WorldWideScience

Sample records for genetic local search

  1. Genetic Algorithms and Local Search

    Science.gov (United States)

    Whitley, Darrell

    1996-01-01

    The first part of this presentation is a tutorial level introduction to the principles of genetic search and models of simple genetic algorithms. The second half covers the combination of genetic algorithms with local search methods to produce hybrid genetic algorithms. Hybrid algorithms can be modeled within the existing theoretical framework developed for simple genetic algorithms. An application of a hybrid to geometric model matching is given. The hybrid algorithm yields results that improve on the current state-of-the-art for this problem.

  2. Genetic local search algorithm for optimization design of diffractive optical elements.

    Science.gov (United States)

    Zhou, G; Chen, Y; Wang, Z; Song, H

    1999-07-10

    We propose a genetic local search algorithm (GLSA) for the optimization design of diffractive optical elements (DOE's). This hybrid algorithm incorporates advantages of both genetic algorithm (GA) and local search techniques. It appears better able to locate the global minimum compared with a canonical GA. Sample cases investigated here include the optimization design of binary-phase Dammann gratings, continuous surface-relief grating array generators, and a uniform top-hat focal plane intensity profile generator. Two GLSA's whose incorporated local search techniques are the hill-climbing method and the simulated annealing algorithm are investigated. Numerical experimental results demonstrate that the proposed algorithm is highly efficient and robust. DOE's that have high diffraction efficiency and excellent uniformity can be achieved by use of the algorithm we propose.

  3. Optimization of distribution piping network in district cooling system using genetic algorithm with local search

    International Nuclear Information System (INIS)

    Chan, Apple L.S.; Hanby, Vic I.; Chow, T.T.

    2007-01-01

    A district cooling system is a sustainable means of distribution of cooling energy through mass production. A cooling medium like chilled water is generated at a central refrigeration plant and supplied to serve a group of consumer buildings through a piping network. Because of the substantial capital investment involved, an optimal design of the distribution piping configuration is one of the crucial factors for successful implementation of the district cooling scheme. In the present study, genetic algorithm (GA) incorporated with local search techniques was developed to find the optimal/near optimal configuration of the piping network in a hypothetical site. The effect of local search, mutation rate and frequency of local search on the performance of the GA in terms of both solution quality and computation time were investigated and presented in this paper

  4. An Improved Hybrid Genetic Algorithm with a New Local Search Procedure

    Directory of Open Access Journals (Sweden)

    Wen Wan

    2013-01-01

    Full Text Available One important challenge of a hybrid genetic algorithm (HGA (also called memetic algorithm is the tradeoff between global and local searching (LS as it is the case that the cost of an LS can be rather high. This paper proposes a novel, simplified, and efficient HGA with a new individual learning procedure that performs a LS only when the best offspring (solution in the offspring population is also the best in the current parent population. Additionally, a new LS method is developed based on a three-directional search (TD, which is derivative-free and self-adaptive. The new HGA with two different LS methods (the TD and Neld-Mead simplex is compared with a traditional HGA. Four benchmark functions are employed to illustrate the improvement of the proposed method with the new learning procedure. The results show that the new HGA greatly reduces the number of function evaluations and converges much faster to the global optimum than a traditional HGA. The TD local search method is a good choice in helping to locate a global “mountain” (or “valley” but may not perform the Nelder-Mead method in the final fine tuning toward the optimal solution.

  5. Process planning optimization on turning machine tool using a hybrid genetic algorithm with local search approach

    Directory of Open Access Journals (Sweden)

    Yuliang Su

    2015-04-01

    Full Text Available A turning machine tool is a kind of new type of machine tool that is equipped with more than one spindle and turret. The distinctive simultaneous and parallel processing abilities of turning machine tool increase the complexity of process planning. The operations would not only be sequenced and satisfy precedence constraints, but also should be scheduled with multiple objectives such as minimizing machining cost, maximizing utilization of turning machine tool, and so on. To solve this problem, a hybrid genetic algorithm was proposed to generate optimal process plans based on a mixed 0-1 integer programming model. An operation precedence graph is used to represent precedence constraints and help generate a feasible initial population of hybrid genetic algorithm. Encoding strategy based on data structure was developed to represent process plans digitally in order to form the solution space. In addition, a local search approach for optimizing the assignments of available turrets would be added to incorporate scheduling with process planning. A real-world case is used to prove that the proposed approach could avoid infeasible solutions and effectively generate a global optimal process plan.

  6. A GENETIC ALGORITHM USING THE LOCAL SEARCH HEURISTIC IN FACILITIES LAYOUT PROBLEM: A MEMETİC ALGORİTHM APPROACH

    Directory of Open Access Journals (Sweden)

    Orhan TÜRKBEY

    2002-02-01

    Full Text Available Memetic algorithms, which use local search techniques, are hybrid structured algorithms like genetic algorithms among evolutionary algorithms. In this study, for Quadratic Assignment Problem (QAP, a memetic structured algorithm using a local search heuristic like 2-opt is developed. Developed in the algorithm, a crossover operator that has not been used before for QAP is applied whereas, Eshelman procedure is used in order to increase thesolution variability. The developed memetic algorithm is applied on test problems taken from QAP-LIB, the results are compared with the present techniques in the literature.

  7. Complete local search with memory

    NARCIS (Netherlands)

    Ghosh, D.; Sierksma, G.

    2000-01-01

    Neighborhood search heuristics like local search and its variants are some of the most popular approaches to solve discrete optimization problems of moderate to large size. Apart from tabu search, most of these heuristics are memoryless. In this paper we introduce a new neighborhood search heuristic

  8. Mathematical programming solver based on local search

    CERN Document Server

    Gardi, Frédéric; Darlay, Julien; Estellon, Bertrand; Megel, Romain

    2014-01-01

    This book covers local search for combinatorial optimization and its extension to mixed-variable optimization. Although not yet understood from the theoretical point of view, local search is the paradigm of choice for tackling large-scale real-life optimization problems. Today's end-users demand interactivity with decision support systems. For optimization software, this means obtaining good-quality solutions quickly. Fast iterative improvement methods, like local search, are suited to satisfying such needs. Here the authors show local search in a new light, in particular presenting a new kind of mathematical programming solver, namely LocalSolver, based on neighborhood search. First, an iconoclast methodology is presented to design and engineer local search algorithms. The authors' concern about industrializing local search approaches is of particular interest for practitioners. This methodology is applied to solve two industrial problems with high economic stakes. Software based on local search induces ex...

  9. Multi-directional local search

    Science.gov (United States)

    Tricoire, Fabien

    2012-01-01

    This paper introduces multi-directional local search, a metaheuristic for multi-objective optimization. We first motivate the method and present an algorithmic framework for it. We then apply it to several known multi-objective problems such as the multi-objective multi-dimensional knapsack problem, the bi-objective set packing problem and the bi-objective orienteering problem. Experimental results show that our method systematically provides solution sets of comparable quality with state-of-the-art methods applied to benchmark instances of these problems, within reasonable CPU effort. We conclude that the proposed algorithmic framework is a viable option when solving multi-objective optimization problems. PMID:25140071

  10. When Gravity Fails: Local Search Topology

    Science.gov (United States)

    Frank, Jeremy; Cheeseman, Peter; Stutz, John; Lau, Sonie (Technical Monitor)

    1997-01-01

    Local search algorithms for combinatorial search problems frequently encounter a sequence of states in which it is impossible to improve the value of the objective function; moves through these regions, called {\\em plateau moves), dominate the time spent in local search. We analyze and characterize {\\em plateaus) for three different classes of randomly generated Boolean Satisfiability problems. We identify several interesting features of plateaus that impact the performance of local search algorithms. We show that local minima tend to be small but occasionally may be very large. We also show that local minima can be escaped without unsatisfying a large number of clauses, but that systematically searching for an escape route may be computationally expensive if the local minimum is large. We show that plateaus with exits, called benches, tend to be much larger than minima, and that some benches have very few exit states which local search can use to escape. We show that the solutions (i.e. global minima) of randomly generated problem instances form clusters, which behave similarly to local minima. We revisit several enhancements of local search algorithms and explain their performance in light of our results. Finally we discuss strategies for creating the next generation of local search algorithms.

  11. Complex Sequencing Problems and Local Search Heuristics

    NARCIS (Netherlands)

    Brucker, P.; Hurink, Johann L.; Osman, I.H.; Kelly, J.P.

    1996-01-01

    Many problems can be formulated as complex sequencing problems. We will present problems in flexible manufacturing that have such a formulation and apply local search methods like iterative improvement, simulated annealing and tabu search to solve these problems. Computational results are reported.

  12. Genetic algorithms as global random search methods

    Science.gov (United States)

    Peck, Charles C.; Dhawan, Atam P.

    1995-01-01

    Genetic algorithm behavior is described in terms of the construction and evolution of the sampling distributions over the space of candidate solutions. This novel perspective is motivated by analysis indicating that the schema theory is inadequate for completely and properly explaining genetic algorithm behavior. Based on the proposed theory, it is argued that the similarities of candidate solutions should be exploited directly, rather than encoding candidate solutions and then exploiting their similarities. Proportional selection is characterized as a global search operator, and recombination is characterized as the search process that exploits similarities. Sequential algorithms and many deletion methods are also analyzed. It is shown that by properly constraining the search breadth of recombination operators, convergence of genetic algorithms to a global optimum can be ensured.

  13. Hybridizing Evolutionary Algorithms with Opportunistic Local Search

    DEFF Research Database (Denmark)

    Gießen, Christian

    2013-01-01

    There is empirical evidence that memetic algorithms (MAs) can outperform plain evolutionary algorithms (EAs). Recently the first runtime analyses have been presented proving the aforementioned conjecture rigorously by investigating Variable-Depth Search, VDS for short (Sudholt, 2008). Sudholt...... of this new operator is demonstrated on the Rastrigin function encoded for binary hypercubes. Our results provide further insight into the problem of how to prevent local search algorithms to get stuck in local optima from a theoretical perspective. The methods stem from discrete probability theory...

  14. Genetic search feature selection for affective modeling

    DEFF Research Database (Denmark)

    Martínez, Héctor P.; Yannakakis, Georgios N.

    2010-01-01

    Automatic feature selection is a critical step towards the generation of successful computational models of affect. This paper presents a genetic search-based feature selection method which is developed as a global-search algorithm for improving the accuracy of the affective models built....... The method is tested and compared against sequential forward feature selection and random search in a dataset derived from a game survey experiment which contains bimodal input features (physiological and gameplay) and expressed pairwise preferences of affect. Results suggest that the proposed method...

  15. On Improving Local Search for Unsatisfiability

    Directory of Open Access Journals (Sweden)

    David Pereira

    2009-10-01

    Full Text Available Stochastic local search (SLS has been an active field of research in the last few years, with new techniques and procedures being developed at an astonishing rate. SLS has been traditionally associated with satisfiability solving, that is, finding a solution for a given problem instance, as its intrinsic nature does not address unsatisfiable problems. Unsatisfiable instances were therefore commonly solved using backtrack search solvers. For this reason, in the late 90s Selman, Kautz and McAllester proposed a challenge to use local search instead to prove unsatisfiability. More recently, two SLS solvers - Ranger and Gunsat - have been developed, which are able to prove unsatisfiability albeit being SLS solvers. In this paper, we first compare Ranger with Gunsat and then propose to improve Ranger performance using some of Gunsat's techniques, namely unit propagation look-ahead and extended resolution.

  16. Stochastic local search foundations and applications

    CERN Document Server

    Hoos, Holger H; Stutzle, Thomas

    2004-01-01

    Stochastic local search (SLS) algorithms are among the most prominent and successful techniques for solving computationally difficult problems in many areas of computer science and operations research, including propositional satisfiability, constraint satisfaction, routing, and scheduling. SLS algorithms have also become increasingly popular for solving challenging combinatorial problems in many application areas, such as e-commerce and bioinformatics. Hoos and Stützle offer the first systematic and unified treatment of SLS algorithms. In this groundbreaking new book, they examine the general concepts and specific instances of SLS algorithms and carefully consider their development, analysis and application. The discussion focuses on the most successful SLS methods and explores their underlying principles, properties, and features. This book gives hands-on experience with some of the most widely used search techniques, and provides readers with the necessary understanding and skills to use this powerful too...

  17. Optimal PMU placement using Iterated Local Search

    Energy Technology Data Exchange (ETDEWEB)

    Hurtgen, M.; Maun, J.-C. [Universite Libre de Bruxelles, Avenue F. Roosevelt 50, B-1050 Brussels (Belgium)

    2010-10-15

    An essential tool for power system monitoring is state estimation. Using PMUs can greatly improve the state estimation process. However, for state estimation, the PMUs should be placed appropriately in the network. The problem of optimal PMU placement for full observability is analysed in this paper. The objective of the paper is to minimise the size of the PMU configuration while allowing full observability of the network. The method proposed initially suggests a PMU distribution which makes the network observable. The Iterated Local Search (ILS) metaheuristic is then used to minimise the size of the PMU configuration needed to observe the network. The algorithm is tested on IEEE test networks with 14, 57 and 118 nodes and compared to the results obtained in previous publications. (author)

  18. 3D protein structure prediction with genetic tabu search algorithm.

    Science.gov (United States)

    Zhang, Xiaolong; Wang, Ting; Luo, Huiping; Yang, Jack Y; Deng, Youping; Tang, Jinshan; Yang, Mary Qu

    2010-05-28

    Protein structure prediction (PSP) has important applications in different fields, such as drug design, disease prediction, and so on. In protein structure prediction, there are two important issues. The first one is the design of the structure model and the second one is the design of the optimization technology. Because of the complexity of the realistic protein structure, the structure model adopted in this paper is a simplified model, which is called off-lattice AB model. After the structure model is assumed, optimization technology is needed for searching the best conformation of a protein sequence based on the assumed structure model. However, PSP is an NP-hard problem even if the simplest model is assumed. Thus, many algorithms have been developed to solve the global optimization problem. In this paper, a hybrid algorithm, which combines genetic algorithm (GA) and tabu search (TS) algorithm, is developed to complete this task. In order to develop an efficient optimization algorithm, several improved strategies are developed for the proposed genetic tabu search algorithm. The combined use of these strategies can improve the efficiency of the algorithm. In these strategies, tabu search introduced into the crossover and mutation operators can improve the local search capability, the adoption of variable population size strategy can maintain the diversity of the population, and the ranking selection strategy can improve the possibility of an individual with low energy value entering into next generation. Experiments are performed with Fibonacci sequences and real protein sequences. Experimental results show that the lowest energy obtained by the proposed GATS algorithm is lower than that obtained by previous methods. The hybrid algorithm has the advantages from both genetic algorithm and tabu search algorithm. It makes use of the advantage of multiple search points in genetic algorithm, and can overcome poor hill-climbing capability in the conventional genetic

  19. Local Search Approaches in Stable Matching Problems

    Directory of Open Access Journals (Sweden)

    Toby Walsh

    2013-10-01

    Full Text Available The stable marriage (SM problem has a wide variety of practical applications, ranging from matching resident doctors to hospitals, to matching students to schools or, more generally, to any two-sided market. In the classical formulation, n men and n women express their preferences (via a strict total order over the members of the other sex. Solving an SM problem means finding a stable marriage where stability is an envy-free notion: no man and woman who are not married to each other would both prefer each other to their partners or to being single. We consider both the classical stable marriage problem and one of its useful variations (denoted SMTI (Stable Marriage with Ties and Incomplete lists where the men and women express their preferences in the form of an incomplete preference list with ties over a subset of the members of the other sex. Matchings are permitted only with people who appear in these preference lists, and we try to find a stable matching that marries as many people as possible. Whilst the SM problem is polynomial to solve, the SMTI problem is NP-hard. We propose to tackle both problems via a local search approach, which exploits properties of the problems to reduce the size of the neighborhood and to make local moves efficiently. We empirically evaluate our algorithm for SM problems by measuring its runtime behavior and its ability to sample the lattice of all possible stable marriages. We evaluate our algorithm for SMTI problems in terms of both its runtime behavior and its ability to find a maximum cardinality stable marriage. Experimental results suggest that for SM problems, the number of steps of our algorithm grows only as O(n log(n, and that it samples very well the set of all stable marriages. It is thus a fair and efficient approach to generate stable marriages. Furthermore, our approach for SMTI problems is able to solve large problems, quickly returning stable matchings of large and often optimal size, despite the

  20. Numerical Search for Local (Partial) Differential Flatness

    Science.gov (United States)

    2016-10-09

    trajectory x∗r (t), while α f lat and α̇ f lat are derived from the matrices product Kr ·Θ(·) (i.e. from the numerical flat model). Fig. 3. Ballbot...in the multimedia material related to this paper. Table I summarizes the time required for solving the nu- merical search and the consequent re

  1. Nigerian Journal of Genetics: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  2. Stochastic search in structural optimization - Genetic algorithms and simulated annealing

    Science.gov (United States)

    Hajela, Prabhat

    1993-01-01

    An account is given of illustrative applications of genetic algorithms and simulated annealing methods in structural optimization. The advantages of such stochastic search methods over traditional mathematical programming strategies are emphasized; it is noted that these methods offer a significantly higher probability of locating the global optimum in a multimodal design space. Both genetic-search and simulated annealing can be effectively used in problems with a mix of continuous, discrete, and integer design variables.

  3. EURISCO: The European search catalogue for plant genetic resources

    NARCIS (Netherlands)

    Weise, Stephan; Oppermann, Markus; Maggioni, Lorenzo; Hintum, van Theo; Knüpffer, Helmut

    2017-01-01

    The European Search Catalogue for Plant Genetic Resources, EURISCO, provides information about 1.8 million crop plant accessions preserved by almost 400 institutes in Europe and beyond. EURISCO is being maintained on behalf of the European Cooperative Programme for Plant Genetic Resources. It is

  4. A Matheuristic Approach Combining Local Search and Mathematical Programming

    Directory of Open Access Journals (Sweden)

    Carolina Lagos

    2016-01-01

    Full Text Available A novel matheuristic approach is presented and tested on a well-known optimisation problem, namely, capacitated facility location problem (CFLP. The algorithm combines local search and mathematical programming. While the local search algorithm is used to select a subset of promising facilities, mathematical programming strategies are used to solve the subproblem to optimality. Proposed local search is influenced by instance-specific information such as installation cost and the distance between customers and facilities. The algorithm is tested on large instances of the CFLP, where neither local search nor mathematical programming is able to find good quality solutions within acceptable computational times. Our approach is shown to be a very competitive alternative to solve large-scale instances for the CFLP.

  5. Local Radon Descriptors for Image Search

    OpenAIRE

    Babaie, Morteza; Tizhoosh, H. R.; Khatami, Amin; Shiri, M. E.

    2017-01-01

    Radon transform and its inverse operation are important techniques in medical imaging tasks. Recently, there has been renewed interest in Radon transform for applications such as content-based medical image retrieval. However, all studies so far have used Radon transform as a global or quasi-global image descriptor by extracting projections of the whole image or large sub-images. This paper attempts to show that the dense sampling to generate the histogram of local Radon projections has a muc...

  6. Partial Symmetry Breaking by Local Search in the Group

    NARCIS (Netherlands)

    Prestwich, S.; Hnich, B.; Simonis, H.; Rossi, R.; Tarim, S.A.

    2012-01-01

    The presence of symmetry in constraint satisfaction problems can cause a great deal of wasted search effort, and several methods for breaking symmetries have been reported. In this paper we describe a new method called Symmetry Breaking by Nonstationary Optimisation, which interleaves local search

  7. Locality in Generic Instance Search from One Example

    NARCIS (Netherlands)

    Tao, R.; Gavves, E.; Snoek, C.G.M.; Smeulders, A.W.M.

    2014-01-01

    This paper aims for generic instance search from a single example. Where the state-of-the-art relies on global image representation for the search, we proceed by including locality at all steps of the method. As the first novelty, we consider many boxes per database image as candidate targets to

  8. the search for local government autonomy in nigeria

    African Journals Online (AJOL)

    RAYAN_

    THE SEARCH FOR LOCAL GOVERNMENT AUTONOMY. IN NIGERIA: LEGAL AND INSTITUTIONAL. PATHWAYS TO ITS REALIZATION. Ifeolu J. Koni*. ABSTRACT. This article examines the status of the local government under the tripartite governmental system in Nigeria that has been in operation since 1979. It reviews ...

  9. Integrating Conflict Driven Clause Learning to Local Search

    Directory of Open Access Journals (Sweden)

    Gilles Audenard

    2009-10-01

    Full Text Available This article introduces SatHyS (SAT HYbrid Solver, a novel hybrid approach for propositional satisfiability. It combines local search and conflict driven clause learning (CDCL scheme. Each time the local search part reaches a local minimum, the CDCL is launched. For SAT problems it behaves like a tabu list, whereas for UNSAT ones, the CDCL part tries to focus on minimum unsatisfiable sub-formula (MUS. Experimental results show good performances on many classes of SAT instances from the last SAT competitions.

  10. Mathematical programming models for solving in equal-sized facilities layout problems. A genetic search method

    International Nuclear Information System (INIS)

    Tavakkoli-Moghaddam, R.

    1999-01-01

    This paper present unequal-sized facilities layout solutions generated by a genetic search program. named Layout Design using a Genetic Algorithm) 9. The generalized quadratic assignment problem requiring pre-determined distance and material flow matrices as the input data and the continuous plane model employing a dynamic distance measure and a material flow matrix are discussed. Computational results on test problems are reported as compared with layout solutions generated by the branch - and bound algorithm a hybrid method merging simulated annealing and local search techniques, and an optimization process of an enveloped block

  11. Modified Biogeography-Based Optimization with Local Search Mechanism

    Directory of Open Access Journals (Sweden)

    Quanxi Feng

    2013-01-01

    Full Text Available Biogeography-based optimization (BBO is a new effective population optimization algorithm based on the biogeography theory with inherently insufficient exploration capability. To address this limitation, we proposed a modified BBO with local search mechanism (denoted as MLBBO. In MLBBO, a modified migration operator is integrated into BBO, which can adopt more information from other habitats, to enhance the exploration ability. Then, a local search mechanism is used in BBO to supplement with modified migration operator. Extensive experimental tests are conducted on 27 benchmark functions to show the effectiveness of the proposed algorithm. The simulation results have been compared with original BBO, DE, improved BBO algorithms, and other evolutionary algorithms. Finally, the performance of the modified migration operator and local search mechanism are also discussed.

  12. An Enhanced Differential Evolution with Elite Chaotic Local Search.

    Science.gov (United States)

    Guo, Zhaolu; Huang, Haixia; Deng, Changshou; Yue, Xuezhi; Wu, Zhijian

    2015-01-01

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

  13. Performance of genetic algorithms in search for water splitting perovskites

    DEFF Research Database (Denmark)

    Jain, A.; Castelli, Ivano Eligio; Hautier, G.

    2013-01-01

    We examine the performance of genetic algorithms (GAs) in uncovering solar water light splitters over a space of almost 19,000 perovskite materials. The entire search space was previously calculated using density functional theory to determine solutions that fulfill constraints on stability, band...

  14. EURISCO: The European search catalogue for plant genetic resources.

    Science.gov (United States)

    Weise, Stephan; Oppermann, Markus; Maggioni, Lorenzo; van Hintum, Theo; Knüpffer, Helmut

    2017-01-04

    The European Search Catalogue for Plant Genetic Resources, EURISCO, provides information about 1.8 million crop plant accessions preserved by almost 400 institutes in Europe and beyond. EURISCO is being maintained on behalf of the European Cooperative Programme for Plant Genetic Resources. It is based on a network of National Inventories of 43 member countries and represents an important effort for the preservation of world's agrobiological diversity by providing information about the large genetic diversity kept by the collaborating collections. Moreover, EURISCO also assists its member countries in fulfilling legal obligations and commitments, e.g. with respect to the International Treaty on Plant Genetic Resources, the Second Global Plan of Action for Plant Genetic Resources for Food and Agriculture of the United Nation's Food and Agriculture Organization, or the Convention on Biological Diversity. EURISCO is accessible at http://eurisco.ecpgr.org. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Constraint-based local search for container stowage slot planning

    DEFF Research Database (Denmark)

    Pacino, Dario; Jensen, Rune Møller; Bebbington, Tom

    2012-01-01

    -sea vessels. This paper describes the constrained-based local search algorithm used in the second phase of this approach where individual containers are assigned to slots in each bay section. The algorithm can solve this problem in an average of 0.18 seconds per bay, corresponding to a 20 seconds runtime...

  16. Global Search and Local Ascent for Large Cournot Games

    Directory of Open Access Journals (Sweden)

    Maria Sarasan

    2010-12-01

    Full Text Available Equilibria detection in large games is a fundamental problem in computational game theory. A memetic algorithm, Global Search and Local Ascent (GSLA, is proposed. GSLA's performance is evaluated by means of numerical experiments within the framework of a Cournot game involving up to 100 players and by comparison with an evolutionary multiobjective optimization algorithm adapted for Nash equilibria detection.

  17. RDEL: Restart Differential Evolution algorithm with Local Search Mutation for global numerical optimization

    Directory of Open Access Journals (Sweden)

    Ali Wagdy Mohamed

    2014-11-01

    Full Text Available In this paper, a novel version of Differential Evolution (DE algorithm based on a couple of local search mutation and a restart mechanism for solving global numerical optimization problems over continuous space is presented. The proposed algorithm is named as Restart Differential Evolution algorithm with Local Search Mutation (RDEL. In RDEL, inspired by Particle Swarm Optimization (PSO, a novel local mutation rule based on the position of the best and the worst individuals among the entire population of a particular generation is introduced. The novel local mutation scheme is joined with the basic mutation rule through a linear decreasing function. The proposed local mutation scheme is proven to enhance local search tendency of the basic DE and speed up the convergence. Furthermore, a restart mechanism based on random mutation scheme and a modified Breeder Genetic Algorithm (BGA mutation scheme is combined to avoid stagnation and/or premature convergence. Additionally, an exponent increased crossover probability rule and a uniform scaling factors of DE are introduced to promote the diversity of the population and to improve the search process, respectively. The performance of RDEL is investigated and compared with basic differential evolution, and state-of-the-art parameter adaptive differential evolution variants. It is discovered that the proposed modifications significantly improve the performance of DE in terms of quality of solution, efficiency and robustness.

  18. An Enhanced Differential Evolution with Elite Chaotic Local Search

    Directory of Open Access Journals (Sweden)

    Zhaolu Guo

    2015-01-01

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

  19. Population genetics models of local ancestry.

    Science.gov (United States)

    Gravel, Simon

    2012-06-01

    Migrations have played an important role in shaping the genetic diversity of human populations. Understanding genomic data thus requires careful modeling of historical gene flow. Here we consider the effect of relatively recent population structure and gene flow and interpret genomes of individuals that have ancestry from multiple source populations as mosaics of segments originating from each population. This article describes general and tractable models for local ancestry patterns with a focus on the length distribution of continuous ancestry tracts and the variance in total ancestry proportions among individuals. The models offer improved agreement with Wright-Fisher simulation data when compared to the state-of-the art and can be used to infer time-dependent migration rates from multiple populations. Considering HapMap African-American (ASW) data, we find that a model with two distinct phases of "European" gene flow significantly improves the modeling of both tract lengths and ancestry variances.

  20. A Hybrid of Modified PSO and Local Search on a Multi-Robot Search System

    Directory of Open Access Journals (Sweden)

    Mohammad Naim Rastgoo

    2015-07-01

    Full Text Available Particle swarm optimization (PSO, a new population-based algorithm, has recently been used on multi-robot systems. Although this algorithm is applied to solve many optimization problems as well as multi-robot systems, it has some drawbacks when it is applied on multi-robot search systems to find a target in a search space containing big static obstacles. One of these defects is premature convergence. This means that one of the properties of basic PSO is that when particles are spread in a search space, as time increases they tend to converge in a small area. This shortcoming is also evident on a multi-robot search system, particularly when there are big static obstacles in the search space that prevent the robots from finding the target easily; therefore, as time increases, based on this property they converge to a small area that may not contain the target and become entrapped in that area. Another shortcoming is that basic PSO cannot guarantee the global convergence of the algorithm. In other words, initially particles explore different areas, but in some cases they are not good at exploiting promising areas, which will increase the search time. This study proposes a method based on the particle swarm optimization (PSO technique on a multi-robot system to find a target in a search space containing big static obstacles. This method is not only able to overcome the premature convergence problem but also establishes an efficient balance between exploration and exploitation and guarantees global convergence, reducing the search time by combining with a local search method, such as A-star. To validate the effectiveness and usefulness of algorithms, a simulation environment has been developed for conducting simulation-based experiments in different scenarios and for reporting experimental results. These experimental results have demonstrated that the proposed method is able to overcome the premature convergence problem and guarantee global

  1. Simulation Optimization by Genetic Search: A Comprehensive Study with Applications to Production Management

    National Research Council Canada - National Science Library

    Yunker, James

    2003-01-01

    In this report, a relatively new simulation optimization technique, the genetic search, is compared to two more established simulation techniques-the pattern search and the response surface methodology search...

  2. Searching for adaptive traits in genetic resources - phenology based approach

    Science.gov (United States)

    Bari, Abdallah

    2015-04-01

    Searching for adaptive traits in genetic resources - phenology based approach Abdallah Bari, Kenneth Street, Eddy De Pauw, Jalal Eddin Omari, and Chandra M. Biradar International Center for Agricultural Research in the Dry Areas, Rabat Institutes, Rabat, Morocco Phenology is an important plant trait not only for assessing and forecasting food production but also for searching in genebanks for adaptive traits. Among the phenological parameters we have been considering to search for such adaptive and rare traits are the onset (sowing period) and the seasonality (growing period). Currently an application is being developed as part of the focused identification of germplasm strategy (FIGS) approach to use climatic data in order to identify crop growing seasons and characterize them in terms of onset and duration. These approximations of growing period characteristics can then be used to estimate flowering and maturity dates for dryland crops, such as wheat, barley, faba bean, lentils and chickpea, and assess, among others, phenology-related traits such as days to heading [dhe] and grain filling period [gfp]. The approach followed here is based on first calculating long term average daily temperatures by fitting a curve to the monthly data over days from beginning of the year. Prior to the identification of these phenological stages the onset is extracted first from onset integer raster GIS layers developed based on a model of the growing period that considers both moisture and temperature limitations. The paper presents some examples of real applications of the approach to search for rare and adaptive traits.

  3. Constraint-based local search for container stowage slot planning

    DEFF Research Database (Denmark)

    Pacino, Dario; Jensen, Rune Møller; Bebbington, Tom

    2012-01-01

    Due to the economical importance of stowage planning, there recently has been an increasing interest in developing optimization algorithms for this problem. We have developed 2-phase approach that in most cases can generate near optimal stowage plans within a few hundred seconds for large deep-sea...... vessels. This paper describes the constrained-based local search algorithm used in the second phase of this approach where individual containers are assigned to slots in each bay section. The algorithm can solve this problem in an average of 0.18 seconds per bay, corresponding to a 20 seconds runtime...

  4. Enhanced Approximate Nearest Neighbor via Local Area Focused Search.

    Energy Technology Data Exchange (ETDEWEB)

    Gonzales, Antonio [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Blazier, Nicholas Paul [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-02-01

    Approximate Nearest Neighbor (ANN) algorithms are increasingly important in machine learning, data mining, and image processing applications. There is a large family of space- partitioning ANN algorithms, such as randomized KD-Trees, that work well in practice but are limited by an exponential increase in similarity comparisons required to optimize recall. Additionally, they only support a small set of similarity metrics. We present Local Area Fo- cused Search (LAFS), a method that enhances the way queries are performed using an existing ANN index. Instead of a single query, LAFS performs a number of smaller (fewer similarity comparisons) queries and focuses on a local neighborhood which is refined as candidates are identified. We show that our technique improves performance on several well known datasets and is easily extended to general similarity metrics using kernel projection techniques.

  5. System network planning expansion using mathematical programming, genetic algorithms and tabu search

    Energy Technology Data Exchange (ETDEWEB)

    Sadegheih, A. [Department of Industrial Engineering, University of Yazd, P.O. Box 89195-741, Yazd (Iran); Drake, P.R. [E-Business and Operations Management Division, University of Liverpool Management School, University of Liverpool, Liverpool (United Kingdom)

    2008-06-15

    In this paper, system network planning expansion is formulated for mixed integer programming, a genetic algorithm (GA) and tabu search (TS). Compared with other optimization methods, GAs are suitable for traversing large search spaces, since they can do this relatively rapidly and because the use of mutation diverts the method away from local minima, which will tend to become more common as the search space increases in size. GA's give an excellent trade off between solution quality and computing time and flexibility for taking into account specific constraints in real situations. TS has emerged as a new, highly efficient, search paradigm for finding quality solutions to combinatorial problems. It is characterized by gathering knowledge during the search and subsequently profiting from this knowledge. The attractiveness of the technique comes from its ability to escape local optimality. The cost function of this problem consists of the capital investment cost in discrete form, the cost of transmission losses and the power generation costs. The DC load flow equations for the network are embedded in the constraints of the mathematical model to avoid sub-optimal solutions that can arise if the enforcement of such constraints is done in an indirect way. The solution of the model gives the best line additions and also provides information regarding the optimal generation at each generation point. This method of solution is demonstrated on the expansion of a 10 bus bar system to 18 bus bars. Finally, a steady-state genetic algorithm is employed rather than generational replacement, also uniform crossover is used. (author)

  6. System network planning expansion using mathematical programming, genetic algorithms and tabu search

    International Nuclear Information System (INIS)

    Sadegheih, A.; Drake, P.R.

    2008-01-01

    In this paper, system network planning expansion is formulated for mixed integer programming, a genetic algorithm (GA) and tabu search (TS). Compared with other optimization methods, GAs are suitable for traversing large search spaces, since they can do this relatively rapidly and because the use of mutation diverts the method away from local minima, which will tend to become more common as the search space increases in size. GA's give an excellent trade off between solution quality and computing time and flexibility for taking into account specific constraints in real situations. TS has emerged as a new, highly efficient, search paradigm for finding quality solutions to combinatorial problems. It is characterized by gathering knowledge during the search and subsequently profiting from this knowledge. The attractiveness of the technique comes from its ability to escape local optimality. The cost function of this problem consists of the capital investment cost in discrete form, the cost of transmission losses and the power generation costs. The DC load flow equations for the network are embedded in the constraints of the mathematical model to avoid sub-optimal solutions that can arise if the enforcement of such constraints is done in an indirect way. The solution of the model gives the best line additions and also provides information regarding the optimal generation at each generation point. This method of solution is demonstrated on the expansion of a 10 bus bar system to 18 bus bars. Finally, a steady-state genetic algorithm is employed rather than generational replacement, also uniform crossover is used

  7. Ant colony system (ACS with hybrid local search to solve vehicle routing problems

    Directory of Open Access Journals (Sweden)

    Suphan Sodsoon

    2016-02-01

    Full Text Available This research applied an Ant Colony System algorithm with a Hybrid Local Search to solve Vehicle Routing Problems (VRP from a single depot when the customers’ requirements are known. VRP is an NP-hard optimization problem and has usually been successfully solved optimum by heuristics. A fleet of vehicles of a specific capacity are used to serve a number of customers at minimum cost, without violating the constraints of vehicle capacity. There are meta-heuristic approaches to solve these problems, such as Simulated Annealing, Genetic Algorithm, Tabu Search and the Ant Colony System algorithm. In this case a hybrid local search was used (Cross-Exchange, Or-Opt and 2-Opt algorithm with an Ant Colony System algorithm. The Experimental Design was tested on 7 various problems from the data set online in the OR-Library. There are five different problems in which customers are randomly distributed with the depot in an approximately central location. The customers were grouped into clusters. The results are evaluated in terms of optimal routes using optimal distances. The experimental results are compared with those obtained from meta-heuristics and they show that the proposed method outperforms six meta-heuristics in the literature.

  8. Iterated local search and record-to-record travel applied to the fixed charge transportation problem

    DEFF Research Database (Denmark)

    Andersen, Jeanne; Klose, Andreas

    , transportation costs do, however, include a fixed charge. Iterated local search and record-to-record travel are both simple local search based meta-heuristics that, to our knowledge, not yet have been applied to the FCTP. In this paper, we apply both types of search strategies and combine them into a single...

  9. Genetic diversity in some local chicken breeds using microsatellite markers

    Directory of Open Access Journals (Sweden)

    M. Cassandro

    2010-04-01

    Full Text Available Genetic relationships among Veneto native breeds of chickens were studied on the basis of microsatellites polymorphisms. A total of 100 DNA samples from 2 local chicken breeds (45 Robusta Lionata and 43 Robusta Maculata and a commercial broiler line (12 Golden Comet were analyzed using 19 microsatellite markers. The average number of alleles per locus was 4.05 and the expected heterozigosity resulted lower for the local breeds than the broiler line. The Robusta Lionata breed and the broiler line showed a significant deficit and excess of heterozygotes, respectively, deviating from Hardy-Weinberg equilibrium. Nei’s standard genetic distances corrected for bias due to sampling of individuals (Da, based on allele frequencies, were calculated among breeds. The local breeds resulted very similar confirming the same genetic origin. The results suggested that microsatellite markers are a useful tool for studying the genetic diversity among local chicken breeds.

  10. The Cellular Differential Evolution Based on Chaotic Local Search

    Directory of Open Access Journals (Sweden)

    Qingfeng Ding

    2015-01-01

    Full Text Available To avoid immature convergence and tune the selection pressure in the differential evolution (DE algorithm, a new differential evolution algorithm based on cellular automata and chaotic local search (CLS or ccDE is proposed. To balance the exploration and exploitation tradeoff of differential evolution, the interaction among individuals is limited in cellular neighbors instead of controlling parameters in the canonical DE. To improve the optimizing performance of DE, the CLS helps by exploring a large region to avoid immature convergence in the early evolutionary stage and exploiting a small region to refine the final solutions in the later evolutionary stage. What is more, to improve the convergence characteristics and maintain the population diversity, the binomial crossover operator in the canonical DE may be instead by the orthogonal crossover operator without crossover rate. The performance of ccDE is widely evaluated on a set of 14 bound constrained numerical optimization problems compared with the canonical DE and several DE variants. The simulation results show that ccDE has better performances in terms of convergence rate and solution accuracy than other optimizers.

  11. Genetic variability in local Brazilian horse lines using microsatellite markers.

    Science.gov (United States)

    Silva, A C M; Paiva, S R; Albuquerque, M S M; Egito, A A; Santos, S A; Lima, F C; Castro, S T; Mariante, A S; Correa, P S; McManus, C M

    2012-04-10

    Genetic variability at 11 microsatellite markers was analyzed in five naturalized/local Brazilian horse breeds or genetic groups. Blood samples were collected from 328 animals of the breeds Campeira (Santa Catarina State), Lavradeira (Roraima State), Pantaneira (Pantanal Mato-Grossense), Mangalarga Marchador (Minas Gerais State), as well as the genetic group Baixadeiro (Maranhão State), and the exotic breeds English Thoroughbred and Arab. We found significant genetic variability within evaluated microsatellite loci, with observed heterozygosis varying between 0.426 and 0.768 and polymorphism information content values of 0.751 to 0.914. All breeds showed high inbreeding coefficients and were not in Hardy-Weinberg equilibrium. The smallest genetic distance was seen between the Pantaneira and Arab breeds. The principal component analyzes and Bayesian approach demonstrated that the exotic breeds have had a significant influence on the genetic formation of the local breeds, with introgression of English Throroughbred in Pantaneira and Lavradeira, as well as genetic proximity between the Arab, Pantaneira and Mangalarga Marchador populations. This study shows the need to conserve traits acquired by naturalized horse breeds over centuries of natural selection in Brazil due to the genetic uniqueness of each group, suggesting a reduced gene flow between them. These results reinforce the need to include these herds in animal genetic resource conservation programs to maximize the genetic variability and conserve useful allele combinations.

  12. Greedy Local Search and Vertex Cover in Sparse Random Graphs

    DEFF Research Database (Denmark)

    Witt, Carsten

    2009-01-01

    . This work starts with a rigorous explanation for this claim based on the refined analysis of the Karp-Sipser algorithm by Aronson et al. Subsequently, theoretical supplements are given to experimental studies of search heuristics on random graphs. For c search heuristic...... finds an optimal cover in polynomial time with a probability arbitrarily close to 1. This behavior relies on the absence of a giant component. As an additional insight into the randomized search, it is shown that the heuristic fails badly also on graphs consisting of a single tree component of maximum......Recently, various randomized search heuristics have been studied for the solution of the minimum vertex cover problem, in particular for sparse random instances according to the G(n, c/n) model, where c > 0 is a constant. Methods from statistical physics suggest that the problem is easy if c

  13. The search for viable local government system in Nigeria: an ...

    African Journals Online (AJOL)

    The history of the Nigerian local government system has been one long episode of trails and errors aimed at achieving viable local government institution without much success. Local government in the country began its long series of reforms from the colonial period when the colonial government attempted to ...

  14. A local search heuristic for the Multi-Commodity k-splittable Maximum Flow Problem

    DEFF Research Database (Denmark)

    Gamst, Mette

    2014-01-01

    , a local search heuristic for solving the problem is proposed. The heuristic is an iterative shortest path procedure on a reduced graph combined with a local search procedure to modify certain path flows and prioritize the different commodities. The heuristic is tested on benchmark instances from...

  15. Variationally localized search direction method for constrained optimization of non-orthogonal, localized orbitals in electronic structure calculations

    Science.gov (United States)

    Ruiz-Serrano, Álvaro; Skylaris, Chris-Kriton

    2013-10-01

    A new method for the constrained optimization of non-orthogonal, spatially localized orbitals using direct energy minimization techniques, in the context of electronic structure calculations, is presented. The variationally localized search direction (VLSD) method, as it was named, ensures that strict localization constraints are imposed upon the search direction vectors exactly, analytically and in a fully variational fashion. In contrast, the truncated search direction (TSD) method, of standard use in many electronic structure approaches with localization constraints, relies on the approximation that the truncated search direction vectors of the unconstrained problem resemble the exact search direction vectors of the constrained problem. With the TSD method, in order to maintain the localization constraints, a part of the pre-calculated information that is stored in the search direction vectors has to be deleted via an ad hoc, non-variational truncation step. The results on an extensive set of test molecules show that, in general, calculations with the VLSD method require less iterations to converge than with the TSD method for any size of the localization region. It was found that in calculations on certain systems where the TSD method is forced to delete a very large amount of information, the VLSD method is capable of achieving convergence in up to three times less iterations. Validation tests show that structural and electronic properties calculated with either method are accurate and in agreement with other electronic structure approaches.

