en cada reacción se analizaron por cromatografía líquida de alta eficacia (HPLC. Los mejores resultados (15.2 %, POP, 30.4 % POS, 15.2 % SOS se obtuvieron empleando la relación molar de sustratos 1:3:3 (OOO: ácido palmítico:ácido esteárico y los parámetros de reacción: tiempo 10h, temperatura 45 °C, carga de enzima 20

  13. Synthesis of 3D Model of a Magnetic Field-Influenced Body from a Single Image

    Science.gov (United States)

    Wang, Cuilan; Newman, Timothy; Gallagher, Dennis

    2006-01-01

    A method for recovery of a 3D model of a cloud-like structure that is in motion and deforming but approximately governed by magnetic field properties is described. The method allows recovery of the model from a single intensity image in which the structure's silhouette can be observed. The method exploits envelope theory and a magnetic field model. Given one intensity image and the segmented silhouette in the image, the method proceeds without human intervention to produce the 3D model. In addition to allowing 3D model synthesis, the method's capability to yield a very compact description offers further utility. Application of the method to several real-world images is demonstrated.

  14. Sound Synthesis of the Harpsichord Using a Computationally Efficient Physical Model

    Science.gov (United States)

    Välimäki, Vesa; Penttinen, Henri; Knif, Jonte; Laurson, Mikael; Erkut, Cumhur

    2004-12-01

    A sound synthesis algorithm for the harpsichord has been developed by applying the principles of digital waveguide modeling. A modification to the loss filter of the string model is introduced that allows more flexible control of decay rates of partials than is possible with a one-pole digital filter, which is a usual choice for the loss filter. A version of the commuted waveguide synthesis approach is used, where each tone is generated with a parallel combination of the string model and a second-order resonator that are excited with a common excitation signal. The second-order resonator, previously proposed for this purpose, approximately simulates the beating effect appearing in many harpsichord tones. The characteristic key-release thump terminating harpsichord tones is reproduced by triggering a sample that has been extracted from a recording. A digital filter model for the soundboard has been designed based on recorded bridge impulse responses of the harpsichord. The output of the string models is injected in the soundboard filter that imitates the reverberant nature of the soundbox and, particularly, the ringing of the short parts of the strings behind the bridge.

  15. Sound Synthesis of the Harpsichord Using a Computationally Efficient Physical Model

    Directory of Open Access Journals (Sweden)

    Vesa Välimäki

    2004-06-01

    Full Text Available A sound synthesis algorithm for the harpsichord has been developed by applying the principles of digital waveguide modeling. A modification to the loss filter of the string model is introduced that allows more flexible control of decay rates of partials than is possible with a one-pole digital filter, which is a usual choice for the loss filter. A version of the commuted waveguide synthesis approach is used, where each tone is generated with a parallel combination of the string model and a second-order resonator that are excited with a common excitation signal. The second-order resonator, previously proposed for this purpose, approximately simulates the beating effect appearing in many harpsichord tones. The characteristic key-release thump terminating harpsichord tones is reproduced by triggering a sample that has been extracted from a recording. A digital filter model for the soundboard has been designed based on recorded bridge impulse responses of the harpsichord. The output of the string models is injected in the soundboard filter that imitates the reverberant nature of the soundbox and, particularly, the ringing of the short parts of the strings behind the bridge.

  16. The integration of Darwinism and evolutionary morphology: Alexej Nikolajevich Sewertzoff (1866-1936) and the developmental basis of evolutionary change.

    Science.gov (United States)

    Levit, George S; Hossfeld, Uwe; Olsson, Lennart

    2004-07-15

    The growth of evolutionary morphology in the late 19th and early 20th centuries was inspired by the work of Carl Gegenbaur (1826-1903) and his protégé and friend Ernst Haeckel (1834-1919). However, neither of them succeeded in creating and applying a strictly Darwinian (selectionist) methodology. This task was left to the next generation of evolutionary morphologists. In this paper we present a relatively unknown researcher, Alexej Nikolajevich Sewertzoff (1866-1936) who made important contributions towards a synthesis of Darwinism and evolutionary morphology. Copyright 2004 Wiley-Liss, Inc.