  16. State-of-the-Art Review on Relevance of Genetic Algorithm to Internet Web Search

    Directory of Open Access Journals (Sweden)

    Kehinde Agbele

    2012-01-01

    Full Text Available People use search engines to find information they desire with the aim that their information needs will be met. Information retrieval (IR is a field that is concerned primarily with the searching and retrieving of information in the documents and also searching the search engine, online databases, and Internet. Genetic algorithms (GAs are robust, efficient, and optimizated methods in a wide area of search problems motivated by Darwin’s principles of natural selection and survival of the fittest. This paper describes information retrieval systems (IRS components. This paper looks at how GAs can be applied in the field of IR and specifically the relevance of genetic algorithms to internet web search. Finally, from the proposals surveyed it turns out that GA is applied to diverse problem fields of internet web search.

  17. Egyptian Journal of Medical Human Genetics: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  18. Solving a chemical batch scheduling problem by local search

    NARCIS (Netherlands)

    Brucker, P.; Hurink, Johann L.

    1999-01-01

    A chemical batch scheduling problem is modelled in two different ways as a discrete optimization problem. Both models are used to solve the batch scheduling problem in a two-phase tabu search procedure. The method is tested on real-world data.

  19. Genetic Diversity of Local and Introduced Sweet Potato [Ipomoea ...

    African Journals Online (AJOL)

    This study was therefore conducted to estimate the genetic diversity of 114 Sweet potato [Ipomoea batatas (L.) Lam] accessions obtained from Nigeria, Asia, Latin America and Local collections along with two improved varieties. Accessions were planted in 2012/13 cropping season at Haramaya University, eastern Ethiopia ...

  20. Genetic structure among the local chicken ecotypes of Tanzania ...

    African Journals Online (AJOL)

    A study was conducted to evaluate the genetic structure of local chicken ecotypes of Tanzania using 20 polymorphic microsatellite DNA markers. A standard PCR was followed by manual genotyping (6% native polyacrylamide gel visualized by silver staining). Phylogenetic analysis of 13 individuals from each of the nine ...

  1. The search for local government autonomy in Nigeria: legal and ...

    African Journals Online (AJOL)

    This article examines the status of the local government under the tripartite governmental system in Nigeria that has been in operation since 1979. It reviews the various reforms that the administration of local government has gone through from the colonial era till 1999 when the extant Constitution of Nigeria came into force.

  2. Modification site localization scoring integrated into a search engine.

    Science.gov (United States)

    Baker, Peter R; Trinidad, Jonathan C; Chalkley, Robert J

    2011-07-01

    Large proteomic data sets identifying hundreds or thousands of modified peptides are becoming increasingly common in the literature. Several methods for assessing the reliability of peptide identifications both at the individual peptide or data set level have become established. However, tools for measuring the confidence of modification site assignments are sparse and are not often employed. A few tools for estimating phosphorylation site assignment reliabilities have been developed, but these are not integral to a search engine, so require a particular search engine output for a second step of processing. They may also require use of a particular fragmentation method and are mostly only applicable for phosphorylation analysis, rather than post-translational modifications analysis in general. In this study, we present the performance of site assignment scoring that is directly integrated into the search engine Protein Prospector, which allows site assignment reliability to be automatically reported for all modifications present in an identified peptide. It clearly indicates when a site assignment is ambiguous (and if so, between which residues), and reports an assignment score that can be translated into a reliability measure for individual site assignments.

  3. Novel search space updating heuristics-based genetic algorithm for optimizing medium-scale airline crew pairing problems

    Directory of Open Access Journals (Sweden)

    Nihan Cetin Demirel

    2017-01-01

    Full Text Available This study examines the crew pairing problem, which is one of the most comprehensive problems encountered in airline planning, to generate a set of crew pairings that has minimal cost, covers all flight legs and fulfils legal criteria. In addition, this study examines current research related to crew pairing optimization. The contribution of this study is developing heuristics based on an improved dynamic-based genetic algorithm, a deadhead-minimizing pairing search and a partial solution approach (less-costly alternative pairing search. This study proposes genetic algorithm variants and a memetic algorithm approach. In addition, computational results based on real-world data from a local airline company in Turkey are presented. The results demonstrate that the proposed approach can successfully handle medium sets of crew pairings and generate higher-quality solutions than previous methods.

  4. PLAST: parallel local alignment search tool for database comparison

    Directory of Open Access Journals (Sweden)

    Lavenier Dominique

    2009-10-01

    Full Text Available Abstract Background Sequence similarity searching is an important and challenging task in molecular biology and next-generation sequencing should further strengthen the need for faster algorithms to process such vast amounts of data. At the same time, the internal architecture of current microprocessors is tending towards more parallelism, leading to the use of chips with two, four and more cores integrated on the same die. The main purpose of this work was to design an effective algorithm to fit with the parallel capabilities of modern microprocessors. Results A parallel algorithm for comparing large genomic banks and targeting middle-range computers has been developed and implemented in PLAST software. The algorithm exploits two key parallel features of existing and future microprocessors: the SIMD programming model (SSE instruction set and the multithreading concept (multicore. Compared to multithreaded BLAST software, tests performed on an 8-processor server have shown speedup ranging from 3 to 6 with a similar level of accuracy. Conclusion A parallel algorithmic approach driven by the knowledge of the internal microprocessor architecture allows significant speedup to be obtained while preserving standard sensitivity for similarity search problems.

  5. PLAST: parallel local alignment search tool for database comparison.

    Science.gov (United States)

    Nguyen, Van Hoa; Lavenier, Dominique

    2009-10-12

    Sequence similarity searching is an important and challenging task in molecular biology and next-generation sequencing should further strengthen the need for faster algorithms to process such vast amounts of data. At the same time, the internal architecture of current microprocessors is tending towards more parallelism, leading to the use of chips with two, four and more cores integrated on the same die. The main purpose of this work was to design an effective algorithm to fit with the parallel capabilities of modern microprocessors. A parallel algorithm for comparing large genomic banks and targeting middle-range computers has been developed and implemented in PLAST software. The algorithm exploits two key parallel features of existing and future microprocessors: the SIMD programming model (SSE instruction set) and the multithreading concept (multicore). Compared to multithreaded BLAST software, tests performed on an 8-processor server have shown speedup ranging from 3 to 6 with a similar level of accuracy. A parallel algorithmic approach driven by the knowledge of the internal microprocessor architecture allows significant speedup to be obtained while preserving standard sensitivity for similarity search problems.

  6. Tunnel Vision: Local Behavioral Influences on Consumer Decisions in Product Search

    NARCIS (Netherlands)

    G. Häubl (Gerald); B.G.C. Dellaert (Benedict); A.C.D. Donkers (Bas)

    2010-01-01

    textabstractWe introduce and test a behavioral model of consumer product search that extends a baseline normative model of sequential search by incorporating nonnormative influences that are local in the sense that they reflect consumers' undue sensitivity to recently encountered alternatives. We

  7. Initialization and Restart in Stochastic Local Search: Computing a Most Probable Explanation in Bayesian Networks

    Science.gov (United States)

    Mengshoel, Ole J.; Wilkins, David C.; Roth, Dan

    2010-01-01

    For hard computational problems, stochastic local search has proven to be a competitive approach to finding optimal or approximately optimal problem solutions. Two key research questions for stochastic local search algorithms are: Which algorithms are effective for initialization? When should the search process be restarted? In the present work we investigate these research questions in the context of approximate computation of most probable explanations (MPEs) in Bayesian networks (BNs). We introduce a novel approach, based on the Viterbi algorithm, to explanation initialization in BNs. While the Viterbi algorithm works on sequences and trees, our approach works on BNs with arbitrary topologies. We also give a novel formalization of stochastic local search, with focus on initialization and restart, using probability theory and mixture models. Experimentally, we apply our methods to the problem of MPE computation, using a stochastic local search algorithm known as Stochastic Greedy Search. By carefully optimizing both initialization and restart, we reduce the MPE search time for application BNs by several orders of magnitude compared to using uniform at random initialization without restart. On several BNs from applications, the performance of Stochastic Greedy Search is competitive with clique tree clustering, a state-of-the-art exact algorithm used for MPE computation in BNs.

  8. Local search heuristics for the probabilistic dial-a-ride problem

    DEFF Research Database (Denmark)

    Ho, Sin C.; Haugland, Dag

    2011-01-01

    evaluation procedure in a pure local search heuristic and in a tabu search heuristic. The quality of the solutions obtained by the two heuristics have been compared experimentally. Computational results confirm that our neighborhood evaluation technique is much faster than the straightforward one...

  9. Visual Search in ASD: Instructed versus Spontaneous Local and Global Processing

    Science.gov (United States)

    Van der Hallen, Ruth; Evers, Kris; Boets, Bart; Steyaert, Jean; Noens, Ilse; Wagemans, Johan

    2016-01-01

    Visual search has been used extensively to investigate differences in mid-level visual processing between individuals with ASD and TD individuals. The current study employed two visual search paradigms with Gaborized stimuli to assess the impact of task distractors (Experiment 1) and task instruction (Experiment 2) on local-global visual…

  10. Precise localizations and counterpart searches of GRBs from the 2nd interplanetary network

    International Nuclear Information System (INIS)

    Hack, F.; Hurley, K.; Atteia, J.; Barat, C.; Niel, M.; Cline, T.; Dennis, B.; Kouveliotou, C.; Klebesadel, R.; Laros, J.; Kurt, V.; Kuznetsov, A.; Zenchenko, V.

    1994-01-01

    The second interplanetary network of GRB detectors operated between 1981 and 1984. It consisted of the Venera 13 and V14 spacecraft (SIGNE detectors), PVO, ICE, and SMM (HXRBS detector). Many of the approximately 90 cosmic GRBs it detected can be localized to a high accuracy. Such localizations will make a better estimate of the burster recurrence time possible and contribute to the search for quiescent counterparts. We will present a number of localizations to illustrate the potential of this network, discuss the techniques we use to perform multi-wavelength counterpart searches, and compare present and promising future localization techniques

  11. The Search for Symmetries in the Genetic Code:

    Science.gov (United States)

    Antoneli, Fernando; Forger, Michael; Hornos, José Eduardo M.

    We give a full classification of the possible schemes for obtaining the distribution of multiplets observed in the standard genetic code by symmetry breaking in the context of finite groups, based on an extended notion of partial symmetry breaking that incorporates the intuitive idea of "freezing" first proposed by Francis Crick, which is given a precise mathematical meaning.

  12. Improved quantum-behaved particle swarm optimization with local search strategy

    Directory of Open Access Journals (Sweden)

    Maolong Xi

    2017-03-01

    Full Text Available Quantum-behaved particle swarm optimization, which was motivated by analysis of particle swarm optimization and quantum system, has shown compared performance in finding the optimal solutions for many optimization problems to other evolutionary algorithms. To address the problem of premature, a local search strategy is proposed to improve the performance of quantum-behaved particle swarm optimization. In proposed local search strategy, a super particle is presented which is a collection body of randomly selected particles’ dimension information in the swarm. The selected probability of particles in swarm is different and determined by their fitness values. To minimization problems, the fitness value of one particle is smaller; the selected probability is more and will contribute more information in constructing the super particle. In addition, in order to investigate the influence on algorithm performance with different local search space, four methods of computing the local search radius are applied in local search strategy and propose four variants of local search quantum-behaved particle swarm optimization. Empirical studies on a suite of well-known benchmark functions are undertaken in order to make an overall performance comparison among the proposed methods and other quantum-behaved particle swarm optimization. The simulation results show that the proposed quantum-behaved particle swarm optimization variants have better advantages over the original quantum-behaved particle swarm optimization.

  13. In Search of Local Knowledge on ICTs in Africa

    Directory of Open Access Journals (Sweden)

    Iginio Gagliardone

    2015-06-01

    Full Text Available This article explores whether, and to what extent, local knowledge features in research on the role of ICTs in statebuilding and peacebuilding in Africa, with a particular focus on neighboring Somalia, Kenya, and Ethiopia. We question whether the claims of the transformative power of ICTs are backed by ‘evidence’ and whether local knowledge – e.g., traditional mechanisms for conflict resolution – is taken into consideration by ICT-based development initiatives. To assess this, we systematically reviewed literature in the region, focusing on academic outputs as well as research published by non-governmental and governmental organizations. Several key findings emerged, including: 1 empirical evidence on the successful use of ICTs to promote peacebuilding and statebuilding is thin; 2 few differences exist between scholarship emanating from the Global North and from Africa; and 3 overall, the literature exhibits a simplistic assumption that ICTs will drive democratic development without sufficient consideration of how ICTs are actually used by the public.

  14. Genetics of osteoporosis: searching for candidate genes for bone fragility.

    Science.gov (United States)

    Rocha-Braz, Manuela G M; Ferraz-de-Souza, Bruno

    2016-08-01

    The pathogenesis of osteoporosis, a common disease with great morbidity and mortality, comprises environmental and genetic factors. As with other complex disorders, the genetic basis of osteoporosis has been difficult to identify. Nevertheless, several approaches have been undertaken in the past decades in order to identify candidate genes for bone fragility, including the study of rare monogenic syndromes with striking bone phenotypes (e.g. osteogenesis imperfecta and osteopetroses), the analysis of individuals or families with extreme osteoporotic phenotypes (e.g. idiopathic juvenile and pregnancy-related osteoporosis), and, chiefly, genome-wide association studies (GWAS) in large populations. Altogether, these efforts have greatly increased the understanding of molecular mechanisms behind bone remodelling, which has rapidly translated into the development of novel therapeutic strategies, exemplified by the tales of cathepsin K (CTSK) and sclerostin (SOST). Additional biological evidence of involvement in bone physiology still lacks for several candidate genes arisen from GWAS, opening an opportunity for the discovery of new mechanisms regulating bone strength, particularly with the advent of high-throughput genomic technologies. In this review, candidate genes for bone fragility will be presented in comprehensive tables and discussed with regard to how their association with osteoporosis emerged, highlighting key players such as LRP5, WNT1 and PLS3. Current limitations in our understanding of the genetic contribution to osteoporosis, such as yet unidentified genetic modifiers, may be overcome in the near future with better genotypic and phenotypic characterisation of large populations and the detailed study of candidate genes in informative individuals with marked phenotype.

  15. Search for Genetic Variants Underlying Musical Aptitude and Related Traits

    OpenAIRE

    Ukkola-Vuoti, Liisa

    2013-01-01

    Music perception and practice represents complex cognitive functions of the brain. There is an abundance of data about the neurophysiological effects of music on the human brain, but heritability and especially molecular studies have been lacking. The development of genome technologies and bioinformatics has enabled the identification of genetic variants underlying complex human traits. These methods can be applied to normal human traits like music perception and performance. Prior to th...

  16. Local weather is associated with rates of online searches for musculoskeletal pain symptoms.

    Directory of Open Access Journals (Sweden)

    Scott Telfer

    Full Text Available Weather conditions are commonly believed to influence musculoskeletal pain, however the evidence for this is mixed. This study aimed to examine the relationship between local meteorological conditions and online search trends for terms related to knee pain, hip pain, and arthritis. Five years of relative online search volumes for these terms were obtained for the 50 most populous cities in the contiguous United States, along with corresponding local weather data for temperature, relative humidity, barometric pressure, and precipitation. Methods from the climate econometrics literature were used to assess the casual impact of these meteorological variables on the relative volumes of searches for pain. For temperatures between -5°C and 30°C, search volumes for hip pain increased by 12 index points, and knee pain increased by 18 index points. Precipitation had a negative effect on search volumes for these terms. At temperatures >30°C, search volumes for arthritis related pain decreased by 7 index points. These patterns were not seen for pain searches unrelated to the musculoskeletal system. In summary, selected local weather conditions are significantly associated with online search volumes for specific musculoskeletal pain symptoms. We believe the predominate driver for this to be the relative changes in physical activity levels associated with meteorological conditions.

  17. Genetic variability of Indonesian local chili pepper: The facts

    Science.gov (United States)

    Arumingtyas, Estri Laras; Kusnadi, Joni; Sari, Dewi Ratih Tirto; Ratih, Nursita

    2017-11-01

    Chili pepper (Capsicum frutescens) is one species of Solanaceae family that is very popular in Indonesia and some other tropical countries because of its pungency. Chili pepper is an important spice in Indonesia and is also eaten fresh as a pickle to increase appetite. In Indonesia, there are various local names for chili pepper includingcabai, cengek, lombok, pedesan etc. These varied local names represent the various morphological shapes of the chili pepper fruit. We have investigated the variability of some chili cultivars based on morphological characteristics, molecular markers, pungency, and capsaicin content. Some biological facts, such as the tendency of chili pepper to outbreed, have also been found. In this paper, the source of variability and the possible mechanism of increasing genetic variability of Indonesian local chili pepper are also discussed.

  18. Entangled local biologies: genetic risk, bodies and inequities in Brazilian cancer genetics.

    Science.gov (United States)

    Gibbon, Sahra

    2017-08-01

    Engaging recent social science work examining the truth making claims of science and biomedicine, this paper explores how biology is being localised in Brazilian cancer genetics. It draws from ethnographic fieldwork in urban regions of southern Brazil working with and alongside patients, families and practitioners in cancer genetic clinics. It examines how different sorts of 'local biologies' are articulated in the context of research, clinical practice and among implicated patient communities and the way these can 'recursively' move across different spheres and scales of social action to extend and transform the meaning of the biological. It shows how the mattering of the biological in Brazilian cancer genetics is fundamentally informed by questions of inequity and care, even while multiple local biologies may obscure rather than reveal the biopolitics of cancer. In an era of epigenetics this raises new opportunities and challenges for anthropological analysis as intervention.

  19. A hybrid approach to protein folding problem integrating constraint programming with local search.

    Science.gov (United States)

    Ullah, Abu Dayem; Steinhöfel, Kathleen

    2010-01-18

    The protein folding problem remains one of the most challenging open problems in computational biology. Simplified models in terms of lattice structure and energy function have been proposed to ease the computational hardness of this optimization problem. Heuristic search algorithms and constraint programming are two common techniques to approach this problem. The present study introduces a novel hybrid approach to simulate the protein folding problem using constraint programming technique integrated within local search. Using the face-centered-cubic lattice model and 20 amino acid pairwise interactions energy function for the protein folding problem, a constraint programming technique has been applied to generate the neighbourhood conformations that are to be used in generic local search procedure. Experiments have been conducted for a few small and medium sized proteins. Results have been compared with both pure constraint programming approach and local search using well-established local move set. Substantial improvements have been observed in terms of final energy values within acceptable runtime using the hybrid approach. Constraint programming approaches usually provide optimal results but become slow as the problem size grows. Local search approaches are usually faster but do not guarantee optimal solutions and tend to stuck in local minima. The encouraging results obtained on the small proteins show that these two approaches can be combined efficiently to obtain better quality solutions within acceptable time. It also encourages future researchers on adopting hybrid techniques to solve other hard optimization problems.

  20. Improved Model Calibration From Genetically Adaptive Multi-Method Search

    Science.gov (United States)

    Vrugt, J. A.; Robinson, B. A.

    2006-12-01

    Evolutionary optimization is a subject of intense interest in many fields of study, including computational chemistry, biology, bio-informatics, economics, computational science, geophysics and environmental science. The goal is to determine values for model parameters or state variables that provide the best possible solution to a predefined cost or objective function, or a set of optimal trade-off values in the case of two or more conflicting objectives. However, locating optimal solutions often turns out to be painstakingly tedious, or even completely beyond current or projected computational capacity. Here we present an innovative concept of genetically adaptive multi-algorithm optimization. Benchmark results show that this new optimization technique is significantly more efficient than current state-of-the-art evolutionary algorithms, approaching a factor of ten improvement for the more complex, higher dimensional optimization problems. Our new algorithm provides new opportunities for solving previously intractable environmental model calibration problems.

  1. The use of quantum molecular calculations to guide a genetic algorithm: a way to search for new chemistry.

    Science.gov (United States)

    Durrant, Marcus C

    2007-01-01

    The process of gene-based molecular evolution has been simulated in silico by using massively parallel density functional theory quantum calculations, coupled with a genetic algorithm, to test for fitness with respect to a target chemical reaction in populations of genetically encoded molecules. The goal of this study was the identification of transition-metal complexes capable of mediating a known reaction, namely the cleavage of N(2) to give the metal nitride. Each complex within the search space was uniquely specified by a nanogene consisting of an eight-digit number. Propagation of an individual nanogene into successive generations was determined by the fitness of its phenotypic molecule to perform the target reaction and new generations were created by recombination and mutation of surviving nanogenes. In its simplest implementation, the quantum-directed genetic algorithm (QDGA) quickly located a local minimum on the evolutionary fitness hypersurface, but proved incapable of progressing towards the global minimum. A strategy for progressing beyond local minima consistent with the Darwinian paradigm by the use of environmental variations coupled with mass extinctions was therefore developed. This allowed for the identification of nitriding complexes that are very closely related to known examples from the chemical literature. Examples of mutations that appear to be beneficial at the genetic level but prove to be harmful at the phenotypic level are described. As well as revealing fundamental aspects of molecular evolution, QDGA appears to be a powerful tool for the identification of lead compounds capable of carrying out a target chemical reaction.

  2. Reduced Search Space Algorithm for Simultaneous Localization and Mapping in Mobile Robots

    Directory of Open Access Journals (Sweden)

    Hesam Omranpour

    2012-03-01

    Full Text Available In this paper, we propose a new algorithm for simultaneous localization and mapping in mobile robots which uses evolutionary algorithm and particle swarm optimization. The proposed method is based on both local and global heuristic search methods. In each step of robot movements, the local search is applied in the small search space of odometry errors to improve the map accuracy. A global search method is applied for loop closing. The proposed algorithm detects loops and closes them, detects and solves correspondence and avoids local extremums. With a proper representation of problem parameters in chromosome, the dimensionality of search space is reduced. The proposed algorithm utilizes occupancy grid and does not require land marks which are not available in most natural environments. A new fitness function is proposed that is computationally efficient and eliminates the need for complex statistical calculations as used in current approaches. Results of experiments on real datasets exhibit the superior performance of the proposed method compared to the current methods.

  3. Genetic Networks of Complex Disorders: from a Novel Search Engine for PubMed Article Database.

    Science.gov (United States)

    Jung, Jae-Yoon; Wall, Dennis Paul

    2013-01-01

    Finding genetic risk factors of complex disorders may involve reviewing hundreds of genes or thousands of research articles iteratively, but few tools have been available to facilitate this procedure. In this work, we built a novel publication search engine that can identify target-disorder specific, genetics-oriented research articles and extract the genes with significant results. Preliminary test results showed that the output of this engine has better coverage in terms of genes or publications, than other existing applications. We consider it as an essential tool for understanding genetic networks of complex disorders.

  4. Search for genetic virulence markers in viral haemorrhagic septicaemia virus (VHSV) using a reverse genetics approach

    DEFF Research Database (Denmark)

    Stegmann, Anders; Biacchesi, S.; Bremont, M.

    2011-01-01

    for virulence to rainbow trout makes it difficult to differentiate between dangerous and harmless VHSV variants. With the aim of identification of genetic virulence markers, we have implemented reverse genetics technology for generation of hybrid virus variants. By substituting different regions in the genome...

  5. On the Use of Local Search in the Evolution of Neural Networks for the Diagnosis of Breast Cancer

    Directory of Open Access Journals (Sweden)

    Agam Gupta

    2015-07-01

    Full Text Available With the advancement in the field of Artificial Intelligence, there have been considerable efforts to develop technologies for pattern recognition related to medical diagnosis. Artificial Neural Networks (ANNs, a significant piece of Artificial Intelligence forms the base for most of the marvels in the former field. However, ANNs face the problem of premature convergence at a local minimum and inability to set hyper-parameters (like the number of neurons, learning rate, etc. while using Back Propagation Algorithm (BPA. In this paper, we have used the Genetic Algorithm (GA for the evolution of the ANN, which overcomes the limitations of the BPA. Since GA alone cannot fit for a high-dimensional, complex and multi-modal optimization landscape of the ANN, BPA is used as a local search algorithm to aid the evolution. The contributions of GA and BPA in the resultant approach are adjudged to determine the magnitude of local search necessary for optimization, striking a clear balance between exploration and exploitation in the evolution. The algorithm was applied to deal with the problem of Breast Cancer diagnosis. Results showed that under optimal settings, hybrid algorithm performs better than BPA or GA alone.

  6. Searching for recursive causal structures in multivariate quantitative genetics mixed models.

    Science.gov (United States)

    Valente, Bruno D; Rosa, Guilherme J M; de Los Campos, Gustavo; Gianola, Daniel; Silva, Martinho A

    2010-06-01

    Biology is characterized by complex interactions between phenotypes, such as recursive and simultaneous relationships between substrates and enzymes in biochemical systems. Structural equation models (SEMs) can be used to study such relationships in multivariate analyses, e.g., with multiple traits in a quantitative genetics context. Nonetheless, the number of different recursive causal structures that can be used for fitting a SEM to multivariate data can be huge, even when only a few traits are considered. In recent applications of SEMs in mixed-model quantitative genetics settings, causal structures were preselected on the basis of prior biological knowledge alone. Therefore, the wide range of possible causal structures has not been properly explored. Alternatively, causal structure spaces can be explored using algorithms that, using data-driven evidence, can search for structures that are compatible with the joint distribution of the variables under study. However, the search cannot be performed directly on the joint distribution of the phenotypes as it is possibly confounded by genetic covariance among traits. In this article we propose to search for recursive causal structures among phenotypes using the inductive causation (IC) algorithm after adjusting the data for genetic effects. A standard multiple-trait model is fitted using Bayesian methods to obtain a posterior covariance matrix of phenotypes conditional to unobservable additive genetic effects, which is then used as input for the IC algorithm. As an illustrative example, the proposed methodology was applied to simulated data related to multiple traits measured on a set of inbred lines.

  7. An Effective Cuckoo Search Algorithm for Node Localization in Wireless Sensor Network.

    Science.gov (United States)

    Cheng, Jing; Xia, Linyuan

    2016-08-31

    Localization is an essential requirement in the increasing prevalence of wireless sensor network (WSN) applications. Reducing the computational complexity, communication overhead in WSN localization is of paramount importance in order to prolong the lifetime of the energy-limited sensor nodes and improve localization performance. This paper proposes an effective Cuckoo Search (CS) algorithm for node localization. Based on the modification of step size, this approach enables the population to approach global optimal solution rapidly, and the fitness of each solution is employed to build mutation probability for avoiding local convergence. Further, the approach restricts the population in the certain range so that it can prevent the energy consumption caused by insignificant search. Extensive experiments were conducted to study the effects of parameters like anchor density, node density and communication range on the proposed algorithm with respect to average localization error and localization success ratio. In addition, a comparative study was conducted to realize the same localization task using the same network deployment. Experimental results prove that the proposed CS algorithm can not only increase convergence rate but also reduce average localization error compared with standard CS algorithm and Particle Swarm Optimization (PSO) algorithm.

  8. Memetic Algorithms with Local Search Chains in R: The Rmalschains Package

    Directory of Open Access Journals (Sweden)

    Christoph Bergmeir

    2016-12-01

    Full Text Available Global optimization is an important field of research both in mathematics and computer sciences. It has applications in nearly all fields of modern science and engineering. Memetic algorithms are powerful problem solvers in the domain of continuous optimization, as they offer a trade-off between exploration of the search space using an evolutionary algorithm scheme, and focused exploitation of promising regions with a local search algorithm. In particular, we describe the memetic algorithms with local search chains (MA-LS-Chains paradigm, and the R package Rmalschains, which implements them. MA-LS-Chains has proven to be effective compared to other algorithms, especially in high-dimensional problem solving. In an experimental study, we demonstrate the advantages of using Rmalschains for high-dimension optimization problems in comparison to other optimization methods already available in R.

  9. A Particle Swarm Optimization-Based Approach with Local Search for Predicting Protein Folding.

    Science.gov (United States)

    Yang, Cheng-Hong; Lin, Yu-Shiun; Chuang, Li-Yeh; Chang, Hsueh-Wei

    2017-10-01

    The hydrophobic-polar (HP) model is commonly used for predicting protein folding structures and hydrophobic interactions. This study developed a particle swarm optimization (PSO)-based algorithm combined with local search algorithms; specifically, the high exploration PSO (HEPSO) algorithm (which can execute global search processes) was combined with three local search algorithms (hill-climbing algorithm, greedy algorithm, and Tabu table), yielding the proposed HE-L-PSO algorithm. By using 20 known protein structures, we evaluated the performance of the HE-L-PSO algorithm in predicting protein folding in the HP model. The proposed HE-L-PSO algorithm exhibited favorable performance in predicting both short and long amino acid sequences with high reproducibility and stability, compared with seven reported algorithms. The HE-L-PSO algorithm yielded optimal solutions for all predicted protein folding structures. All HE-L-PSO-predicted protein folding structures possessed a hydrophobic core that is similar to normal protein folding.

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

    DEFF Research Database (Denmark)

    Neumann, Frank; Witt, Carsten

    2015-01-01

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

  11. A reduced-cost iterated local search heuristic for the fixed-charge transportation problem

    NARCIS (Netherlands)

    Buson, Erika; Roberti, Roberto; Toth, Paolo

    2014-01-01

    The fixed-charge transportation problem (FCTP) is a generalization of the transportation problem where an additional fixed cost is paid for sending a flow from an origin to a destination. We propose an iterated local search heuristic based on the utilization of reduced costs for guiding the restart

  12. Genetic diversity of Echinococcus multilocularis on a local scale.

    Science.gov (United States)

    Knapp, J; Guislain, M-H; Bart, J M; Raoul, F; Gottstein, B; Giraudoux, P; Piarroux, R

    2008-05-01

    Echinococcusmultilocularis is the causative agent of human Alveolar Echinococcosis (AE), and it is one of the most lethal zoonotic infections in the Northern Hemisphere. In France, the eastern and central regions are endemic areas; Franche-Comté, Lorraine and Auvergne are particularly contaminated. Recently, several human cases were recorded in the French Ardennes area, a region adjacent to the western border of the E. multilocularis range in France. A previous study in this focus described a prevalence of over 50% of the parasite in red foxes. The present study investigated the genetic diversity of adult worms collected from foxes in a 900km(2) area in the Ardennes. Instead of a conventional mitochondrial target (ATP6), two microsatellite targets (EmsB and NAK1) were used. A total of 140 adult worms isolated from 25 red foxes were genotyped. After hierarchical clustering analyses, the EmsB target enabled us to distinguish two main assemblages, each divided into sub-groups, yielding the differentiation of six clusters or assemblage profiles. Thirteen foxes (52% of the foxes) each harbored worms from at least two different assemblage profiles, suggesting they had become infected by several sources. Using the NAK1 target, we identified 3 alleles, two found in association with the two EmsB assemblages. With the NAK1 target, we investigated the parasite breeding system and the possible causes of genetic diversification. Only one fox harbored hybrid worms, indicative of a possible (and rare) occurrence of recombination, although multiple infections have been observed in foxes. These results confirm the usefulness of microsatellite targets for assessing genetic polymorphism in a geographically restricted local range.

  13. Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST

    Directory of Open Access Journals (Sweden)

    Oliver Melvin J

    2005-04-01

    Full Text Available Abstract Background BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST, which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. Results W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN. W.ND-BLAST provides intuitive Graphic User Interfaces (GUI for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. Conclusion W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is

  14. Bilayer Local Search Enhanced Particle Swarm Optimization for the Capacitated Vehicle Routing Problem

    Directory of Open Access Journals (Sweden)

    A. K. M. Foysal Ahmed

    2018-03-01

    Full Text Available The classical capacitated vehicle routing problem (CVRP is a very popular combinatorial optimization problem in the field of logistics and supply chain management. Although CVRP has drawn interests of many researchers, no standard way has been established yet to obtain best known solutions for all the different problem sets. We propose an efficient algorithm Bilayer Local Search-based Particle Swarm Optimization (BLS-PSO along with a novel decoding method to solve CVRP. Decoding method is important to relate the encoded particle position to a feasible CVRP solution. In bilayer local search, one layer of local search is for the whole population in any iteration whereas another one is applied only on the pool of the best particles generated in different generations. Such searching strategies help the BLS-PSO to perform better than the existing proposals by obtaining best known solutions for most of the existing benchmark problems within very reasonable computational time. Computational results also show that the performance achieved by the proposed algorithm outperforms other PSO-based approaches.

  15. A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences.

    Science.gov (United States)

    Othman, Razib M; Deris, Safaai; Illias, Rosli M

    2008-02-01

    A genetic similarity algorithm is introduced in this study to find a group of semantically similar Gene Ontology terms. The genetic similarity algorithm combines semantic similarity measure algorithm with parallel genetic algorithm. The semantic similarity measure algorithm is used to compute the similitude strength between the Gene Ontology terms. Then, the parallel genetic algorithm is employed to perform batch retrieval and to accelerate the search in large search space of the Gene Ontology graph. The genetic similarity algorithm is implemented in the Gene Ontology browser named basic UTMGO to overcome the weaknesses of the existing Gene Ontology browsers which use a conventional approach based on keyword matching. To show the applicability of the basic UTMGO, we extend its structure to develop a Gene Ontology -based protein sequence annotation tool named extended UTMGO. The objective of developing the extended UTMGO is to provide a simple and practical tool that is capable of producing better results and requires a reasonable amount of running time with low computing cost specifically for offline usage. The computational results and comparison with other related tools are presented to show the effectiveness of the proposed algorithm and tools.

  16. Linkage-Based Distance Metric in the Search Space of Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Yong-Hyuk Kim

    2015-01-01

    Full Text Available We propose a new distance metric, based on the linkage of genes, in the search space of genetic algorithms. This second-order distance measure is derived from the gene interaction graph and first-order distance, which is a natural distance in chromosomal spaces. We show that the proposed measure forms a metric space and can be computed efficiently. As an example application, we demonstrate how this measure can be used to estimate the extent to which gene rearrangement improves the performance of genetic algorithms.

  17. searchSCF: Using MongoDB to Enable Richer Searches of Locally Hosted Science Data Repositories

    Science.gov (United States)

    Knosp, B.

    2016-12-01

    Science teams today are in the unusual position of almost having too much data available to them. Modern sensors and models are capable of outputting terabytes of data per day, which can make it difficult to find specific subsets of data. The sheer size of files can also make it time consuming to retrieve this big data from national data archive centers. Thus, many science teams choose to store what data they can on their local systems, but they are not always equipped with tools to help them intelligently organize and search their data. In its local data repository, the Aura Microwave Limb Sounder (MLS) science team at NASA's Jet Propulsion Laboratory has collected over 300TB of atmospheric science data from 71 missions/models that aid in validation, algorithm development, and research activities. When the project began, the team developed a MySQL database to aid in data queries, but this database was only designed to keep track of MLS and a few ancillary data sets, leving much of the data uncatalogued. The team has also seen database query time rise over the life of the mission. Even though the MLS science team's data holdings are not the size of a national data center's, team members still need tools to help them discover and utilize the data that they have on-hand. Over the past year, members of the science team have been looking for solutions to (1) store information on all the data sets they have collected in a single database, (2) store more metadata about each data file, (3) develop queries that can find relationships among these disparate data types, and (4) plug any new functions developed around this database into existing analysis, visualization, and web tools, transparently to users. In this presentation, I will discuss the searchSCF package that is currently under development. This package includes a NoSQL database management system (MongoDB) and a set of Python tools that both ingests data into the database and supports user queries. I will also

  18. Genetic Algorithm-based Dynamic Vehicle Route Search using Car-to-Car Communication

    Directory of Open Access Journals (Sweden)

    KIM, J.

    2010-11-01

    Full Text Available Suggesting more efficient driving routes generate benefits not only for individuals by saving commute time, but also for society as a whole by reducing accident rates and social costs by lessening traffic congestion. In this paper, we suggest a new route search algorithm based on a genetic algorithm which is more easily installable into mutually communicating car navigation systems, and validate its usefulness through experiments reflecting real-world situations. The proposed algorithm is capable of searching alternative routes dynamically in unexpected events of system malfunctioning or traffic slow-downs due to accidents. Experimental results demonstrate that our algorithm searches the best route more efficiently and evolves with universal adaptability.

  19. Pipelining Memetic Algorithms, Constraint Satisfaction, and Local Search for Course Timetabling

    Science.gov (United States)

    Conant-Pablos, Santiago E.; Magaña-Lozano, Dulce J.; Terashima-Marín, Hugo

    This paper introduces a hybrid algorithm that combines local search and constraint satisfaction techniques with memetic algorithms for solving Course Timetabling hard problems. These problems require assigning a set of courses to a predetermined finite number of classrooms and periods of time, complying with a complete set of hard constraints while maximizing the consistency with a set of preferences (soft constraints). The algorithm works in a three-stage sequence: first, it creates an initial population of approximations to the solution by partitioning the variables that represent the courses and solving each partition as a constraint-satisfaction problem; second, it reduces the number of remaining hard and soft constraint violations applying a memetic algorithm; and finally, it obtains a complete and fully consistent solution by locally searching around the best memetic solution. The approach produces competitive results, always getting feasible solutions with a reduced number of soft constraints inconsistencies, when compared against the methods running independently.

  20. Iterated Local Search Algorithm with Strategic Oscillation for School Bus Routing Problem with Bus Stop Selection

    Directory of Open Access Journals (Sweden)

    Mohammad Saied Fallah Niasar

    2017-02-01

    Full Text Available he school bus routing problem (SBRP represents a variant of the well-known vehicle routing problem. The main goal of this study is to pick up students allocated to some bus stops and generate routes, including the selected stops, in order to carry students to school. In this paper, we have proposed a simple but effective metaheuristic approach that employs two features: first, it utilizes large neighborhood structures for a deeper exploration of the search space; second, the proposed heuristic executes an efficient transition between the feasible and infeasible portions of the search space. Exploration of the infeasible area is controlled by a dynamic penalty function to convert the unfeasible solution into a feasible one. Two metaheuristics, called N-ILS (a variant of the Nearest Neighbourhood with Iterated Local Search algorithm and I-ILS (a variant of Insertion with Iterated Local Search algorithm are proposed to solve SBRP. Our experimental procedure is based on the two data sets. The results show that N-ILS is able to obtain better solutions in shorter computing times. Additionally, N-ILS appears to be very competitive in comparison with the best existing metaheuristics suggested for SBRP

  1. DNA markers reveal genetic structure and localized diversity of ...

    African Journals Online (AJOL)

    High genetic diversity was observed among the landraces for both marker systems. STRUCTURE analysis revealed 4 clusters of genetically differentiated groups of landraces. Cluster analysis revealed a close relationship between landraces along geographic proximity with genetic distance between landraces increasing ...

  2. Localized search cues in corn roots for western corn rootworm (Coleoptera: Chrysomelidae) larvae.

    Science.gov (United States)

    Bernklau, E J; Bjostad, L B; Meihls, L N; Coudron, T A; Lim, E; Hibbard, B E

    2009-04-01

    Cues that elicit a characteristic localized search behavior by neonate larvae of the western corn rootworm, Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), were extracted from living corn, Zea mays L., roots with acetone. Larvae were exposed to corn roots or to an acetone extract of corn roots and then transferred into a bioassay arena where their movements were tracked and recorded. After a 5-min exposure to live corn roots, larvae produced highly convoluted tracks that were indicative of a localized search behavior, and these distinctive tracks were also produced by larvae exposed to an acetone extract of corn roots. Larvae exposed to a filter paper control moved in relatively straight paths that were indicative of ranging behavior. Larval tracks were recorded by means of a videocamera and tracking software, and four parameters of movement were used to quantify the tracks: mean turn angle, mean meander, total distance, and maximum distance from origin. For every parameter measured, tracks resulting from exposure to the control were significantly different from tracks resulting from exposure to live corn roots and to all doses of the corn root extract. In a separate experiment, larvae exposed to corn root pieces or corn root juice exhibited the localized search behavior, but larvae exposed to oat root pieces and oat root juice (nonhost) exhibited ranging behavior.

  3. Hybridization of Adaptive Differential Evolution with an Expensive Local Search Method

    Directory of Open Access Journals (Sweden)

    Rashida Adeeb Khanum

    2016-01-01

    Full Text Available Differential evolution (DE is an effective and efficient heuristic for global optimization problems. However, it faces difficulty in exploiting the local region around the approximate solution. To handle this issue, local search (LS techniques could be hybridized with DE to improve its local search capability. In this work, we hybridize an updated version of DE, adaptive differential evolution with optional external archive (JADE with an expensive LS method, Broydon-Fletcher-Goldfarb-Shano (BFGS for solving continuous unconstrained global optimization problems. The new hybrid algorithm is denoted by DEELS. To validate the performance of DEELS, we carried out extensive experiments on well known test problems suits, CEC2005 and CEC2010. The experimental results, in terms of function error values, success rate, and some other statistics, are compared with some of the state-of-the-art algorithms, self-adaptive control parameters in differential evolution (jDE, sequential DE enhanced by neighborhood search for large-scale global optimization (SDENS, and differential ant-stigmergy algorithm (DASA. These comparisons reveal that DEELS outperforms jDE and SDENS except DASA on the majority of test instances.

  4. Comparison of Genetic Algorithm and Harmony Search for Generator Maintenance Scheduling

    Directory of Open Access Journals (Sweden)

    Laiq Khan

    2012-10-01

    Full Text Available GMS (Generator Maintenance Scheduling ranks very high in decision making of power generation management. Generators maintenance schedule decides the time period of maintenance tasks and a reliable reserve margin is also maintained during this time period. In this paper, a comparison of GA (Genetic Algorithm and HS (Harmony Search algorithm is presented to solve generators maintenance scheduling problem for WAPDA (Water And Power Development Authority Pakistan. GA is a search procedure, which is used in search problems to compute exact and optimized solution. GA is considered as global search heuristic technique. HS algorithm is quite efficient, because the convergence rate of this algorithm is very fast. HS algorithm is based on the concept of music improvisation process of searching for a perfect state of harmony. The two algorithms generate feasible and optimal solutions and overcome the limitations of the conventional methods including extensive computational effort, which increases exponentially as the size of the problem increases. The proposed methods are tested, validated and compared on the WAPDA electric system.

  5. Ultrafast localization of the optic disc using dimensionality reduction of the search space.

    Science.gov (United States)

    Mahfouz, Ahmed Essam; Fahmy, Ahmed S

    2009-01-01

    Optic Disc (OD) localization is an important pre-processing step that significantly simplifies subsequent segmentation of the OD and other retinal structures. Current OD localization techniques suffer from impractically-high computation times (few minutes/image). In this work, we present an ultrafast technique that requires less than a second to localize the OD. The technique is based on reducing the dimensionality of the search space by projecting the 2D image feature space onto two orthogonal (x- and y-) axes. This results in two 1D signals that can be used to determine the x- and y- coordinates of the OD. Image features such as retinal vessels orientation and the OD brightness and shape are used in the current method. Four publicly-available databases, including STARE and DRIVE, were used to evaluate the proposed technique. The OD was successfully located in 330 images out of 340 images (97%) with an average computation time of 0.65 seconds.