  17. Evolutionary algorithms for mobile ad hoc networks

    CERN Document Server

    Dorronsoro, Bernabé; Danoy, Grégoire; Pigné, Yoann; Bouvry, Pascal

    2014-01-01

    Describes how evolutionary algorithms (EAs) can be used to identify, model, and minimize day-to-day problems that arise for researchers in optimization and mobile networking. Mobile ad hoc networks (MANETs), vehicular networks (VANETs), sensor networks (SNs), and hybrid networks—each of these require a designer’s keen sense and knowledge of evolutionary algorithms in order to help with the common issues that plague professionals involved in optimization and mobile networking. This book introduces readers to both mobile ad hoc networks and evolutionary algorithms, presenting basic concepts as well as detailed descriptions of each. It demonstrates how metaheuristics and evolutionary algorithms (EAs) can be used to help provide low-cost operations in the optimization process—allowing designers to put some “intelligence” or sophistication into the design. It also offers efficient and accurate information on dissemination algorithms topology management, and mobility models to address challenges in the ...

  18. The influence of deterministic and stochastic waiting time for triggering mortality and colonization events on the coexistence of cooperators and defectors in an evolutionary game model

    Directory of Open Access Journals (Sweden)

    YouHua Chen

    2014-06-01

    waiting time, both defectors and cooperators could coexist, regardless of the types of waiting time for colonization events. Defense (or cooperation rewards could determine the persistence time of both game players. When the defense reward is low, cooperators could persist better in the simulation. But when the defense reward becomes sufficiently higher, defectors would persist better. Overall, non-coexistence of cooperators and defectors in the present evolutionary game model is dependent on the stochastic mortality events, but not colonization events. In conclusion, my present study quantifies the influence of the temporally fluctuating motility-colonization dynamic on modeling the coexistence of species in the spatial evolutionary game.

  19. The modern synthesis, Ronald Fisher and creationism.

    Science.gov (United States)

    Leigh

    1999-12-01

    The 'modern evolutionary synthesis' convinced most biologists that natural selection was the only directive influence on adaptive evolution. Today, however, dissatisfaction with the synthesis is widespread, and creationists and antidarwinians are multiplying. The central problem with the synthesis is its failure to show (or to provide distinct signs) that natural selection of random mutations could account for observed levels of adaptation.

  20. Financial Markets as Nonlinear Adaptive Evolutionary Systems

    OpenAIRE

    Hommes, C.H.

    2001-01-01

    This paper gives an overview of joint work with Buz Brock, on evolutionary adaptive belief systems (ABS) for modelling financial markets. Recent work with Andrea Gaunersdorfer is also reviewed and some recent experimental work on expectation formation in financial markets is also discussed. Financial markets are viewed as evolutionary systems between different, competing trading strategies. Agents are boundedly rational in the sense that they tend to follow strategies that have performed well...

  1. Oxygen spectral line synthesis: 3D non-LTE with CO5BOLD hydrodynamical model atmospheres.

    Science.gov (United States)

    Prakapavičius, D.; Steffen, M.; Kučinskas, A.; Ludwig, H.-G.; Freytag, B.; Caffau, E.; Cayrel, R.

    In this work we present first results of our current project aimed at combining the 3D hydrodynamical stellar atmosphere approach with non-LTE (NLTE) spectral line synthesis for a number of key chemical species. We carried out a full 3D-NLTE spectrum synthesis of the oxygen IR 777 nm triplet, using a modified and improved version of our NLTE3D package to calculate departure coefficients for the atomic levels of oxygen in a CO5BOLD 3D hydrodynamical solar model atmosphere. Spectral line synthesis was subsequently performed with the Linfor3D code. In agreement with previous studies, we find that the lines of the oxygen triplet produce deeper cores under NLTE conditions, due to the diminished line source function in the line forming region. This means that the solar oxygen IR 777 nm lines should be stronger in NLTE, leading to negative 3D NLTE-LTE abundance corrections. Qualitatively this result would support previous claims for a relatively low solar oxygen abundance. Finally, we outline several further steps that need to be taken in order to improve the physical realism and numerical accuracy of our current 3D-NLTE calculations.