  6. Analysis of Genetic diversity and reltionships in local Tunisian barley ...

    African Journals Online (AJOL)

    Yomi

    Genetic diversity and environmental associations of wild barley, Hordeum spontaneum, in Turkey. Genetica, 68: 203-213. Nagaoka T, Ogihara Y (1997). Applicability of inter-simple sequence repeat polymorphism in wheat for use as DNA markers in comparison to RFLP and RAPD markers. Theor. Appl. Genet. 94: 597-602.

  7. DNA markers reveal genetic structure and localized diversity of ...

    African Journals Online (AJOL)

    uqhdesma

    2016-10-12

    Oct 12, 2016 ... with genetic distance between landraces increasing with an increase in geographic distance. The ... the extent and structure of crop genetic diversity is ...... Ribosomal DNA spacer length polymorphism in barley. Mendelian inheritance, chromosomal location and population dynamics. Proc. Natl. Acad. Sci.

  8. A Local and Global Search Combined Particle Swarm Optimization Algorithm and Its Convergence Analysis

    Directory of Open Access Journals (Sweden)

    Weitian Lin

    2014-01-01

    Full Text Available Particle swarm optimization algorithm (PSOA is an advantage optimization tool. However, it has a tendency to get stuck in a near optimal solution especially for middle and large size problems and it is difficult to improve solution accuracy by fine-tuning parameters. According to the insufficiency, this paper researches the local and global search combine particle swarm algorithm (LGSCPSOA, and its convergence and obtains its convergence qualification. At the same time, it is tested with a set of 8 benchmark continuous functions and compared their optimization results with original particle swarm algorithm (OPSOA. Experimental results indicate that the LGSCPSOA improves the search performance especially on the middle and large size benchmark functions significantly.

  9. Comparison of a constraint directed search to a genetic algorithm in a scheduling application

    International Nuclear Information System (INIS)

    Abbott, L.

    1993-01-01

    Scheduling plutonium containers for blending is a time-intensive operation. Several constraints must be taken into account; including the number of containers in a dissolver run, the size of each dissolver run, and the size and target purity of the blended mixture formed from these runs. Two types of algorithms have been used to solve this problem: a constraint directed search and a genetic algorithm. This paper discusses the implementation of these two different approaches to the problem and the strengths and weaknesses of each algorithm

  10. A Rule-Based Local Search Algorithm for General Shift Design Problems in Airport Ground Handling

    DEFF Research Database (Denmark)

    Clausen, Tommy

    We consider a generalized version of the shift design problem where shifts are created to cover a multiskilled demand and fit the parameters of the workforce. We present a collection of constraints and objectives for the generalized shift design problem. A local search solution framework with mul...... with multiple neighborhoods and a loosely coupled rule engine based on simulated annealing is presented. Computational experiments on real-life data from various airport ground handling organization show the performance and flexibility of the proposed algorithm....

  11. Efficient Top-k Locality Search for Co-located Spatial Web Objects

    DEFF Research Database (Denmark)

    Qu, Qiang; Liu, Siyuan; Yang, Bin

    2014-01-01

    In step with the web being used widely by mobile users, user location is becoming an essential signal in services, including local intent search. Given a large set of spatial web objects consisting of a geographical location and a textual description (e.g., online business directory entries...... of restaurants, bars, and shops), how can we find sets of objects that are both spatially and textually relevant to a query? Most of existing studies solve the problem by requiring that all query keywords are covered by the returned objects and then rank the sets by spatial proximity. The needs for identifying...

  12. SEARCH

    International Development Research Centre (IDRC) Digital Library (Canada)

    Chaitali Sinha

    Anexo B: Lista de verificación para presentar una nota conceptual en el marco de IDRC-SEARCH ....... 17 .... incluir investigación primaria y/o síntesis de estudios existentes, para generar nuevo conocimiento. Los .... de datos entre grupos diferentes de usuarios (trabajadores de la salud comunitaria, funcionarios de salud.

  13. Population differentiation in Pacific salmon: local adaptation, genetic drift, or the environment?

    Science.gov (United States)

    Adkison, Milo D.

    1995-01-01

    Morphological, behavioral, and life-history differences between Pacific salmon (Oncorhynchus spp.) populations are commonly thought to reflect local adaptation, and it is likewise common to assume that salmon populations separated by small distances are locally adapted. Two alternatives to local adaptation exist: random genetic differentiation owing to genetic drift and founder events, and genetic homogeneity among populations, in which differences reflect differential trait expression in differing environments. Population genetics theory and simulations suggest that both alternatives are possible. With selectively neutral alleles, genetic drift can result in random differentiation despite many strays per generation. Even weak selection can prevent genetic drift in stable populations; however, founder effects can result in random differentiation despite selective pressures. Overlapping generations reduce the potential for random differentiation. Genetic homogeneity can occur despite differences in selective regimes when straying rates are high. In sum, localized differences in selection should not always result in local adaptation. Local adaptation is favored when population sizes are large and stable, selection is consistent over large areas, selective diffeentials are large, and straying rates are neither too high nor too low. Consideration of alternatives to local adaptation would improve both biological research and salmon conservation efforts.

  14. Landscape genomics in Atlantic salmon (Salmo salar): searching for gene-environment interactions driving local adaptation.

    Science.gov (United States)

    Vincent, Bourret; Dionne, Mélanie; Kent, Matthew P; Lien, Sigbjørn; Bernatchez, Louis

    2013-12-01

    A growing number of studies are examining the factors driving historical and contemporary evolution in wild populations. By combining surveys of genomic variation with a comprehensive assessment of environmental parameters, such studies can increase our understanding of the genomic and geographical extent of local adaptation in wild populations. We used a large-scale landscape genomics approach to examine adaptive and neutral differentiation across 54 North American populations of Atlantic salmon representing seven previously defined genetically distinct regional groups. Over 5500 genome-wide single nucleotide polymorphisms were genotyped in 641 individuals and 28 bulk assays of 25 pooled individuals each. Genome scans, linkage map, and 49 environmental variables were combined to conduct an innovative landscape genomic analysis. Our results provide valuable insight into the links between environmental variation and both neutral and potentially adaptive genetic divergence. In particular, we identified markers potentially under divergent selection, as well as associated selective environmental factors and biological functions with the observed adaptive divergence. Multivariate landscape genetic analysis revealed strong associations of both genetic and environmental structures. We found an enrichment of growth-related functions among outlier markers. Climate (temperature-precipitation) and geological characteristics were significantly associated with both potentially adaptive and neutral genetic divergence and should be considered as candidate loci involved in adaptation at the regional scale in Atlantic salmon. Hence, this study significantly contributes to the improvement of tools used in modern conservation and management schemes of Atlantic salmon wild populations. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  15. Searching Online Mendelian Inheritance in Man (OMIM): A Knowledgebase of Human Genes and Genetic Phenotypes.

    Science.gov (United States)

    Amberger, Joanna S; Hamosh, Ada

    2017-06-27

    Online Mendelian Inheritance in Man (OMIM) at OMIM.org is the primary repository of comprehensive, curated information on genes and genetic phenotypes and the relationships between them. This unit provides an overview of the types of information in OMIM and optimal strategies for searching and retrieving the information. OMIM.org has links to many related and complementary databases, providing easy access to more information on a topic. The relationship between genes and genetic disorders is highlighted in this unit. The basic protocol explains searching OMIM both from a gene perspective and a clinical features perspective. Two alternate protocols provide strategies for viewing gene-phenotype relationships: a gene map table and Quick View or Side-by-Side format for clinical features. OMIM.org is updated nightly, and the MIMmatch service, described in the support protocol, provides a convenient way to follow updates to entries, gene-phenotype relationships, and collaborate with other researchers. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  16. A GPU Implementation of Local Search Operators for Symmetric Travelling Salesman Problem

    Directory of Open Access Journals (Sweden)

    Juraj Fosin

    2013-06-01

    Full Text Available The Travelling Salesman Problem (TSP is one of the most studied combinatorial optimization problem which is significant in many practical applications in transportation problems. The TSP problem is NP-hard problem and requires large computation power to be solved by the exact algorithms. In the past few years, fast development of general-purpose Graphics Processing Units (GPUs has brought huge improvement in decreasing the applications’ execution time. In this paper, we implement 2-opt and 3-opt local search operators for solving the TSP on the GPU using CUDA. The novelty presented in this paper is a new parallel iterated local search approach with 2-opt and 3-opt operators for symmetric TSP, optimized for the execution on GPUs. With our implementation large TSP problems (up to 85,900 cities can be solved using the GPU. We will show that our GPU implementation can be up to 20x faster without losing quality for all TSPlib problems as well as for our CRO TSP problem.

  17. A Framework for Similarity Search with Space-Time Tradeoffs using Locality Sensitive Filtering

    DEFF Research Database (Denmark)

    Christiani, Tobias Lybecker

    2017-01-01

    that satisfies certain locality-sensitivity properties, we can construct a dynamic data structure that solves the approximate near neighbor problem in $d$-dimensional space with query time $dn^{\\rho_q + o(1)}$, update time $dn^{\\rho_u + o(1)}$, and space usage $dn + n^{1 + \\rho_u + o(1)}$ where $n$ denotes......We present a framework for similarity search based on Locality-Sensitive Filtering~(LSF),generalizing the Indyk-Motwani (STOC 1998) Locality-Sensitive Hashing~(LSH) framework to support space-time tradeoffs. Given a family of filters, defined as a distribution over pairs of subsets of space...... the number of points in the data structure.The space-time tradeoff is tied to the tradeoff between query time and update time (insertions/deletions), controlled by the exponents $\\rho_q, \\rho_u$ that are determined by the filter family. \\\\ Locality-sensitive filtering was introduced by Becker et al. (SODA...

  18. Searching for globally optimal functional forms for interatomic potentials using genetic programming with parallel tempering.

    Science.gov (United States)

    Slepoy, A; Peters, M D; Thompson, A P

    2007-11-30

    Molecular dynamics and other molecular simulation methods rely on a potential energy function, based only on the relative coordinates of the atomic nuclei. Such a function, called a force field, approximately represents the electronic structure interactions of a condensed matter system. Developing such approximate functions and fitting their parameters remains an arduous, time-consuming process, relying on expert physical intuition. To address this problem, a functional programming methodology was developed that may enable automated discovery of entirely new force-field functional forms, while simultaneously fitting parameter values. The method uses a combination of genetic programming, Metropolis Monte Carlo importance sampling and parallel tempering, to efficiently search a large space of candidate functional forms and parameters. The methodology was tested using a nontrivial problem with a well-defined globally optimal solution: a small set of atomic configurations was generated and the energy of each configuration was calculated using the Lennard-Jones pair potential. Starting with a population of random functions, our fully automated, massively parallel implementation of the method reproducibly discovered the original Lennard-Jones pair potential by searching for several hours on 100 processors, sampling only a minuscule portion of the total search space. This result indicates that, with further improvement, the method may be suitable for unsupervised development of more accurate force fields with completely new functional forms. Copyright (c) 2007 Wiley Periodicals, Inc.

  19. DNA markers reveal genetic structure and localized diversity of ...

    African Journals Online (AJOL)

    uqhdesma

    2016-10-12

    Oct 12, 2016 ... of high-throughput sequencing (or next-generation sequencing-NGS) technologies in recent years, .... data [ln Pr(X/K)], was used to estimate K. Admixture ancestry model and correlated population allele ..... Dje Y, Forcioli D, Ater M, Lefebvre C, Vekemans X (1999). Assessing population genetic structure of ...

  20. Genetic diversity and population structure of locally adapted South African chicken lines: Implications for conservation.

    NARCIS (Netherlands)

    Marle-Koster, van E.; Hefer, C.A.; Nel, L.H.; Groenen, M.A.M.

    2008-01-01

    In this study microsatellite markers were applied to investigate the genetic diversity and population structure of the six local chicken lines kept in the “Fowls for Africa” program, for better clarification of parameters for breed differentiation and genetic conservation of this valuable resource.

  1. Search of molecular ground state via genetic algorithm: Implementation on a hybrid SIMD-MIMD platform

    International Nuclear Information System (INIS)

    Pucello, N.; D'Agostino, G.; Pisacane, F.

    1997-01-01

    A genetic algorithm for the optimization of the ground-state structure of a metallic cluster has been developed and ported on a SIMD-MIMD parallel platform. The SIMD part of the parallel platform is represented by a Quadrics/APE100 consisting of 512 floating point units, while the MIMD part is formed by a cluster of workstations. The proposed algorithm is composed by a part where the genetic operators are applied to the elements of the population and a part which performs a further local relaxation and the fitness calculation via Molecular Dynamics. These parts have been implemented on the MIMD and on the SIMD part, respectively. Results have been compared to those generated by using Simulated Annealing

  2. Iterated local search algorithm for solving the orienteering problem with soft time windows.

    Science.gov (United States)

    Aghezzaf, Brahim; Fahim, Hassan El

    2016-01-01

    In this paper we study the orienteering problem with time windows (OPTW) and the impact of relaxing the time windows on the profit collected by the vehicle. The way of relaxing time windows adopted in the orienteering problem with soft time windows (OPSTW) that we study in this research is a late service relaxation that allows linearly penalized late services to customers. We solve this problem heuristically by considering a hybrid iterated local search. The results of the computational study show that the proposed approach is able to achieve promising solutions on the OPTW test instances available in the literature, one new best solution is found. On the newly generated test instances of the OPSTW, the results show that the profit collected by the OPSTW is better than the profit collected by the OPTW.

  3. Optimizing heliostat positions with local search metaheuristics using a ray tracing optical model

    Science.gov (United States)

    Reinholz, Andreas; Husenbeth, Christof; Schwarzbözl, Peter; Buck, Reiner

    2017-06-01

    The life cycle costs of solar tower power plants are mainly determined by the investment costs of its construction. Significant parts of these investment costs are used for the heliostat field. Therefore, an optimized placement of the heliostats gaining the maximal annual power production has a direct impact on the life cycle costs revenue ratio. We present a two level local search method implemented in MATLAB utilizing the Monte Carlo raytracing software STRAL [1] for the evaluation of the annual power output for a specific weighted annual time scheme. The algorithm was applied to a solar tower power plant (PS10) with 624 heliostats. Compared to former work of Buck [2], we were able to improve both runtime of the algorithm and quality of the output solutions significantly. Using the same environment for both algorithms, we were able to reach Buck's best solution with a speed up factor of about 20.

  4. Searching of fuel recharges by means of genetic algorithms and neural networks in BWRs

    International Nuclear Information System (INIS)

    Ortiz S, J.J.; Montes T, J.L.; Castillo M, J.A.; Perusquia del C, R.

    2004-01-01

    In this work improvements to the systems RENOR and RECOPIA are presented, that were developed to optimize fuel recharges in boiling water reactors. The RENOR system is based on a Multi state recurrent neural network while RECOPIA is based on a Genetic Algorithm. In the new versions of these systems there is incorporate the execution of the Turned off Margin in Cold and the Excess of Reactivity in Hot. The new systems were applied to an operation cycle of the Unit 1 of the Nuclear Power station of Laguna Verde. The recharges of fuel obtained by both methods are compared among if being observed that RENOR has better performance that RECOPIA, due to the nature of its search process. RECOPIA requires of approximately 1.4 times more time that RENOR to find a satisfactory recharge of fuel. (Author)

  5. Genetic algorithm with small population size for search feasible control parameters for parallel hybrid electric vehicles

    Directory of Open Access Journals (Sweden)

    Yu-Huei Cheng

    2017-11-01

    Full Text Available The control strategy is a major unit in hybrid electric vehicles (HEVs. In order to provide suitable control parameters for reducing fuel consumptions and engine emissions while maintaining vehicle performance requirements, the genetic algorithm (GA with small population size is applied to search for feasible control parameters in parallel HEVs. The electric assist control strategy (EACS is used as the fundamental control strategy of parallel HEVs. The dynamic performance requirements stipulated in the Partnership for a New Generation of Vehicles (PNGV is considered to maintain the vehicle performance. The known ADvanced VehIcle SimulatOR (ADVISOR is used to simulate a specific parallel HEV with urban dynamometer driving schedule (UDDS. Five population sets with size 5, 10, 15, 20, and 25 are used in the GA. The experimental results show that the GA with population size of 25 is the best for selecting feasible control parameters in parallel HEVs.

  6. Hooke–Jeeves Method-used Local Search in a Hybrid Global Optimization Algorithm

    Directory of Open Access Journals (Sweden)

    V. D. Sulimov

    2014-01-01

    Full Text Available Modern methods for optimization investigation of complex systems are based on development and updating the mathematical models of systems because of solving the appropriate inverse problems. Input data desirable for solution are obtained from the analysis of experimentally defined consecutive characteristics for a system or a process. Causal characteristics are the sought ones to which equation coefficients of mathematical models of object, limit conditions, etc. belong. The optimization approach is one of the main ones to solve the inverse problems. In the main case it is necessary to find a global extremum of not everywhere differentiable criterion function. Global optimization methods are widely used in problems of identification and computation diagnosis system as well as in optimal control, computing to-mography, image restoration, teaching the neuron networks, other intelligence technologies. Increasingly complicated systems of optimization observed during last decades lead to more complicated mathematical models, thereby making solution of appropriate extreme problems significantly more difficult. A great deal of practical applications may have the problem con-ditions, which can restrict modeling. As a consequence, in inverse problems the criterion functions can be not everywhere differentiable and noisy. Available noise means that calculat-ing the derivatives is difficult and unreliable. It results in using the optimization methods without calculating the derivatives.An efficiency of deterministic algorithms of global optimization is significantly restrict-ed by their dependence on the extreme problem dimension. When the number of variables is large they use the stochastic global optimization algorithms. As stochastic algorithms yield too expensive solutions, so this drawback restricts their applications. Developing hybrid algo-rithms that combine a stochastic algorithm for scanning the variable space with deterministic local search

  7. Genetic diversity of Ghanaian local chicken populations based on ...

    African Journals Online (AJOL)

    In Ghana, local chickens are raised across distinct agro-ecological zones and constitute unique populations with variable phenotypes that need to be characterized to provide needed information for the conservation of useful genotypes against future needs. In particular, the Interior Savannah (GHIS) in the north, the Forest ...

  8. Development of Future Rule Curves for Multipurpose Reservoir Operation Using Conditional Genetic and Tabu Search Algorithms

    Directory of Open Access Journals (Sweden)

    Anongrit Kangrang

    2018-01-01

    Full Text Available Optimal rule curves are necessary guidelines in the reservoir operation that have been used to assess performance of any reservoir to satisfy water supply, irrigation, industrial, hydropower, and environmental conservation requirements. This study applied the conditional genetic algorithm (CGA and the conditional tabu search algorithm (CTSA technique to connect with the reservoir simulation model in order to search optimal reservoir rule curves. The Ubolrat Reservoir located in the northeast region of Thailand was an illustrative application including historic monthly inflow, future inflow generated by the SWAT hydrological model using 50-year future climate data from the PRECIS regional climate model in case of B2 emission scenario by IPCC SRES, water demand, hydrologic data, and physical reservoir data. The future and synthetic inflow data of reservoirs were used to simulate reservoir system for evaluating water situation. The situations of water shortage and excess water were shown in terms of frequency magnitude and duration. The results have shown that the optimal rule curves from CGA and CTSA connected with the simulation model can mitigate drought and flood situations than the existing rule curves. The optimal future rule curves were more suitable for future situations than the other rule curves.

  9. Local Climate Heterogeneity Shapes Population Genetic Structure of Two Undifferentiated Insular Scutellaria Species.

    Science.gov (United States)

    Hsiung, Huan-Yi; Huang, Bing-Hong; Chang, Jui-Tse; Huang, Yao-Moan; Huang, Chih-Wei; Liao, Pei-Chun

    2017-01-01

    Spatial climate heterogeneity may not only affect adaptive gene frequencies but could also indirectly shape the genetic structure of neutral loci by impacting demographic dynamics. In this study, the effect of local climate on population genetic variation was tested in two phylogenetically close Scutellaria species in Taiwan. Scutellaria taipeiensis , which was originally assumed to be an endemic species of Taiwan Island, is shown to be part of the widespread species S. barbata based on the overlapping ranges of genetic variation and climatic niches as well as their morphological similarity. Rejection of the scenario of "early divergence with secondary contact" and the support for multiple origins of populations of S. taipeiensis from S. barbata provide strong evolutionary evidence for a taxonomic revision of the species combination. Further tests of a climatic effect on genetic variation were conducted. Regression analyses show nonlinear correlations among any pair of geographic, climatic, and genetic distances. However, significantly, the bioclimatic variables that represent the precipitation from late summer to early autumn explain roughly 13% of the genetic variation of our sampled populations. These results indicate that spatial differences of precipitation in the typhoon season may influence the regeneration rate and colonization rate of local populations. The periodic typhoon episodes explain the significant but nonlinear influence of climatic variables on population genetic differentiation. Although, the climatic difference does not lead to species divergence, the local climate variability indeed impacts the spatial genetic distribution at the population level.

  10. Genetic diversity measures of local European beef cattle breeds for conservation purposes

    Directory of Open Access Journals (Sweden)

    Pereira Albano

    2001-05-01

    Full Text Available Abstract This study was undertaken to determine the genetic structure, evolutionary relationships, and the genetic diversity among 18 local cattle breeds from Spain, Portugal, and France using 16 microsatellites. Heterozygosities, estimates of Fst, genetic distances, multivariate and diversity analyses, and assignment tests were performed. Heterozygosities ranged from 0.54 in the Pirenaica breed to 0.72 in the Barrosã breed. Seven percent of the total genetic variability can be attributed to differences among breeds (mean Fst = 0.07; P

  11. Dark Matter Searches with Cherenkov Telescopes: Nearby Dwarf Galaxies or Local Galaxy Clusters?

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez-Conde, Miguel A.; /KIPAC, Menlo Park /SLAC /IAC, La Laguna /Laguna U., Tenerife; Cannoni, Mirco; /Huelva U.; Zandanel, Fabio; /IAA, Granada; Gomez, Mario E.; /Huelva U.; Prada, Francisco; /IAA, Granada

    2012-06-06

    In this paper, we compare dwarf galaxies and galaxy clusters in order to elucidate which object class is the best target for gamma-ray DM searches with imaging atmospheric Cherenkov telescopes (IACTs). We have built a mixed dwarfs+clusters sample containing some of the most promising nearby dwarf galaxies (Draco, Ursa Minor, Wilman 1 and Segue 1) and local galaxy clusters (Perseus, Coma, Ophiuchus, Virgo, Fornax, NGC 5813 and NGC 5846), and then compute their DM annihilation flux profiles by making use of the latest modeling of their DM density profiles. We also include in our calculations the effect of DM substructure. Willman 1 appears as the best candidate in the sample. However, its mass modeling is still rather uncertain, so probably other candidates with less uncertainties and quite similar fluxes, namely Ursa Minor and Segue 1, might be better options. As for galaxy clusters, Virgo represents the one with the highest flux. However, its large spatial extension can be a serious handicap for IACT observations and posterior data analysis. Yet, other local galaxy cluster candidates with more moderate emission regions, such as Perseus, may represent good alternatives. After comparing dwarfs and clusters, we found that the former exhibit annihilation flux profiles that, at the center, are roughly one order of magnitude higher than those of clusters, although galaxy clusters can yield similar, or even higher, integrated fluxes for the whole object once substructure is taken into account. Even when any of these objects are strictly point-like according to the properties of their annihilation signals, we conclude that dwarf galaxies are best suited for observational strategies based on the search of point-like sources, while galaxy clusters represent best targets for analyses that can deal with rather extended emissions. Finally, we study the detection prospects for present and future IACTs in the framework of the constrained minimal supersymmetric standard model. We

  12. The star formation histories of local group dwarf galaxies. II. Searching for signatures of reionization

    Energy Technology Data Exchange (ETDEWEB)

    Weisz, Daniel R. [Department of Astronomy, University of California at Santa Cruz, 1156 High Street, Santa Cruz, CA 95064 (United States); Dolphin, Andrew E. [Raytheon Company, 1151 East Hermans Road, Tucson, AZ 85756 (United States); Skillman, Evan D. [Minnesota Institute for Astrophysics, University of Minnesota, 116 Church Street SE, Minneapolis, MN 55455 (United States); Holtzman, Jon [Department of Astronomy, New Mexico State University, Box 30001, 1320 Frenger Street, Las Cruces, NM 88003 (United States); Gilbert, Karoline M.; Dalcanton, Julianne J.; Williams, Benjamin F., E-mail: drw@ucsc.edu [Department of Astronomy, University of Washington, Box 351580, Seattle, WA 98195 (United States)

    2014-07-10

    We search for signatures of reionization in the star formation histories (SFHs) of 38 Local Group dwarf galaxies (10{sup 4} < M{sub *} < 10{sup 9} M{sub ☉}). The SFHs are derived from color-magnitude diagrams using archival Hubble Space Telescope/Wide Field Planetary Camera 2 imaging. Only five quenched galaxies (And V, And VI, And XIII, Leo IV, and Hercules) are consistent with forming the bulk of their stars before reionization, when full uncertainties are considered. Observations of 13 of the predicted 'true fossils' identified by Bovill and Ricotti show that only two (Hercules and Leo IV) indicate star formation quenched by reionization. However, both are within the virial radius of the Milky Way and evidence of tidal disturbance complicates this interpretation. We argue that the late-time gas capture scenario posited by Ricotti for the low mass, gas-rich, and star-forming fossil candidate Leo T is observationally indistinguishable from simple gas retention. Given the ambiguity between environmental effects and reionization, the best reionization fossil candidates are quenched low mass field galaxies (e.g., KKR 25).

  13. Local search for optimal global map generation using mid-decadal landsat images

    Science.gov (United States)

    Khatib, L.; Gasch, J.; Morris, Robert; Covington, S.

    2007-01-01

    NASA and the US Geological Survey (USGS) are seeking to generate a map of the entire globe using Landsat 5 Thematic Mapper (TM) and Landsat 7 Enhanced Thematic Mapper Plus (ETM+) sensor data from the "mid-decadal" period of 2004 through 2006. The global map is comprised of thousands of scene locations and, for each location, tens of different images of varying quality to chose from. Furthermore, it is desirable for images of adjacent scenes be close together in time of acquisition, to avoid obvious discontinuities due to seasonal changes. These characteristics make it desirable to formulate an automated solution to the problem of generating the complete map. This paper formulates a Global Map Generator problem as a Constraint Optimization Problem (GMG-COP) and describes an approach to solving it using local search. Preliminary results of running the algorithm on image data sets are summarized. The results suggest a significant improvement in map quality using constraint-based solutions. Copyright ?? 2007, Association for the Advancement of Artificial Intelligence (www.aaai.org). All rights reserved.

  14. A Sustainable City Planning Algorithm Based on TLBO and Local Search

    Science.gov (United States)

    Zhang, Ke; Lin, Li; Huang, Xuanxuan; Liu, Yiming; Zhang, Yonggang

    2017-09-01

    Nowadays, how to design a city with more sustainable features has become a center problem in the field of social development, meanwhile it has provided a broad stage for the application of artificial intelligence theories and methods. Because the design of sustainable city is essentially a constraint optimization problem, the swarm intelligence algorithm of extensive research has become a natural candidate for solving the problem. TLBO (Teaching-Learning-Based Optimization) algorithm is a new swarm intelligence algorithm. Its inspiration comes from the “teaching” and “learning” behavior of teaching class in the life. The evolution of the population is realized by simulating the “teaching” of the teacher and the student “learning” from each other, with features of less parameters, efficient, simple thinking, easy to achieve and so on. It has been successfully applied to scheduling, planning, configuration and other fields, which achieved a good effect and has been paid more and more attention by artificial intelligence researchers. Based on the classical TLBO algorithm, we propose a TLBO_LS algorithm combined with local search. We design and implement the random generation algorithm and evaluation model of urban planning problem. The experiments on the small and medium-sized random generation problem showed that our proposed algorithm has obvious advantages over DE algorithm and classical TLBO algorithm in terms of convergence speed and solution quality.

  15. Hitting times of local and global optima in genetic algorithms with very high selection pressure

    Directory of Open Access Journals (Sweden)

    Eremeev Anton V.

    2017-01-01

    Full Text Available The paper is devoted to upper bounds on the expected first hitting times of the sets of local or global optima for non-elitist genetic algorithms with very high selection pressure. The results of this paper extend the range of situations where the upper bounds on the expected runtime are known for genetic algorithms and apply, in particular, to the Canonical Genetic Algorithm. The obtained bounds do not require the probability of fitness-decreasing mutation to be bounded by a constant which is less than one.

  16. Combining local search with co-evolution in a remarkably simple way

    Energy Technology Data Exchange (ETDEWEB)

    Boettcher, S.; Percus, A.

    2000-05-01

    The authors explore a new general-purpose heuristic for finding high-quality solutions to hard optimization problem. The method, called extremal optimization, is inspired by self-organized criticality, a concept introduced to describe emergent complexity in physical systems. In contrast to genetic algorithms, which operate on an entire gene-pool of possible solutions, extremal optimization successively replaces extremely undesirable elements of a single sub-optimal solution with new, random ones. Large fluctuations, or avalanches, ensue that efficiently explore many local optima. Drawing upon models used to simulate far-from-equilibrium dynamics, extremal optimization complements heuristics inspired by equilibrium statistical physics, such as simulated annealing. With only one adjustable parameter, its performance has proved competitive with more elaborate methods, especially near phase transitions. Phase transitions are found in many combinatorial optimization problems, and have been conjectured to occur in the region of parameter space containing the hardest instances. We demonstrate how extremal optimization can be implemented for a variety of hard optimization problems. We believe that this will be a useful tool in the investigation of phase transitions in combinatorial optimization, thereby helping to elucidate the origin of computational complexity.

  17. SIMMER extension for multigroup energy structure search using genetic algorithm with different fitness functions

    Directory of Open Access Journals (Sweden)

    Mattia Massone

    2017-09-01

    Full Text Available The multigroup transport theory is the basis for many neutronics modules. A significant point of the cross-section (XS generation procedure is the choice of the energy groups' boundaries in the XS libraries, which must be carefully selected as an unsuitable energy meshing can easily lead to inaccurate results. This decision can require considerable effort and is particularly difficult for the common user, especially if not well-versed in reactor physics. This work investigates a genetic algorithm-based tool which selects an appropriate XS energy structure (ES specific for the considered problem, to be used for the condensation of a fine multigroup library. The procedure is accelerated by results storage and fitness calculation speed-up and can be easily parallelized. The extension is applied to the coupled code SIMMER and tested on the European Sustainable Nuclear Industrial Initiative (ESNII+ Advanced Sodium Technological Reactor for Industrial Demonstration (ASTRID-like reactor system with different fitness functions. The results show that, when the libraries are condensed based on the ESs suggested by the algorithm, the code actually returns the correct multiplication factor, in both reference and voided conditions. The computational effort reduction obtained by using the condensed library rather than the fine one is assessed and is much higher than the time required for the ES search.

  18. PRODUCTIVITY AND GENETIC DIVERSITY OF LOCAL CATTLE IN CIAMIS-WEST JAVA

    Directory of Open Access Journals (Sweden)

    N. Hilmia

    2013-03-01

    Full Text Available The objectives of this study were to identify the productivity and genetic diversity of local cattle in Ciamis West Java based on DNA microsatellite, in order to provide the basic information for its rearing, conservation and development. Eighteen of local cattle were kept for 58 days by feeding concentrates and rice straw. The measured parameters were weekly body weight as well as carcass percentage. The percentage of comparing carcass was taken from PO, Bali and crossbred cattle from local cattle with Limousin, Simmental, Brahman and Angus cattle. Data were analyzed using Excel software and SAS (2004. Blood samples were taken from two subpopulations i.e., 46 and 52 samples from Tambaksari and Cijulang areas, respectively. Other DNA samples were collected from Bali, PO, Limousin, Simental, Brahman and Angus cattle. Genetic diversity and phylogenetic analysis were analyzed using 3 microsatellite loci, that were INRA35, HEL9 and BM2113. The genotyping data were analyzed using POPGENE.32 program, while phylogenetic trees were analyzed by MEGA 4. Average daily gain (ADG of local cattle in Ciamis was 0.62±0.23 kg/head/day with a carcass percentage was 51.62±1.80%. The carcasses percentage of local cattle in Ciamis was not significantly different from those of Bali, PO, and crossbred cattle. The genetic diversity of local cattle in Ciamis was categorized in the medium level, the diversity of local cattle in Tambaksari subpopulation was higher than in Cijulang subpopulation. Local cattle in Ciamis had a closer genetic distance with the PO cattle.

  19. Genetic Localization of Foraging (For): A Major Gene for Larval Behavior in Drosophila Melanogaster

    OpenAIRE

    de-Belle, J. S.; Hilliker, A. J.; Sokolowski, M. B.

    1989-01-01

    Localizing genes for quantitative traits by conventional recombination mapping is a formidable challenge because environmental variation, minor genes, and genetic markers have modifying effects on continuously varying phenotypes. We describe ``lethal tagging,'' a method used in conjunction with deficiency mapping for localizing major genes associated with quantitative traits. Rover/sitter is a naturally occurring larval foraging polymorphism in Drosophila melanogaster which has a polygenic pa...

  20. Genetic Algorithm-Based Relevance Feedback for Image Retrieval Using Local Similarity Patterns.

    Science.gov (United States)

    Stejic, Zoran; Takama, Yasufumi; Hirota, Kaoru

    2003-01-01

    Proposes local similarity pattern (LSP) as a new method for computing digital image similarity. Topics include optimizing similarity computation based on genetic algorithm; relevance feedback; and an evaluation of LSP on five databases that showed an increase in retrieval precision over other methods for computing image similarity. (Author/LRW)

  1. Global to local genetic diversity indicators of evolutionary potential in tree species within and outside forests

    DEFF Research Database (Denmark)

    Graudal, Lars; Aravanopoulos, Filippos; Bennadji, Zohra

    2014-01-01

    There is a general trend of biodiversity loss at global, regional, national and local levels. To monitor this trend, international policy processes have created a wealth of indicators over the last two decades. However, genetic diversity indicators are regrettably absent from comprehensive bio...

  2. Genetic diversity of Hajar1 and Hajar2 local Saudi chicken lines ...

    African Journals Online (AJOL)

    This study was conducted to assess genetic diversity of Hajar1 and Hajar2 local Saudi chicken lines using mitochondrial DNA (mtDNA) D-loop partial sequences. One hundred blood samples were obtained equally from Hajar1 and Hajar2 Saudi chicken lines as 50 samples from each line. The D-loop region was partially ...

  3. PRODUCTIVITY AND GENETIC DIVERSITY OF LOCAL CATTLE IN CIAMIS-WEST JAVA

    Directory of Open Access Journals (Sweden)

    N. Hilmia

    2014-10-01

    Full Text Available The objectives of this study were to identify the productivity and genetic diversity of local cattle inCiamis West Java based on DNA microsatellite, in order to provide the basic information for its rearing,conservation and development. Eighteen of local cattle were kept for 58 days by feeding concentratesand rice straw. The measured parameters were weekly body weight as well as carcass percentage. Thepercentage of comparing carcass was taken from PO, Bali and crossbred cattle from local cattle withLimousin, Simmental, Brahman and Angus cattle. Data were analyzed using Excel software and SAS(2004. Blood samples were taken from two subpopulations i.e., 46 and 52 samples from Tambaksariand Cijulang areas, respectively. Other DNA samples were collected from Bali, PO, Limousin, Simental,Brahman and Angus cattle. Genetic diversity and phylogenetic analysis were analyzed using 3microsatellite loci, that were INRA35, HEL9 and BM2113. The genotyping data were analyzed usingPOPGENE.32 program, while phylogenetic trees were analyzed by MEGA 4. Average daily gain (ADGof local cattle in Ciamis was 0.62±0.23 kg/head/day with a carcass percentage was 51.62±1.80%. Thecarcasses percentage of local cattle in Ciamis was not significantly different from those of Bali, PO, andcrossbred cattle. The genetic diversity of local cattle in Ciamis was categorized in the medium level, thediversity of local cattle in Tambaksari subpopulation was higher than in Cijulang subpopulation. Localcattle in Ciamis had a closer genetic distance with the PO cattle.

  4. A new method for decoding an encrypted text by genetic algorithms and its comparison with tabu search and simulated annealing

    Directory of Open Access Journals (Sweden)

    Mahdi Sadeghzadeh

    2014-02-01

    Full Text Available Genetic Algorithm is an algorithm based on population and many optimization problems are solved with this method, successfully. With increasing demand for computer attacks, security, efficient and reliable Internet has increased. Cryptographic systems have studied the science of communication is hidden, and includes two case categories including encryption, password and analysis. In this paper, several code analyses based on genetic algorithms, tabu search and simulated annealing for a permutation of encrypted text are investigated. The study also attempts to provide and to compare the performance in terms of the amount of check and control algorithms and the results are compared.

  5. Search for Active-State Conformation of Drug Target GPCR Using Real-Coded Genetic Algorithm

    Science.gov (United States)

    Ishino, Yoko; Harada, Takanori; Aida, Misako

    G-Protein coupled receptors (GPCRs) comprise a large superfamily of proteins and are a target for nearly 50% of drugs in clinical use today. GPCRs have a unique structural motif, seven transmembrane helices, and it is known that agonists and antagonists dock with a GPCR in its ``active'' and ``inactive'' condition, respectively. Knowing conformations of both states is eagerly anticipated for elucidation of drug action mechanism. Since GPCRs are difficult to crystallize, the 3D structures of these receptors have not yet been determined by X-ray crystallography, except the inactive-state conformation of two proteins. The conformation of them enabled the inactive form of other GPCRs to be modeled by computer-aided homology modeling. However, to date, the active form of GPCRs has not been solved. This paper describes a novel method to predict the 3D structure of an active-state GPCR aiming at molecular docking-based virtual screening using real-coded genetic algorithm (real-coded GA), receptor-ligand docking simulations, and molecular dynamics (MD) simulations. The basic idea of the method is that the MD is first used to calculate an average 3D coordinates of all atoms of a GPCR protein against heat fluctuation on the pico- or nano- second time scale, and then real-coded GA involving receptor-ligand docking simulations functions to determine the rotation angle of each helix as a movement on wider time scale. The method was validated using human leukotriene B4 receptor BLT1 as a sample GPCR. Our study demonstrated that the established evolutionary search for the active state of the leukotriene receptor provided the appropriate 3D structure of the receptor to dock with its agonists.

  6. NSGA-II Algorithm with a Local Search Strategy for Multiobjective Optimal Design of Dry-Type Air-Core Reactor

    Directory of Open Access Journals (Sweden)

    Chengfen Zhang

    2015-01-01

    Full Text Available Dry-type air-core reactor is now widely applied in electrical power distribution systems, for which the optimization design is a crucial issue. In the optimization design problem of dry-type air-core reactor, the objectives of minimizing the production cost and minimizing the operation cost are both important. In this paper, a multiobjective optimal model is established considering simultaneously the two objectives of minimizing the production cost and minimizing the operation cost. To solve the multi-objective optimization problem, a memetic evolutionary algorithm is proposed, which combines elitist nondominated sorting genetic algorithm version II (NSGA-II with a local search strategy based on the covariance matrix adaptation evolution strategy (CMA-ES. NSGA-II can provide decision maker with flexible choices among the different trade-off solutions, while the local-search strategy, which is applied to nondominated individuals randomly selected from the current population in a given generation and quantity, can accelerate the convergence speed. Furthermore, another modification is that an external archive is set in the proposed algorithm for increasing the evolutionary efficiency. The proposed algorithm is tested on a dry-type air-core reactor made of rectangular cross-section litz-wire. Simulation results show that the proposed algorithm has high efficiency and it converges to a better Pareto front.

  7. The Nearby Galaxies Supernova Search project: The rate of supernovae in the local universe

    Science.gov (United States)

    Strolger, Louis-Gregory

    2003-08-01

    Over 2200 supernova events have been discovered in the past millenium—nearly half of which have been found in only the last decade. The rise in interest in these events has been sparked, in large part, by the sample of distant Type Ia supernovae which are giving unprecedented information about the cosmological parameters of our Universe. However, when one considers that very little is known about several SN Types including the Type Ia events, it is clear that there remains much to be understood in the detailed analysis of supernovae. Currently, this analysis is best done through relatively low redshift supernova surveys. Here I present the results from the Nearby Galaxies Supernova Search project (NGSS), a three-year survey for SNe in equatorial field galaxies. Through the bulk analysis of these SNe, I have determined the local SN rates in field galaxies (in Supernova Units [SNu]; Supernovae per century per 1010 LB⊙ ) to be 0.192 ± 0.045 (Poisson) ± 0.094 (systematic) for Type Ia SNe, 0.678 ± 0.164 ± 0.278 to 1.242 ± 0.301 ± 0.514 for Type II SNe, and 1.166 ± 0.178 ± 0.498 to 1.924 ± 0.293 ± 0.887 for all supernova types (depending on assumed intrinsic extinction distributions for core-collapse events). A small number of SNe from this survey were also attributed to Abell galaxy clusters. Although there was not a sufficient sample in which to draw conclusive rates, through simple assumptions about galaxy cluster mass, size, and luminosity parameters, I estimate the supernova rate to be 0.46 ± 0.14 (Poisson) to 0.84 ± 0.26 SNu in these environments (also dependent on extinction distributions). In the course of this survey, we discovered a number of rare SN types, including SN 1999aw, a SN 1999aa-like Type Ia in a very low-luminosity host galaxy. We have completed a very thorough analysis of this luminous and peculiar event, which I include in this dissertation. The NGSS project has successfully discovered one of the largest samples of SNe from a

  8. Evaluation of genetic diversity of Katingan catlle and their genetic relationship with some other local catlle through DNA microsatellite analysis

    Directory of Open Access Journals (Sweden)

    Bambang Ngaji Utomo

    2011-06-01

    Full Text Available Katingan cattle is one of Indonesian animal genetic resources located in Katingan District, Central Kalimantan. The Katingan cattle is predicted to be extint, therefore it is necessary to conserve the cattle. Breed characterization is the primary step in any conservation program. Characterization was done using 10 microsatellite markers to evaluate the genetic diversity of Katingan Cattle in three subpopulations and their genetic relationship with some other local cattle. A total number of 72 random whole blood of Katingan samples consisted of Pendahara (20 samples, Buntut Bali (20 samples, and Tumbang Lahang (32 samples were used. The samples of Bali, PO, and Limousine Cattle were 11, 6, and 3 respectivelly. The number of 136 aleles were found with the variation from 9 aleles (ILSTS089 to 18 aleles (ILSTS013 and the average of the alele was 13.6 aleles per locus. A number of alel from Tumbang Lahang was higher (10.8 aleles than Pendahara (10.4 aleles and Buntut Bali subpopulation (7.3 aleles. Some loci produced polymorphic diagnostic aleles which varied from 1-7 types of allele. HEL013 and BM1818 had four aleles, while ILSTS026 and ILSTS089 had five and six aleles respectively. ILSTS029 and ILSTS036 had seven aleles. The diagnostic aleles were also found in Tumbang Lahang subpopulastion, as well as in Pendahara, and Buntut Bali. Heterozigositas values of Pendahara, Buntut Bali, and Tumbang Lahang subpopulation were 0.454, 0.478, and 0.529 respectively. While the average of heterozigositas (Ĥ was 0.492. Subpopulation of Tumbang Lahang was closer genetically to Pendahara (0.169 than Buntut Bali (0.173 and also the subpopulation was closer genetically to PO cattle (0.259 when compared to Buntut Bali (0.311 and Pendahara (0.329. The population of Katingan cattle was within one kluster with PO Cattle.