  2. [On the problems of the evolutionary optimization of life history. I. A Markov model of the Leslie life history and optimization of fertility].

    Science.gov (United States)

    Pasekov, V P

    2013-03-01

    The paper considers the properties of individual life history corresponding to the Leslie model of age-structured population. The life history is simulated as a finite Markov chain with absorption at a death state of individual. In this model, individual longevity, average number of offspring R(L) (produced by an individual over the entire life), and some other known parameters of the life history have been derived using simple probability methods that do not involve matrix calculus and their individual components have been interpreted. In the Leslie linear population model (derived by simple modification of a Markov chain), R(L) determines the growth or decline of a population. Individuals with higher R(L) values have evolutionary advantages in the population due to accelerated growth in their number The selection of fertility as a factor of the increase in R(L) is considered. In the Leslie model, fertility is a set of correlated quantitative traits, where the age-specific fertility components determined both by multipl loci and the environment. According to the genetic theory of quantitative trait selection, they evolve towards an increase in R(L). Taking into account the limited resources for reproduction, selection optimizes the fertility distribution according to age. Optimal distribution corresponds to the attainment of the maximum R(L). This complies with the maximization of the rate of population growth (r-selection), which is characteristic of linear population models. The search for the RL maximum and optimal distribution of fertility belongs to the field of linear programming.

  3. Preventive evolutionary medicine of cancers.

    Science.gov (United States)

    Hochberg, Michael E; Thomas, Frédéric; Assenat, Eric; Hibner, Urszula

    2013-01-01

    Evolutionary theory predicts that once an individual reaches an age of sufficiently low Darwinian fitness, (s)he will have reduced chances of keeping cancerous lesions in check. While we clearly need to better understand the emergence of precursor states and early malignancies as well as their mitigation by the microenvironment and tissue architecture, we argue that lifestyle changes and preventive therapies based in an evolutionary framework, applied to identified high-risk populations before incipient neoplasms become clinically detectable and chemoresistant lineages emerge, are currently the most reliable way to control or eliminate early tumours. Specifically, the relatively low levels of (epi)genetic heterogeneity characteristic of many if not most incipient lesions will mean a relatively limited set of possible adaptive traits and associated costs compared to more advanced cancers, and thus a more complete and predictable understanding of treatment options and outcomes. We propose a conceptual model for preventive treatments and discuss the many associated challenges.

  4. Multi-Objective Analysis Applied to Mixed-Model Assembly Line Sequencing Problem through Elite Induced Evolutionary Method

    Science.gov (United States)

    Shimizu, Yoshiaki; Sakaguchi, Tatsuhiko; Pralomkarn, Theerayoth

    To meet higher customer satisfaction and shorter production lead time, assembly lines are shifting to mixed-model assembly lines. Accordingly, sequencing is becoming an increasingly important operation scheduling that directly affects on efficiency of the entire process. In this study, such sequencing problem at the mixed-model assembly line has been formulated as a bi-objective integer programming problem so that decision making through trade-off analysis can bring about significant production improvements. Then we have developed a multi-objective analysis method by hybridizing conventional and recent meta-heuristic methods. After showing its generic idea, the car mixed-model assembly line sequencing problem is concerned as a case study. Certain measures are also introduced to quantitatively evaluate the performances of the method through comparison.

  5. Evolutionary Mechanisms for Loneliness

    Science.gov (United States)

    Cacioppo, John T.; Cacioppo, Stephanie; Boomsma, Dorret I.

    2013-01-01

    Robert Weiss (1973) conceptualized loneliness as perceived social isolation, which he described as a gnawing, chronic disease without redeeming features. On the scale of everyday life, it is understandable how something as personally aversive as loneliness could be regarded as a blight on human existence. However, evolutionary time and evolutionary forces operate at such a different scale of organization than we experience in everyday life that personal experience is not sufficient to understand the role of loneliness in human existence. Research over the past decade suggests a very different view of loneliness than suggested by personal experience, one in which loneliness serves a variety of adaptive functions in specific habitats. We review evidence on the heritability of loneliness and outline an evolutionary theory of loneliness, with an emphasis on its potential adaptive value in an evolutionary timescale. PMID:24067110

  6. Evolutionary behavioral genetics.

    Science.gov (United States)

    Zietsch, Brendan P; de Candia, Teresa R; Keller, Matthew C

    2015-04-01

    We describe the scientific enterprise at the intersection of evolutionary psychology and behavioral genetics-a field that could be termed Evolutionary Behavioral Genetics-and how modern genetic data is revolutionizing our ability to test questions in this field. We first explain how genetically informative data and designs can be used to investigate questions about the evolution of human behavior, and describe some of the findings arising from these approaches. Second, we explain how evolutionary theory can be applied to the investigation of behavioral genetic variation. We give examples of how new data and methods provide insight into the genetic architecture of behavioral variation and what this tells us about the evolutionary processes that acted on the underlying causal genetic variants.

  7. Marine mammals: evolutionary biology

    National Research Council Canada - National Science Library

    Berta, Annalisa; Sumich, James L; Kovacs, Kit M

    2015-01-01

    The third edition of Marine Mammals: Evolutionary Biology provides a comprehensive and current assessment of the diversity, evolution, and biology of marine mammals, while highlighting the latest tools and techniques for their study...

  8. Evolutionary Modeling Predicts a Decrease in Postcopulatory Sperm Viability as a Response to Increasing Levels of Sperm Competition

    NARCIS (Netherlands)

    Engqvist, Leif

    Sperm competition has been found to have a strong influence on the evolution of many male and female reproductive traits. Theoretical models have shown that, with increasing levels of sperm competition, males are predicted to increase ejaculate investment, and there is ample empirical evidence

  9. Evidence for Karyotype Polymorphism in the Free-Living Flatworm, Macrostomum lignano, a Model Organism for Evolutionary and Developmental Biology

    NARCIS (Netherlands)

    Zadesenets, Kira S.; Vizoso, Dita B.; Schlatter, Aline; Konopatskaia, Irina D.; Berezikov, Eugene; Scharer, Lukas; Rubtsov, Nikolay B.

    2016-01-01

    Over the past decade, the free-living flatworm Macrostomum lignano has been successfully used in many areas of biology, including embryology, stem cells, sexual selection, bioadhesion and aging. The increased use of this powerful laboratory model, including the establishment of genomic resources and

  10. Stylus: a system for evolutionary experimentation based on a protein/proteome model with non-arbitrary functional constraints.

    Directory of Open Access Journals (Sweden)

    Douglas D Axe

    Full Text Available The study of protein evolution is complicated by the vast size of protein sequence space, the huge number of possible protein folds, and the extraordinary complexity of the causal relationships between protein sequence, structure, and function. Much simpler model constructs may therefore provide an attractive complement to experimental studies in this area. Lattice models, which have long been useful in studies of protein folding, have found increasing use here. However, while these models incorporate actual sequences and structures (albeit non-biological ones, they incorporate no actual functions--relying instead on largely arbitrary structural criteria as a proxy for function. In view of the central importance of function to evolution, and the impossibility of incorporating real functional constraints without real function, it is important that protein-like models be developed around real structure-function relationships. Here we describe such a model and introduce open-source software that implements it. The model is based on the structure-function relationship in written language, where structures are two-dimensional ink paths and functions are the meanings that result when these paths form legible characters. To capture something like the hierarchical complexity of protein structure, we use the traditional characters of Chinese origin. Twenty coplanar vectors, encoded by base triplets, act like amino acids in building the character forms. This vector-world model captures many aspects of real proteins, including life-size sequences, a life-size structural repertoire, a realistic genetic code, secondary, tertiary, and quaternary structure, structural domains and motifs, operon-like genetic structures, and layered functional complexity up to a level resembling bacterial genomes and proteomes. Stylus is a full-featured implementation of the vector world for Unix systems. To demonstrate the utility of Stylus, we generated a sample set of