  9. Genetic specificity and potential for local adaptation between dengue viruses and mosquito vectors

    Directory of Open Access Journals (Sweden)

    Richardson Jason H

    2009-07-01

    Full Text Available Abstract Background Several observations support the hypothesis that vector-driven selection plays an important role in shaping dengue virus (DENV genetic diversity. Clustering of DENV genetic diversity at a particular location may reflect underlying genetic structure of vector populations, which combined with specific vector genotype × virus genotype (G × G interactions may promote adaptation of viral lineages to local mosquito vector genotypes. Although spatial structure of vector polymorphism at neutral genetic loci is well-documented, existence of G × G interactions between mosquito and virus genotypes has not been formally demonstrated in natural populations. Here we measure G × G interactions in a system representative of a natural situation in Thailand by challenging three isofemale families from field-derived Aedes aegypti with three contemporaneous low-passage isolates of DENV-1. Results Among indices of vector competence examined, the proportion of mosquitoes with a midgut infection, viral RNA concentration in the body, and quantity of virus disseminated to the head/legs (but not the proportion of infected mosquitoes with a disseminated infection strongly depended on the specific combinations of isofemale families and viral isolates, demonstrating significant G × G interactions. Conclusion Evidence for genetic specificity of interactions in our simple experimental design indicates that vector competence of Ae. aegypti for DENV is likely governed to a large extent by G × G interactions in genetically diverse, natural populations. This result challenges the general relevance of conclusions from laboratory systems that consist of a single combination of mosquito and DENV genotypes. Combined with earlier evidence for fine-scale genetic structure of natural Ae. aegypti populations, our finding indicates that the necessary conditions for local DENV adaptation to mosquito vectors are met.

  10. Local-regional control in breast cancer patients with a possible genetic predisposition

    International Nuclear Information System (INIS)

    Freedman, Laura M.; Buchholz, Thomas A.; Thames, Howard D.; Strom, Eric A.; McNeese, Marsha D.; Hortobagyi, Gabriel N.; Singletary, S. Eva; Heaton, Keith M.; Hunt, Kelly K.

    2000-01-01

    Purpose: Local control rates for breast cancer in genetically predisposed women are poorly defined. Because such a small percentage of breast cancer patients have proven germline mutations, surrogates, such as a family history for breast cancer, have been used to examine this issue. The purpose of this study was to evaluate local-regional control following breast conservation therapy (BCT) in patients with bilateral breast cancer and a breast cancer family history. Methods and Materials: We retrospectively reviewed records of all 58 patients with bilateral breast cancer and a breast cancer family history treated in our institution between 1959 and 1998. The primary surgical treatment was a breast-conserving procedure in 55 of the 116 breast cancer cases and a mastectomy in 61. The median follow-up was 68 months for the BCT patients and 57 months for the mastectomy-treated patients. Results: Eight local-regional recurrences occurred in the 55 cases treated with BCT, resulting in 5- and 10-year actuarial local-regional control rates of 86% and 76%, respectively. In the nine cases that did not receive radiation as a component of their BCT, four developed local-regional recurrences (5- and 10-year local-regional control rates of BCT without radiation: 49% and 49%). The 5- and 10-year actuarial local-regional control rates for the 46 cases treated with BCT and radiation were 94% and 83%, respectively. In these cases, there were two late local recurrences, developing at 8 years and 9 years, respectively. A log rank comparison of radiation versus no radiation actuarial data was significant at p = 0.009. In the cases treated with BCT, a multivariate analysis of radiation use, patient age, degree of family history, margin status, and stage revealed that only the use of radiation was associated with improved local control (Cox regression analysis p = 0.021). The 10-year actuarial rates of local-regional control following mastectomy with and without radiation were 91% and 89

  11. An Efficient Two-Objective Hybrid Local Search Algorithm for Solving the Fuel Consumption Vehicle Routing Problem

    Directory of Open Access Journals (Sweden)

    Weizhen Rao

    2016-01-01

    Full Text Available The classical model of vehicle routing problem (VRP generally minimizes either the total vehicle travelling distance or the total number of dispatched vehicles. Due to the increased importance of environmental sustainability, one variant of VRPs that minimizes the total vehicle fuel consumption has gained much attention. The resulting fuel consumption VRP (FCVRP becomes increasingly important yet difficult. We present a mixed integer programming model for the FCVRP, and fuel consumption is measured through the degree of road gradient. Complexity analysis of FCVRP is presented through analogy with the capacitated VRP. To tackle the FCVRP’s computational intractability, we propose an efficient two-objective hybrid local search algorithm (TOHLS. TOHLS is based on a hybrid local search algorithm (HLS that is also used to solve FCVRP. Based on the Golden CVRP benchmarks, 60 FCVRP instances are generated and tested. Finally, the computational results show that the proposed TOHLS significantly outperforms the HLS.

  12. A Hybrid Evolutionary Algorithm to Quadratic Three-Dimensional Assignment Problem with Local Search for Many-Core Graphics Processors

    Science.gov (United States)

    Lipinski, Piotr

    This paper concerns the quadratic three-dimensional assignment problem (Q3AP), an extension of the quadratic assignment problem (QAP), and proposes an efficient hybrid evolutionary algorithm combining stochastic optimization and local search with a number of crossover operators, a number of mutation operators and an auto-adaptation mechanism. Auto-adaptation manages the pool of evolutionary operators applying different operators in different computation phases to better explore the search space and to avoid premature convergence. Local search additionally optimizes populations of candidate solutions and accelerates evolutionary search. It uses a many-core graphics processor to optimize a number of solutions in parallel, which enables its incorporation into the evolutionary algorithm without excessive increases in the computation time. Experiments performed on benchmark Q3AP instances derived from the classic QAP instances proposed by Nugent et al. confirmed that the proposed algorithm is able to find optimal solutions to Q3AP in a reasonable time and outperforms best known results found in the literature.

  13. Simulating local adaptation to climate of forest trees with a Physio-Demo-Genetics model.

    Science.gov (United States)

    Oddou-Muratorio, Sylvie; Davi, Hendrik

    2014-04-01

    One challenge of evolutionary ecology is to predict the rate and mechanisms of population adaptation to environmental variations. The variations in most life history traits are shaped both by individual genotypic and by environmental variation. Forest trees exhibit high levels of genetic diversity, large population sizes, and gene flow, and they also show a high level of plasticity for life history traits. We developed a new Physio-Demo-Genetics model (denoted PDG) coupling (i) a physiological module simulating individual tree responses to the environment; (ii) a demographic module simulating tree survival, reproduction, and pollen and seed dispersal; and (iii) a quantitative genetics module controlling the heritability of key life history traits. We used this model to investigate the plastic and genetic components of the variations in the timing of budburst (TBB) along an elevational gradient of Fagus sylvatica (the European beech). We used a repeated 5 years climatic sequence to show that five generations of natural selection were sufficient to develop nonmonotonic genetic differentiation in the TBB along the local climatic gradient but also that plastic variation among different elevations and years was higher than genetic variation. PDG complements theoretical models and provides testable predictions to understand the adaptive potential of tree populations.

  14. Using particle swarm optimization to search for locally $D$-optimal designs for mixed factor experiments with binary response

    OpenAIRE

    Lukemire, Joshua; Mandal, Abhyuday; Wong, Weng Kee

    2016-01-01

    Identifying optimal designs for generalized linear models with a binary response can be a challenging task, especially when there are both continuous and discrete independent factors in the model. Theoretical results rarely exist for such models, and the handful that do exist come with restrictive assumptions. This paper investigates the use of particle swarm optimization (PSO) to search for locally $D$-optimal designs for generalized linear models with discrete and continuous factors and a b...

  15. High and distinct range-edge genetic diversity despite local bottlenecks.

    Directory of Open Access Journals (Sweden)

    Jorge Assis

    Full Text Available The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhiza polyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines.

  16. Analysis of an iterated local search algorithm for vertex cover in sparse random graphs

    DEFF Research Database (Denmark)

    Witt, Carsten

    2012-01-01

    based on the refined analysis of the Karp–Sipser algorithm by Aronson et al. (1998) [1]. Subsequently, theoretical supplements are given to experimental studies of search heuristics on random graphs. For csearch heuristic...... finds an optimal cover in polynomial time with a probability arbitrarily close to 1. This behavior relies on the absence of a giant component. As an additional insight into the randomized search, it is shown that the heuristic fails badly also on graphs consisting of a single tree component of maximum......Recently, various randomized search heuristics have been studied for the solution of the minimum vertex cover problem, in particular for sparse random instances according to the G(n,c/n) model, where c>0 is a constant. Methods from statistical physics suggest that the problem is easy if c...

  17. Heirloom tomato cultivars and local populations as sources of genetic variability for breeding

    Directory of Open Access Journals (Sweden)

    Glogovac Svetlana

    2010-01-01

    Full Text Available Five local tomato populations and fourteen heirloom cultivars were analyzed in this study. The analyzed genotypes represent a part of tomato collection of Institute of Field and Vegetable Crops in Novi Sad. The following fruit and plant traits were analyzed: growth type, fruit color, fruit shape index, fruit weight, number of locules and dry matter content. Cluster analysis was performed so as to group the analyzed genotypes by homology and divergence. The aim of this article was to determine the importance of heirloom cultivars and local populations as sources of genetic variability in tomato breeding process.

  18. Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups

    OpenAIRE

    Cesconeto, Robson Jose; Joost, Stéphane; McManus, Concepta Margaret; Paiva, Samuel Rezende; Cobuci, Jaime Araujo; Braccini, Jose

    2017-01-01

    Abstract Samples of 191 animals from 18 different Brazilian locally adapted swine genetic groups were genotyped using Illumina Porcine SNP60 BeadChip in order to identify selection signatures related to the monthly variation of Brazilian environmental variables. Using BayeScan software, 71 SNP markers were identified as FST outliers and 60 genotypes (58 markers) were found by Samβada software in 371 logistic models correlated with 112 environmental variables. Five markers were identified in b...

  19. Indexing constitutional accountability in local governance: the search for the water-power interface

    NARCIS (Netherlands)

    Regmi, A.

    2004-01-01

    This paper cites an example from a case study of the first small 2.4 MW anauti hydropower system in Nepal. Designed and implemented by Russian technical assistence in 1965, this power plant has impacted on several local irrigation systems and has become a site of contestation for local people, both

  20. Memetic Algorithm with Local Search as Modified Swine Influenza Model-Based Optimization and Its Use in ECG Filtering

    Directory of Open Access Journals (Sweden)

    Devidas G. Jadhav

    2014-01-01

    Full Text Available The Swine Influenza Model Based Optimization (SIMBO family is a newly introduced speedy optimization technique having the adaptive features in its mechanism. In this paper, the authors modified the SIMBO to make the algorithm further quicker. As the SIMBO family is faster, it is a better option for searching the basin. Thus, it is utilized in local searches in developing the proposed memetic algorithms (MAs. The MA has a faster speed compared to SIMBO with the balance in exploration and exploitation. So, MAs have small tradeoffs in convergence velocity for comprehensively optimizing the numerical standard benchmark test bed having functions with different properties. The utilization of SIMBO in the local searching is inherently the exploitation of better characteristics of the algorithms employed for the hybridization. The developed MA is applied to eliminate the power line interference (PLI from the biomedical signal ECG with the use of adaptive filter whose weights are optimized by the MA. The inference signal required for adaptive filter is obtained using the selective reconstruction of ECG from the intrinsic mode functions (IMFs of empirical mode decomposition (EMD.

  1. Effective and extensible feature extraction method using genetic algorithm-based frequency-domain feature search for epileptic EEG multiclassification.

    Science.gov (United States)

    Wen, Tingxi; Zhang, Zhongnan

    2017-05-01

    In this paper, genetic algorithm-based frequency-domain feature search (GAFDS) method is proposed for the electroencephalogram (EEG) analysis of epilepsy. In this method, frequency-domain features are first searched and then combined with nonlinear features. Subsequently, these features are selected and optimized to classify EEG signals. The extracted features are analyzed experimentally. The features extracted by GAFDS show remarkable independence, and they are superior to the nonlinear features in terms of the ratio of interclass distance and intraclass distance. Moreover, the proposed feature search method can search for features of instantaneous frequency in a signal after Hilbert transformation. The classification results achieved using these features are reasonable; thus, GAFDS exhibits good extensibility. Multiple classical classifiers (i.e., k-nearest neighbor, linear discriminant analysis, decision tree, AdaBoost, multilayer perceptron, and Naïve Bayes) achieve satisfactory classification accuracies by using the features generated by the GAFDS method and the optimized feature selection. The accuracies for 2-classification and 3-classification problems may reach up to 99% and 97%, respectively. Results of several cross-validation experiments illustrate that GAFDS is effective in the extraction of effective features for EEG classification. Therefore, the proposed feature selection and optimization model can improve classification accuracy.

  2. Local genetic structure on breeding grounds of a long-distance migrant passerine: the bluethroat (Luscinia svecica) in Spain.

    Science.gov (United States)

    Alda, Fernando; García, Javier; García, Jesús T; Suárez-Seoane, Susana

    2013-01-01

    Breeding site fidelity can be determined by environmental features, which depending on their heterogeneous distribution may shape the genetic landscape of a population. We used 10 microsatellite loci to study the genetic variation of 83 bluethroats (Luscinia svecica azuricollis) across 14 localities within the Spanish breeding population and assess the relative influence of different habitat characteristics (physiography and vegetation) on genetic differentiation. Based on the genetic variation of this population, we identified 3 geographically consistent genetic clusters that on average showed a higher genetic differentiation than among other north European populations, even those belonging to different subspecies. The inferred genetic clusters occurred in geographic areas that significantly differed in elevation. The highest genetic differentiation was observed between sites at different mountain ranges, as well as between the highest altitude sites in the northeastern locale, whereas vegetation type did not explain a significant percentage of genetic variation. The lack of correlation between geographic and genetic distances suggests that this pattern of genetic structure cannot be explained as a consequence of isolation by distance. Finally, we discuss the importance of preserving areas encompassing high environmental and genetic variation as a means of preserving evolutionary processes and adaptive potential.

  3. Phylogeny, genetic relationships and population structure of five Italian local chicken breeds

    Directory of Open Access Journals (Sweden)

    Simone Ceccobelli

    2013-09-01

    Full Text Available Number and population size of local chicken breeds in Italy is considered to be critical. Molecular data can be used to provide reliable insight into the diversity of chicken breeds. The first aim of this study was to investigate the maternal genetic origin of five Italian local chicken breeds (Ancona, Livorno, Modenese, Romagnola and Valdarnese bianca based on mitochondrial DNA (mtDNA information. Secondly, the extent of the genetic diversity, population structure and the genetic relationships among these chicken populations, by using 27 microsatellite markers, were assessed. To achieve these targets, a 506 bp fragment of the D-loop region was sequenced in 50 chickens of the five breeds. Eighteen variable sites were observed which defined 12 haplotypes. They were assigned to three clades and two maternal lineages. Results indicated that 90% of the haplotypes are related to clade E, which has been described to originate from the Indian subcontinent. For the microsatellite analysis, 137 individual blood samples from the five Italian breeds were included. A total of 147 alleles were detected at 27 microsatellite loci. The five Italian breeds showed a slightly higher degree of inbreeding (FIS=0.08 than the commercial populations that served as reference. Structure analysis showed a separation of the Italian breeds from the reference populations. A further sub-clustering allowed discriminating among the five different Italian breeds. This research provides insight into population structure, relatedness and variability of the five studied breeds.

  4. The local enhancement conundrum: in search of the adaptive value of a social learning mechanism.

    Science.gov (United States)

    Arbilly, Michal; Laland, Kevin N

    2014-02-01

    Social learning mechanisms are widely thought to vary in their degree of complexity as well as in their prevalence in the natural world. While learning the properties of a stimulus that generalize to similar stimuli at other locations (stimulus enhancement) prima facie appears more useful to an animal than learning about a specific stimulus at a specific location (local enhancement), empirical evidence suggests that the latter is much more widespread in nature. Simulating populations engaged in a producer-scrounger game, we sought to deploy mathematical models to identify the adaptive benefits of reliance on local enhancement and/or stimulus enhancement, and the alternative conditions favoring their evolution. Surprisingly, we found that while stimulus enhancement readily evolves, local enhancement is advantageous only under highly restricted conditions: when generalization of information was made unreliable or when error in social learning was high. Our results generate a conundrum over how seemingly conflicting empirical and theoretical findings can be reconciled. Perhaps the prevalence of local enhancement in nature is due to stimulus enhancement costs independent of the learning task itself (e.g. predation risk), perhaps natural habitats are often characterized by unreliable yet highly rewarding payoffs, or perhaps local enhancement occurs less frequently, and stimulus enhancement more frequently, than widely believed. Copyright © 2013 Elsevier Inc. All rights reserved.

  5. Searching for the preferred backlight intensity in liquid crystal displays with local backlight dimming

    DEFF Research Database (Denmark)

    Korhonen, Jari; Mantel, Claire; Burini, Nino

    2013-01-01

    Local backlight dimming is one of the most promising techniques for reducing power consumption and improving contrast characteristics of liquid crystal displays (LCD). In practice, due to light diffusion and a smaller number of backlight sources than pixels, local backlight dimming must often trade......-off between leakage of light in dark pixels and clipping of luminance in bright pixels. Only few studies have analyzed the subjective preferences between different luminance and contrast levels. In this paper, we present a method for defining the perceptually optimal backlight level via subjective...

  6. Local literature bias in genetic epidemiology: an empirical evaluation of the Chinese literature.

    Directory of Open Access Journals (Sweden)

    Zhenglun Pan

    2005-12-01

    Full Text Available BACKGROUND: Postulated epidemiological associations are subject to several biases. We evaluated whether the Chinese literature on human genome epidemiology may offer insights on the operation of selective reporting and language biases. METHODS AND FINDINGS: We targeted 13 gene-disease associations, each already assessed by meta-analyses, including at least 15 non-Chinese studies. We searched the Chinese Journal Full-Text Database for additional Chinese studies on the same topics. We identified 161 Chinese studies on 12 of these gene-disease associations; only 20 were PubMed-indexed (seven English full-text. Many studies (14-35 per topic were available for six topics, covering diseases common in China. With one exception, the first Chinese study appeared with a time lag (2-21 y after the first non-Chinese study on the topic. Chinese studies showed significantly more prominent genetic effects than non-Chinese studies, and 48% were statistically significant per se, despite their smaller sample size (median sample size 146 versus 268, p < 0.001. The largest genetic effects were often seen in PubMed-indexed Chinese studies (65% statistically significant per se. Non-Chinese studies of Asian-descent populations (27% significant per se also tended to show somewhat more prominent genetic effects than studies of non-Asian descent (17% significant per se. CONCLUSION: Our data provide evidence for the interplay of selective reporting and language biases in human genome epidemiology. These biases may not be limited to the Chinese literature and point to the need for a global, transparent, comprehensive outlook in molecular population genetics and epidemiologic studies in general.

  7. A systematic review of local vulnerability to climate change: In search of transparency, coherence and comparability

    NARCIS (Netherlands)

    Delaney, A.; Chesterman, S.; Crane, T.A.; Tamas, P.A.; Ericksen, P.J.

    2014-01-01

    Because vulnerability is a conceptual construct rather than a directly observable phenomenon, most vulnerability assessments measure a set of “vulnerability indicators”. In order to identify the core approaches and range of variation in the field, we conducted a systematic literature review on local

  8. Limited Pollen Dispersal Contributes to Population Genetic Structure but Not Local Adaptation in Quercus oleoides Forests of Costa Rica.

    Directory of Open Access Journals (Sweden)

    Nicholas John Deacon

    Full Text Available Quercus oleoides Cham. and Schlect., tropical live oak, is a species of conservation importance in its southern range limit of northwestern Costa Rica. It occurs in high-density stands across a fragmented landscape spanning a contrasting elevation and precipitation gradient. We examined genetic diversity and spatial genetic structure in this geographically isolated and genetically distinct population. We characterized population genetic diversity at 11 nuclear microsatellite loci in 260 individuals from 13 sites. We monitored flowering time at 10 sites, and characterized the local environment in order to compare observed spatial genetic structure to hypotheses of isolation-by-distance and isolation-by-environment. Finally, we quantified pollen dispersal distances and tested for local adaptation through a reciprocal transplant experiment in order to experimentally address these hypotheses.High genetic diversity is maintained in the population and the genetic variation is significantly structured among sampled sites. We identified 5 distinct genetic clusters and average pollen dispersal predominately occurred over short distances. Differences among sites in flowering phenology and environmental factors, however, were not strictly associated with genetic differentiation. Growth and survival of upland and lowland progeny in their native and foreign environments was expected to exhibit evidence of local adaptation due to the more extreme dry season in the lowlands. Seedlings planted in the lowland garden experienced much higher mortality than seedlings in the upland garden, but we did not identify evidence for local adaptation.Overall, this study indicates that the Costa Rican Q. oleoides population has a rich population genetic history. Despite environmental heterogeneity and habitat fragmentation, isolation-by-distance and isolation-by-environment alone do not explain spatial genetic structure. These results add to studies of genetic structure by

  9. Genetic and proteomic evidences support the localization of yeast enolase in the cell surface

    DEFF Research Database (Denmark)

    López-Villar, Elena; Monteoliva, Lucía; Larsen, Martin Røssel

    2006-01-01

    protein (GFP) as reporter proteins, proved that the 169 N-terminal amino acids are sufficient to target the protein to the cell surface. Furthermore, the enolase-GFP fusion co-localized with a plasma membrane marker. Enolase was also identified among membrane proteins obtained by a purification protocol...... that different experimental approaches (genetics, cellular biology and proteomics) show that yeast enolase can reach the cell surface and describe the protein regions involved in its cell surface targeting. Hybrid enolase truncates, fused at their C terminus with the yeast internal invertase or green fluorescent...

  10. Search for unstable DNA in schizophrenia families with evidence for genetic anticipation

    Energy Technology Data Exchange (ETDEWEB)

    Petronis, A.; Vincent, J.B.; Tatuch, Y.; Sasaki, Tsukasa [Univ. of British Columbia, Vancouver (Canada)] [and others

    1996-10-01

    Evidence for genetic anticipation has recently become an important subject of research in clinical psychiatric genetics. Renewed interest in anticipation was evoked by molecular genetic findings of a novel type of mutation termed {open_quotes}unstable DNA.{close_quotes} The unstable DNA model can be construed as the {open_quotes}best fit{close_quotes} for schizophrenia twin and family epidemiological data. We have performed a large-scale Southern blot hybridization, asymmetrical PCR-based, and repeat expansion-detection screening for (CAG){sub n}/(CTG){sub n} and (CCG){sub n}/(CGG){sub n} expansions in eastern Canadian schizophrenia multiplex families demonstrating genetic anticipation. There were no differences in (CAG){sub n}/(CTG){sub n} and (CCG){sub n}/(CGG){sub n} pattern distribution either between affected and unaffected individuals or across generations. Our findings do not support the hypothesis that large (CAG){sub n}/(CTG){sub n} or (CCG){sub n}/(CGG){sub n} expansions are the major etiologic factor in schizophrenia. A separate set of experiments directed to the analysis of small (30-130 trinucleotides), Huntington disease-type expansions in individual genes is required in order to fully exclude the presence of (CAG){sub n}/(CTG){sub n}- or (CCG){sub n}/(CGG){sub n}-type unstable mutation. 38 refs., 2 figs.

  11. Capital dynamics and local health systems: searching for a comprehensive analysis of the health sector

    Directory of Open Access Journals (Sweden)

    Maria de Fátima Siliansky de Andreazzi

    2006-01-01

    Full Text Available The article presents a proposal of a methodology aimed to analyze the health care sector according to the dynamics of capital accumulation. That approach could be summed up to more traditional approaches founded in the Public Health field, based in a political perspective. The proposal departs from concepts and methods of Industrial Organization, already used for health care markets, in the European and Latin-American (CEPAL contexts. We aggregated economic and historical variables to these approaches, which delimitate possibilities and impose constraints to the strategies of the local agents. The objective of the paper is to give methodological support to public managers at state and local level, whose role as the single commander in their territories is prescribed by the present health policy in Brazil. That includes all the fields related to private sector regulation in health: from planning the supply to quality control of providers.

  12. Genetic diversity and phylogenetic relationships in local cattle breeds of Senegal based on autosomal microsatellite markers.

    Science.gov (United States)

    Ndiaye, Ndèye Penda; Sow, Adama; Dayo, Guiguigbaza-Kossigan; Ndiaye, Saliou; Sawadogo, Germain Jerôme; Sembène, Mbacké

    2015-08-01

    the development of sustainable breeding and crossbreeding programs of Senegalese local breeds, effective management is needed towards genetic selection and transhumance to ensure their long-term survival.

  13. Genetic diversity and phylogenetic relationships in local cattle breeds of Senegal based on autosomal microsatellite markers

    Directory of Open Access Journals (Sweden)

    Ndèye Penda Ndiaye

    2015-08-01

    productivity and adaptation relative to global changes. For the development of sustainable breeding and crossbreeding programs of Senegalese local breeds, effective management is needed towards genetic selection and transhumance to ensure their long-term survival.

  14. Traditional genetic improvement and use of biotechnological techniques in searching of resistance to main fungi pathogens of Musa spp.

    Directory of Open Access Journals (Sweden)

    Michel Leiva-Mora

    2006-07-01

    Full Text Available Bananas and plantain are important food staple in human diet, even cooked or consumed fresh. Fungal diseases caused by Fusarium oxysporum f. sp. cubense (Foc and Mycosphaerella fijiensis have threated to distroy Musa spp. Those crops are difficult to breed genetically because they are steriles, do not produce fertil seeds and they are partenocarpic. Genetic crossing by hibridization have been used successfully in FHIA and IITA Musa breeding programs, they have released numerous improved hybrids to those diseases. Plant Biotechnology has developed a set of techniques for Musa micropropagation to increase multiplication rates, healthy and safety plant material for plantation. Mutagenic techniques, somaclonal variation, somatic embryogenesis and more recient genetic transformation have enabled advances and complementation with clasical Musa breeding for searching resistance to principal fungal pathogen of Musa spp. Field evaluation systems to find Musa resistant genotypes to Foc and M. fijiensis have demostrated to be usefull but laborious. Nevertheless to enhance eficacy in selection of promissory genotypes the development of reproducible early evaluation methodologies by using fungal pathogens or their derivates is needed. Key words: evaluation and selection, Fusarium oxysporum, improvement

  15. HBLAST: Parallelised sequence similarity--A Hadoop MapReducable basic local alignment search tool.

    Science.gov (United States)

    O'Driscoll, Aisling; Belogrudov, Vladislav; Carroll, John; Kropp, Kai; Walsh, Paul; Ghazal, Peter; Sleator, Roy D

    2015-04-01

    The recent exponential growth of genomic databases has resulted in the common task of sequence alignment becoming one of the major bottlenecks in the field of computational biology. It is typical for these large datasets and complex computations to require cost prohibitive High Performance Computing (HPC) to function. As such, parallelised solutions have been proposed but many exhibit scalability limitations and are incapable of effectively processing "Big Data" - the name attributed to datasets that are extremely large, complex and require rapid processing. The Hadoop framework, comprised of distributed storage and a parallelised programming framework known as MapReduce, is specifically designed to work with such datasets but it is not trivial to efficiently redesign and implement bioinformatics algorithms according to this paradigm. The parallelisation strategy of "divide and conquer" for alignment algorithms can be applied to both data sets and input query sequences. However, scalability is still an issue due to memory constraints or large databases, with very large database segmentation leading to additional performance decline. Herein, we present Hadoop Blast (HBlast), a parallelised BLAST algorithm that proposes a flexible method to partition both databases and input query sequences using "virtual partitioning". HBlast presents improved scalability over existing solutions and well balanced computational work load while keeping database segmentation and recompilation to a minimum. Enhanced BLAST search performance on cheap memory constrained hardware has significant implications for in field clinical diagnostic testing; enabling faster and more accurate identification of pathogenic DNA in human blood or tissue samples. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. Properties of global- and local-ancestry adjustments in genetic association tests in admixed populations.

    Science.gov (United States)

    Martin, Eden R; Tunc, Ilker; Liu, Zhi; Slifer, Susan H; Beecham, Ashley H; Beecham, Gary W

    2018-03-01

    Population substructure can lead to confounding in tests for genetic association, and failure to adjust properly can result in spurious findings. Here we address this issue of confounding by considering the impact of global ancestry (average ancestry across the genome) and local ancestry (ancestry at a specific chromosomal location) on regression parameters and relative power in ancestry-adjusted and -unadjusted models. We examine theoretical expectations under different scenarios for population substructure; applying different regression models, verifying and generalizing using simulations, and exploring the findings in real-world admixed populations. We show that admixture does not lead to confounding when the trait locus is tested directly in a single admixed population. However, if there is more complex population structure or a marker locus in linkage disequilibrium (LD) with the trait locus is tested, both global and local ancestry can be confounders. Additionally, we show the genotype parameters of adjusted and unadjusted models all provide tests for LD between the marker and trait locus, but in different contexts. The local ancestry adjusted model tests for LD in the ancestral populations, while tests using the unadjusted and the global ancestry adjusted models depend on LD in the admixed population(s), which may be enriched due to different ancestral allele frequencies. Practically, this implies that global-ancestry adjustment should be used for screening, but local-ancestry adjustment may better inform fine mapping and provide better effect estimates at trait loci. © 2017 WILEY PERIODICALS, INC.

  17. The population genomic landscape of human genetic structure, admixture history and local adaptation in Peninsular Malaysia.

    Science.gov (United States)

    Deng, Lian; Hoh, Boon Peng; Lu, Dongsheng; Fu, Ruiqing; Phipps, Maude E; Li, Shilin; Nur-Shafawati, Ab Rajab; Hatin, Wan Isa; Ismail, Endom; Mokhtar, Siti Shuhada; Jin, Li; Zilfalil, Bin Alwi; Marshall, Christian R; Scherer, Stephen W; Al-Mulla, Fahd; Xu, Shuhua

    2014-09-01

    Peninsular Malaysia is a strategic region which might have played an important role in the initial peopling and subsequent human migrations in Asia. However, the genetic diversity and history of human populations--especially indigenous populations--inhabiting this area remain poorly understood. Here, we conducted a genome-wide study using over 900,000 single nucleotide polymorphisms (SNPs) in four major Malaysian ethnic groups (MEGs; Malay, Proto-Malay, Senoi and Negrito), and made comparisons of 17 world-wide populations. Our data revealed that Peninsular Malaysia has greater genetic diversity corresponding to its role as a contact zone of both early and recent human migrations in Asia. However, each single Orang Asli (indigenous) group was less diverse with a smaller effective population size (N(e)) than a European or an East Asian population, indicating a substantial isolation of some duration for these groups. All four MEGs were genetically more similar to Asian populations than to other continental groups, and the divergence time between MEGs and East Asian populations (12,000--6,000 years ago) was also much shorter than that between East Asians and Europeans. Thus, Malaysian Orang Asli groups, despite their significantly different features, may share a common origin with the other Asian groups. Nevertheless, we identified traces of recent gene flow from non-Asians to MEGs. Finally, natural selection signatures were detected in a batch of genes associated with immune response, human height, skin pigmentation, hair and facial morphology and blood pressure in MEGs. Notable examples include SYN3 which is associated with human height in all Orang Asli groups, a height-related gene (PNPT1) and two blood pressure-related genes (CDH13 and PAX5) in Negritos. We conclude that a long isolation period, subsequent gene flow and local adaptations have jointly shaped the genetic architectures of MEGs, and this study provides insight into the peopling and human migration

  18. Local and global genetic diversity of protozoan parasites: Spatial distribution of Cryptosporidium and Giardia genotypes.

    Science.gov (United States)

    Garcia-R, Juan C; French, Nigel; Pita, Anthony; Velathanthiri, Niluka; Shrestha, Rima; Hayman, David

    2017-07-01

    Cryptosporidiosis and giardiasis are recognized as significant enteric diseases due to their long-term health effects in humans and their economic impact in agriculture and medical care. Molecular analysis is essential to identify species and genotypes causing these infectious diseases and provides a potential tool for monitoring. This study uses information on species and genetic variants to gain insights into the geographical distribution and spatial patterns of Cryptosporidium and Giardia parasites. Here, we describe the population heterogeneity of genotypic groups within Cryptosporidium and Giardia present in New Zealand using gp60 and gdh markers to compare the observed variation with other countries around the globe. Four species of Cryptosporidium (C. hominis, C. parvum, C. cuniculus and C. erinacei) and one species of Giardia (G. intestinalis) were identified. These species have been reported worldwide and there are not unique Cryptosporidium gp60 subtype families and Giardia gdh assemblages in New Zealand, most likely due to high gene flow of historical and current human activity (travel and trade) and persistence of large host population sizes. The global analysis revealed that genetic variants of these pathogens are widely distributed. However, genetic variation is underestimated by data biases (e.g. neglected submission of sequences to genetic databases) and low sampling. New genotypes are likely to be discovered as sampling efforts increase according to accumulation prediction analyses, especially for C. parvum. Our study highlights the need for greater sampling and archiving of genotypes globally to allow comparative analyses that help understand the population dynamics of these protozoan parasites. Overall our study represents a comprehensive overview for exploring local and global protozoan genotype diversity and advances our understanding of the importance for surveillance and potential risk associated with these infectious diseases.

  19. Local and global genetic diversity of protozoan parasites: Spatial distribution of Cryptosporidium and Giardia genotypes.

    Directory of Open Access Journals (Sweden)

    Juan C Garcia-R

    2017-07-01

    Full Text Available Cryptosporidiosis and giardiasis are recognized as significant enteric diseases due to their long-term health effects in humans and their economic impact in agriculture and medical care. Molecular analysis is essential to identify species and genotypes causing these infectious diseases and provides a potential tool for monitoring. This study uses information on species and genetic variants to gain insights into the geographical distribution and spatial patterns of Cryptosporidium and Giardia parasites. Here, we describe the population heterogeneity of genotypic groups within Cryptosporidium and Giardia present in New Zealand using gp60 and gdh markers to compare the observed variation with other countries around the globe. Four species of Cryptosporidium (C. hominis, C. parvum, C. cuniculus and C. erinacei and one species of Giardia (G. intestinalis were identified. These species have been reported worldwide and there are not unique Cryptosporidium gp60 subtype families and Giardia gdh assemblages in New Zealand, most likely due to high gene flow of historical and current human activity (travel and trade and persistence of large host population sizes. The global analysis revealed that genetic variants of these pathogens are widely distributed. However, genetic variation is underestimated by data biases (e.g. neglected submission of sequences to genetic databases and low sampling. New genotypes are likely to be discovered as sampling efforts increase according to accumulation prediction analyses, especially for C. parvum. Our study highlights the need for greater sampling and archiving of genotypes globally to allow comparative analyses that help understand the population dynamics of these protozoan parasites. Overall our study represents a comprehensive overview for exploring local and global protozoan genotype diversity and advances our understanding of the importance for surveillance and potential risk associated with these infectious diseases.

  20. A search for genetic effects of atomic bomb radiation on the growth and development of the F1 generation, 1

    International Nuclear Information System (INIS)

    Furusho, Toshiyuki; Otake, Masanori.

    1978-10-01

    In a search for possible genetic effects of atomic bomb radiation on the growth and development of offspring of A-bomb survivors a survey was made in 1965 on approximately 200,000 children of all primary schools, junior high schools, and senior high schools in the cities of Hiroshima and Nagasaki. Of the collected data, those pertaining to senior high school students 15 to 17 years of age of Hiroshima City were analyzed to determine if there was any genetic effect of A-bomb radiation on stature. Comparisons were made with regard to the mean stature and variance of the offspring and the covariance and correlation between one parent or the sum for both parents and offspring for the exposed group and the nonexposed group. The observed differences included those with both positive and negative signs, but none were statistically significant nor did they demonstrate any specific tendency. A comparison was made with a similar study reported by Neel and Schull. Furthermore, estimation of the regression coefficients of the mean stature, variance, covariance, and correlation between one parent or the sum for both parents and offspring by parental radiation dose also did not show any specific tendency. Though the genetic effects of A-bomb radiation on stature could not be accurately estimated in the current series of analyses, the stature data of 6- to 14-year-old children in Hiroshima and those of 6- to 17-year-old children in Nagasaki Will soon be studied, which should permit a more comprehensive and extensive analysis and evaluation of the possible genetic effects of radiation on stature. (author)

  1. Improving search for low energy protein structures with an iterative niche genetic algorithm

    DEFF Research Database (Denmark)

    Helles, Glennie

    2010-01-01

    . Particularly parallel implementations have been demonstrated to generally outperform their sequential counterparts, but they are nevertheless used to a much lesser extent for protein structure prediction. In this work we focus strictly on parallel algorithms for protein structure prediction and propose......In attempts to predict the tertiary structure of proteins we use almost exclusively metaheuristics. However, despite known differences in performance of metaheuristics for different problems, the effect of the choice of metaheuristic has received precious little attention in this field...... that the iterative niche algorithm converges much faster at lower energy structures than both the traditional niche genetic algorithm and the parallel tempering algorithm....

  2. Environmental and Genetic Factors Regulating Localization of the Plant Plasma Membrane H+-ATPase.

    Science.gov (United States)

    Haruta, Miyoshi; Tan, Li Xuan; Bushey, Daniel B; Swanson, Sarah J; Sussman, Michael R

    2018-01-01

    A P-type H + -ATPase is the primary transporter that converts ATP to electrochemical energy at the plasma membrane of higher plants. Its product, the proton-motive force, is composed of an electrical potential and a pH gradient. Many studies have demonstrated that this proton-motive force not only drives the secondary transporters required for nutrient uptake, but also plays a direct role in regulating cell expansion. Here, we have generated a transgenic Arabidopsis ( Arabidopsis thaliana ) plant expressing H + -ATPase isoform 2 (AHA2) that is translationally fused with a fluorescent protein and examined its cellular localization by live-cell microscopy. Using a 3D imaging approach with seedlings grown for various times under a variety of light intensities, we demonstrate that AHA2 localization at the plasma membrane of root cells requires light. In dim light conditions, AHA2 is found in intracellular compartments, in addition to the plasma membrane. This localization profile was age-dependent and specific to cell types found in the transition zone located between the meristem and elongation zones. The accumulation of AHA2 in intracellular compartments is consistent with reduced H + secretion near the transition zone and the suppression of root growth. By examining AHA2 localization in a knockout mutant of a receptor protein kinase, FERONIA, we found that the intracellular accumulation of AHA2 in the transition zone is dependent on a functional FERONIA-dependent inhibitory response in root elongation. Overall, this study provides a molecular underpinning for understanding the genetic, environmental, and developmental factors influencing root growth via localization of the plasma membrane H + -ATPase. © 2018 American Society of Plant Biologists. All Rights Reserved.

  3. Optimal clustering of MGs based on droop controller for improving reliability using a hybrid of harmony search and genetic algorithms.

    Science.gov (United States)

    Abedini, Mohammad; Moradi, Mohammad H; Hosseinian, S M

    2016-03-01

    This paper proposes a novel method to address reliability and technical problems of microgrids (MGs) based on designing a number of self-adequate autonomous sub-MGs via adopting MGs clustering thinking. In doing so, a multi-objective optimization problem is developed where power losses reduction, voltage profile improvement and reliability enhancement are considered as the objective functions. To solve the optimization problem a hybrid algorithm, named HS-GA, is provided, based on genetic and harmony search algorithms, and a load flow method is given to model different types of DGs as droop controller. The performance of the proposed method is evaluated in two case studies. The results provide support for the performance of the proposed method. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

  4. A novel chaotic particle swarm optimization approach using Henon map and implicit filtering local search for economic load dispatch

    International Nuclear Information System (INIS)

    Coelho, Leandro dos Santos; Mariani, Viviana Cocco

    2009-01-01

    Particle swarm optimization (PSO) is a population-based swarm intelligence algorithm driven by the simulation of a social psychological metaphor instead of the survival of the fittest individual. Based on the chaotic systems theory, this paper proposed a novel chaotic PSO combined with an implicit filtering (IF) local search method to solve economic dispatch problems. Since chaotic mapping enjoys certainty, ergodicity and the stochastic property, the proposed PSO introduces chaos mapping using Henon map sequences which increases its convergence rate and resulting precision. The chaotic PSO approach is used to produce good potential solutions, and the IF is used to fine-tune of final solution of PSO. The hybrid methodology is validated for a test system consisting of 13 thermal units whose incremental fuel cost function takes into account the valve-point loading effects. Simulation results are promising and show the effectiveness of the proposed approach.

  5. A matter of timing: identifying significant multi-dose radiotherapy improvements by numerical simulation and genetic algorithm search.