  11. Inferring the Growth of Massive Galaxies Using Bayesian Spectral Synthesis Modeling

    Science.gov (United States)

    Stillman, Coley Michael; Poremba, Megan R.; Moustakas, John

    2018-01-01

    The most massive galaxies in the universe are typically found at the centers of massive galaxy clusters. Studying these galaxies can provide valuable insight into the hierarchical growth of massive dark matter halos. One of the key challenges of measuring the stellar mass growth of massive galaxies is converting the measured light profiles into stellar mass. We use Prospector, a state-of-the-art Bayesian spectral synthesis modeling code, to infer the total stellar masses of a pilot sample of massive central galaxies selected from the Sloan Digital Sky Survey. We compare our stellar mass estimates to previous measurements, and present some of the quantitative diagnostics provided by Prospector.

  12. Design and synthesis of model transparent aqueous colloids with optimal scattering properties.

    Science.gov (United States)

    Perro, Adeline; Meng, Guangnan; Fung, Jerome; Manoharan, Vinothan N

    2009-10-06

    We demonstrate the synthesis and self-assembly of colloidal particles with independently controlled diameter and scattering cross section. We show that it is possible to prepare bulk colloidal suspensions that are nearly transparent in water, while the particles themselves can be individually resolved using optical microscopy. These particles may be ideal model colloids for real-space studies of self-assembly in aqueous media. Moreover, they illustrate the degree to which the optical properties of colloids can be engineered through straightforward chemistry.

  13. Model Research On Synthesis Of Al2O3-C Layers By MOCVD

    Directory of Open Access Journals (Sweden)

    Sawka A.

    2015-06-01

    Full Text Available These are model studies whose aim is to obtain information that would allow development of new technology for synthesizing monolayers of Al2O3-C with adjusted microstructure on cemented carbides. The Al2O3-C layer will constitute an intermediate layer on which the outer layer of Al2O3 without carbon is synthesized. The purpose of the intermediate layer is to block the cobalt diffusion to the synthesized outer layer of Al2O3 and to stop the diffusion of air oxygen to the substrate during the synthesis of the outer layer. This layer should be thin, continuous, dense and uniform in thickness.

  14. Toward an integration of evolutionary biology and ecosystem science.

    Science.gov (United States)

    Matthews, Blake; Narwani, Anita; Hausch, Stephen; Nonaka, Etsuko; Peter, Hannes; Yamamichi, Masato; Sullam, Karen E; Bird, Kali C; Thomas, Mridul K; Hanley, Torrance C; Turner, Caroline B

    2011-07-01

    At present, the disciplines of evolutionary biology and ecosystem science are weakly integrated. As a result, we have a poor understanding of how the ecological and evolutionary processes that create, maintain, and change biological diversity affect the flux of energy and materials in global biogeochemical cycles. The goal of this article was to review several research fields at the interfaces between ecosystem science, community ecology and evolutionary biology, and suggest new ways to integrate evolutionary biology and ecosystem science. In particular, we focus on how phenotypic evolution by natural selection can influence ecosystem functions by affecting processes at the environmental, population and community scale of ecosystem organization. We develop an eco-evolutionary model to illustrate linkages between evolutionary change (e.g. phenotypic evolution of producer), ecological interactions (e.g. consumer grazing) and ecosystem processes (e.g. nutrient cycling). We conclude by proposing experiments to test the ecosystem consequences of evolutionary changes. © 2011 Blackwell Publishing Ltd/CNRS.

  15. Eco-Evolutionary Theory and Insect Outbreaks.

    Science.gov (United States)

    Páez, David J; Dukic, Vanja; Dushoff, Jonathan; Fleming-Davies, Arietta; Dwyer, Greg

    2017-06-01

    Eco-evolutionary theory argues that population cycles in consumer-resource interactions are partly driven by natural selection, such that changes in densities and changes in trait values are mutually reinforcing. Evidence that the theory explains cycles in nature, however, is almost nonexistent. Experimental tests of model assumptions are logistically impractical for most organisms, while for others, evidence that population cycles occur in nature is lacking. For insect baculoviruses in contrast, tests of model assumptions are straightforward, and there is strong evidence that baculoviruses help drive population cycles in many insects, including the gypsy moth that we study here. We therefore used field experiments with the gypsy moth baculovirus to test two key assumptions of eco-evolutionary models of host-pathogen population cycles: that reduced host infection risk is heritable and that it is costly. Our experiments confirm both assumptions, and inserting parameters estimated from our data into eco-evolutionary insect-outbreak models gives cycles closely resembling gypsy moth outbreak cycles in North America, whereas standard models predict unrealistic stable equilibria. Our work shows that eco-evolutionary models are useful for explaining outbreaks of forest insect defoliators, while widespread observations of intense selection on defoliators in nature and of heritable and costly resistance in defoliators in the lab together suggest that eco-evolutionary dynamics may play a general role in defoliator outbreaks.

  16. Assessing extreme models of the Stoeber synthesis using transients under a range of initial composition

    Energy Technology Data Exchange (ETDEWEB)

    Lee, K.; McCormick, A.V. [Univ. of Minnesota, Minneapolis, MN (United States); Look, J.L. [Oak Ridge National Lab., TN (United States); Harris, M.T. [Univ. of Maryland, College Park, MD (United States). Dept. of Chemical Engineering

    1997-10-01

    Monodispersely sized micrometer-scale spherical colloids of metal oxides are important for the controlled fabrication of high quality ceramic materials. Their synthesis by the hydrolysis of metal alkoxides is of particular interest. {sup 29}Si-NMR, conductimetry, and photon correlation spectroscopy are used to monitor the temporal profile of intermediate concentrations in Stoeber synthesis (i.e., ammonia-catalyzed hydrolysis of tetraethoxysilane in a batch reactor). Extreme models of the process are assessed by examining the effect of initial composition on these transients (over a wider range of composition than attempted previously). The trends with initial composition suggest that the nucleation is rate-limited by the hydrolysis of the singly hydrolyzed monomer, the product of which probably phase separates. Moreover, the trends are consistent with the aggregation model discussed by G.H. Bogush and C.F. Zukoski (J. Colloid Interface Sci. 142, 1, 19, 1991) and by M.T. Harris (Ph.D. dissertation, Univ. of Tennessee, 1992). The trends are not consistent with a growth model without aggregation.

  17. Evidence for Karyotype Polymorphism in the Free-Living Flatworm, Macrostomum lignano, a Model Organism for Evolutionary and Developmental Biology

    OpenAIRE

    Zadesenets, Kira S.; Vizoso, Dita B.; Schlatter, Aline; Konopatskaia, Irina D.; Berezikov, Eugene; Scharer, Lukas; Rubtsov, Nikolay B.

    2016-01-01

    Over the past decade, the free-living flatworm Macrostomum lignano has been successfully used in many areas of biology, including embryology, stem cells, sexual selection, bioadhesion and aging. The increased use of this powerful laboratory model, including the establishment of genomic resources and tools, makes it essential to have a detailed description of the chromosome organization of this species, previously suggested to have a karyotype with 2n = 8 and one pair of large and three pairs ...