    Directory of Open Access Journals (Sweden)

    Simon D Angus

    Full Text Available Multi-dose radiotherapy protocols (fraction dose and timing currently used in the clinic are the product of human selection based on habit, received wisdom, physician experience and intra-day patient timetabling. However, due to combinatorial considerations, the potential treatment protocol space for a given total dose or treatment length is enormous, even for relatively coarse search; well beyond the capacity of traditional in-vitro methods. In constrast, high fidelity numerical simulation of tumor development is well suited to the challenge. Building on our previous single-dose numerical simulation model of EMT6/Ro spheroids, a multi-dose irradiation response module is added and calibrated to the effective dose arising from 18 independent multi-dose treatment programs available in the experimental literature. With the developed model a constrained, non-linear, search for better performing cadidate protocols is conducted within the vicinity of two benchmarks by genetic algorithm (GA techniques. After evaluating less than 0.01% of the potential benchmark protocol space, candidate protocols were identified by the GA which conferred an average of 9.4% (max benefit 16.5% and 7.1% (13.3% improvement (reduction on tumour cell count compared to the two benchmarks, respectively. Noticing that a convergent phenomenon of the top performing protocols was their temporal synchronicity, a further series of numerical experiments was conducted with periodic time-gap protocols (10 h to 23 h, leading to the discovery that the performance of the GA search candidates could be replicated by 17-18 h periodic candidates. Further dynamic irradiation-response cell-phase analysis revealed that such periodicity cohered with latent EMT6/Ro cell-phase temporal patterning. Taken together, this study provides powerful evidence towards the hypothesis that even simple inter-fraction timing variations for a given fractional dose program may present a facile, and highly cost

  6. A matter of timing: identifying significant multi-dose radiotherapy improvements by numerical simulation and genetic algorithm search.

    Science.gov (United States)

    Angus, Simon D; Piotrowska, Monika Joanna

    2014-01-01

    Multi-dose radiotherapy protocols (fraction dose and timing) currently used in the clinic are the product of human selection based on habit, received wisdom, physician experience and intra-day patient timetabling. However, due to combinatorial considerations, the potential treatment protocol space for a given total dose or treatment length is enormous, even for relatively coarse search; well beyond the capacity of traditional in-vitro methods. In constrast, high fidelity numerical simulation of tumor development is well suited to the challenge. Building on our previous single-dose numerical simulation model of EMT6/Ro spheroids, a multi-dose irradiation response module is added and calibrated to the effective dose arising from 18 independent multi-dose treatment programs available in the experimental literature. With the developed model a constrained, non-linear, search for better performing cadidate protocols is conducted within the vicinity of two benchmarks by genetic algorithm (GA) techniques. After evaluating less than 0.01% of the potential benchmark protocol space, candidate protocols were identified by the GA which conferred an average of 9.4% (max benefit 16.5%) and 7.1% (13.3%) improvement (reduction) on tumour cell count compared to the two benchmarks, respectively. Noticing that a convergent phenomenon of the top performing protocols was their temporal synchronicity, a further series of numerical experiments was conducted with periodic time-gap protocols (10 h to 23 h), leading to the discovery that the performance of the GA search candidates could be replicated by 17-18 h periodic candidates. Further dynamic irradiation-response cell-phase analysis revealed that such periodicity cohered with latent EMT6/Ro cell-phase temporal patterning. Taken together, this study provides powerful evidence towards the hypothesis that even simple inter-fraction timing variations for a given fractional dose program may present a facile, and highly cost-effecitive means

  7. 3D maps of the local interstellar medium: searching for the imprints of past events

    Science.gov (United States)

    Lallement, R.

    2015-01-01

    Inversion of interstellar (IS) gas or dust absorbing columns measured along the path to stars distributed in distance and direction allows reconstructing the distribution of interstellar matter (ISM) in three dimensions. A low resolution IS dust map based on reddening measurements towards 23,000 nearby stars is used to illustrate the potential of the more detailed maps that are expected within the next several years. The map reveals the location of the main IS cloud complexes up to distances on the order of 600 to 1200 pc depending on directions. Owing to target selection biases towards weakly reddened, brighter stars, the map is especially revealing in terms of regions devoid of IS matter. It traces the Local Bubble and its neighboring cavities, including a conspicuous, giant, >=1000 pc long cavity in the third quadrant located beyond the so-called βMa tunnel. This cavity is bordered by the main constituents of the Gould belt, the well-known and still unexplained rotating and expanding ring of clouds and young stars, inclined by ~ 20° to the galactic plane. Comparing the dust distribution with X-ray emission maps and IS gas observations shows that the giant cavity contains a large fraction of warm, fully ionized and dust-poor gas in addition to million K, X-ray bright gas. This set of structures must reflect the main events that occurred in the past; today however even the formation of the Gould belt is still a matter of controversy. It has been suggested recently that the Cretaceus-Tertiary (KT) mass extinction is potentially due to a gamma-ray burst (GRB) that occurred in the massive globular cluster (GC) 47 Tuc during its close encounter with the Sun ~70 Myrs ago. Such a hypothesis is based on computations of the cluster and Sun trajectories and the frequency of short GRBs in GC's. Given the mass, speed and size of 47 Tuc, wherever it crossed the Galactic plane it must have produced at the crossing site significant dynamical effects on the disk stars and IS

  8. Optimal filter design with progressive genetic algorithm for local damage detection in rolling bearings

    Science.gov (United States)

    Wodecki, Jacek; Michalak, Anna; Zimroz, Radoslaw

    2018-03-01

    Harsh industrial conditions present in underground mining cause a lot of difficulties for local damage detection in heavy-duty machinery. For vibration signals one of the most intuitive approaches of obtaining signal with expected properties, such as clearly visible informative features, is prefiltration with appropriately prepared filter. Design of such filter is very broad field of research on its own. In this paper authors propose a novel approach to dedicated optimal filter design using progressive genetic algorithm. Presented method is fully data-driven and requires no prior knowledge of the signal. It has been tested against a set of real and simulated data. Effectiveness of operation has been proven for both healthy and damaged case. Termination criterion for evolution process was developed, and diagnostic decision making feature has been proposed for final result determinance.

  9. [Genetic diversity and mating system Pinus brutia var. Stankewiczii sukacz. in small localities of Sudak (Crimea)].

    Science.gov (United States)

    Korshikov, I I; Kalafat, L A; Milchevskaya, Ya G

    2015-01-01

    A comparative analysis of genetic variation at 12 polymorphic isozyme loci, and the mating system has been carried out in mature trees and their seed progeny in three small localities of Pinus brutia var. stankewiczii Sukacz. near the town of Sudak--settlement of Novyi Svet in the Crimea. We found that embryos maintain the same allelic diversity as mother plants but their observed heterozygosity is lower on the average by 37.4%. The significant deviation of genotype distribution from the theoretically expected ratios caused by the deficiency of heterozygotes was observed at 8 out of 12 loci. Multilocus estimate of outcrossing rate (t(m)) in populations varied from 68.9 to 94.9% making on the average 80.7%.

  10. Determination of genetic polymorphism in Guney Karaman local Turkish sheep breed by using STR markers

    Science.gov (United States)

    Karslı, Taki; Balcıoǧlu, Murat Soner

    2017-04-01

    The objective of this study was to assess genetic diversity of Güney Karaman Turkish local sheep breed. A total of 29 samples were genotyped by using 14 STR markers. All markers were polymorphic. The number of alleles in Güney Karaman sheep breed ranged from 3 to 11 per locus, with a mean of 7.42. The average observed and expected heterozygosity was 0.659 and 0.794, respectively. Mean inbreeding coefficient (Fis) value was found 0.175. The PIC values ranged from 0.569 to 0.860 with a mean of 0.743. The findings of this research demonstrate at moderate level gene diversity and heterozygosity with lower inbreeding in Güney Karaman sheep breed.

  11. Genetic variation in two conserved local Romanian pig breeds using type 1 DNA markers

    Directory of Open Access Journals (Sweden)

    Wales Richard

    2001-07-01

    Full Text Available Abstract Analysis of the genetic variation of an endangered population is an important component for the success of conservation. Animals from two local Romanian pig breeds, the Mangalitsa and Bazna, were analysed for variation at a number of genetic loci using PCR-based DNA tests. Polymorphism was assessed at loci which 1 are known to cause phenotypic variation, 2 are potentially involved in trait differences or 3 are putative candidate genes. The traits considered are disease resistance, growth, coat colour, meat quality and prolificacy. Even though the populations are small and the markers are limited to specific genes, we found significant differences in five of the ten characterised loci. In some cases the observed allele frequencies were interesting in relation to gene function and the phenotype of the breed. These breeds are part of a conservation programme in Romania and marker information may be useful in preserving a representative gene pool in the populations. The use of polymorphisms in type 1 (gene markers may be a useful complement to analysis based on anonymous markers.

  12. Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups.

    Science.gov (United States)

    Cesconeto, Robson Jose; Joost, Stéphane; McManus, Concepta Margaret; Paiva, Samuel Rezende; Cobuci, Jaime Araujo; Braccini, Jose

    2017-11-01

    Samples of 191 animals from 18 different Brazilian locally adapted swine genetic groups were genotyped using Illumina Porcine SNP60 BeadChip in order to identify selection signatures related to the monthly variation of Brazilian environmental variables. Using BayeScan software, 71 SNP markers were identified as F ST outliers and 60 genotypes (58 markers) were found by Samβada software in 371 logistic models correlated with 112 environmental variables. Five markers were identified in both methods, with a Kappa value of 0.073 (95% CI: 0.011-0.134). The frequency of these markers indicated a clear north-south country division that reflects Brazilian environmental differences in temperature, solar radiation, and precipitation. Global spatial territory correlation for environmental variables corroborates this finding (average Moran's I = 0.89, range from 0.55 to 0.97). The distribution of alleles over the territory was not strongly correlated with the breed/genetic groups. These results are congruent with previous mtDNA studies and should be used to direct germplasm collection for the National gene bank.

  13. Information-Fusion Methods Based Simultaneous Localization and Mapping for Robot Adapting to Search and Rescue Postdisaster Environments

    Directory of Open Access Journals (Sweden)

    Hongling Wang

    2018-01-01

    Full Text Available The first application of utilizing unique information-fusion SLAM (IF-SLAM methods is developed for mobile robots performing simultaneous localization and mapping (SLAM adapting to search and rescue (SAR environments in this paper. Several fusion approaches, parallel measurements filtering, exploration trajectories fusing, and combination sensors’ measurements and mobile robots’ trajectories, are proposed. The novel integration particle filter (IPF and optimal improved EKF (IEKF algorithms are derived for information-fusion systems to perform SLAM task in SAR scenarios. The information-fusion architecture consists of multirobots and multisensors (MAM; multiple robots mount on-board laser range finder (LRF sensors, localization sonars, gyro odometry, Kinect-sensor, RGB-D camera, and other proprioceptive sensors. This information-fusion SLAM (IF-SLAM is compared with conventional methods, which indicates that fusion trajectory is more consistent with estimated trajectories and real observation trajectories. The simulations and experiments of SLAM process are conducted in both cluttered indoor environment and outdoor collapsed unstructured scenario, and experimental results validate the effectiveness of the proposed information-fusion methods in improving SLAM performances adapting to SAR scenarios.

  14. Optimization In Searching Daily Rule Curve At Mosul Regulating Reservoir, North Iraq Using Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Thair M. Al-Taiee

    2013-05-01

    Full Text Available To obtain optimal operating rules for storage reservoirs, large numbers of simulation and optimization models have been developed over the past several decades, which vary significantly in their mechanisms and applications. Rule curves are guidelines for long term reservoir operation. An efficient technique is required to find the optimal rule curves that can mitigate water shortage in long term operation. The investigation of developed Genetic Algorithm (GA technique, which is an optimization approach base on the mechanics of natural selection, derived from the theory of natural evolution, was carried out to through the application to predict the daily rule curve of  Mosul regulating reservoir in Iraq.  Record daily inflows, outflow, water level in the reservoir for 19 year (1986-1990 and (1994-2007 were used in the developed model for assessing the optimal reservoir operation. The objective function is set to minimize the annual sum of squared deviation from the desired downstream release and desired storage volume in the reservoir. The decision variables are releases, storage volume, water level and outlet (demand from the reservoir. The results of the GA model gave a good agreement during the comparison with the actual rule curve and the designed rating curve of the reservoir. The simulated result shows that GA-derived policies are promising and competitive and can be effectively used for daily reservoir operation in addition to the rational monthly operation and predicting also rating curve of reservoirs.

  15. GENETIC VARIATION IN THREE BREEDS OF INDONESIAN LOCAL DUCKS BASED ON BLOOD AND EGG WHITE PROTEIN POLYMORPHISM

    Directory of Open Access Journals (Sweden)

    S. Johari

    2013-03-01

    Full Text Available A study of genetic variation of four blood protein loci and three egg white loci in three breeds of Indonesian local ducks (Magelang duck = MAD, Tegal duck = TED and Mojosari duck= MOD was investigated by using polyacrilamide gel electrophoresis (PAGE. The result showed that four blood protein loci (Pre-albumin, Albumin, Transferrin and Post-transferrin and three egg white loci (Ovalbumin, Ovoglobulin and Conalbumin were found to be polymorphic in three breeds of local ducks. There was no difference on blood and egg white protein polyimorphism. The average value of heterozygosity on three breeds of local ducks had a genetic potential to determine the controlled mating system and selection to obtain pure line. The closest phylogenetic relationship among the three breeds of local ducks occurred between MAD and TED.

  16. A hypothesis-generating search for new genetic breast cancer syndromes - a national study in 803 Swedish families

    Directory of Open Access Journals (Sweden)

    von Wachenfeldt Anna

    2007-03-01

    Full Text Available Abstract Among Swedish families with an inherited predisposition for breast cancer, less than one third segregate mutations in genes known to be associated with an increased risk of breast cancer in combination with other types of tumours. In a search for new putative familial breast cancer syndromes we studied Swedish families undergoing genetic counselling during 1992-2000. Four thousand families from counselling clinics in Sweden were eligible for study. Families with breast cancer only were excluded, as were families with mutations in genes already known to be associated with malignant diseases. We identified 803 families with two or more cases of breast cancer and at least one other type of cancer. The observed proportion of different types of non-breast cancer was compared with the percentage distribution of non-breast cancer tumours in Sweden in 1958 and 1999. We found tumours in the colon, ovary, endometrium, pancreas and liver, as well as leukaemia in a significantly larger proportion of the study population than in the general population in both years. These tumours were also seen among families where several members had one additional tumour, suggesting that malignancies at these sites, in combination with breast tumours, could constitute genetic syndromes. Endometrial carcinoma has not previously been described in the context of breast cancer syndromes and the excess of malignancies at this site could not be explained by secondary tumours. Thus, we suggest that endometrial carcinoma and breast cancer constitute a new breast cancer syndrome. Further investigation is warranted to categorize phenotypes of both breast and endometrial tumours in this subgroup.

  17. Incremental artificial bee colony with local search to economic dispatch problem with ramp rate limits and prohibited operating zones

    International Nuclear Information System (INIS)

    Özyön, Serdar; Aydin, Doğan

    2013-01-01

    Highlights: ► Prohibited operating zone economic dispatch problem has been solved by IABC-LS. ► The losses used in the solution of the problem have been computed by B-loss matrix. ► IABC-LS method has been applied to three test systems in literature. ► The values obtained by IABC and IABC-LS are better than the results in literature. - Abstract: In this study, prohibited operating zone economic power dispatch problem which considers ramp rate limit, has been solved by incremental artificial bee colony algorithm (IABC) and incremental artificial bee colony algorithm with local search (IABC-LS) methods. The transmission line losses used in the solution of the problem have been computed by B-loss matrix. IABC, IABC-LS methods have been applied to three different test systems in literature which consist of 6, 15 and 40 generators. The attained optimum solution values have been compared with the optimum results in literature and have been discussed.

  18. Dengue Baidu Search Index data can improve the prediction of local dengue epidemic: A case study in Guangzhou, China.

    Science.gov (United States)

    Li, Zhihao; Liu, Tao; Zhu, Guanghu; Lin, Hualiang; Zhang, Yonghui; He, Jianfeng; Deng, Aiping; Peng, Zhiqiang; Xiao, Jianpeng; Rutherford, Shannon; Xie, Runsheng; Zeng, Weilin; Li, Xing; Ma, Wenjun

    2017-03-01

    Dengue fever (DF) in Guangzhou, Guangdong province in China is an important public health issue. The problem was highlighted in 2014 by a large, unprecedented outbreak. In order to respond in a more timely manner and hence better control such potential outbreaks in the future, this study develops an early warning model that integrates internet-based query data into traditional surveillance data. A Dengue Baidu Search Index (DBSI) was collected from the Baidu website for developing a predictive model of dengue fever in combination with meteorological and demographic factors. Generalized additive models (GAM) with or without DBSI were established. The generalized cross validation (GCV) score and deviance explained indexes, intraclass correlation coefficient (ICC) and root mean squared error (RMSE), were respectively applied to measure the fitness and the prediction capability of the models. Our results show that the DBSI with one-week lag has a positive linear relationship with the local DF occurrence, and the model with DBSI (ICC:0.94 and RMSE:59.86) has a better prediction capability than the model without DBSI (ICC:0.72 and RMSE:203.29). Our study suggests that a DSBI combined with traditional disease surveillance and meteorological data can improve the dengue early warning system in Guangzhou.

  19. A novel cooperative localization algorithm using enhanced particle filter technique in maritime search and rescue wireless sensor network.

    Science.gov (United States)

    Wu, Huafeng; Mei, Xiaojun; Chen, Xinqiang; Li, Junjun; Wang, Jun; Mohapatra, Prasant

    2017-09-29

    Maritime search and rescue (MSR) play a significant role in Safety of Life at Sea (SOLAS). However, it suffers from scenarios that the measurement information is inaccurate due to wave shadow effect when utilizing wireless Sensor Network (WSN) technology in MSR. In this paper, we develop a Novel Cooperative Localization Algorithm (NCLA) in MSR by using an enhanced particle filter method to reduce measurement errors on observation model caused by wave shadow effect. First, we take into account the mobility of nodes at sea to develop a motion model-Lagrangian model. Furthermore, we introduce both state model and observation model to constitute a system model for particle filter (PF). To address the impact of the wave shadow effect on the observation model, we develop an optimal parameter derived by Kullback-Leibler divergence (KLD) to mitigate the error. After the optimal parameter is acquired, an improved likelihood function is presented. Finally, the estimated position is acquired. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

  20. HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching.

    Science.gov (United States)

    Bi, Guiqi; Mao, Yunxiang; Xing, Qikun; Cao, Min

    2018-01-01

    Organelle phylogenomic analysis requires precisely constructed multi-gene alignment matrices concatenated by pre-aligned single gene datasets. For non-bioinformaticians, it can take days to weeks to manually create high-quality multi-gene alignments comprising tens or hundreds of homologous genes. Here, we describe a new and highly efficient pipeline, HomBlocks, which uses a homologous block searching method to construct multiple sequence alignment. This approach can automatically recognize locally collinear blocks among organelle genomes and excavate phylogenetically informative regions to construct multiple sequence alignment in a few hours. In addition, HomBlocks supports organelle genomes without annotation and makes adjustment to different taxon datasets, thereby enabling the inclusion of as many common genes as possible. Topology comparison of trees built by conventional multi-gene and HomBlocks alignments implemented in different taxon categories shows that the same efficiency can be achieved by HomBlocks as when using the traditional method. The availability of Homblocks makes organelle phylogenetic analyses more accessible to non-bioinformaticians, thereby promising to lead to a better understanding of phylogenic relationships at an organelle genome level. HomBlocks is implemented in Perl and is supported by Unix-like operative systems, including Linux and macOS. The Perl source code is freely available for download from https://github.com/fenghen360/HomBlocks.git, and documentation and tutorials are available at https://github.com/fenghen360/HomBlocks. yxmao@ouc.edu.cn or fenghen360@126.com. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Calculating all local minima on liquidus surfaces using the FactSage software and databases and the Mesh Adaptive Direct Search algorithm

    International Nuclear Information System (INIS)

    Gheribi, Aimen E.; Robelin, Christian; Digabel, Sebastien Le; Audet, Charles; Pelton, Arthur D.

    2011-01-01

    Highlights: → Systematic search of low melting temperatures in multicomponent systems. → Calculation of eutectic in multicomponent systems. → The FactSage software and the direct search algorithm are used simultaneously. - Abstract: It is often of interest, for a multicomponent system, to identify the low melting compositions at which local minima of the liquidus surface occur. The experimental determination of these minima can be very time-consuming. An alternative is to employ the CALPHAD approach using evaluated thermodynamic databases containing optimized model parameters giving the thermodynamic properties of all phases as functions of composition and temperature. Liquidus temperatures are then calculated by Gibbs free energy minimization algorithms which access the databases. Several such large databases for many multicomponent systems have been developed over the last 40 years, and calculated liquidus temperatures are generally quite accurate. In principle, one could then search for local liquidus minima by simply calculating liquidus temperatures over a compositional grid. In practice, such an approach is prohibitively time-consuming for all but the simplest systems since the required number of grid points is extremely large. In the present article, the FactSage database computing system is coupled with the powerful Mesh Adaptive Direct Search (MADS) algorithm in order to search for and calculate automatically all liquidus minima in a multicomponent system. Sample calculations for a 4-component oxide system, a 7-component chloride system, and a 9-component ferrous alloy system are presented. It is shown that the algorithm is robust and rapid.

  2. GENETIC VARIATION IN THREE BREEDS OF INDONESIAN LOCAL DUCKS BASED ON BLOOD AND EGG WHITE PROTEIN POLYMORPHISM

    Directory of Open Access Journals (Sweden)

    S. Johari

    2014-10-01

    Full Text Available A study of genetic variation of four blood protein loci and three egg white loci in three breeds ofIndonesian local ducks (Magelang duck = MAD, Tegal duck = TED and Mojosari duck= MOD wasinvestigated by using polyacrilamide gel electrophoresis (PAGE. The result showed that four bloodprotein loci (Pre-albumin, Albumin, Transferrin and Post-transferrin and three egg white loci(Ovalbumin, Ovoglobulin and Conalbumin were found to be polymorphic in three breeds of localducks. There was no difference on blood and egg white protein polyimorphism. The average value ofheterozygosity on three breeds of local ducks had a genetic potential to determine the controlled matingsystem and selection to obtain pure line. The closest phylogenetic relationship among the three breeds oflocal ducks occurred between MAD and TED.

  3. Analysis of genetic and cultural conservation value of three indigenous Croatian cattle breeds in a local and global context.

    Science.gov (United States)

    Ramljak, J; Ivanković, A; Veit-Kensch, C E; Förster, M; Medugorac, I

    2011-02-01

    It is widely accepted that autochthonous cattle breeds can be important genetic resources for unforeseeable environmental conditions in the future. Apart from that, they often represent local culture and tradition and thus assist in the awareness of ethnic identity of a country. In Croatia, there are only three indigenous cattle breeds, Croatian Buša, Slavonian Syrmian Podolian and Istrian Cattle. All of them are threatened but specialized in a particular habitat and production system. We analysed 93 microsatellites in 51 animals of each breed to get thorough information about genetic diversity and population structure. We further set them within an existing frame of additional 16 breeds that have been genotyped for the same marker set and cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the north-west of Europe. The cultural value was evaluated regarding the role in landscape, gastronomy, folklore and handicraft. The overall results recognize Croatian Buša being partly admixed but harbouring an enormous genetic diversity comparable with other traditional unselected Buša breeds in the Anatolian and Balkan areas. The Podolian cattle showed the lowest genetic diversity at the highest genetic distance to all remaining breeds but are playing an important role as part of the cultural landscape and thus contribute to the tourist industry. The genetic diversity of the Istrian cattle was found in the middle range of this study. It is already included in the tourist industry as a local food speciality. Current and future conservation strategies are discussed. © 2010 Blackwell Verlag GmbH.

  4. Influence of genetic architecture on contemporary local evolution in the soapberry bug, Jadera haematoloma: artificial selection on beak length.

    Science.gov (United States)

    Dingle, H; Carroll, S P; Famula, T R

    2009-10-01

    Little is known about the influence of genetic architecture on local adaptation. We investigated the genetic architecture of the rapid contemporary evolution of mouthparts, the flight polymorphism and life history traits in the soapberry bug Jadera haematoloma (Hemiptera) using laboratory selection. The mouthparts of these seed-feeding bugs have adapted in 40-50 years by decreasing in length following novel natural selection induced by a host switch to the seeds of an introduced tree with smaller fruits than those of the native host vine. Laboratory selection on beak length in both an ancestral population feeding on the native host and a derived population feeding on the introduced host reveals genetic variance allowing a rapid response (heritabilities of 0.51-0.87) to selection for either longer or shorter beaks. This selection resulted in reverse evolution by restoring long beaks in the derived population and forward evolution by re-creating short beaks in the ancestral bugs. There were strong genetic correlations (0.68-0.84) in both populations between beak lengths and the frequency of flight morphs, with short beaks associated with short wings. The results reveal a genetically interrelated set of adaptive multivariate traits including both beak length and flight morph. This suite of traits reflects host plant patchiness and seeding phenology. Weaker evidence suggests that egg mass and early egg production may be elements of the same suite. Reversible or forward evolution thus may occur in a broad set of genetically correlated multivariate traits undergoing rapid contemporary adaptation to altered local environments.

  5. Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Kirsten Bomblies

    2010-03-01

    Full Text Available As Arabidopsis thaliana is increasingly employed in evolutionary and ecological studies, it is essential to understand patterns of natural genetic variation and the forces that shape them. Previous work focusing mostly on global and regional scales has demonstrated the importance of historical events such as long-distance migration and colonization. Far less is known about the role of contemporary factors or environmental heterogeneity in generating diversity patterns at local scales. We sampled 1,005 individuals from 77 closely spaced stands in diverse settings around Tübingen, Germany. A set of 436 SNP markers was used to characterize genome-wide patterns of relatedness and recombination. Neighboring genotypes often shared mosaic blocks of alternating marker identity and divergence. We detected recent outcrossing as well as stretches of residual heterozygosity in largely homozygous recombinants. As has been observed for several other selfing species, there was considerable heterogeneity among sites in diversity and outcrossing, with rural stands exhibiting greater diversity and heterozygosity than urban stands. Fine-scale spatial structure was evident as well. Within stands, spatial structure correlated negatively with observed heterozygosity, suggesting that the high homozygosity of natural A. thaliana may be partially attributable to nearest-neighbor mating of related individuals. The large number of markers and extensive local sampling employed here afforded unusual power to characterize local genetic patterns. Contemporary processes such as ongoing outcrossing play an important role in determining distribution of genetic diversity at this scale. Local "outcrossing hotspots" appear to reshuffle genetic information at surprising rates, while other stands contribute comparatively little. Our findings have important implications for sampling and interpreting diversity among A. thaliana accessions.

  6. Estimating detection rates for the LIGO-Virgo search for gravitational-wave burst counterparts to gamma-ray bursts using inferred local GRB rates

    International Nuclear Information System (INIS)

    Leonor, I; Frey, R; Sutton, P J; Jones, G; Marka, S; Marka, Z

    2009-01-01

    One of the ongoing searches performed using the LIGO-Virgo network of gravitational-wave interferometers is the search for gravitational-wave burst (GWB) counterparts to gamma-ray bursts (GRBs). This type of analysis makes use of GRB time and position information from gamma-ray satellite detectors to trigger the GWB search, and the GWB detection rates possible for such an analysis thus strongly depend on the GRB detection efficiencies of the satellite detectors. Using local GRB rate densities inferred from observations which are found in the science literature, we calculate estimates of the GWB detection rates for different configurations of the LIGO-Virgo network for this type of analysis.

  7. Genetic Structure and Molecular Diversity of Cacao Plants Established as Local Varieties for More than Two Centuries: The Genetic History of Cacao Plantations in Bahia, Brazil.

    Science.gov (United States)

    Santos, Elisa S L; Cerqueira-Silva, Carlos Bernard M; Mori, Gustavo M; Ahnert, Dário; Mello, Durval L N; Pires, José Luis; Corrêa, Ronan X; de Souza, Anete P

    2015-01-01

    Bahia is the most important cacao-producing state in Brazil, which is currently the sixth-largest country worldwide to produce cacao seeds. In the eighteenth century, the Comum, Pará and Maranhão varieties of cacao were introduced into southern Bahia, and their descendants, which are called 'Bahian cacao' or local Bahian varieties, have been cultivated for over 200 years. Comum plants have been used to start plantations in African countries and extended as far as countries in South Asia and Oceania. In Brazil, two sets of clones selected from Bahian varieties and their mutants, the Agronomic Institute of East (SIAL) and Bahian Cacao Institute (SIC) series, represent the diversity of Bahian cacao in germplasm banks. Because the genetic diversity of Bahian varieties, which is essential for breeding programs, remains unknown, the objective of this work was to assess the genetic structure and diversity of local Bahian varieties collected from farms and germplasm banks. To this end, 30 simple sequence repeat (SSR) markers were used to genotype 279 cacao plants from germplasm and local farms. The results facilitated the identification of 219 cacao plants of Bahian origin, and 51 of these were SIAL or SIC clones. Bahian cacao showed low genetic diversity. It could be verified that SIC and SIAL clones do not represent the true diversity of Bahian cacao, with the greatest amount of diversity found in cacao trees on the farms. Thus, a core collection to aid in prioritizing the plants to be sampled for Bahian cacao diversity is suggested. These results provide information that can be used to conserve Bahian cacao plants and applied in breeding programs to obtain more productive Bahian cacao with superior quality and tolerance to major diseases in tropical cacao plantations worldwide.

  8. Natural habitats uncovered? – Genetic structure of known and newly found localities of the endangered bitterling Pseudorhodeus tanago (Cyprinidae

    Directory of Open Access Journals (Sweden)

    Kenji Saitoh

    2017-03-01

    Full Text Available Overuse of natural resources by humans is a major threat to biodiversity. Overuse often involves species of economic or esthetic value, and fish are a typical example for a group that is exploited both for economic reasons (for human consumption and for esthetic reasons (e.g. by aquarists. Pseudorhodeus tanago (Tanaka, 1909 (formerly known as Tanakia tanago is a small colorful but legally protected (fishing, keeping and transfer are banned bitterling fish distributed around Tokyo, Japan. Whereas it is critically endangered and more and more habitat loss has occurred, at least four stocks have been newly found during the last decade. To explore whether emergence of these newly found habitats is a consequence of incomplete survey, we genotyped mitochondrial cytochrome b sequence of P. tanago from 17 localities and an illegal home aquarium. Populations known by the past extensive survey (13 localities showed geographically structured population genetic characteristics. Population-specific haplotypes were common indicating past divergence and bottleneck events. Four (north, {center + west}, south_1, south_2 or five (north, center, west, south_1, south_2 geographic groups were detectable as for these known localities. On the other hand, newly found stocks were polymorphic and showed identical haplotypes from distant known localities. If we assume historical basis of distribution and genetic characteristics of these newly found stocks, it must be a series of unlikely geological events and haplotype sorting. We discuss potential issues posed by these questionable stocks.

  9. High-precision approach to localization scheme of visible light communication based on artificial neural networks and modified genetic algorithms

    Science.gov (United States)

    Guan, Weipeng; Wu, Yuxiang; Xie, Canyu; Chen, Hao; Cai, Ye; Chen, Yingcong

    2017-10-01

    An indoor positioning algorithm based on visible light communication (VLC) is presented. This algorithm is used to calculate a three-dimensional (3-D) coordinate of an indoor optical wireless environment, which includes sufficient orders of multipath reflections from reflecting surfaces of the room. Leveraging the global optimization ability of the genetic algorithm (GA), an innovative framework for 3-D position estimation based on a modified genetic algorithm is proposed. Unlike other techniques using VLC for positioning, the proposed system can achieve indoor 3-D localization without making assumptions about the height or acquiring the orientation angle of the mobile terminal. Simulation results show that an average localization error of less than 1.02 cm can be achieved. In addition, in most VLC-positioning systems, the effect of reflection is always neglected and its performance is limited by reflection, which makes the results not so accurate for a real scenario and the positioning errors at the corners are relatively larger than other places. So, we take the first-order reflection into consideration and use artificial neural network to match the model of a nonlinear channel. The studies show that under the nonlinear matching of direct and reflected channels the average positioning errors of four corners decrease from 11.94 to 0.95 cm. The employed algorithm is emerged as an effective and practical method for indoor localization and outperform other existing indoor wireless localization approaches.

  10. The Knowledge of Local Communities and School Knowledge: In Search of a Didactic Transposition in Natural Sciences

    Science.gov (United States)

    Capece, Jó António

    2018-01-01

    This article is the result of an ongoing research under the project entitled "The local curriculum in Mozambican schools: epistemological and didactic-methodological strategies for its implementation". Based on ethnographic research, the collection is being made. Systematization of knowledge and cultural experiences of local communities…

  11. Genetic diversity in a population of rhinoclemmys nasuta (Testudines: Geoemydidae) associated with an insular locality in the Choco biogeographic region

    International Nuclear Information System (INIS)

    Castillo Cutiva, Leslie Anais; Giraldo, Alan; Barreto, Guillermo

    2014-01-01

    Characterization of the genetic diversity of Rhinoclemmys nasuta population inhabits Isla Palma (Malaga Bay, Valle del Cauca) was carried out using three microsatellite systems (cm72, cm58 and cm 3 ). In this locality, individuals of R. nasuta are widely distributed in the inland streams and creeks system. 100 to 200 ml of peripheral blood was taken off from ten turtles in five streams of the island, preserving samples in a 0.5 m EDTA. DNA was extracted using salting-out and chelex solution techniques. PCR amplified products were visualized and measured in polyacrylamide gels stained with silver nitrate. successful amplification products were obtained for all systems analyzed, two of which (cm72 and cm3) were found to be monomorphic, while the system cm58 had a high pic (0.698) allowing to estimate the genetic diversity of this population. The observed heterozygosity was low (ho = 0.26) and inbreeding indices fis and fit were high (0.67857 and 0.67881), indicating an excess of homozygotes in each of the rivers and for the all population. The molecular analysis of variance suggested that there is no difference in genetic structure of the population (FST = 0.00075, p= 0.95112). Therefore, the results suggest that the genetic diversity of R. nasutapopulation in Isla Palma was low and exhibited a highly inbred index.

  12. Genetic variation of the Turnip mosaic virus population of Vietnam: a case study of founder, regional and local influences.

    Science.gov (United States)

    Nguyen, Huy Duc; Tran, Hoa Thi Nhu; Ohshima, Kazusato

    2013-01-01

    Turnip mosaic virus (TuMV) is one of the most important viruses infecting a wide range of plant species, primarily from the family Brassicaceae. Thirty TuMV isolates were collected from Brassica and Raphanus plants in Vietnam during 2006-2008. Host reaction studies showed that many of the isolates belonged to Brassica/Raphanus (BR) host-infecting type. Sequence-based phylogenetic and population genetic analyses were made of the complete polyprotein gene sequences, and of four non-recombinogenic regions of those sequences (i.e. genes of the helper-component proteinase protein, protein 3, nuclear inclusion b protein and coat protein). These were used to assess the subpopulation differentiation and divergence between Vietnamese TuMV populations and those of nearby Asian countries. Nine inter- and intralineage recombination type patterns were identified in the genomes of the Vietnamese isolates, of which seven were novel. All the Vietnamese non-recombinant isolates fell into the world-B group of TuMV and clustered with Chinese isolates. The estimates of genetic differentiation and gene flow reveal that the TuMV populations of Vietnam, China and Japan are genetically linked but have clear local founder effects. This, the first population genetic study of a TuMV population in Southeast Asia, indicates the importance of such studies for providing the scientific basis of control strategies. Copyright © 2012 Elsevier B.V. All rights reserved.

  13. AN INTEGRATED MAP OF HUMAN-CHROMOSOME-13 ALLOWING REGIONAL LOCALIZATION OF GENETIC-MARKERS

    NARCIS (Netherlands)

    KOOY, RF; WIJNGAARD, A; VERLIND, E; SCHEFFER, H; BUYS, CHCM

    1995-01-01

    37 CA repeats, 5 STSs, 9 ESTs, and 4 genes were mapped to 19 different intervals of chromosome 13 determined by the cytogenetic breakpoints of 19 different cell lines with interstitial deletions or translocations involving various parts of chromosome 13. A framework genetic linkage map was

  14. Variability in seed traits, oil content and genetic diversity in local and ...

    African Journals Online (AJOL)

    Variability in seed traits, oil content and genetic diversity of Jatropha curcas L. according to rainfall gradient in Senegal are hereby reported and discussed. Seed oil variability ranged from 58.61% in Sudanian zone to 46.94% in Sahelian zone. Seed oil content and seed thickness were correlated to rainfall with a correlation ...

  15. Search for major genes with progeny test data to accelerate the development of genetically superior loblolly pine. Technical progress report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-02-15

    This report details the progress of the three tasks of this project. The tasks are: (1) develop genetic models and analytical methods; (2) molecular confirmation of major gene segregation; and (3) develop strategies for marker-assisted breeding.

  16. SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database

    International Nuclear Information System (INIS)

    Ginzinger, Simon W.; Coles, Murray

    2009-01-01

    We present SimShiftDB, a new program to extract conformational data from protein chemical shifts using structural alignments. The alignments are obtained in searches of a large database containing 13,000 structures and corresponding back-calculated chemical shifts. SimShiftDB makes use of chemical shift data to provide accurate results even in the case of low sequence similarity, and with even coverage of the conformational search space. We compare SimShiftDB to HHSearch, a state-of-the-art sequence-based search tool, and to TALOS, the current standard tool for the task. We show that for a significant fraction of the predicted similarities, SimShiftDB outperforms the other two methods. Particularly, the high coverage afforded by the larger database often allows predictions to be made for residues not involved in canonical secondary structure, where TALOS predictions are both less frequent and more error prone. Thus SimShiftDB can be seen as a complement to currently available methods

  17. Search for major genes with progeny test data to accelerate the development of genetically superior loblolly pine

    Energy Technology Data Exchange (ETDEWEB)

    NCSU

    2003-12-30

    This research project is to develop a novel approach that fully utilized the current breeding materials and genetic test information available from the NCSU-Industry Cooperative Tree Improvement Program to identify major genes that are segregating for growth and disease resistance in loblolly pine. If major genes can be identified in the existing breeding population, they can be utilized directly in the conventional loblolly pine breeding program. With the putative genotypes of parents identified, tree breeders can make effective decisions on management of breeding populations and operational deployment of genetically superior trees. Forest productivity will be significantly enhanced if genetically superior genotypes with major genes for economically important traits could be deployed in an operational plantation program. The overall objective of the project is to develop genetic model and analytical methods for major gene detection with progeny test data and accelerate the development of genetically superior loblolly pine. Specifically, there are three main tasks: (1) Develop genetic models for major gene detection and implement statistical methods and develop computer software for screening progeny test data; (2) Confirm major gene segregation with molecular markers; and (3) Develop strategies for using major genes for tree breeding.

  18. Increased fire frequency promotes stronger spatial genetic structure and natural selection at regional and local scales in Pinus halepensis Mill.

    Science.gov (United States)

    Budde, Katharina B; González-Martínez, Santiago C; Navascués, Miguel; Burgarella, Concetta; Mosca, Elena; Lorenzo, Zaida; Zabal-Aguirre, Mario; Vendramin, Giovanni G; Verdú, Miguel; Pausas, Juli G; Heuertz, Myriam

    2017-04-01

    The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies. Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation. Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime. An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits

  19. Genetics

    Science.gov (United States)

    ... Likelihood of getting certain diseases Mental abilities Natural talents An abnormal trait (anomaly) that is passed down ... one of them has a genetic disorder. Information Human beings have cells with 46 chromosomes . These consist ...

  20. Further genetic localization of the transforming sequences of the p21 v-ras gene of Harvey murine sarcoma virus

    DEFF Research Database (Denmark)

    Willumsen, B M; Ellis, R W; Scolnick, E M

    1984-01-01

    The sequences encoding the 21-kilodalton transforming protein (p21 ras) of Harvey murine sarcoma virus have previously been localized genetically to a 1.3-kilobase segment of the viral DNA (E. H. Chang, R. W. Ellis, E. M. Scolnick, and D. R. Lowy, Science 210:1249-1251, 1980). Within this segment...... of this open reading frame. By constructing a mutant of Harvey murine sarcoma virus DNA from which the first two ATG codons of this open reading frame have been deleted, we now show by transfection of the mutant viral DNA into NIH 3T3 cells that only the third ATG codon is necessary and sufficient...

  1. Disease and genetic contributions toward local tissue volume disturbances in schizophrenia: a tensor-based morphometry study.

    Science.gov (United States)

    Yang, Yaling; Nuechterlein, Keith H; Phillips, Owen R; Gutman, Boris; Kurth, Florian; Dinov, Ivo; Thompson, Paul M; Asarnow, Robert F; Toga, Arthur W; Narr, Katherine L

    2012-09-01

    Structural brain deficits, especially frontotemporal volume reduction and ventricular enlargement, have been repeatedly reported in patients with schizophrenia. However, it remains unclear whether brain structural deformations may be attributable to disease-related or genetic factors. In this study, the structural magnetic resonance imaging data of 48 adult-onset schizophrenia patients, 65 first-degree nonpsychotic relatives of schizophrenia patients, 27 community comparison (CC) probands, and 73 CC relatives were examined using tensor-based morphometry (TBM) to isolate global and localized differences in tissue volume across the entire brain between groups. We found brain tissue contractions most prominently in frontal and temporal regions and expansions in the putamen/pallidum, and lateral and third ventricles in schizophrenia patients when compared with unrelated CC probands. Results were similar, though less prominent when patients were compared with their nonpsychotic relatives. Structural deformations observed in unaffected patient relatives compared to age-similar CC relatives were suggestive of schizophrenia-related genetic liability and were pronounced in the putamen/pallidum and medial temporal regions. Schizophrenia and genetic liability effects for the putamen/pallidum were confirmed by regions-of-interest analysis. In conclusion, TBM findings complement reports of frontal, temporal, and ventricular dysmorphology in schizophrenia and further indicate that putamen/pallidum enlargements, originally linked mainly with medication exposure in early studies, also reflect a genetic predisposition for schizophrenia. Thus, brain deformation profiles revealed in this study may help to clarify the role of specific genetic or environmental risk factors toward altered brain morphology in schizophrenia.

  2. Three-year monitoring of genetic diversity reveals a micro-connectivity pattern and local recruitment in the broadcast marine species Paracentrotus lividus.

    Science.gov (United States)

    Couvray, Sylvain; Coupé, Stéphane

    2018-01-01

    In conservation and management of marine biological resources, a knowledge of connectivity is necessary to understand how local populations are naturally replenished by the arrival of new recruits from source populations. At small geographical scales, species experiencing moderate to long pelagic larval phases are mostly genetically homogeneous, which hinders inferences about local connectivity. Recent studies demonstrated that assessing genetic relatedness and kinship could provide information about local connectivity in populations with high levels of gene flow. Here, we were interested in deciphering the structure and connectivity of populations of the sea urchin Paracentrotus lividus, by monitoring populations at 11 localities distributed along a 225-km coast-line in the south-eastern French Mediterranean Sea. Using 12 microsatellite loci, we found a weak but significant genetic differentiation and observed a transient genetic differentiation among locations within temporal cohorts, without any correlation with the distance between locations, interpreted as unexplainable chaotic genetic patchiness. Among temporal cohorts, the more related individuals were mainly found within locations and the observed local differentiation (F ST ) correlated with the proportion of kin within locations, suggesting that larvae dispersed cohesively. Specifically, we could also reveal that populations flanking Cape Sicié were influenced by eastern populations and that local recruitment was a frequent occurrence. Overall, our results contribute to the growing number of studies showing that connectivity can be reliably assessed at a fine spatial scale even in genetically homogenous populations.