  18. Modelling formation of disinfection by-products in water distribution: Optimisation using a multi-objective evolutionary algorithm

    KAUST Repository

    Radhakrishnan, Mohanasundar

    2012-05-01

    Concerns have been raised regarding disinfection by-products (DBPs) formed as a result of the reaction of halogen-based disinfectants with DBP precursors. In order to appreciate the chemical and biological tradeoffs, it is imperative to understand the formation trends of DBPs and their spread in the distribution network. However, the water at a point in a complex distribution system is a mixture from various sources, whose proportions are complex to estimate and requires advanced hydraulic analysis. To understand the risks of DBPs and to develop mitigation strategies, it is important to understand the distribution of DBPs in a water network, which requires modelling. The goal of this research was to integrate a steady-state water network model with a particle backtracking algorithm and chlorination as well as DBPs models in order to assess the tradeoffs between biological and chemical risks in the distribution network. A multi-objective optimisation algorithm was used to identify the optimal proportion of water from various sources, dosages of alum, and dosages of chlorine in the treatment plant and in booster locations to control the formation of chlorination DBPs and to achieve a balance between microbial and chemical risks. © IWA Publishing 2012.

  19. The ecological and evolutionary drivers of female-biased sex ratios: two-sex models of perennial seagrasses.

    Science.gov (United States)

    Shelton, Andrew Olaf

    2010-03-01

    Among sexually reproducing species, differences between the sexes within species are ubiquitous. Despite the clear effect of sex differences on sex ratios and population growth rates, demographic models rarely consider both sexes explicitly. Here I explore the causes of extreme female-biased sex ratios in two marine angiosperms (Phyllospadix spp.). Using demographic data, I develop two-sex matrix projection models to assess the magnitude of demographic differences necessary to generate observed sex ratios and the consequences of sex differences for population growth rates. I demonstrate that small sex differences in survival can generate biased sex ratios, but the importance of sexual reproduction differs markedly between species. Even in the absence of a direct trade-off between sexual and asexual reproduction, the presence of two reproductive modes affects both the importance of sex and the sex-ratio bias. Using sensitivity analyses, I quantify the contribution of shared and sex-specific vital rates and show that until males become rare, the sensitivity of sex-specific vital rates is small relative to that of shared vital rates. I demonstrate that placing sex differences in the context of a demographic model that includes biologically motivated life-history trade-offs can explain the maintenance of sex-specific life histories and the persistence of skewed sex ratios.

  20. Driving developmental and evolutionary change: A systems biology view.

    Science.gov (United States)

    Bard, Jonathan

    2013-04-01

    Embryonic development is underpinned by ∼50 core processes that drive morphogenesis, growth, patterning and differentiation, and each is the functional output of a complex molecular network. Processes are thus the natural and parsimonious link between genotype and phenotype and the obvious focus for any discussion of biological change. Here, the implications of this approach are explored. One is that many features of developmental change can be modeled as mathematical graphs, or sets of connected triplets of the general form . In these, the verbs (edges) are the outputs of the processes that drive change and the nouns (nodes) are the time-dependent states of biological entities (from molecules to tissues). Such graphs help unpick the multi-level complexity of developmental phenomena and may help suggest new experiments. Another comes from analyzing the effect of mutation that lead to tinkering with the dynamic properties of these processes and to congenital abnormalities; if these changes are both inherited and advantageous, they become evolutionary modifications. In this context, protein networks often represents what classical evolutionary genetics sees as genes, and the realization that traits reflect the output processes of complex networks, particularly for growth, patterning and pigmentation, rather than anything simpler clarifies some problems that the evolutionary synthesis of the 1950s has found hard to solve. In the wider context, most processes are used many times in development and cooperate to produce tissue modules (bones, branching duct systems, muscles etc.). Their underlying generative networks can thus be thought of as genomic modules or subroutines. Copyright © 2012 Elsevier Ltd. All rights reserved.