  3. PMD2HD--a web tool aligning a PubMed search results page with the local German Cancer Research Centre library collection.

    Science.gov (United States)

    Bohne-Lang, Andreas; Lang, Elke; Taube, Anke

    2005-06-27

    Web-based searching is the accepted contemporary mode of retrieving relevant literature, and retrieving as many full text articles as possible is a typical prerequisite for research success. In most cases only a proportion of references will be directly accessible as digital reprints through displayed links. A large number of references, however, have to be verified in library catalogues and, depending on their availability, are accessible as print holdings or by interlibrary loan request. The problem of verifying local print holdings from an initial retrieval set of citations can be solved using Z39.50, an ANSI protocol for interactively querying library information systems. Numerous systems include Z39.50 interfaces and therefore can process Z39.50 interactive requests. However, the programmed query interaction command structure is non-intuitive and inaccessible to the average biomedical researcher. For the typical user, it is necessary to implement the protocol within a tool that hides and handles Z39.50 syntax, presenting a comfortable user interface. PMD2HD is a web tool implementing Z39.50 to provide an appropriately functional and usable interface to integrate into the typical workflow that follows an initial PubMed literature search, providing users with an immediate asset to assist in the most tedious step in literature retrieval, checking for subscription holdings against a local online catalogue. PMD2HD can facilitate literature access considerably with respect to the time and cost of manual comparisons of search results with local catalogue holdings. The example presented in this article is related to the library system and collections of the German Cancer Research Centre. However, the PMD2HD software architecture and use of common Z39.50 protocol commands allow for transfer to a broad range of scientific libraries using Z39.50-compatible library information systems.

  4. Collective identity, associative dynamics and social participation of migrant communities in Switzerland: the search for a local citizenship

    Directory of Open Access Journals (Sweden)

    Claudio Bolzman

    2016-10-01

    Full Text Available The purpose of this article is the study of the significance of the new forms of collective identity developed by Spanish an Italian immigrants in Swiss society. The immigrants direct their efforts at local level and rely largely on their own resources to achieve greater social recognition. They express themselves both at the cultural and political levels, through organisations of different sorts and fight for their political rights at the local level. Our analysis establishes a relationship between socio-historical changes and changes in the immigrants’ways of collective expression.

  5. Genetics

    International Nuclear Information System (INIS)

    Hubitschek, H.E.

    1975-01-01

    Progress is reported on the following research projects: genetic effects of high LET radiations; genetic regulation, alteration, and repair; chromosome replication and the division cycle of Escherichia coli; effects of radioisotope decay in the DNA of microorganisms; initiation and termination of DNA replication in Bacillus subtilis; mutagenesis in mouse myeloma cells; lethal and mutagenic effects of near-uv radiation; effect of 8-methoxypsoralen on photodynamic lethality and mutagenicity in Escherichia coli; DNA repair of the lethal effects of far-uv; and near uv irradiation of bacterial cells

  6. Genetic Diversity and Local Connectivity in the Mediterranean Red Gorgonian Coral after Mass Mortality Events.

    Science.gov (United States)

    Pilczynska, Joanna; Cocito, Silvia; Boavida, Joana; Serrão, Ester; Queiroga, Henrique

    2016-01-01

    Estimating the patterns of connectivity in marine taxa with planktonic dispersive stages is a challenging but crucial task because of its conservation implications. The red gorgonian Paramuricea clavata is a habitat forming species, characterized by short larval dispersal and high reproductive output, but low recruitment. In the recent past, the species was impacted by mass mortality events caused by increased water temperatures in summer. In the present study, we used 9 microsatellites to investigate the genetic structure and connectivity in the highly threatened populations from the Ligurian Sea (NW Mediterranean). No evidence for a recent bottleneck neither decreased genetic diversity in sites impacted by mass mortality events were found. Significant IBD pattern and high global FST confirmed low larval dispersal capability in the red gorgonian. The maximum dispersal distance was estimated at 20-60 km. Larval exchange between sites separated by hundreds of meters and between different depths was detected at each site, supporting the hypothesis that deeper subpopulations unaffected by surface warming peaks may provide larvae for shallower ones, enabling recovery after climatically induced mortality events.

  7. The Breda Study: Search for genetic factors involved in type 2 diabetes mellitus in a defined Dutch population

    NARCIS (Netherlands)

    Tilburg, Jonathan Hendrik Otto van

    2002-01-01

    Little is known about the nature of genetic variation underlying complex diseases in humans. The recognition that susceptibility to type 2 diabetes mellitus has a strong inherited component provides a mechanism for developing the molecular understanding of the pathogenesis of type 2 diabetes

  8. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  9. Genetic variation and population structure of American mink Neovison vison from PCB-contaminated and non-contaminated locales in eastern North America.

    Science.gov (United States)

    Wirgin, Isaac; Maceda, Lorraine; Waldman, John; Mayack, David T

    2015-11-01

    American mink Neovison vison may be particularly vulnerable to toxicities of persistent contaminants such as PCBs because of their aquatic-based diet, position near the top of the food web, and small deme sizes. Furthermore, ranched mink are sensitive to reproductive toxicities of fish diets from PCB-polluted sites. The upper Hudson River is highly contaminated with PCBs and previous studies have shown elevated hepatic burdens of total and coplanar PCBs in mink collected near the river compared with those from more distant locales in New York and elsewhere. We hypothesized that bioaccumulation of PCBs in Hudson River mink has reduced their levels of genetic diversity or altered their genetic population structure. To address this, we conducted microsatellite DNA analysis on collections made in proximity to and from more distant locales in the Hudson River watershed, elsewhere in New York State, and at other sites in eastern North America including New Brunswick, four locales in Ontario, multiple drainages in Maine, and two ecoregions in Rhode Island. We did not find reduced genetic diversity at the individual or population levels in mink collected near (<6 km) to PCB hotspots in the Hudson River nor evidence of altered population structure. Consistent with their distribution in small localized and isolated demes, we did find significant genetic population structure among many mink collections in New York State and elsewhere. Depending on the analytical approach used, genetically distinct populations numbered between 16 when using STRUCTURE to 19-20 when using Exact G tests, F ST, or AMOVA analyses. Genetically distinct population units were found among major ecoregions and minor ecoregions in New York State, among different hydrologic subunits within the Hudson River watershed, among spatially separate locales in Ontario, and among most watersheds in Maine. However, despite this localization and potential heightened impact of stressors, genetic diversity and genetic

  10. Genetic diversity of Mycobacterium tuberculosis isolates from Tochigi prefecture, a local region of Japan.

    Science.gov (United States)

    Mizukoshi, Fuminori; Miyoshi-Akiyama, Tohru; Iwai, Hiroki; Suzuki, Takako; Kiritani, Reiko; Kirikae, Teruo; Funatogawa, Keiji

    2017-05-25

    Foreign-born patients with tuberculosis (TB) may introduce globally disseminated isolates of Mycobacterium tuberculosis into large cities in Japan. The risk of dissemination of these isolates into local regions, however, has not been determined. This study analyzed the molecular epidemiology of M. tuberculosis isolates obtained from TB patients living in a local region of Japan. Whole genome sequences of 169 M. tuberculosis isolates, obtained from 148 Japanese-born and 21 foreign-born patients living in Tochigi, Japan, were analyzed using the Comprehensive analysis server for the Mycobacterium t u b erculosis complex (CASTB). The 169 isolates were clustered into four clades; Lineage 2 (111 isolates 65.7%), Lineage 4 (43 isolates, 25.4%), Lineage 1 (13 isolates, 7.7%), and Lineage 3 (2 isolates, 1.2%). Of the 111 isolates belonging to Lineage 2, 79 (71.2%) were of the atypical Beijing sub-genotype. Of the 13 Lineage 1 isolates, nine (69.2%) were from foreign-born patients. The isolates belonging to Lineage 4 were further clustered into three clades, two containing isolates shared by both Japanese- and foreign-born patients. The two isolates belonging to Lineage 3 were obtained from foreign-born patients. The genotypic diversity of M. tuberculosis in a local region of Japan is increased primarily by the presence of isolates obtained from foreign-born patients.

  11. Search for sterile neutrinos in holographic dark energy cosmology: Reconciling Planck observation with the local measurement of the Hubble constant

    Science.gov (United States)

    Zhao, Ming-Ming; He, Dong-Ze; Zhang, Jing-Fei; Zhang, Xin

    2017-08-01

    We search for sterile neutrinos in the holographic dark energy cosmology by using the latest observational data. To perform the analysis, we employ the current cosmological observations, including the cosmic microwave background temperature power spectrum data from the Planck mission, the baryon acoustic oscillation measurements, the type Ia supernova data, the redshift space distortion measurements, the shear data of weak lensing observation, the Planck lensing measurement, and the latest direct measurement of H0 as well. We show that, compared to the Λ CDM cosmology, the holographic dark energy cosmology with sterile neutrinos can relieve the tension between the Planck observation and the direct measurement of H0 much better. Once we include the H0 measurement in the global fit, we find that the hint of the existence of sterile neutrinos in the holographic dark energy cosmology can be given. Under the constraint of the all-data combination, we obtain Neff=3.76 ±0.26 and mν,sterile eff0 in the holographic dark energy cosmology is at the 2.75 σ level and the massless or very light sterile neutrino is favored by the current observations.

  12. Microsatellite Analysis of Perch (Perca fluviatilis) and its Genetic Authentication of Geographical Localization.

    Science.gov (United States)

    Rolli, Joelle; Girardet, Sylvie; Monachon, Cédric; Richard, Christian

    2014-10-01

    European perch (Perca fluviatilis) is an economically important freshwater species in Europe. In Switzerland, where the demand largely exceeds the production coming from Swiss lakes, nearly 90% of the requirements come from importation with the majority of perch originating from Estonia and Russia. The price of perch fillet varies considerably depending on the origin. Therefore traceability in the fish food sector plays an increasingly important role for consumer protection. Currently the traceability of perch can be assessed through chemical isotopic analysis. The 180/160 isotopic abundance ratio is used as geographical traceability marker, but several aspects affect the accuracy of the method, i.e. the distinct geographical area ratio differs only very slightly with overlapping standard deviation, the need for a large amount of fish material requires the mix of many fillets, the impossibility of analyzing processed matrix, the comparison of the ratio with the ratio of a sample of the presumed originating water makes the analyses more complicated. New application of DNA markers for the traceability of food products plays an increasingly important role for consumer protection. Microsatellites, which are short tandemly repetitive DNA sequences, are genetic markers of choice for traceability because of their abundance and high polymorphism. Moreover, fluorescent labelling and capillary electrophoresis separation increase efficiency and precision of genotyping microsatellites. The method can also be efficiently applied in processed food products where other methods have limited applications. In this study, we tested the efficiency of three polymorphic microsatellites and their combinations for their ability to correctly assign or exclude 195 reference perch to their origin population. Using the maximum likelihood and Bayesian methods computed by the software GeneClass2, the three loci microsatellite were optimized and allowed the correct assignation of all but two

  13. The joint effects of background selection and genetic recombination on local gene genealogies.

    Science.gov (United States)

    Zeng, Kai; Charlesworth, Brian

    2011-09-01

    Background selection, the effects of the continual removal of deleterious mutations by natural selection on variability at linked sites, is potentially a major determinant of DNA sequence variability. However, the joint effects of background selection and genetic recombination on the shape of the neutral gene genealogy have proved hard to study analytically. The only existing formula concerns the mean coalescent time for a pair of alleles, making it difficult to assess the importance of background selection from genome-wide data on sequence polymorphism. Here we develop a structured coalescent model of background selection with recombination and implement it in a computer program that efficiently generates neutral gene genealogies for an arbitrary sample size. We check the validity of the structured coalescent model against forward-in-time simulations and show that it accurately captures the effects of background selection. The model produces more accurate predictions of the mean coalescent time than the existing formula and supports the conclusion that the effect of background selection is greater in the interior of a deleterious region than at its boundaries. The level of linkage disequilibrium between sites is elevated by background selection, to an extent that is well summarized by a change in effective population size. The structured coalescent model is readily extendable to more realistic situations and should prove useful for analyzing genome-wide polymorphism data.

  14. Computer-aided diagnostic scheme for the detection of lung nodules on chest radiographs: Localized search method based on anatomical classification

    International Nuclear Information System (INIS)

    Shiraishi, Junji; Li Qiang; Suzuki, Kenji; Engelmann, Roger; Doi, Kunio

    2006-01-01

    We developed an advanced computer-aided diagnostic (CAD) scheme for the detection of various types of lung nodules on chest radiographs intended for implementation in clinical situations. We used 924 digitized chest images (992 noncalcified nodules) which had a 500x500 matrix size with a 1024 gray scale. The images were divided randomly into two sets which were used for training and testing of the computerized scheme. In this scheme, the lung field was first segmented by use of a ribcage detection technique, and then a large search area (448x448 matrix size) within the chest image was automatically determined by taking into account the locations of a midline and a top edge of the segmented ribcage. In order to detect lung nodule candidates based on a localized search method, we divided the entire search area into 7x7 regions of interest (ROIs: 64x64 matrix size). In the next step, each ROI was classified anatomically into apical, peripheral, hilar, and diaphragm/heart regions by use of its image features. Identification of lung nodule candidates and extraction of image features were applied for each localized region (128x128 matrix size), each having its central part (64x64 matrix size) located at a position corresponding to a ROI that was classified anatomically in the previous step. Initial candidates were identified by use of the nodule-enhanced image obtained with the average radial-gradient filtering technique, in which the filter size was varied adaptively depending on the location and the anatomical classification of the ROI. We extracted 57 image features from the original and nodule-enhanced images based on geometric, gray-level, background structure, and edge-gradient features. In addition, 14 image features were obtained from the corresponding locations in the contralateral subtraction image. A total of 71 image features were employed for three sequential artificial neural networks (ANNs) in order to reduce the number of false-positive candidates. All

  15. Genetic algorithms optimized fuzzy controller for the indoor environmental management in buildings implemented using PLC and local operating networks

    Energy Technology Data Exchange (ETDEWEB)

    Kolokotsa, D. [Technological Educational Institute of Crete (Greece). Dept. of Natural Resources Engineering; Stavrakakis, G.S.; Kalaitzakis, K. [Technical University of Crete (Greece). Dept. of Electronics and Computer Engineering; Agoris, D. [University of Patras (Greece). Dept. of Electrical and Computer Engineering

    2002-09-01

    In this paper, an optimized fuzzy controller is presented for the control of the environmental parameters at the building zone level. The occupants' preferences are monitored via a smart card unit. Genetic algorithm optimization techniques are applied to shift properly the membership functions of the fuzzy controller in order to satisfy the occupants' preferences while minimizing energy consumption. The implementation of the system integrates a smart card unit, sensors, actuators, interfaces, a programmable logic controller (PLC), local operating network (LON) modules and devices, and a central PC that monitors the performance of the system. The communication of the PLC with the smart card unit is performed using an RS 485 port, while the PLC-PC communication is performed via the LON network. The integrated system is installed and tested in the building of the Laboratory of Electronics of the Technical University of Crete. (author)

  16. Melinda - A custom search engine that provides access to locally-developed content using the HL7 Infobutton standard.

    Science.gov (United States)

    Wan, Yik-Ki J; Staes, Catherine J

    2016-01-01

    Healthcare organizations use care pathways to standardize care, but once developed, adoption rates often remain low. One challenge for usage concerns clinicians' difficulty in accessing guidance when it is most needed. Although the HL7 'Infobutton Standard' allows clinicians easier access to external references, access to locally-developed resources often requires clinicians to deviate from their normal electronic health record (EHR) workflow to use another application. To address this gap between internal and external resources, we reviewed the literature and existing practices at the University of Utah Health Care. We identify the requirements to meet the needs of a healthcare enterprise and clinicians, describe the design and development of a prototype to aggregate both internal and external resources from within or outside the EHR, and evaluated strengths and limitations of the prototype. The system is functional but not implemented in a live EHR environment. We suggest next steps and enhancements.

  17. Search for genetic factors in bicuspid aortic valve disease: ACTA2 mutations do not play a major role.

    Science.gov (United States)

    Tortora, Giada; Wischmeijer, Anita; Berretta, Paolo; Alfonsi, Jacopo; Di Marco, Luca; Barbieri, Andrea; Marconi, Caterina; Isidori, Federica; Rossi, Cesare; Leone, Ornella; Di Bartolomeo, Roberto; Seri, Marco; Pacini, Davide

    2017-11-01

    Mutations in ACTA2 have been reported as a cause of familiar thoracic aortic aneurysm (TAA) with associated bicuspid aortic valve (BAV) in some individuals. Our aim is to investigate the role of ACTA2 mutations in BAV associated with TAA in 20 patients. We recruited 20 patients who underwent surgery for BAV and TAA; clinical genetic evaluation and ACTA2 mutation analysis were performed on each patient, along with next-generation sequencing analysis of BAV-related genes. Available first-degree relatives were enrolled and evaluated with echocardiography and clinical genetic examination. No mutations were found in ACTA2 or in BAV-related genes in our probands nor any common clinical signs possibly related to their heart disease. One-third of probands did not have any cardiovascular risk factor. Surgery was required at a young age (mean age 47.2 years) and at relatively small ascending aortic diameters (mean size 49.7 mm). In 77 first-degree relatives, 1 new diagnosis of TAA requiring surgery was made and 8 previous BAV/TAA diagnoses (9/77 = 11.7%) were confirmed. The phenotype BAV ± TAA segregated in 25% of our families. Although based on a small cohort, our results seemed to justify the conclusion that ACTA2 did not play a significant role in the pathogenesis of BAV aortopathy. The underlying genetic factors of this condition remain elusive and both large association studies and exome or genome sequencing could represent promising tools to unravel its pathogenesis. Aortic resection of TAA at elective surgery in these patients should be recommended as well as echocardiography in their first-degree relatives. © The Author 2017. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

  18. A hybrid color space for skin detection using genetic algorithm heuristic search and principal component analysis technique.

    Science.gov (United States)

    Maktabdar Oghaz, Mahdi; Maarof, Mohd Aizaini; Zainal, Anazida; Rohani, Mohd Foad; Yaghoubyan, S Hadi

    2015-01-01

    Color is one of the most prominent features of an image and used in many skin and face detection applications. Color space transformation is widely used by researchers to improve face and skin detection performance. Despite the substantial research efforts in this area, choosing a proper color space in terms of skin and face classification performance which can address issues like illumination variations, various camera characteristics and diversity in skin color tones has remained an open issue. This research proposes a new three-dimensional hybrid color space termed SKN by employing the Genetic Algorithm heuristic and Principal Component Analysis to find the optimal representation of human skin color in over seventeen existing color spaces. Genetic Algorithm heuristic is used to find the optimal color component combination setup in terms of skin detection accuracy while the Principal Component Analysis projects the optimal Genetic Algorithm solution to a less complex dimension. Pixel wise skin detection was used to evaluate the performance of the proposed color space. We have employed four classifiers including Random Forest, Naïve Bayes, Support Vector Machine and Multilayer Perceptron in order to generate the human skin color predictive model. The proposed color space was compared to some existing color spaces and shows superior results in terms of pixel-wise skin detection accuracy. Experimental results show that by using Random Forest classifier, the proposed SKN color space obtained an average F-score and True Positive Rate of 0.953 and False Positive Rate of 0.0482 which outperformed the existing color spaces in terms of pixel wise skin detection accuracy. The results also indicate that among the classifiers used in this study, Random Forest is the most suitable classifier for pixel wise skin detection applications.

  19. [Search for bacterial contamination of the aqueous humor during cataract surgery with and without local antibiotic prophylaxis].

    Science.gov (United States)

    Saint-Blancat, P; Burucoa, C; Boissonnot, M; Gobert, F; Risse, J F

    1995-01-01

    Bacterial contamination of anterior chamber at the end of cataract surgery, was compared between two techniques: extracapsular extraction and phacoemulsification. The effectiveness of preoperative antibiotic eyedrops using Norfloxacine 0.3% (Chibroxine) was also evaluated. The study focused on 101 patients grouped according to surgical technique and presence of preoperative antibiotic eyedrops. Conjunctival sampling was made the day prior the surgery, as well as in the operating room, after skin and conjunctival desinfection with povidone iodine in all the patients included in the study. Aqueous humour was collected at the end of surgery. Eight samples out of 101 were positive which represents 7.9% of the cases. In 75% of the cases, the anterior chamber aspirate showed a different germ or non-recurrent germ in the second conjunctival sample. None of the included patients developed endophthalmitis. The two most frequent pathogens were Propionibacterium acnes in 62.5% of the cases, and Staphylococcus epidermidis in 50%. Another pathogen was found in a culture environment: Micrococcus roseus. In two samples, two different bacteria grew: Propionibacterium acnes and Staphylococcus epidermidis. Whatever the surgical technique, no statistically significant bacterial contamination was found. There was no significant statistical difference between patients who had local antibiotic eyedrops and those who did not. This study confirms the poor reliability of local antibiotic eyedrops to prevent surgical contamination. Furthermore performing an anterior chamber aspirate at the end of the surgery for risk patients would help the physician identify the pathogens involved in endophthalmitis in order to begin antibiotic treatment as soon as possible.

  20. Searching of fuel recharges by means of genetic algorithms and neural networks in BWRs; Busqueda de recargas de combustible mediante algoritmos geneticos y redes neuronales en BWRs

    Energy Technology Data Exchange (ETDEWEB)

    Ortiz S, J.J.; Montes T, J.L.; Castillo M, J.A.; Perusquia del C, R. [ININ, Carretera Mexico-Toluca Km. 36.5, 52045 Estado de Mexico (Mexico)

    2004-07-01

    In this work improvements to the systems RENOR and RECOPIA are presented, that were developed to optimize fuel recharges in boiling water reactors. The RENOR system is based on a Multi state recurrent neural network while RECOPIA is based on a Genetic Algorithm. In the new versions of these systems there is incorporate the execution of the Turned off Margin in Cold and the Excess of Reactivity in Hot. The new systems were applied to an operation cycle of the Unit 1 of the Nuclear Power station of Laguna Verde. The recharges of fuel obtained by both methods are compared among if being observed that RENOR has better performance that RECOPIA, due to the nature of its search process. RECOPIA requires of approximately 1.4 times more time that RENOR to find a satisfactory recharge of fuel. (Author)

  1. Search for positron localization near transition-metal solutes of negative effective charge in Ni and Cu

    International Nuclear Information System (INIS)

    Hunter, D.M.; Grynszpan, R.I.; Arrott, A.S.

    1993-01-01

    Results of an early (1973) angular correlation (ACAR) study of dilute (0.5 at.%) Cu based alloys by a Japanese group were interpreted in terms of an attraction of e + by transition metal solutes of effective negative charge. Doppler Broadening (DB) measurements reveal no such an effect for Cu(Mn) and Cu(Ni) solid solutions as well as for Ni alloys with 3d, 4d and 5d transition metal solutes (0.1 to 1.5 at.%) i.e. no evidence of e + localization near these impurities is seen. Our results strongly suggest that the ACAR results are due to the metallurgical state of the samples. In contrast, significant DB lineshape parameter variations, observed for our Ni(Zr) alloys, are attributed to positron trapping in and near Ni 5 Zr precipitates. Our DB results for a series of Ni(Au) alloys are understood in terms of a combination of the effect of an overall lattice expansion and a positron preference for clusters of Au atoms. The above comparison between DB and ACAR results is supported by our 'spin polarized' DB results for a (001) Ni single crystal which resemble those obtained by other groups using a 'spin polarized' 2D-ACAR technique. (orig.)

  2. Search for genetic markers determining the efficiency of therapy with bisphosphonates in Russian women with postmenopausal osteoporosis: A pilot study

    Directory of Open Access Journals (Sweden)

    M. Yu. Krylov

    2016-01-01

    Full Text Available Many clinical observations show that patient’s genetic background is of great importance in determining the efficiency of treatment.Subjects and methods. The instigation included 50 postmenopausal women with osteoporosis (OP, who were followed up at the Laboratory of osteoporosis, V.A. Nasonova Research Institute of Rheumatology. Body mineral density (BMD in the lumbar spine (LI-IV, femoral neck (FN, and total hip was measured using dual-energy X-ray absorptiometry before and 12 months after treatment with bisphosphonates (BP. To estimate BMD changes, the investigators used ΔBMD in percent (Δ, %.Results and discussion. The whole group showed a positive effect of BP therapy during a year, which was most pronounced in the lumbar spine (mean ΔBMD, about 4%, and a small increment in the proximal hip BMD (mean ΔBMD, about 2%. An analysis indicated a statistically significant correlation of MCP1 -2518A>G polymorphism with changes in LI-IV BMD after 12-month BP therapy. Thus, the female patients who were A allele carriers had a twice lower increase in LI-IV BMD due to BP therapy than those without this allele. The genetic variants of the CCR5 gene, which were related to Δ32 deletion, and IL1β -511C/T polymorphism were also associated with changes in FN BMD following 12-month BP therapy. The BMD increase due to BP therapy in the carriers of the CCR5 Δ32 mutation (wt/Δ32 genotype was 3.5-fold than that in the carriers of the wild type gene (wt/wt genotype. Examination of IL1 -511C/T polymorphism demonstrated that the FN BMD increment in the carriers of the CC genotype was significantly higher than in those of the CT genotype (4.2±4.8 and 1.0±3.7%, respectively; р = 0.023. Our investigation revealed no significant relationship between VDR, LEPR, IL10, MHTFR, PPARG, SPP1, and CCR5(G/A gene polymorphisms and 12-month BP therapy-induced BMD changes in the three study skeletal regions. The findings may suggest that genetic testing may be used to

  3. Key Challenges in the Search for Innovative Drug Treatments for Special Populations. Converging Needs in Neonatology, Pediatrics, and Medical Genetics.

    Science.gov (United States)

    MacLeod, Stuart

    2017-08-04

    The explosion of knowledge concerning the interplay of genetic and environmental factors determining pathophysiology and guiding therapeutic choice has altered the landscape in pediatric clinical pharmacology and pharmacy. The need for innovative research methods and design expertise for small clinical trials to be undertaken in sparse populations has been accentuated. At the same time, shortfalls in critical human resources represent a key challenge, especially in low- and middle-income countries where the need for new research and education directions is greatest. Unless a specific action plan is urgently developed, there will be a continuing gap in availability of the essential expertise needed to address treatment challenges in special patient populations such as neonates, patients suffering from rare or neglected diseases, and children of all ages.

  4. A DFT-based genetic algorithm search for AuCu nanoalloy electrocatalysts for CO2 reduction

    DEFF Research Database (Denmark)

    Lysgaard, Steen; Mýrdal, Jón Steinar Garðarsson; Hansen, Heine Anton

    2015-01-01

    Using a DFT-based genetic algorithm (GA) approach, we have determined the most stable structure and stoichiometry of a 309-atom icosahedral AuCu nanoalloy, for potential use as an electrocatalyst for CO2 reduction. The identified core–shell nano-particle consists of a copper core interspersed....... This shows that the mixed Cu135@Au174 core–shell nanoalloy has a similar adsorption energy, for the most favorable site, as a pure gold nano-particle. Cu, however, has the effect of stabilizing the icosahedral structure because Au particles are easily distorted when adding adsorbates....... that it is possible to use the LCAO mode to obtain a realistic estimate of the molecular chemisorption energy for systems where the computation in normal grid mode is not computationally feasible. These corrections are employed when calculating adsorption energies on the Cu, Au and most stable mixed particles...

  5. A modified gravitational search algorithm based on a non-dominated sorting genetic approach for hydro-thermal-wind economic emission dispatching

    International Nuclear Information System (INIS)

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

    2017-01-01

    Wind power is a type of clean and renewable energy, and reasonable utilization of wind power is beneficial to environmental protection and economic development. Therefore, a short-term hydro-thermal-wind economic emission dispatching (SHTW-EED) problem is presented in this paper. The proposed problem aims to distribute the load among hydro, thermal and wind power units to simultaneously minimize economic cost and pollutant emission. To solve the SHTW-EED problem with complex constraints, a modified gravitational search algorithm based on the non-dominated sorting genetic algorithm-III (MGSA-NSGA-III) is proposed. In the proposed MGSA-NSGA-III, a non-dominated sorting approach, reference-point based selection mechanism and chaotic mutation strategy are applied to improve the evolutionary process of the original gravitational search algorithm (GSA) and maintain the distribution diversity of Pareto optimal solutions. Moreover, a parallel computing strategy is introduced to improve the computational efficiency. Finally, the proposed MGSA-NSGA-III is applied to a typical hydro-thermal-wind system to verify its feasibility and effectiveness. The simulation results indicate that the proposed algorithm can obtain low economic cost and small pollutant emission when dealing with the SHTW-EED problem. - Highlights: • A hybrid algorithm is proposed to handle hydro-thermal-wind power dispatching. • Several improvement strategies are applied to the algorithm. • A parallel computing strategy is applied to improve computational efficiency. • Two cases are analyzed to verify the efficiency of the optimize mode.

  6. Feature Selection for Object-Based Classification of High-Resolution Remote Sensing Images Based on the Combination of a Genetic Algorithm and Tabu Search

    Directory of Open Access Journals (Sweden)

    Lei Shi

    2018-01-01

    Full Text Available In object-based image analysis of high-resolution images, the number of features can reach hundreds, so it is necessary to perform feature reduction prior to classification. In this paper, a feature selection method based on the combination of a genetic algorithm (GA and tabu search (TS is presented. The proposed GATS method aims to reduce the premature convergence of the GA by the use of TS. A prematurity index is first defined to judge the convergence situation during the search. When premature convergence does take place, an improved mutation operator is executed, in which TS is performed on individuals with higher fitness values. As for the other individuals with lower fitness values, mutation with a higher probability is carried out. Experiments using the proposed GATS feature selection method and three other methods, a standard GA, the multistart TS method, and ReliefF, were conducted on WorldView-2 and QuickBird images. The experimental results showed that the proposed method outperforms the other methods in terms of the final classification accuracy.

  7. Search for methods and materials for practical use of residential radiation doses calculated via a standardized local methodology

    International Nuclear Information System (INIS)

    Cho, D.; Rhee, I.; Lee, G.-B.

    2003-01-01

    The aim of this work is on determination of standard parameters for computing residential doses per year near the nuclear power plants with consideration of local circumstances in Korea that may not be similar to those in the foreign developed power plants. All the data presented here was originated from four Korean nuclear power plants that are located along the seashore in the south provinces of Korea. We have selected critical nuclei, pathways and human organs related to the human exposure via simulated estimation with K-DOSE 60 based on the updated ICRP-60 with laborious addition of experimental input from key other Korean nuclear research organizations. From those results, we found that 1) the critical nuclides were found to be 3 H, 133 Xe, 60 Co for Kori plant and 14 C, 41 Ar for Wolsung plant. The most critical pathway was 'vegetable intake' for adults and 'milk intake' for infants. However, there was no preference in the effective organs, and 2) sensitivity analyses showed that the chemical composition in a nuclide much more influenced upon the radiation dose than any other input parameters such as food intake, radiation discharge, and transfer/concentration coefficients by more than 102 factor. The effect of transfer/concentration coefficients on the radiation dose was negligible. All input parameters showed highly estimated correlation with the radiation dose, approximated to 1.0, except for food intake in Wolsung power plant (partial correlation coefficient (PCC)=0.877). Consequently, we suggest that a prediction model or scenarios for food intake reflecting the current living trend and formal publications including details of chemical components in the critical nuclei from each plant are needed. Also, standardized domestic values of the parameters used in the calculation must replace the values of the existed or default-set imported factors via properly designed experiments and/or modelling such as transport of liquid discharge in waters nearby the

  8. A search for genetic effects of atomic bomb radiation on the growth and development of the F1 generation, 2

    International Nuclear Information System (INIS)

    Furusho, Toshiyuki; Otake, Masanori.

    1978-08-01

    A comparative study to detect possible genetic effects of atomic bomb radiation on the growth and development of offspring of A-bomb survivors was made on a group of senior high school students 15 to 17 years of age born to survivors and to nonexposed parents in Hiroshima using as variables weight, sitting height, and chest circumference. Using data from students born to nonexposed parents, regression analysis was made to determine the effect of parental age on the weight, sitting height, and chest circumference of the offspring, but no statistically significant relation was observed. The mean and variance values of weight, sitting height, and chest circumference of offspring of nonexposed parents were compared to those of offspring born to exposed father and nonexposed mother, and of offspring born to exposed mother and nonexposed father, but very few statistically significant differences were found. The mean and variance values of weight, sitting height, and chest circumference of offspring born to nonexposed parents were compared to those of offspring born to parents both exposed, and again there were very few statistically significant differences. No specific tendency was observed in relation to the combined radiation dose of both parents. (author)

  9. Genetic distinctiveness of the Herdwick sheep breed and two other locally adapted hill breeds of the UK.

    Science.gov (United States)

    Bowles, Dianna; Carson, Amanda; Isaac, Peter

    2014-01-01

    There is considerable interest in locally adapted breeds of livestock as reservoirs of genetic diversity that may provide important fitness traits for future use in agriculture. In marginal areas, these animals contribute to food security and extract value from land unsuitable for other systems of farming. In England, close to 50% of the national sheep flock is farmed on grassland designated as disadvantaged areas for agricultural production. Many of these areas are in the uplands, where some native breeds of sheep continue to be commercially farmed only in highly localised geographical regions to which they are adapted. This study focuses on three of these breeds, selected for their adaptation to near identical environments and their geographical concentration in regions close to one another. Our objective has been to use retrotyping, microsatellites and single nucleotide polymorphisms to explore the origins of the breeds and whether, despite their similar adaptations and proximity, they are genetically distinctive. We find the three breeds each have a surprisingly different pattern of retrovirus insertions into their genomes compared with one another and with other UK breeds. Uniquely, there is a high incidence of the R0 retrotype in the Herdwick population, characteristic of a primitive genome found previously in very few breeds worldwide and none in the UK mainland. The Herdwick and Rough Fells carry two rare retroviral insertion events, common only in Texels, suggesting sheep populations in the northern uplands have a historical association with the original pin-tail sheep of Texel Island. Microsatellite data and analyses of SNPs associated with RXFP2 (horn traits) and PRLR (reproductive performance traits) also distinguished the three breeds. Significantly, an SNP linked to TMEM154, a locus controlling susceptibility to infection by Maedi-Visna, indicated that all three native hill breeds have a lower than average risk of infection to the lentivirus.

  10. Expression and Genetic Variation in Neuroendocrine Signaling Pathways in Lethal and Nonlethal Prostate Cancer among Men Diagnosed with Localized Disease.

    Science.gov (United States)

    Lu, Donghao; Carlsson, Jessica; Penney, Kathryn L; Davidsson, Sabina; Andersson, Swen-Olof; Mucci, Lorelei A; Valdimarsdóttir, Unnur; Andrén, Ove; Fang, Fang; Fall, Katja

    2017-12-01

    Background: Recent data suggest that neuroendocrine signaling pathways may play a role in the progression of prostate cancer, particularly for early-stage disease. We aimed to explore whether expression of selected genes in the adrenergic, serotoninergic, glucocorticoid, and dopaminergic pathways differs in prostate tumor tissue from men with lethal disease compared with men with nonlethal disease. Methods: On the basis of the Swedish Watchful Waiting Cohort, we included 511 men diagnosed with incidental prostate cancer through transurethral resection of the prostate during 1977-1998 with follow-up up to 30 years. For those with tumor tissue ( N = 262), we measured mRNA expression of 223 selected genes included in neuroendocrine pathways. Using DNA from normal prostate tissue ( N = 396), we genotyped 36 SNPs from 14 receptor genes. Lethal prostate cancer was the primary outcome in analyses with pathway gene expression and genetic variants. Results: Differential expression of genes in the serotoninergic pathway was associated with risk of lethal prostate cancer ( P = 0.007); similar but weaker associations were noted for the adrenergic ( P = 0.014) and glucocorticoid ( P = 0.020) pathways. Variants of the HTR2A (rs2296972; P = 0.002) and NR3CI (rs33388; P = 0.035) genes (within the serotoninergic and glucocorticoid pathways) were associated with lethal cancer in overdominant models. These genetic variants were correlated with expression of several genes in corresponding pathways ( P pathways, particularly serotoninergic pathway, are associated with lethal outcome in the natural course of localized prostate cancer. Impact: This study provides evidence of the role of neuroendocrine pathways in prostate cancer progression that may have clinical utility. Cancer Epidemiol Biomarkers Prev; 26(12); 1781-7. ©2017 AACR . ©2017 American Association for Cancer Research.

  11. Genetic distinctiveness of the Herdwick sheep breed and two other locally adapted hill breeds of the UK.

    Directory of Open Access Journals (Sweden)

    Dianna Bowles

    Full Text Available There is considerable interest in locally adapted breeds of livestock as reservoirs of genetic diversity that may provide important fitness traits for future use in agriculture. In marginal areas, these animals contribute to food security and extract value from land unsuitable for other systems of farming. In England, close to 50% of the national sheep flock is farmed on grassland designated as disadvantaged areas for agricultural production. Many of these areas are in the uplands, where some native breeds of sheep continue to be commercially farmed only in highly localised geographical regions to which they are adapted. This study focuses on three of these breeds, selected for their adaptation to near identical environments and their geographical concentration in regions close to one another. Our objective has been to use retrotyping, microsatellites and single nucleotide polymorphisms to explore the origins of the breeds and whether, despite their similar adaptations and proximity, they are genetically distinctive. We find the three breeds each have a surprisingly different pattern of retrovirus insertions into their genomes compared with one another and with other UK breeds. Uniquely, there is a high incidence of the R0 retrotype in the Herdwick population, characteristic of a primitive genome found previously in very few breeds worldwide and none in the UK mainland. The Herdwick and Rough Fells carry two rare retroviral insertion events, common only in Texels, suggesting sheep populations in the northern uplands have a historical association with the original pin-tail sheep of Texel Island. Microsatellite data and analyses of SNPs associated with RXFP2 (horn traits and PRLR (reproductive performance traits also distinguished the three breeds. Significantly, an SNP linked to TMEM154, a locus controlling susceptibility to infection by Maedi-Visna, indicated that all three native hill breeds have a lower than average risk of infection to the

  12. Ice Cover Prediction of a Power Grid Transmission Line Based on Two-Stage Data Processing and Adaptive Support Vector Machine Optimized by Genetic Tabu Search

    Directory of Open Access Journals (Sweden)

    Xiaomin Xu

    2017-11-01

    Full Text Available With the increase in energy demand, extreme climates have gained increasing attention. Ice disasters on transmission lines can cause gap discharge and icing flashover electrical failures, which can lead to mechanical failure of the tower, conductor, and insulators, causing significant harm to people’s daily life and work. To address this challenge, an intelligent combinational model is proposed based on improved empirical mode decomposition and support vector machine for short-term forecasting of ice cover thickness. Firstly, in light of the characteristics of ice cover thickness data, fast independent component analysis (FICA is implemented to smooth the abnormal situation on the curve trend of the original data for prediction. Secondly, ensemble empirical mode decomposition (EEMD decomposes data after denoising it into different components from high frequency to low frequency, and support vector machine (SVM is introduced to predict the sequence of different components. Then, some modifications are performed on the standard SVM algorithm to accelerate the convergence speed. Combined with the advantages of genetic algorithm and tabu search, the combination algorithm is introduced to optimize the parameters of support vector machine. To improve the prediction accuracy, the kernel function of the support vector machine is adaptively adopted according to the complexity of different sequences. Finally, prediction results for each component series are added to obtain the overall ice cover thickness. A 220 kV DC transmission line in the Hunan Region is taken as the case study to verify the practicability and effectiveness of the proposed method. Meanwhile, we select SVM optimized by genetic algorithm (GA-SVM and traditional SVM algorithm for comparison, and use the error function of mean absolute percentage error (MAPE, root mean square error (RMSE and mean absolute error (MAE to compare prediction accuracy. Finally, we find that these improvements

  13. Intervention of genetic flow of the foreign cattle toward diversity of phenotype expressions of local cattle in the District of Banyuwangi

    Directory of Open Access Journals (Sweden)

    MOHAMAD AMIN

    2010-04-01

    Full Text Available Amin M (2010 Intervention of genetic flow of the foreign cattle toward diversity of phenotype expressions of local cattle in the District of Banyuwangi. Biodiversitas 10: 69-74. The aims of the present research are two folds: to know the phenotypic diversity and to reconstruct the cross-breeding pattern of local cattle in Banyuwangi. Based on three sampling areas, it was found that there were 32 phenotypic cattle (10 in the sub districts of Rogojampi, 16 in Tegaldlimo and 6 in Glagah areas. The phenotypic varieties were caused by two factors, namely the flow of genetic intervention of the other local cattle (Bali, Ongole, and Brahman cattle and the artificial insemination program using the semen of Limousine, Simmental, Aberdeen Angus and Santa Gertrudis cattle.

  14. Aberrant nuclear localization of β-catenin without genetic alterations in β-catenin or Axin genes in esophageal cancer

    Directory of Open Access Journals (Sweden)

    Shinoda Noriyuki

    2007-02-01

    Full Text Available Abstract Background β-catenin is a multifunctional protein involved in two apparently independent processes: cell-cell adhesion and signal transduction. β-catenin is involved in Wnt signaling pathway that regulates cellular differentiation and proliferation. In this study, we investigated the expression pattern of β-catenin and cyclin D1 using immunohistochemistry and searched for mutations in exon 3 of the β-catenin gene and Axin gene in esophageal squamous cell carcinoma. Materials and methods Samples were obtained from 50 esophageal cancer patients. Immunohistochemical staining for β-catenin and cyclin D1 was done. Mutational analyses of the exon3 of the β-catenin gene and Axin gene were performed on tumors with nuclear β-catenin expression. Results Four (8% esophageal cancer tissues showed high nuclear β-catenin staining. Overexpression of cyclin D1 was observed in 27 out of 50 (54% patients. All four cases that showed nuclear β-catenin staining overexpressed cyclin D1. No relationship was observed between the expression pattern of β-catenin and cyclin D1 and age, sex, tumor size, stage, differentiation grade, lymph node metastasis, response to chemotherapy, or survival. No mutational change was found in β-catenin exon 3 in the four cases with nuclear β-catenin staining. Sequencing analysis of the Axin cDNA revealed only a splicing variant (108 bp deletion, position 2302–2409 which was present in the paired normal mucosa. Conclusion A fraction of esophageal squamous cell carcinomas have abnormal nuclear accumulation of β-catenin accompanied with increased cyclin D1 expression. Mutations in β-catenin or axin genes are not responsible for this abnormal localization of β-catenin.

  15. Searching for non-genetic molecular and imaging PTSD risk and resilience markers: Systematic review of literature and design of the German Armed Forces PTSD biomarker study.

    Science.gov (United States)

    Schmidt, Ulrike; Willmund, Gerd-Dieter; Holsboer, Florian; Wotjak, Carsten T; Gallinat, Jürgen; Kowalski, Jens T; Zimmermann, Peter

    2015-01-01

    Biomarkers allowing the identification of individuals with an above average vulnerability or resilience for posttraumatic stress disorder (PTSD) would especially serve populations at high risk for trauma exposure like firefighters, police officers and combat soldiers. Aiming to identify the most promising putative PTSD vulnerability markers, we conducted the first systematic review on potential imaging and non-genetic molecular markers for PTSD risk and resilience. Following the PRISMA guidelines, we systematically screened the PubMed database for prospective longitudinal clinical studies and twin studies reporting on pre-trauma and post-trauma PTSD risk and resilience biomarkers. Using 25 different combinations of search terms, we retrieved 8151 articles of which we finally included and evaluated 9 imaging and 27 molecular studies. In addition, we briefly illustrate the design of the ongoing prospective German Armed Forces (Bundeswehr) PTSD biomarker study (Bw-BioPTSD) which not only aims to validate these previous findings but also to identify novel and clinically applicable molecular, psychological and imaging risk, resilience and disease markers for deployment-related psychopathology in a cohort of German soldiers who served in Afghanistan. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Genetic Discrimination

    Science.gov (United States)

    Skip to main content Genetic Discrimination Enter Search Term(s): Español Research Funding An Overview Bioinformatics Current Grants Education and Training Funding Extramural Research News Features Funding Divisions ...

  17. Search for buildings with high radon levels in Sweden: measurements carried out by local authorities in both older and newly built homes

    International Nuclear Information System (INIS)

    Swedjemark, G.A.

    1988-01-01

    Local authorities in Sweden have made about 58,000 radon daughter measurements with the following aims: (1) to search for houses with high radon daughter levels, (2) to determine the level above which the house would be regarded as an insanitary dwelling, and (3) to check that the radon daughter concentrations in newly built houses are below the established limit. The sampling of dwellings is therefore not representative for Swedish homes. 5300 homes were found to have levels above the limit 400 Bq.m -3 EER. The highest level found was 28,000 Bq.m -3 . In about one third of the homes found to have levels exceeding the limit, measures had been carried out to decrease the radon daughter concentration. About half of the homes in which the levels were decreased had levels below the limit for rebuilding, e.g. 200 Bq.m -3 . Measurements in order to ascertain levels in newly built houses were made in about 1100 homes out of 200,000 built since 1981 which was the year in which requirements for newly built houses came into force. Of those built with radon-protective foundations, 94% had concentrations below the 70 Bq.m -3 EER limit, compared to 80% for traditional building techniques. (author)

  18. A targeted approach to genetic counseling in breast cancer patients: the experience of an Italian local project.

    Science.gov (United States)

    La Verde, Nicla; Corsi, Fabio; Moretti, Anna; Peissel, Bernard; Dalu, Davide; Girelli, Serena; Fasola, Cinzia; Gambaro, Anna; Roversi, Gaia; Azzollini, Jacopo; Radice, Paolo; Pensotti, Valeria; Farina, Gabriella; Manoukian, Siranoush

    2016-01-01

    Patients with hereditary breast cancer (BC) may benefit from genetic counseling and testing for detection of causative mutations, definition of therapeutic and preventive strategies, and identification of at-risk relatives. Italy has few oncogenetic centers and genetic evaluation of all patients with BC is not feasible. Moreover, lack of uniformity in the selection of patients generates inappropriate referral to the geneticist. We designed a model that may represent a reproducible way to select patients at risk for hereditary BC, with the aims of rationalizing access to genetic centers and improving clinical management and surveillance. The genetic unit of a Cancer Center and the Departments of Oncology from 2 public Hospitals in Milan were involved in the project. After training sessions at the genetic unit, operators from the 2 hospitals evaluated all patients with BC attending a first oncologic visit, through a specific interview. Patients considered at risk of hereditary BC attended counseling at the genetic unit. Of 419 patients, 61 (14.5%) were eligible for genetic counseling after the interview. Of these, 46 (10.9%) strictly met testing criteria. Overall, 52 (12.4%) patients underwent genetic counseling and 47 were tested for BRCA1/BRCA2 mutation. After genetic test results, the available options for treatment/surveillance were discussed by a multidisciplinary team, according to the level of genetic risk. It is possible to improve the process of referring patients with suspected hereditary BC for genetic risk assessment. The application of clinical screening reduced the genetics unit's workload and enabled optimization of time and resources.

  19. Search Help

    Science.gov (United States)

    Guidance and search help resource listing examples of common queries that can be used in the Google Search Appliance search request, including examples of special characters, or query term seperators that Google Search Appliance recognizes.

  20. IN SITU COMPARISON OF TREE-RING RESPONSES TO CLIMATE AND POPULATION GENETICS: THE NEED TO CONTROL FOR LOCAL CLIMATE AND SITE VARIABLES

    Directory of Open Access Journals (Sweden)

    Johann Mathias Housset

    2016-10-01

    Full Text Available Tree species responses to climate change will be greatly influenced by their evolutionary potential and their phenotypic plasticity. Investigating tree-rings responses to climate and population genetics at the regional scale is therefore crucial in assessing the tree behaviour to climate change. This study combined in situ dendroclimatology and population genetics over a latitudinal gradient and compared the variations between the two at the intra- and inter-population levels. This approach was applied on the northern marginal populations of Thuja occidentalis (eastern white-cedar in the Canadian boreal forest. We aimed first to assess the radial growth variability (response functional trait within populations across the gradient and to compare it with the genetic diversity (microsatellites. Second, we investigated the variability in the growth response to climate at the regional scale through the radial growth-climate relationships, and tested its correlation with environmental variables and population genetic structure. Model selection based on the Akaike Information Criteria revealed that the growth synchronicity between pairs of trees of a population covariates with both the genetic diversity of this population and the amount of precipitation (inverse correlation, although these variables only explained a small fraction of the observed variance. At the regional scale, variance partitioning and partial redundancy analysis indicate that the growth response to climate was greatly modulated by stand environmental variables, suggesting predominant plastic variations in growth-response to climate. Combining in situ dendroclimatology and population genetics is a promising way to investigate species’ response capacity to climate change in natural stands. We stress the need to control for local climate and site conditions effects on dendroclimatic response to climate to avoid misleading conclusions regarding the associations with genetic variables.

  1. 2nd International Conference on Harmony Search Algorithm

    CERN Document Server

    Geem, Zong

    2016-01-01

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

  2. In search of the genetic footprints of Sumerians: a survey of Y-chromosome and mtDNA variation in the Marsh Arabs of Iraq

    Directory of Open Access Journals (Sweden)

    Olivieri Anna

    2011-10-01

    Full Text Available Abstract Background For millennia, the southern part of the Mesopotamia has been a wetland region generated by the Tigris and Euphrates rivers before flowing into the Gulf. This area has been occupied by human communities since ancient times and the present-day inhabitants, the Marsh Arabs, are considered the population with the strongest link to ancient Sumerians. Popular tradition, however, considers the Marsh Arabs as a foreign group, of unknown origin, which arrived in the marshlands when the rearing of water buffalo was introduced to the region. Results To shed some light on the paternal and maternal origin of this population, Y chromosome and mitochondrial DNA (mtDNA variation was surveyed in 143 Marsh Arabs and in a large sample of Iraqi controls. Analyses of the haplogroups and sub-haplogroups observed in the Marsh Arabs revealed a prevalent autochthonous Middle Eastern component for both male and female gene pools, with weak South-West Asian and African contributions, more evident in mtDNA. A higher male than female homogeneity is characteristic of the Marsh Arab gene pool, likely due to a strong male genetic drift determined by socio-cultural factors (patrilocality, polygamy, unequal male and female migration rates. Conclusions Evidence of genetic stratification ascribable to the Sumerian development was provided by the Y-chromosome data where the J1-Page08 branch reveals a local expansion, almost contemporary with the Sumerian City State period that characterized Southern Mesopotamia. On the other hand, a more ancient background shared with Northern Mesopotamia is revealed by the less represented Y-chromosome lineage J1-M267*. Overall our results indicate that the introduction of water buffalo breeding and rice farming, most likely from the Indian sub-continent, only marginally affected the gene pool of autochthonous people of the region. Furthermore, a prevalent Middle Eastern ancestry of the modern population of the marshes of

  3. Range-edge genetic diversity: locally poor extant southern patches maintain a regionally diverse hotspot in the seagrass Zostera marina.

    Science.gov (United States)

    Diekmann, Onno E; Serrão, Ester A

    2012-04-01

    Refugial populations at the rear edge are predicted to contain higher genetic diversity than those resulting from expansion, such as in post-glacial recolonizations. However, peripheral populations are also predicted to have decreased diversity compared to the centre of a species' distribution. We aim to test these predictions by comparing genetic diversity in populations at the limits of distribution of the seagrass Zostera marina, with populations in the species' previously described central diversity 'hotspot'. Zostera marina populations show decreased allelic richness, heterozygosity and genotypic richness in both the 'rear' edge and the 'leading' edge compared to the diversity 'hotspot' in the North Sea/Baltic region. However, when populations are pooled, genetic diversity at the southern range is as high as in the North Sea/Baltic region while the 'leading edge' remains low in genetic diversity. The decreased genetic diversity in these southern Iberian populations compared to more central populations is possibly the effect of drift because of small effective population size, as a result of reduced habitat, low sexual reproduction and low gene flow. However, when considering the whole southern edge of distribution rather than per population, diversity is as high as in the central 'hotspot' in the North Sea/Baltic region. We conclude that diversity patterns assessed per population can mask the real regional richness that is typical of rear edge populations, which have played a key role in the species biogeographical history and as marginal diversity hotspots have very high conservation value. © 2012 Blackwell Publishing Ltd.

  4. Adaptive color polymorphism and unusually high local genetic diversity in the side-blotched lizard, Uta stansburiana.

    Directory of Open Access Journals (Sweden)

    Steven Micheletti

    Full Text Available Recently, studies of adaptive color variation have become popular as models for examining the genetics of natural selection. We examined color pattern polymorphism and genetic variation in a population of side-blotched lizards (Uta stansburiana that is found in habitats with both dark (lava and light colored (granite substrates. We conducted a limited experiment for adult phenotypic plasticity in laboratory conditions. We recorded both substrate and lizard color patterns in the field to determine whether lizards tended to match their substrate. Finally we examined genetic variation in a gene (melanocortin 1 receptor that has been shown to affect lizard color in other species and in a presumably neutral gene (mitochondrial cytochrome b. Populations were sampled in the immediate area of the lava flows as well as from a more distant site to examine the role of population structure. Our captive Uta did not change color to match their background. We show that side-blotched lizards tend to match the substrate on which it was caught in the field and that variation in the melanocortin 1 receptor gene does not correlate well with color pattern in this population. Perhaps the most remarkable result is that this population of side-blotched lizards shows extremely high levels of variation at both genetic markers, in the sense of allele numbers, with relatively low levels of between-allele sequence variation. Genetic variation across this small region was as great or greater than that seen in samples of pelagic fish species collected worldwide. Statistical analysis of genetic variation suggests rapid population expansion may be responsible for the high levels of variation.

  5. Adaptive color polymorphism and unusually high local genetic diversity in the side-blotched lizard, Uta stansburiana.

    Science.gov (United States)

    Micheletti, Steven; Parra, Eliseo; Routman, Eric J

    2012-01-01

    Recently, studies of adaptive color variation have become popular as models for examining the genetics of natural selection. We examined color pattern polymorphism and genetic variation in a population of side-blotched lizards (Uta stansburiana) that is found in habitats with both dark (lava) and light colored (granite) substrates. We conducted a limited experiment for adult phenotypic plasticity in laboratory conditions. We recorded both substrate and lizard color patterns in the field to determine whether lizards tended to match their substrate. Finally we examined genetic variation in a gene (melanocortin 1 receptor) that has been shown to affect lizard color in other species and in a presumably neutral gene (mitochondrial cytochrome b). Populations were sampled in the immediate area of the lava flows as well as from a more distant site to examine the role of population structure. Our captive Uta did not change color to match their background. We show that side-blotched lizards tend to match the substrate on which it was caught in the field and that variation in the melanocortin 1 receptor gene does not correlate well with color pattern in this population. Perhaps the most remarkable result is that this population of side-blotched lizards shows extremely high levels of variation at both genetic markers, in the sense of allele numbers, with relatively low levels of between-allele sequence variation. Genetic variation across this small region was as great or greater than that seen in samples of pelagic fish species collected worldwide. Statistical analysis of genetic variation suggests rapid population expansion may be responsible for the high levels of variation.

  6. A molecular analysis of the patterns of genetic diversity in local chickens from western Algeria in comparison with commercial lines and wild jungle fowls.

    Science.gov (United States)

    Mahammi, F Z; Gaouar, S B S; Laloë, D; Faugeras, R; Tabet-Aoul, N; Rognon, X; Tixier-Boichard, M; Saidi-Mehtar, N

    2016-02-01

    The objectives of this study were to characterize the genetic variability of village chickens from three agro-ecological regions of western Algeria: coastal (CT), inland plains (IP) and highlands (HL), to reveal any underlying population structure, and to evaluate potential genetic introgression from commercial lines into local populations. A set of 233 chickens was genotyped with a panel of 23 microsatellite markers. Geographical coordinates were individually recorded. Eight reference populations were included in the study to investigate potential gene flow: four highly selected commercial pure lines and four lines of French slow-growing chickens. Two populations of wild red jungle fowls were also genotyped to compare the range of diversity between domestic and wild fowls. A genetic diversity analysis was conducted both within and between populations. Multivariate redundancy analyses were performed to assess the relative influence of geographical location among Algerian ecotypes. The results showed a high genetic variability within the Algerian population, with 184 alleles and a mean number of 8.09 alleles per locus. The values of heterozygosity (He and Ho) ranged from 0.55 to 0.62 in Algerian ecotypes and were smaller than values found in Jungle fowl populations and higher than values found in commercial populations. Although the structuring analysis of genotypes did not reveal clear subpopulations within Algerian ecotypes, the supervised approach using geographical data showed a significant (p < 0.01) differentiation between the three ecotypes which was mainly due to altitude. Thus, the genetic diversity of Algerian ecotypes may be under the influence of two factors with contradictory effects: the geographical location and climatic conditions may induce some differentiation, whereas the high level of exchanges and gene flow may suppress it. Evidence of gene flow between commercial and Algerian local populations was observed, which may be due to unrecorded

  7. Inferring local adaptation from QST–FST comparisons: neutral genetic and quantitative trait variation in European populations of great snipe

    NARCIS (Netherlands)

    Saether, S.A.; Fiske, P.; Kålås, J.A.; Kuresoo, A.; Luigujõe, L.; Piertney, S.; Sahlman, T.; Höglund, J.

    2007-01-01

    We applied a phenotypic QST (PST) vs. FST approach to study spatial variation in selection among great snipe (Gallinago media) populations in two regions of northern Europe. Morphological divergence between regions was high despite low differentiation in selectively neutral genetic markers, whereas

  8. Measuring local genetic variability in populations of codling moth (Lepidoptera: Tortricidae) across an unmanaged / commercial orchard interface

    Science.gov (United States)

    The genetic structure of adult codling moth Cydia pomonella L., populations was characterized both inside a managed apple, Malus domestica Borkdhausen, orchard and in surrounding unmanaged hosts and non-host trees in central Chile during 2006-2007. Adult males were collected using an array of sex ph...

  9. Random searching

    International Nuclear Information System (INIS)

    Shlesinger, Michael F

    2009-01-01

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

  10. Modified harmony search

    Science.gov (United States)

    Mohamed, Najihah; Lutfi Amri Ramli, Ahmad; Majid, Ahmad Abd; Piah, Abd Rahni Mt

    2017-09-01

    A metaheuristic algorithm, called Harmony Search is quite highly applied in optimizing parameters in many areas. HS is a derivative-free real parameter optimization algorithm, and draws an inspiration from the musical improvisation process of searching for a perfect state of harmony. Propose in this paper Modified Harmony Search for solving optimization problems, which employs a concept from genetic algorithm method and particle swarm optimization for generating new solution vectors that enhances the performance of HS algorithm. The performances of MHS and HS are investigated on ten benchmark optimization problems in order to make a comparison to reflect the efficiency of the MHS in terms of final accuracy, convergence speed and robustness.

  11. Search Patterns

    CERN Document Server

    Morville, Peter

    2010-01-01

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

  12. Prenatal Genetic Testing Chart

    Science.gov (United States)

    ... Management Education & Events Advocacy For Patients About ACOG Prenatal Genetic Testing Chart (Infographic) Home For Patients Search FAQs Prenatal Genetic Testing Chart (Infographic) PFSI010 ››› Weeks 1–4 ...

  13. Local adaptations in bryophytes revisited: the genetic structure of the calcium-tolerant peatmoss Sphagnum warnstorfii along geographic and pH gradients

    Science.gov (United States)

    Mikulášková, Eva; Hájek, Michal; Veleba, Adam; Johnson, Matthew G; Hájek, Tomáš; Shaw, Jonathan A

    2015-01-01

    Bryophytes dominate some ecosystems despite their extraordinary sensitivity to habitat quality. Nevertheless, some species behave differently across various regions. The existence of local adaptations is questioned by a high dispersal ability, which is thought to redistribute genetic variability among populations. Although Sphagnum warnstorfii is an important ecosystem engineer in fen peatlands, the causes of its rather wide niche along the pH/calcium gradient are poorly understood. Here, we studied the genetic variability of its global populations, with a detailed focus on the wide pH/calcium gradient in Central Europe. Principal coordinates analysis of 12 polymorphic microsatellite loci revealed a significant gradient coinciding with water pH, but independent of geography; even samples from the same fens were clearly separated along this gradient. However, most of the genetic variations remained unexplained, possibly because of the introgression from phylogenetically allied species. This explanation is supported by the small heterogeneous cluster of samples that appeared when populations morphologically transitional to S. subnites, S. rubellum, or S. russowii were included into the analysis. Alternatively, this unexplained variation might be attributed to a legacy of glacial refugia with recently dissolved ecological and biogeographic consequences. Isolation by distance appeared at the smallest scale only (up to 43 km). Negative spatial correlations occurred more frequently, mainly at long distances (up to 950 km), implying a genetic similarity among samples which are very distant geographically. Our results confirm the high dispersal ability of peatmosses, but simultaneously suggested that their ability to cope with a high pH/calcium level is at least partially determined genetically, perhaps via specific physiological mechanisms or a hummock-forming ability. PMID:25628880

  14. Search on Rugged Landscapes

    DEFF Research Database (Denmark)

    Billinger, Stephan; Stieglitz, Nils; Schumacher, Terry

    2014-01-01

    This paper presents findings from a laboratory experiment on human decision-making in a complex combinatorial task. We find strong evidence for a behavioral model of adaptive search. Success narrows down search to the neighborhood of the status quo, while failure promotes gradually more explorative...... search. Task complexity does not have a direct effect on behavior, but systematically affects the feedback conditions that guide success-induced exploitation and failure-induced exploration. The analysis also shows that human participants were prone to over-exploration, since they broke off the search...... for local improvements too early. We derive stylized decision rules that generate the search behavior observed in the experiment and discuss the implications of our findings for individual decision-making and organizational search....

  15. The significance of protecting domestic native corn from genetically modified seeds: a perspective from local Mexican NGOs

    Directory of Open Access Journals (Sweden)

    Juanamaria Vazquez

    2016-12-01

    Full Text Available During the last decades, there has been an ongoing global discussion about the use of genetically modified organisms (GMO and their insertion in geographic regions where there is a vast pool of native landraces such as Mexican corn, Indian rice, Peruvian potato. This discussion takes place between those who defend native landraces along with traditional farming knowledge (TK and those who defend genetic engineering products (GMO, turning the discussion into a running social confrontation between large corporations and domestic NGO’s network. Both sides are accompanied by leading scientific communities.Based on the Political Economy perspective of K. Polanyi and his analytical categories, this paper examines the case of the Mexican GMO controversy between predominantly US agroindustry and Mexican NGOs. It shows the performance of NGO’s in trying to avoid the insertion of GM corn in México through a legal injunction that is banning the commercialization of this GM corn in the whole territory.

  16. Differential Cotton leaf crumple virus-VIGS-mediated gene silencing and viral genome localization in different Gossypium hirsutum genetic backgrounds

    KAUST Repository

    Idris, Ali

    2010-12-01

    A Cotton leaf crumple virus (CLCrV)-based gene silencing vector containing a fragment of the Gossypium hirsutum Magnesium chelatase subunit I was used to establish endogenous gene silencing in cotton of varied genetic backgrounds. Biolistic inoculation resulted in systemic and persistent photo-bleaching of the leaves and bolls of the seven cultivars tested, however, the intensity of silencing was variable. CLCrV-VIGS-mediated expression of green fluorescent protein was used to monitor the in planta distribution of the vector, indicating successful phloem invasion in all cultivars tested. Acala SJ-1, one of the cotton cultivars, was identified as a particularly optimal candidate for CLCrV-VIGS-based cotton reverse-genetics. © 2010 Elsevier Ltd.

  17. Genetic evidence of local exploitation of Atlantic salmon in a coastal subsistence fishery in the Northwest Atlantic

    Science.gov (United States)

    Bradbury, Ian R.; Hamilton, Lorraine C.; Rafferty, Sara; Meerburg, David; Poole, Rebecca; Dempson, J. Brian; Robertson, Martha J.; Reddin, David G.; Bourret, Vincent; Dionne, Mélanie; Chaput, Gerald J.; Sheehan, Timothy F.; King, Tim L.; Candy, John R.; Bernatchez, Louis

    2014-01-01

    Fisheries targeting mixtures of populations risk the over utilization of minor stock constituents unless harvests are monitored and managed. We evaluated stock composition and exploitation of Atlantic salmon in a subsistence fishery in coastal Labrador, Canada using genetic mixture analysis and individual assignment with a microsatellite baseline (15 loci, 11 829 individuals, 12 regional groups) encompassing the species western Atlantic range. Bayesian and maximum likelihood mixture analyses of fishery samples over six years (2006-2011; 1 772 individuals) indicate contributions of adjacent stocks of 96-97%. Estimates of fishery associated exploitation were highest for Labrador salmon (4.2-10.6% per year) and generally work illustrates how genetic analysis of mixed stock Atlantic salmon fisheries in the northwest Atlantic using this new baseline can disentangle exploitation and reveal complex migratory behaviours.

  18. The impact of local extinction on genetic structure of wild populations of lima beans (Phaseolus lunatus in the Central Valley of Costa Rica: consequences for the conservation of plant genetic resources

    Directory of Open Access Journals (Sweden)

    Daniel Barrantes

    2008-09-01

    Full Text Available Plant populations may experience local extinction and at the same time new populations may appear in nearby suitable locations. Species may also colonize the same site on multiple occasions. Here, we examined the impact of local extinction and recolonization on the genetic structure of wild populations of lima beans (Phaseolus lunatus in the Central valley of Costa Rica. We compared genetic diversity from the samples taken from the populations before and after extinction at 13 locations using microsatellite markers. Locations were classified according to the occurrence of extinction episodes during the previous five years into three groups: 1 populations that experienced extinction for more than one year, and were later recolonized (recolonized, 2 populations that did not experience local extinction (control, and 3 populations that did not experience local extinction during the study, but were cut to experimentally simulate extinction (experimental. Our data did not show a clear tendency in variation in allele frequencies, expected heterozygosity, and effective number of alleles within and between groups of populations. However, we found that the level of genetic differentiation between samples collected at different times at the same location was different in the three groups of populations. Recolonized locations showed the highest level of genetic differentiation (mean Fst= 0.2769, followed by control locations (mean Fst= 0.0576 and experimental locations (mean Fst= 0.0189. Similar findings were observed for Nei’s genetic distance between samples (di,j= 0.1786, 0.0400, and 0.0037, respectively. Our results indicate that genetic change in lima beans depends on the duration and frequency of local extinction episodes. These findings also showed that control populations are not in equilibrium. Implications of these results for the establishment of conservation strategies of genetic resources of lima beans are discussed. Rev. Biol. Trop. 56 (3

  19. Occurrence and genetic relatedness of Listeria spp. in two brands of locally processed ready-to-eat meats in Trinidad.

    Science.gov (United States)

    Syne, S M; Ramsubhag, A; Adesiyun, A A

    2011-05-01

    Contamination of locally produced, ready-to-eat meats by Listeria spp. has been previously reported at one processing plant in Trinidad. However, the status of this pathogen in locally produced products sold at retail outlets is unknown. This study was conducted to establish whether there is a risk to consumers of locally processed meats caused by the presence of Listeria spp., and whether a link exists between the presence of the pathogen in retail products and the manufacturing plant of one brand (B). Four hundred and eighty ready-to-eat meat products of two popular local brands (A and B) were collected from retail outlets and analysed for the presence of Listeria spp. together with food samples and surfaces from one manufacturing plant (B). Eighty-eight of the retail products (18·3%) were contaminated with Listeria spp., of which, 52·3% were L. innocua, 44·3% were L. monocytogenes and 3·4% belonged to the L. seeligeri-L. welshimeri-L. ivanovii (Siwi) group. L. innocua was found in 15 in-process food samples and on three surfaces of equipment at plant B. Four in-process food samples were also contaminated with Siwi isolates. Repetitive extragenic palindromic PCR DNA fingerprinting showed a possible association between strains of different Listeria spp. and brand as well as with manufacturing plant B.

  20. Personalized Search

    CERN Document Server

    AUTHOR|(SzGeCERN)749939

    2015-01-01

    As the volume of electronically available information grows, relevant items become harder to find. This work presents an approach to personalizing search results in scientific publication databases. This work focuses on re-ranking search results from existing search engines like Solr or ElasticSearch. This work also includes the development of Obelix, a new recommendation system used to re-rank search results. The project was proposed and performed at CERN, using the scientific publications available on the CERN Document Server (CDS). This work experiments with re-ranking using offline and online evaluation of users and documents in CDS. The experiments conclude that the personalized search result outperform both latest first and word similarity in terms of click position in the search result for global search in CDS.

  1. Localized past, globalized future: towards an effective bioethical framework using examples from population genetics and medical tourism.

    Science.gov (United States)

    Widdows, Heather

    2011-02-01

    This paper suggests that many of the pressing dilemmas of bioethics are global and structural in nature. Accordingly, global ethical frameworks are required which recognize the ethically significant factors of all global actors. To this end, ethical frameworks must recognize the rights and interests of both individuals and groups (and the interrelation of these). The paper suggests that the current dominant bioethical framework is inadequate to this task as it is over-individualist and therefore unable to give significant weight to the ethical demands of groups (and by extension communal and public goods). It will explore this theme by considering the inadequacy of informed consent (the 'global standard' of bioethics) to address two pressing global bioethical issues: medical tourism and population genetics. Using these examples it will show why consent is inadequate to address all the significant features of these ethical dilemmas. Four key failures will be explored, namely, • That the rights and interests of those related (and therefore affected) are neglected; • That consent fails to take account of the context and commitments of individuals which may constitute inducement and coercion; • That consent alone does not have the ethical weight to negate exploitation or make an unjust action just ('the fallacy of sufficiency'); • That consent is a single one-off act which is inappropriate for the types of decision being made. It will conclude by suggesting that more appropriate models are emerging, particularly in population genetics, which can supplement consent. © 2010 Blackwell Publishing Ltd.

  2. Temporal change in genetic integrity suggests loss of local adaptation in a wild Atlantic salmon (Salmo salar) population following introgression by farmed escapees.

    Science.gov (United States)

    Bourret, V; O'Reilly, P T; Carr, J W; Berg, P R; Bernatchez, L

    2011-03-01

    In some wild Atlantic salmon populations, rapid declines in numbers of wild returning adults has been associated with an increase in the prevalence of farmed salmon. Studies of phenotypic variation have shown that interbreeding between farmed and wild salmon may lead to loss of local adaptation. Yet, few studies have attempted to assess the impact of interbreeding at the genome level, especially among North American populations. Here, we document temporal changes in the genetic makeup of the severely threatened Magaguadavic River salmon population (Bay of Fundy, Canada), a population that might have been impacted by interbreeding with farmed salmon for nearly 20 years. Wild and farmed individuals caught entering the river from 1980 to 2005 were genotyped at 112 single-nucleotide polymorphisms (SNPs), and/or eight microsatellite loci, to scan for potential shifts in adaptive genetic variation. No significant temporal change in microsatellite-based estimates of allele richness or gene diversity was detected in the wild population, despite its precipitous decline in numbers over the last two decades. This might reflect the effect of introgression from farmed salmon, which was corroborated by temporal change in linkage-disequilibrium. Moreover, SNP genome scans identified a temporal decrease in candidate loci potentially under directional selection. Of particular interest was a SNP previously shown to be strongly associated with an important quantitative trait locus for parr mark number, which retained its genetic distinctiveness between farmed and wild fish longer than other outliers. Overall, these results indicate that farmed escapees have introgressed with wild Magaguadavic salmon resulting in significant alteration of the genetic integrity of the native population, including possible loss of adaptation to wild conditions.

  3. Genetic localization of Cd63, a member of the transmembrane 4 superfamily, reveals two distinct loci in the mouse genome

    Energy Technology Data Exchange (ETDEWEB)

    Gwynn, B.; Eicher, E.M.; Peters, L.L. [Jackson Lab., Bar Harbor, ME (United States)

    1996-07-15

    The membrane protein CD63, a molecular marker for early stages of melanoma progression, has been associated with platelet storage pool deficiency disorders (SPD). CD63 localizes to the membranes of platelets, lysosomes, and melanosomes, all of which are affected in a specific subgroup of SPD. The cDNA encoding CD63 detects two closely related sequences that map to different regions of the mouse genome. One locus maps to mouse Chromosome (Chr) 10 in a region that shares linkage homology with the human chromosome encoding human CD63. The second locus maps to mouse Chr 18 in a region that bears no known human CD63-related genes. No SPD has been localized to these regions of either the mouse or the human chromosomes. 15 refs., 2 figs.

  4. Dual-flow-RootChip reveals local adaptations of roots towards environmental asymmetry at the physiological and genetic levels.

    Science.gov (United States)

    Stanley, Claire E; Shrivastava, Jagriti; Brugman, Rik; Heinzelmann, Elisa; van Swaay, Dirk; Grossmann, Guido

    2018-02-01

    Roots grow in highly dynamic and heterogeneous environments. Biological activity as well as uneven nutrient availability or localized stress factors result in diverse microenvironments. Plants adapt their root morphology in response to changing environmental conditions, yet it remains largely unknown to what extent developmental adaptations are based on systemic or cell-autonomous responses. We present the dual-flow-RootChip, a microfluidic platform for asymmetric perfusion of Arabidopsis roots to investigate root-environment interactions under simulated environmental heterogeneity. Applications range from investigating physiology, root hair development and calcium signalling upon selective exposure to environmental stresses to tracing molecular uptake, performing selective drug treatments and localized inoculations with microbes. Using the dual-flow-RootChip, we revealed cell-autonomous adaption of root hair development under asymmetric phosphate (Pi) perfusion, with unexpected repression in root hair growth on the side exposed to low Pi and rapid tip-growth upregulation when Pi concentrations increased. The asymmetric root environment further resulted in an asymmetric gene expression of RSL4, a key transcriptional regulator of root hair growth. Our findings demonstrate that roots possess the capability to locally adapt to heterogeneous conditions in their environment at the physiological and transcriptional levels. Being able to generate asymmetric microenvironments for roots will help further elucidate decision-making processes in root-environment interactions. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  5. Global and local genetic diversity at two microsatellite loci in Plasmodium vivax parasites from Asia, Africa and South America

    DEFF Research Database (Denmark)

    Schousboe, Mette L; Ranjitkar, Samir; Rajakaruna, Rupika S

    2014-01-01

    diversity are vital to the evaluation of drug and vaccine efficacy, tracking of P. vivax outbreaks, and assessing geographical differentiation between parasite populations. METHODS: The genetic diversity of eight P. vivax populations (n = 543) was investigated by using two microsatellites (MS), m1501 and m......3502, chosen because of their seven and eight base-pair (bp) repeat lengths, respectively. These were compared with published data of the same loci from six other P. vivax populations. RESULTS: In total, 1,440 P. vivax samples from 14 countries on three continents were compared. There was highest...... heterozygosity within Asian populations, where expected heterozygosity (He) was 0.92-0.98, and alleles with a high repeat number were more common. Pairwise FST revealed significant differentiation between most P. vivax populations, with the highest divergence found between Asian and South American populations...

  6. Policy implications for familial searching

    OpenAIRE

    Kim, Joyce; Mammo, Danny; Siegel, Marni B; Katsanis, Sara H

    2011-01-01

    Abstract In the United States, several states have made policy decisions regarding whether and how to use familial searching of the Combined DNA Index System (CODIS) database in criminal investigations. Familial searching pushes DNA typing beyond merely identifying individuals to detecting genetic relatedness, an application previously reserved for missing persons identifications and custody battles. The intentional search of CODIS for partial matches to an item of evidence offers law enforce...

  7. Human growth hormone-related latrogenic Creutzfeldt-Jakob disease: Search for a genetic susceptibility by analysis of the PRNP coding region

    Energy Technology Data Exchange (ETDEWEB)

    Jaegly, A.; Boussin, F.; Deslys, J.P. [CEA/CRSSA/DSV/DPTE, Fontenay-aux-Roses (France)] [and others

    1995-05-20

    The human PRNP gene encoding PrP is located on chromosome 20 and consists of two exons and a single intron. The open reading frame is entirely fitted into the second exon. Genetic studies indicate that all of the familial and several sporadic forms of TSSEs are associated with mutations in the PRNP 759-bp coding region. Moreover, homozygosity at codon 129, a locus harboring a polymorphism among the general population, was proposed as a genetic susceptibility marker for both sporadic and iatrogenic CJD. To assess whether additional genetic predisposition markers exist in the PRNP gene, the authors sequenced the PRNP coding region of 17 of the 32 French patients who developed a hGH-related CJD.

  8. Genetics of cosQ, the DNA-packaging termination site of phage lambda: local suppressors and methylation effects.

    OpenAIRE

    Wieczorek, Douglas J; Feiss, Michael

    2003-01-01

    The cos site of the bacteriophage lambda chromosome contains the sites required for DNA processing and packaging during virion assembly. cos is composed of three subsites, cosQ, cosN, and cosB. cosQ is required for the termination of chromosome packaging. Previous studies have shown cosQ mutations to be suppressed in three ways: by a local suppressor within cosQ; by an increase in the length of the lambda chromosome; and by missense mutations affecting the prohead's portal protein, gpB. In th...

  9. A search for genetic diversity among Italian Greyhounds from Continental Europe and the USA and the effect of inbreeding on susceptibility to autoimmune disease.

    Science.gov (United States)

    Pedersen, Niels C; Liu, Hongwei; Leonard, Angela; Griffioen, Layle

    2015-01-01

    Previous studies documented the problem of inbreeding among Italian Greyhounds (IG) from the USA and its possible role in a multiple autoimmune disease syndrome. The present study is an extension of these earlier experiments and had two objectives: 1) to identify pockets of additional genetic diversity that might still exist among IG from the USA and Continental Europe, and 2) to determine how loss of genetic diversity within the genome and in the dog leukocyte antigen (DLA) complex relates to the problem of autoimmune disease in IG from the USA. Genetic testing was conducted using 33 short tandem repeat (STR) loci across 25 chromosomes and 7 STR loci that associated with specific dog leukocyte antigen (DLA) class I and II haplotypes. Standard genetic assessment tests based on allele frequencies and internal relatedness (IR) were used as measures of breed-wide and individual heterozygosity. The results of these tests demonstrated that IG from the USA and Continental Europe belonged to a single breed but were genetically distinguishable by genomic allele frequencies, DLA class I and II haplotypes, and principal coordinate analysis (PCoA). In the second part of the study, 85 IG from the USA that had suffered various autoimmune disorders (case) and 104 healthy dogs (control) of comparable age were studied for genetic associations with disease. Case dogs were found to be significantly more homozygous in the DLA regions than control dogs. Principal coordinate analysis did not differentiate case from control populations. No specific STR-associated DLA-class I or II haplotype was associated with increased autoimmune disease risks. Reasons for the loss of genetic diversity and increased homozygosity among IG from the USA were studied using registration data and deep pedigrees. The breed in the USA started from a small number of founders from Europe and has remained relatively isolated and small in numbers, limiting breeding choices especially in the period before modern

  10. Acetylglutamate synthase in Neurospora crassa: characterization, localization, and genetic behavior of a regulatory enzyme of arginine biosynthesis

    International Nuclear Information System (INIS)

    Jacobson, J.A.

    1988-01-01

    This study describes the characterization and localization of the first enzyme of arginine biosynthesis in Neurospora crassa. A radioactive assay was developed to detect this enzyme whereby radioactive substrate and product molecules could be separated by ion-exchange chromatography. The enzyme was found to have a pH optimum of 9.0 and K/sub m/ values for glutamate and acetyl-CoA of approximately 4.7 and 0.45 mM, respectively. The enzyme was shown to be feedback inhibited by arginine. Half-maximal inhibition was observed at 0.13 mM arginine, a concentration which is similar to be in vivo cytosolic concentration of 0.2 mM. Arginine was found to act as a competitive inhibitor with respect to acetyl-CoA. Acetylglutamate synthase was localized to the mitochondrion. However, in contrast to the mitochondrial matrix location of the other ornithine biosynthetic enzymes, this enzyme was found to reside on the mitochondrial inner membrane

  11. A genome-wide search for linkage to asthma phenotypes in the genetics of asthma international network families : evidence for a major susceptibility locus on chromosome 2p

    NARCIS (Netherlands)

    Pillai, SG; Chiano, MN; White, NJ; Speer, M; Barnes, KC; Carlsen, K; Gerritsen, Jorrit; Helms, P; Lenney, W; Silverman, M; Sly, P; Sundy, J; Tsanakas, J; von Berg, A; Whyte, M; Varsani, S; Skelding, P; Hauser, M; Vance, J; Pericak-Vance, M; Burns, DK; Middleton, LT; Brewster, [No Value; Anderson, WH; Riley, JH

    Asthma is a complex disease and the intricate interplay between genetic and environmental factors underlies the overall phenotype of the disease. Families with at least two siblings with asthma were collected from Europe, Australia and the US. A genome scan using a set of 364 families with a panel

  12. In search of shared and non-shared influences on infant attachment: A behavior-genetic study of the association between sensitivity and attachment

    NARCIS (Netherlands)

    Fearon, R.M.; van IJzendoorn, M.H.; Fonagy, P.; Bakermans-Kranenburg, M.J.; Schuengel, C.; Bokhorst, C.L.

    2006-01-01

    The current article presents results from a twin study of genetic and environmental components of maternal sensitivity and infant attachment and their association. The sample consisted of 136 twin pairs from 2 sites: Leiden, the Netherlands, and London, UK. Maternal sensitivity was assessed in the

  13. A binary genetic programing model for teleconnection identification between global sea surface temperature and local maximum monthly rainfall events

    Science.gov (United States)

    Danandeh Mehr, Ali; Nourani, Vahid; Hrnjica, Bahrudin; Molajou, Amir

    2017-12-01

    The effectiveness of genetic programming (GP) for solving regression problems in hydrology has been recognized in recent studies. However, its capability to solve classification problems has not been sufficiently explored so far. This study develops and applies a novel classification-forecasting model, namely Binary GP (BGP), for teleconnection studies between sea surface temperature (SST) variations and maximum monthly rainfall (MMR) events. The BGP integrates certain types of data pre-processing and post-processing methods with conventional GP engine to enhance its ability to solve both regression and classification problems simultaneously. The model was trained and tested using SST series of Black Sea, Mediterranean Sea, and Red Sea as potential predictors as well as classified MMR events at two locations in Iran as predictand. Skill of the model was measured in regard to different rainfall thresholds and SST lags and compared to that of the hybrid decision tree-association rule (DTAR) model available in the literature. The results indicated that the proposed model can identify potential teleconnection signals of surrounding seas beneficial to long-term forecasting of the occurrence of the classified MMR events.

  14. Localization and the interface between quantum mechanics, quantum field theory and quantum gravity II. (The search of the interface between QFT and QG)

    International Nuclear Information System (INIS)

    Schroer, Bert; Freie Universitaet, Berlin

    2010-02-01

    The main topics of this second part of a two-part essay are some consequences of the phenomenon of vacuum polarization as the most important physical manifestation of modular localization. Besides philosophically unexpected consequences, it has led to a new constructive 'outside-inwards approach' in which the pointlike fields and the compactly localized operator algebras which they generate only appear from intersecting much simpler algebras localized in noncompact wedge regions whose generators have extremely mild almost free field behavior. Another consequence of vacuum polarization presented in this essay is the localization entropy near a causal horizon which follows a logarithmically modified area law in which a dimensionless area (the area divided by the square of dR where dR is the thickness of a light sheet) appears. There are arguments that this logarithmically modified area law corresponds to the volume law of the standard heat bath thermal behavior. We also explain the symmetry enhancing effect of holographic projections onto the causal horizon of a region and show that the resulting infinite dimensional symmetry groups contain the Bondi-Metzner-Sachs group. This essay is the second part of a partitioned longer paper. (author)

  15. Localization and the interface between quantum mechanics, quantum field theory and quantum gravity II (The search of the interface between QFT and QG)

    International Nuclear Information System (INIS)

    Schroer, Bert

    2010-01-01

    The main topics of this second part of a two-part essay are some consequences of the phenomenon of vacuum polarization as the most important physical manifestation of modular localization. Besides philosophically unexpected consequences, it has led to a new constructive 'outside-inwards approach' in which the pointlike fields and the compactly localized operator algebras which they generate only appear from intersecting much simpler algebras localized in noncompact wedge regions whose generators have extremely mild almost free field behavior. Another consequence of vacuum polarization presented in this essay is the localization entropy near a causal horizon which follows a logarithmically modified area law in which a dimensionless area (the area divided by the square of dR where dR is the thickness of a light sheet) appears. There are arguments that this logarithmically modified area law corresponds to the volume law of the standard heat bath thermal behavior. We also explain the symmetry enhancing effect of holographic projections onto the causal horizon of a region and show that the resulting infinite dimensional symmetry groups contain the Bondi-Metzner-Sachs group. This essay is the second part of a partitioned longer paper. (author)

  16. Is Arc mRNA Unique: A Search for mRNAs That Localize to the Distal Dendrites of Dentate Gyrus Granule Cells Following Neural Activity

    Directory of Open Access Journals (Sweden)

    Christopher A. de Solis

    2017-10-01

    Full Text Available There have been several attempts to identify which RNAs are localized to dendrites; however, no study has determined which RNAs localize to the dendrites following the induction of synaptic activity. We sought to identify all RNA transcripts that localize to the distal dendrites of dentate gyrus granule cells following unilateral high frequency stimulation of the perforant pathway (pp-HFS using Sprague Dawley rats. We then utilized laser microdissection (LMD to very accurately dissect out the distal 2/3rds of the molecular layer (ML, which contains these dendrites, without contamination from the granule cell layer, 2 and 4 h post pp-HFS. Next, we purified and amplified RNA from the ML and performed an unbiased screen for 27,000 RNA transcripts using Affymetrix microarrays. We determined that Activity Regulated Cytoskeletal Protein (Arc/Arg3.1 mRNA, exhibited the greatest fold increase in the ML at both timepoints (2 and 4 h. In total, we identified 31 transcripts that increased their levels within the ML following pp-HFS across the two timepoints. Of particular interest is that one of these identified transcripts was an unprocessed micro-RNA (pri-miR132. Fluorescent in situ hybridization and qRT-PCR were used to confirm some of these candidate transcripts. Our data indicate Arc is a unique activity dependent gene, due to the magnitude that its activity dependent transcript localizes to the dendrites. Our study determined other activity dependent transcripts likely localize to the dendrites following neural activity, but do so with lower efficiency compared to Arc.

  17. Genetically Modified Neural Stem Cells for a Local and Sustained Delivery of Neuroprotective Factors to the Dystrophic Mouse Retina

    Science.gov (United States)

    Jung, Gila; Sun, Jing; Petrowitz, Bettina; Riecken, Kristoffer; Kruszewski, Katharina; Jankowiak, Wanda; Kunst, Frank; Skevas, Christos; Richard, Gisbert; Fehse, Boris

    2013-01-01

    A continuous intraocular delivery of neurotrophic factors (NFs) is being explored as a strategy to rescue photoreceptor cells and visual functions in degenerative retinal disorders that are currently untreatable. To establish a cell-based intraocular delivery system for a sustained administration of NFs to the dystrophic mouse retina, we used a polycistronic lentiviral vector to genetically modify adherently cultivated murine neural stem (NS) cells. The vector concurrently encoded a gene of interest, a reporter gene, and a resistance gene and thus facilitated the selection, cloning, and in vivo tracking of the modified cells. To evaluate whether modified NS cells permit delivery of functionally relevant quantities of NFs to the dystrophic mouse retina, we expressed a secretable variant of ciliary neurotrophic factor (CNTF) in NS cells and grafted the cells into the vitreous space of Pde6brd1 and Pde6brd10 mice, two animal models of retinitis pigmentosa. In both mouse lines, grafted cells attached to the retina and lens, where they differentiated into astrocytes and some neurons. Adverse effects of the transplanted cells on the morphology of host retinas were not observed. Importantly, the CNTF-secreting NS cells significantly attenuated photoreceptor degeneration in both mutant mouse lines. The neuroprotective effect was significantly more pronounced when clonally derived NS cell lines selected for high expression levels of CNTF were grafted into Pde6brd1 mice. Intravitreal transplantations of modified NS cells may thus represent a useful method for preclinical studies aimed at evaluating the therapeutic potential of a cell-based intraocular delivery of NFs in mouse models of photoreceptor degeneration. PMID:24167317

  18. Faceted Search

    CERN Document Server

    Tunkelang, Daniel

    2009-01-01

    We live in an information age that requires us, more than ever, to represent, access, and use information. Over the last several decades, we have developed a modern science and technology for information retrieval, relentlessly pursuing the vision of a "memex" that Vannevar Bush proposed in his seminal article, "As We May Think." Faceted search plays a key role in this program. Faceted search addresses weaknesses of conventional search approaches and has emerged as a foundation for interactive information retrieval. User studies demonstrate that faceted search provides more

  19. Virulence characteristics and genetic affinities of multiple drug resistant uropathogenic Escherichia coli from a semi urban locality in India.

    Directory of Open Access Journals (Sweden)

    Savita Jadhav

    genetically distinct with no evidence to espouse expansion of E. coli from India to the west or vice-versa.

  20. Morphological, Phenological And Agronomical Characterisation Of Variability Among Common Bean (Phaseolus Vulgaris L. Local Populations From The National Centre For Plant Genetic Resources: Polish Genebank

    Directory of Open Access Journals (Sweden)

    Boros Lech

    2014-12-01

    Full Text Available The main purpose of this work was to analyse the morphological, phenological and agronomical variability among common bean local populations from The National Centre for Plant Genetic Resources, Polish Genebank, in order to know the relation among them, and to identify potentially useful accessions for future production and breeding. A considerable genotypic variation for number of seeds per plant, number of pods per plant and weight of seeds per plant were found. Studied bean accessions differed significantly in terms of thousand seeds weight (TSW as well as severity of bacterial halo blight and anthracnose, the major bean diseases. The lowest genotypic diversity was found for the percentage of protein in the seeds, the length of the vegetation period and lodging. The cluster analysis allowed identification of five groups of bean accessions. Genotypes from the first cluster (POLPOD 98-77, KOS 002 and Raba cv. and from the second cluster (WUKR 06-573a, KRA 4, WUKR 06-0534 together with Prosna cv. are of the highest usefulness for breeding purposes. There was no grouping of local populations depending on region of origin.

  1. Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  2. Involvement of two genetic lineages of Sarcoptes scabiei mites in a local mange epizootic of wild mammals in Japan.

    Science.gov (United States)

    Makouloutou, Patrice; Suzuki, Kazuo; Yokoyama, Mayumi; Takeuchi, Masahiko; Yanagida, Tetsuya; Sato, Hiroshi

    2015-01-01

    Similar to wild mammals on the continents, mange caused by the mange mite, Sarcoptes scabiei (Acari: Sarcoptidae) is spreading in wild mammals in most of Japan. We collected crusted or alopetic skin from 120 raccoon dogs (Nyctereutes procyonoides viverrinus), three raccoons (Procyon lotor), six Japanese badgers (Meles anakuma), one Japanese marten (Martes melampus), one stray dog (Canis lupus familiaris), four wild boars (Sus scrofa leucomystax), and one Japanese serow (Capricornis crispus), mainly in an area where mangy wild animals have been increasingly noted in the past 4 yr. The second internal transcribed spacer (ITS2) region of the ribosomal RNA gene and the partial 16S and cytochrome c oxidase subunit I (cox-1) genes of mitochondrial DNA (mtDNA) were characterized in these skin samples. The ITS2 sequencing (404 base pairs [bp]) identified the causative mite for mangy skin lesions of 128 animals as S. scabiei, regardless of host origin. The cat mite (Notoedres cati) was the cause in one raccoon dog and one raccoon. Most mites had almost identical ITS2 nucleotide sequences to those recorded in a variety of mammals worldwide. Partial 16S and cox-1 fragments of mtDNA amplified and sequenced successfully (331 bp and 410 bp, respectively) showed an identical nucleotide sequence except for one site (C vs. T) for the former and four sites (G, C, C, C vs. A, T, T, T, respectively) for the latter fragment. These substitutions were always synchronized, with the two mitochondrial DNA haplotypes (i.e., C/GCCC and T/ATTT) appearing to separately colonize in geographic units. The T/ATTT haplotype fell into a clade where animal-derived mites worldwide dominated, whereas the C/GCCC haplotype formed a geographic branch unique to Japanese isolates. These results suggest that heterologous populations of monospecific S. scabiei are expanding their populations and distributions regardless of host species in an apparently local mange epizootic of wild mammals in Japan.

  3. Journal of Genetics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Search. Search. Journal of Genetics. Title. Author. Keywords. Fulltext. Submit. Journal of Genetics. Current Issue : Vol. 97, Issue 1. Current Issue Volume 97 | Issue 1. March 2018. Home · Volumes & Issues · Online Resources · Special Issues · Forthcoming Articles · Search · Editorial ...

  4. A discrete particle swarm optimization algorithm with local search for a production-based two-echelon single-vendor multiple-buyer supply chain

    Science.gov (United States)

    Seifbarghy, Mehdi; Kalani, Masoud Mirzaei; Hemmati, Mojtaba

    2016-03-01

    This paper formulates a two-echelon single-producer multi-buyer supply chain model, while a single product is produced and transported to the buyers by the producer. The producer and the buyers apply vendor-managed inventory mode of operation. It is assumed that the producer applies economic production quantity policy, which implies a constant production rate at the producer. The operational parameters of each buyer are sales quantity, sales price and production rate. Channel profit of the supply chain and contract price between the producer and each buyer is determined based on the values of the operational parameters. Since the model belongs to nonlinear integer programs, we use a discrete particle swarm optimization algorithm (DPSO) to solve the addressed problem; however, the performance of the DPSO is compared utilizing two well-known heuristics, namely genetic algorithm and simulated annealing. A number of examples are provided to verify the model and assess the performance of the proposed heuristics. Experimental results indicate that DPSO outperforms the rival heuristics, with respect to some comparison metrics.

  5. Numeral eddy current sensor modelling based on genetic neural network

    International Nuclear Information System (INIS)

    Yu Along

    2008-01-01

    This paper presents a method used to the numeral eddy current sensor modelling based on the genetic neural network to settle its nonlinear problem. The principle and algorithms of genetic neural network are introduced. In this method, the nonlinear model parameters of the numeral eddy current sensor are optimized by genetic neural network (GNN) according to measurement data. So the method remains both the global searching ability of genetic algorithm and the good local searching ability of neural network. The nonlinear model has the advantages of strong robustness, on-line modelling and high precision. The maximum nonlinearity error can be reduced to 0.037% by using GNN. However, the maximum nonlinearity error is 0.075% using the least square method

  6. In search of the pre- and post-neolithic genetic substrates in Iberia: evidence from Y-chromosome in Pyrenean populations.

    Science.gov (United States)

    López-Parra, A M; Gusmão, L; Tavares, L; Baeza, C; Amorim, A; Mesa, M S; Prata, M J; Arroyo-Pardo, E

    2009-01-01

    The male-mediated genetic legacy of the Pyrenean population was assessed through the analysis of 12 Y-STR and 27 Y-SNP loci in a sample of 169 males from 5 main geographical areas in the Spanish Pyrenees: Cinco Villas (Western Pyrenees), Jacetania and Valle de Arán (Central Pyrenees) and Alto Urgel and Cerdaña (Eastern Pyrenees). In the Iberian context, the Pyrenean samples present some specificities, being characterizeded by a high proportion of chromosomes R1b1b2-M269 (including the usually uncommon R1b1b2d-SRY(2627) and R1b1b2c-M153 types) or I2a2-M26 and low proportions of other haplogroups. Our results indicate that an old pre-Neolithic substrate is preponderant in populations of the whole Pyrenean fringe. However, AMOVA revealed a high level of substructure within Pyrenean populations, partially explained by drift effects as well as by the signature of an ancient genetic differentiation between Western and Eastern Pyrenees.

  7. Localization of a gene (CMT2A) for autosomal dominant Charcot-Marie-Tooth disease type 2 to chromosome 1p and evidence of genetic heterogeneity

    Energy Technology Data Exchange (ETDEWEB)

    Othmane, K.B.; Loprest, L.J.; Wilkinson, K.M. (Duke Univ. Medical Center, Durham, NC (United States)); Middleton, L.T. (Cyprus Institute of Neurology and Genetics, Nicosia (Cyprus)) (and others)

    1993-08-01

    Charcot-Marie-Tooth (CMT) disease type 2 (CMT2) is an inherited peripheral neuropathy characterized by variable age of onset and normal or slightly diminished nerve conduction velocity. CMT2 is pathologically and genetically distinct from CMT type 1 (CMT1). While CMT1 has been shown to be genetically heterogeneous, no chromosomal localization has been established for CMT2. The authors have performed pedigree linkage analysis in six large autosomal dominant CMT2 families and have demonstrated linkage and heterogeneity to a series of microsatellites (D1S160, D1S170, D1S244, D1S228 and D1S199) in the distal region of the short arm of chromosome 1. Significant evidence for heterogeneity was found using admixture analyses and the two-point lod scores. Admixture analyses using the multipoint results for the markers D1S244, D1S228, and D1S199 supported the two-point findings. Three families, DUK662, DUK1241, and 1523 gave posterior probabilities of 1.0, 0.98, and 0.88 of being of the linked type. Multipoint analysis examining the [open quotes]linked[close quotes] families showed that the most favored location for the CMT2A gene is within the interval flanked by D1S244 and D1S228 (odds approximately 70:1 of lying within versus outside that interval). These findings suggest that the CMT2 phenotype is secondary to at least two different genes and demonstrate further heterogeneity in the CMT phenotype.

  8. Policy implications for familial searching.

    Science.gov (United States)

    Kim, Joyce; Mammo, Danny; Siegel, Marni B; Katsanis, Sara H

    2011-11-01

    In the United States, several states have made policy decisions regarding whether and how to use familial searching of the Combined DNA Index System (CODIS) database in criminal investigations. Familial searching pushes DNA typing beyond merely identifying individuals to detecting genetic relatedness, an application previously reserved for missing persons identifications and custody battles. The intentional search of CODIS for partial matches to an item of evidence offers law enforcement agencies a powerful tool for developing investigative leads, apprehending criminals, revitalizing cold cases and exonerating wrongfully convicted individuals. As familial searching involves a range of logistical, social, ethical and legal considerations, states are now grappling with policy options for implementing familial searching to balance crime fighting with its potential impact on society. When developing policies for familial searching, legislators should take into account the impact of familial searching on select populations and the need to minimize personal intrusion on relatives of individuals in the DNA database. This review describes the approaches used to narrow a suspect pool from a partial match search of CODIS and summarizes the economic, ethical, logistical and political challenges of implementing familial searching. We examine particular US state policies and the policy options adopted to address these issues. The aim of this review is to provide objective background information on the controversial approach of familial searching to inform policy decisions in this area. Herein we highlight key policy options and recommendations regarding effective utilization of familial searching that minimize harm to and afford maximum protection of US citizens.

  9. Autonomous search

    CERN Document Server

    Hamadi, Youssef; Saubion, Frédéric

    2012-01-01

    Autonomous combinatorial search (AS) represents a new field in combinatorial problem solving. Its major standpoint and originality is that it considers that problem solvers must be capable of self-improvement operations. This is the first book dedicated to AS.

  10. Low genetic diversity and local adaptive divergence of Dracaena cambodiana (Liliaceae) populations associated with historical population bottlenecks and natural selection: an endangered long-lived tree endemic to Hainan Island, China.

    Science.gov (United States)

    Zheng, D-J; Xie, L-S; Zhu, J-H; Zhang, Z-L

    2012-09-01

    Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long-lived trees. Dracaena cambodiana is an endangered, long-lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D. cambodiana were detected using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D. cambodiana populations, which was further supported by habitat-private fragments. We suggest that the current genetic diversity and population differentiation of D. cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D. cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  11. Multidisciplinary team approach for the management of patients with locally advanced non-small cell lung cancer: Searching the evidence to guide the decision

    Energy Technology Data Exchange (ETDEWEB)

    Oh, In Jae; Ahn, Sung Ja [Chonnam National University Hwasun Hospital, Hwasun (Korea, Republic of)

    2017-03-15

    Locally advanced non-small cell lung cancer (LA-NSCLC) is composed of heterogeneous subgroups that require a multidisciplinary team approach in order to ensure optimal therapy for each patient. Since 2010, the National Comprehensive Cancer Network has recommended chemoradiation therapy (CRT) for bulky mediastinal disease and surgical combination for those patients with single-station N2 involvement who respond to neoadjuvant therapy. According to lung cancer tumor boards, thoracic surgeons make a decision on the resectability of the tumor, if it is determined to be unresectable, concurrent CRT (CCRT) is considered the next choice. However, the survival benefit of CCRT over sequential CRT or radiotherapy alone carries the risk of additional toxicity. Considering severe adverse events that may lead to death, fit patients who are able to tolerate CCRT must be identified by multidisciplinary tumor board. Decelerated approaches, such as sequential CRT or high-dose radiation alone may be a valuable alternative for patients who are not eligible for CCRT. As a new treatment strategy, investigators are interested in the application of the innovative radiation techniques, trimodality therapy combining surgery after high-dose definitive CCRT, and the combination of radiation with targeted or immunotherapy agents. The updated results and on-going studies are thoroughly reviewed in this article.

  12. Oceanographic Currents and Local Ecological Knowledge Indicate, and Genetics Does Not Refute, a Contemporary Pattern of Larval Dispersal for The Ornate Spiny Lobster, Panulirus ornatus in the South-East Asian Archipelago.

    Directory of Open Access Journals (Sweden)

    Hoc Tan Dao

    Full Text Available Here we utilize a combination of genetic data, oceanographic data, and local ecological knowledge to assess connectivity patterns of the ornate spiny lobster Panulirus ornatus (Fabricius, 1798 in the South-East Asian archipelago from Vietnam to Australia. Partial mitochondrial DNA control region and 10 polymorphic microsatellites did not detect genetic structure of 216 wild P. ornatus samples from Australia, Indonesia and Vietnam. Analyses show no evidence for genetic differentiation among populations (mtDNA control region sequences ΦST = -0.008; microsatellite loci FST = 0.003. A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow in P. ornatus throughout the South-East Asian Archipelago. This lack of genetic structure may be due to the oceanography-driven connectivity of the pelagic lobster larvae between spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. The connectivity cycle necessitates three generations. The lack of genetic structure of P. ornatus population in the South-East Asian archipelago has important implications for the sustainable management of this lobster in that the species within the region needs to be managed as one genetic stock.

  13. Journal of Genetics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 80; Issue 1. Testing quantum dynamics in genetic information processing ... Keywords. assembly; computation; database search; DNA replication; genetic information; nucleotide base; polymerase enzyme; quantum coherence; quantum mechanics; quantum superposition.

  14. Genetic aspects of female reproduction

    NARCIS (Netherlands)

    Collins, J.; Diedrich, K.; Franks, S.; Geraedts, J. P. M.; Jacobs, P. A.; Karges, B.; Kennedy, S.; Marozzi, A.; Regan, L.; Baird, D. T.; Crosignani, P. G.; Devroey, P.; Diczfalusy, E.; Evers, J. L. H.; Fauser, B. C. J. M.; Fraser, L.; Gianaroli, L.; Glasier, A.; Liebaers, I.; Ragni, G.; Sunde, A.; Tarlatzis, B.; Van Steirteghem, A.

    2008-01-01

    BACKGROUND: Sexual reproduction provides the means for preserving genetic identity and in turn, genetic variability may affect the ability to reproduce. This review aims to summarize current research on genetic diagnosis and genetic causes of reproductive disorders.METHODS: Searches were done by

  15. Prenatal Genetic Counseling (For Parents)

    Science.gov (United States)

    ... Safe Videos for Educators Search English Español Prenatal Genetic Counseling KidsHealth / For Parents / Prenatal Genetic Counseling What's in ... how can they help your family? What Is Genetic Counseling? Genetic counseling is the process of: evaluating family ...

  16. A hybrid search algorithm for swarm robots searching in an unknown environment.

    Science.gov (United States)

    Li, Shoutao; Li, Lina; Lee, Gordon; Zhang, Hao

    2014-01-01

    This paper proposes a novel method to improve the efficiency of a swarm of robots searching in an unknown environment. The approach focuses on the process of feeding and individual coordination characteristics inspired by the foraging behavior in nature. A predatory strategy was used for searching; hence, this hybrid approach integrated a random search technique with a dynamic particle swarm optimization (DPSO) search algorithm. If a search robot could not find any target information, it used a random search algorithm for a global search. If the robot found any target information in a region, the DPSO search algorithm was used for a local search. This particle swarm optimization search algorithm is dynamic as all the parameters in the algorithm are refreshed synchronously through a communication mechanism until the robots find the target position, after which, the robots fall back to a random searching mode. Thus, in this searching strategy, the robots alternated between two searching algorithms until the whole area was covered. During the searching process, the robots used a local communication mechanism to share map information and DPSO parameters to reduce the communication burden and overcome hardware limitations. If the search area is very large, search efficiency may be greatly reduced if only one robot searches an entire region given the limited resources available and time constraints. In this research we divided the entire search area into several subregions, selected a target utility function to determine which subregion should be initially searched and thereby reduced the residence time of the target to improve search efficiency.

  17. Searching for an environmental effect of parental alcoholism on offspring alcohol use disorder: A genetically-informed study of children of alcoholics

    Science.gov (United States)

    Slutske, Wendy S.; D’Onofrio, Brian M.; Turkheimer, Eric; Emery, Robert E.; Harden, K. Paige; Heath, Andrew C.; Martin, Nicholas G.

    2009-01-01

    The children-of-twins design was used to isolate a potentially causal environmental impact of having an alcoholic parent on offspring alcohol use disorder by examining whether the children of alcoholics were at a higher risk for alcohol use disorders than the children of non-alcoholic parents even after correlated familial factors were controlled. Participants were 1,224 male and female twins from 836 twin pairs selected from the Australian Twin Registry, 2,334 of their 18–39 year-old offspring, and 983 spouses of the twins. Lifetime histories of DSM-IV alcohol use disorders were obtained by structured psychiatric telephone interviews conducted individually with each of the family members. Comparisons of the offspring of twins discordant for alcoholism indicated that there was no longer a statistically significant difference between the children of alcoholics and the children of non-alcoholics after genetic and family environmental factors correlated with having an alcoholic parent were controlled. The results of this study suggest that the direct causal effect of being exposed to an alcoholic parent on offspring alcohol use disorder is modest at best. PMID:18729607

  18. Searching in clutter : visual attention strategies of expert pilots

    Science.gov (United States)

    2012-10-22

    Clutter can slow visual search. However, experts may develop attention strategies that alleviate the effects of clutter on search performance. In the current study we examined the effects of global and local clutter on visual search performance and a...

  19. Genetics Home Reference: microphthalmia

    Science.gov (United States)

    ... navigation Home Page Search Home Health Conditions Genes Chromosomes & mtDNA Resources Help Me Understand Genetics Share: Email ... COLOBOMA 9 MICROPHTHALMIA, ISOLATED, WITH CORECTOPIA OPTIC DISC ANOMALIES WITH RETINAL AND/OR MACULAR DYSTROPHY Sources for ...

  20. Ship Collision Avoidance by Distributed Tabu Search

    Directory of Open Access Journals (Sweden)

    Dong-Gyun Kim

    2015-03-01

    Full Text Available More than 90% of world trade is transported by sea. The size and speed of ships is rapidly increasing in order to boost economic efficiency. If ships collide, the damage and cost can be astronomical. It is very difficult for officers to ascertain routes that will avoid collisions, especially when multiple ships travel the same waters. There are several ways to prevent ship collisions, such as lookouts, radar, and VHF radio. More advanced methodologies, such as ship domain, fuzzy theory, and genetic algorithm, have been proposed. These methods work well in one-on-one situations, but are more difficult to apply in multiple-ship situations. Therefore, we proposed the Distributed Local Search Algorithm (DLSA to avoid ship collisions as a precedent study. DLSA is a distributed algorithm in which multiple ships communicate with each other within a certain area. DLSA computes collision risk based on the information received from neighboring ships. However, DLSA suffers from Quasi-Local Minimum (QLM, which prevents a ship from changing course even when a collision risk arises. In our study, we developed the Distributed Tabu Search Algorithm (DTSA. DTSA uses a tabu list to escape from QLM that also exploits a modified cost function and enlarged domain of next-intended courses to increase its efficiency. We conducted experiments to compare the performance of DLSA and DTSA. The results showed that DTSA outperformed DLSA.

  1. Search strategies in structural bioinformatics.

    Science.gov (United States)

    Oakley, Mark T; Barthel, Daniel; Bykov, Yuri; Garibaldi, Jonathan M; Burke, Edmund K; Krasnogor, Natalio; Hirst, Jonathan D

    2008-06-01

    Optimisation problems pervade structural bioinformatics. In this review, we describe recent work addressing a selection of bioinformatics challenges. We begin with a discussion of research into protein structure comparison, and highlight the utility of Kolmogorov complexity as a measure of structural similarity. We then turn to research into de novo protein structure prediction, in which structures are generated from first principles. In this endeavour, there is a compromise between the detail of the model and the extent to which the conformational space of the protein can be sampled. We discuss some developments in this area, including off-lattice structure prediction using the great deluge algorithm. One strategy to reduce the size of the search space is to restrict the protein chain to sites on a regular lattice. In this context, we highlight the use of memetic algorithms, which combine genetic algorithms with local optimisation, to the study of simple protein models on the two-dimensional square lattice and the face-centred cubic lattice.

  2. An efficient method of agrobacterium-mediated genetic transformation and regeneration in local Indian cultivar of groundnut (Arachis hypogaea) using grafting.

    Science.gov (United States)

    Tiwari, Vivekanand; Chaturvedi, Amit Kumar; Mishra, Avinash; Jha, Bhavanath

    2015-01-01

    Groundnut (Arachis hypogaea L.) is an industrial crop used as a source of edible oil and nutrients. In this study, an efficient method of regeneration and Agrobacterium-mediated genetic transformation is reported for a local cultivar GG-20 using de-embryonated cotyledon explant. A high regeneration 52.69 ± 2.32 % was achieved by this method with 66.6 μM 6-benzylaminopurine (BAP), while the highest number of shoot buds per explant, 17.67 ± 3.51, was found with 20 μM BAP and 10 μM 2,4-dichlorophenoxyacetic acid (2,4-D). The bacterial culture OD, acetosyringone and L-cysteine concentration were optimized as 1.8, 200 μM and 50 mg L(-1), respectively, in co-cultivation media. It was observed that the addition of 2,4-D in co-cultivation media induced accumulation of endogenous indole-3-acetic acid (IAA). The optimized protocol exhibited 85 % transformation efficiency followed by 14.65 ± 1.06 % regeneration, of which 3.82 ± 0.6 % explants were survived on hygromycin after selection. Finally, 14.58 ± 2.95 % shoots (regenerated on survived explants) were rooted on rooting media (RM3). In grafting method, regenerated shoots (after hygromycin selection) were grafted on the non-transformed stocks with 100 % survival and new leaves emerged in 3 weeks. The putative transgenic plants were then confirmed by PCR, Southern hybridization, reverse transcriptase PCR (RT-PCR) and β-glucuronidase (GUS) histochemical assay. The reported method is efficient and rapid and can also be applied to other crops which are recalcitrant and difficult in rooting.

  3. Research and Applications of Shop Scheduling Based on Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Hang ZHAO

    Full Text Available ABSTRACT Shop Scheduling is an important factor affecting the efficiency of production, efficient scheduling method and a research and application for optimization technology play an important role for manufacturing enterprises to improve production efficiency, reduce production costs and many other aspects. Existing studies have shown that improved genetic algorithm has solved the limitations that existed in the genetic algorithm, the objective function is able to meet customers' needs for shop scheduling, and the future research should focus on the combination of genetic algorithm with other optimized algorithms. In this paper, in order to overcome the shortcomings of early convergence of genetic algorithm and resolve local minimization problem in search process,aiming at mixed flow shop scheduling problem, an improved cyclic search genetic algorithm is put forward, and chromosome coding method and corresponding operation are given.The operation has the nature of inheriting the optimal individual ofthe previous generation and is able to avoid the emergence of local minimum, and cyclic and crossover operation and mutation operation can enhance the diversity of the population and then quickly get the optimal individual, and the effectiveness of the algorithm is validated. Experimental results show that the improved algorithm can well avoid the emergency of local minimum and is rapid in convergence.

  4. Optimum energy re-establishment in distribution systems: a comparison between the search performance using fuzzy heuristics and genetic algorithms; Restabelecimento otimo de energia em sistemas de distribuicao: uma comparacao entre o desempenho de busca com heuristica fuzzy e algoritmos geneticos

    Energy Technology Data Exchange (ETDEWEB)

    Delbem, Alexandre C.B.; Bretas, Newton G. [Sao Paulo Univ., Sao Carlos, SP (Brazil). Dept. de Engenharia Eletrica; Carvalho, Andre C.P.L.F. [Sao Paulo Univ., Sao Carlos, SP (Brazil). Dept. de Ciencias de Computacao e Estatistica

    1996-11-01

    A search approach using fuzzy heuristics and a neural network parameter was developed for service restoration of a distribution system. The goal was to restore energy for an un-faulted zone after a fault had been identified and isolated. The restoration plan must be carried out in a very short period. However, the combinatorial feature of the problem constrained the application of automatic energy restoration planners. To overcome this problem, an heuristic search approach using fuzzy heuristics was proposed. As a result, a genetic algorithm approach was developed to achieve the optimal energy restoration plan. The effectiveness of these approaches were tested in a simplified distribution system based on the complex distribution system of Sao Carlos city, Sao Paulo State - southeast Brazil. It was noticed that the genetic algorithm provided better performance than the fuzzy heuristic search in this problem. 11 refs., 10 figs.

  5. Basic Local Alignment Search Tool (BLAST)

    Data.gov (United States)

    U.S. Department of Health & Human Services — BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the...

  6. Smoothed Analysis of Local Search Algorithms

    NARCIS (Netherlands)

    Manthey, Bodo; Dehne, Frank; Sack, Jörg-Rüdiger; Stege, Ulrike

    2015-01-01

    Smoothed analysis is a method for analyzing the performance of algorithms for which classical worst-case analysis fails to explain the performance observed in practice. Smoothed analysis has been applied to explain the performance of a variety of algorithms in the last years. One particular class of

  7. Algebraic Algorithm Design and Local Search

    National Research Council Canada - National Science Library

    Graham, Robert

    1996-01-01

    .... Algebraic techniques have been applied successfully to algorithm synthesis by the use of algorithm theories and design tactics, an approach pioneered in the Kestrel Interactive Development System (KIDS...

  8. Internet Search Engines

    OpenAIRE

    Fatmaa El Zahraa Mohamed Abdou

    2004-01-01

    A general study about the internet search engines, the study deals main 7 points; the differance between search engines and search directories, components of search engines, the percentage of sites covered by search engines, cataloging of sites, the needed time for sites appearance in search engines, search capabilities, and types of search engines.

  9. Phenylketonuria Genetic Screening Simulation

    Science.gov (United States)

    Erickson, Patti

    2012-01-01

    After agreeing to host over 200 students on a daylong genetics field trip, the author needed an easy-to-prepare genetics experiment to accompany the DNA-necklace and gel-electrophoresis activities already planned. One of the student's mothers is a pediatric physician at the local hospital, and she suggested exploring genetic-disease screening…

  10. Visualizing Search Behavior with Adaptive Discriminations

    OpenAIRE

    Cook, Robert G.; Qadri, Muhammad A. J.

    2013-01-01

    We examined different aspects of the visual search behavior of a pigeon using an open-ended, adaptive testing procedure controlled by a genetic algorithm. The animal had to accurately search for and peck a gray target element randomly located from among a variable number of surrounding darker and lighter distractor elements. Display composition was controlled by a genetic algorithm involving the multivariate configuration of different parameters or genes (number of distractors, element size, ...

  11. Multi Population Hybrid Genetic Algorithms for University Course Timetabling

    Directory of Open Access Journals (Sweden)

    Mehrnaz Shirani LIRI

    2012-08-01

    Full Text Available University course timetabling is one of the important and time consuming issues that each University is involved with at the beginning of each university year. This problem is in class of NP-hard problem and is very difficult to solve by classic algorithms. Therefore optimization techniques are used to solve them and produce optimal or almost optimal feasible solutions instead of exact solutions. Genetic algorithms, because of their multidirectional search property, are considered as an efficient approach for solving this type of problems. In this paper three new hybrid genetic algorithms for solving the university course timetabling problem (UCTP are proposed: FGARI, FGASA and FGATS. In the proposed algorithms, fuzzy logic is used to measure violation of soft constraints in fitness function to deal with inherent uncertainty and vagueness involved in real life data. Also, randomized iterative local search, simulated annealing and tabu search are applied, respectively, to improve exploitive search ability and prevent genetic algorithm to be trapped in local optimum. The experimental results indicate that the proposed algorithms are able to produce promising results for the UCTP

  12. Keep Searching and You’ll Find

    DEFF Research Database (Denmark)

    Laursen, Keld

    2012-01-01

    This article critically reviews and synthesizes the contributions found in theoretical and empirical studies of firm-level innovation search processes. It explores the advantages and disadvantages of local and non-local search, discusses organizational responses, and identifies potential exogenous...... triggers for different kinds of search. It argues that the initial focus on local search was a consequence, in part, of the attention in evolutionary economics to path-dependent behavior, but that as localized behavior was increasingly accepted as the standard mode, studies began to question whether local...... different search strategies, but end up with very similar technological profiles in fast-growing technologies. The article concludes by highlighting what we have learnt from the literature and suggesting some new avenues for research....

  13. Genetic Algorithms in Noisy Environments

    OpenAIRE

    THEN, T. W.; CHONG, EDWIN K. P.

    1993-01-01

    Genetic Algorithms (GA) have been widely used in the areas of searching, function optimization, and machine learning. In many of these applications, the effect of noise is a critical factor in the performance of the genetic algorithms. While it hals been shown in previous siiudies that genetic algorithms are still able to perform effectively in the presence of noise, the problem of locating the global optimal solution at the end of the search has never been effectively addressed. Furthermore,...

  14. Accelerated Profile HMM Searches.

    Directory of Open Access Journals (Sweden)

    Sean R Eddy

    2011-10-01

    Full Text Available Profile hidden Markov models (profile HMMs and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the "multiple segment Viterbi" (MSV algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call "sparse rescaling". These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches.

  15. Focused Crawler Optimization Using Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Hartanto Kusuma Wardana

    2011-12-01

    Full Text Available As the size of the Web continues to grow, searching it for useful information has become more difficult. Focused crawler intends to explore the Web conform to a specific topic. This paper discusses the problems caused by local searching algorithms. Crawler can be trapped within a limited Web community and overlook suitable Web pages outside its track. A genetic algorithm as a global searching algorithm is modified to address the problems. The genetic algorithm is used to optimize Web crawling and to select more suitable Web pages to be fetched by the crawler. Several evaluation experiments are conducted to examine the effectiveness of the approach. The crawler delivers collections consist of 3396 Web pages from 5390 links which had been visited, or filtering rate of Roulette-Wheel selection at 63% and precision level at 93% in 5 different categories. The result showed that the utilization of genetic algorithm had empowered focused crawler to traverse the Web comprehensively, despite it relatively small collections. Furthermore, it brought up a great potential for building an exemplary collections compared to traditional focused crawling methods.

  16. Harmony Search for Balancing Two-sided Assembly Lines

    Directory of Open Access Journals (Sweden)

    Hindriyanto Dwi Purnomo

    2012-01-01

    Full Text Available Two-sided assembly lines balancing problems are important problem for large-sized products such as cars and buses, in which, tasks operations can be performed in the two sides of the line. In this paper, Harmony Search algorithm is proposed to solve two-sided assembly lines balancing problems type-I (TALBP-I. The proposed method adopts the COMSOAL heuristic and specific features of TALBP in the Harmony operators – the harmony memory consideration, random selection and pitch adjustment – in order to maintain the local and global search. The proposed method is evaluated based on 6 benchmark problems that are commonly used in TALBP. The experiment results show that the proposed method work well and produces better solution than the heuristic method and genetic algorithm.

  17. In situ Comparison of Tree-Ring Responses to Climate and Population Genetics: The Need to Control for Local Climate and Site Variables

    OpenAIRE

    Housset, Johann M.; Carcaillet, Christopher; Girardin, Martin P.; Xu, Huaitong; Tremblay, Francine; Bergeron, Yves

    2016-01-01

    Tree species responses to climate change will be greatly influenced by their evolutionary potential and their phenotypic plasticity. Investigating tree-rings responses to climate and population genetics at the regional scale is crucial in assessing the tree behavior to climate change. This study combined in situ dendroclimatology and population genetics over a latitudinal gradient and compared the variations between the two at the intra- and inter-population levels. This approach was applied ...

  18. Histochemical studies on genetical control of hormonal enzyme inducibility in the mouse. IV: Cellular localization of androgen sensitive nonspecific esterase in the epididymis

    DEFF Research Database (Denmark)

    Kirkeby, S; Blecher, S R

    1981-01-01

    Nonspecific esterase of mouse epididymis has previously been studied histochemically, using alpha naphthyl-acetate and 5-bromoindoxyl acetate techniques, as well as certain inhibitors. Epithelial cell types of the epididymis have been characterized, and certain esterase isozymes in a particular c...... to normal. This method can now be applied to the study of epididymides of genetically sex-reversed chromosomal female, to analyze genetic control of X-chromosomal activation....

  19. Optimization of the Thermosetting Pultrusion Process by Using Hybrid and Mixed Integer Genetic Algorithms

    DEFF Research Database (Denmark)

    Baran, Ismet; Tutum, Cem Celal; Hattel, Jesper Henri

    2013-01-01

    to the pultrusion domain of a composite part and thermal contact resistance (TCR) regions at the die-part interface are defined. Two optimization case studies are performed on this new configuration. In the first one, optimal die radius and TCR values are found by using a hybrid genetic algorithm based...... on a sequential combination of a genetic algorithm (GA) and a local search technique to fit the centerline temperature of the composite with the one calculated in the validation case. In the second optimization study, the productivity of the process is improved by using a mixed integer genetic algorithm (MIGA...

  20. Interrupted Visual Searches Reveal Volatile Search Memory

    Science.gov (United States)

    Shen, Y. Jeremy; Jiang, Yuhong V.

    2006-01-01

    This study investigated memory from interrupted visual searches. Participants conducted a change detection search task on polygons overlaid on scenes. Search was interrupted by various disruptions, including unfilled delay, passive viewing of other scenes, and additional search on new displays. Results showed that performance was unaffected by…

  1. Comparison tomography relocation hypocenter grid search and guided grid search method in Java island

    International Nuclear Information System (INIS)

    Nurdian, S. W.; Adu, N.; Palupi, I. R.; Raharjo, W.

    2016-01-01

    The main data in this research is earthquake data recorded from 1952 to 2012 with 9162 P wave and 2426 events are recorded by 30 stations located around Java island. Relocation hypocenter processed using grid search and guidded grid search method. Then the result of relocation hypocenter become input for tomography pseudo bending inversion process. It can be used to identification the velocity distribution in subsurface. The result of relocation hypocenter by grid search and guided grid search method after tomography process shown in locally and globally. In locally area grid search method result is better than guided grid search according to geological reseach area. But in globally area the result of guided grid search method is better for a broad area because the velocity variation is more diverse than the other one and in accordance with local geological research conditions. (paper)

  2. OpenSearch and SRU: A Continuum of Searching

    Directory of Open Access Journals (Sweden)

    Ralph LeVan

    2006-09-01

    Full Text Available Not all library content can be exposed as HTML pages for harvesting by search engines such as Google and Yahoo!. If a library instead exposes its content through a local search interface, that content can then be found by users of metasearch engines such as A9 and Vivísimo. The functionality provided by the local search engine will affect the functionality of the metasearch engine and the findability of the library’s content. This paper describes that situation and some emerging standards in the metasearch arena that choose different balance points between functionality and ease of implementation.

  3. Evacuation route planning during nuclear emergency using genetic algorithm

    International Nuclear Information System (INIS)

    Suman, Vitisha; Sarkar, P.K.

    2012-01-01

    In nuclear industry the routing in case of any emergency is a cause of concern and of great importance. Even the smallest of time saved in the affected region saves a huge amount of otherwise received dose. Genetic algorithm an optimization technique has great ability to search for the optimal path from the affected region to a destination station in a spatially addressed problem. Usually heuristic algorithms are used to carry out these types of search strategy, but due to the lack of global sampling in the feasible solution space, these algorithms have considerable possibility of being trapped into local optima. Routing problems mainly are search problems for finding the shortest distance within a time limit to cover the required number of stations taking care of the traffics, road quality, population size etc. Lack of any formal mechanisms to help decision-makers explore the solution space of their problem and thereby challenges their assumptions about the number and range of options available. The Genetic Algorithm provides a way to optimize a multi-parameter constrained problem with an ease. Here use of Genetic Algorithm to generate a range of options available and to search a solution space and selectively focus on promising combinations of criteria makes them ideally suited to such complex spatial decision problems. The emergency response and routing can be made efficient, in accessing the closest facilities and determining the shortest route using genetic algorithm. The accuracy and care in creating database can be used to improve the result of the final output. The Genetic algorithm can be used to improve the accuracy of result on the basis of distance where other algorithm cannot be obtained. The search space can be utilized to its great extend

  4. Genetics Home Reference: eosinophil peroxidase deficiency

    Science.gov (United States)

    ... navigation Home Page Search Home Health Conditions Genes Chromosomes & mtDNA Resources Help Me Understand Genetics Share: Email ... EPXD peroxidase and phospholipid deficiency in eosinophils Presentey anomaly Related Information How are genetic conditions and genes ...

  5. A hybrid search algorithm for swarm robots searching in an unknown environment.

    Directory of Open Access Journals (Sweden)

    Shoutao Li

    Full Text Available This paper proposes a novel method to improve the efficiency of a swarm of robots searching in an unknown environment. The approach focuses on the process of feeding and individual coordination characteristics inspired by the foraging behavior in nature. A predatory strategy was used for searching; hence, this hybrid approach integrated a random search technique with a dynamic particle swarm optimization (DPSO search algorithm. If a search robot could not find any target information, it used a random search algorithm for a global search. If the robot found any target information in a region, the DPSO search algorithm was used for a local search. This particle swarm optimization search algorithm is dynamic as all the parameters in the algorithm are refreshed synchronously through a communication mechanism until the robots find the target position, after which, the robots fall back to a random searching mode. Thus, in this searching strategy, the robots alternated between two searching algorithms until the whole area was covered. During the searching process, the robots used a local communication mechanism to share map information and DPSO parameters to reduce the communication burden and overcome hardware limitations. If the search area is very large, search efficiency may be greatly reduced if only one robot searches an entire region given the limited resources available and time constraints. In this research we divided the entire search area into several subregions, selected a target utility function to determine which subregion should be initially searched and thereby reduced the residence time of the target to improve search efficiency.

  6. The Impact of Parametrization on Randomized Search Heuristics

    DEFF Research Database (Denmark)

    Gießen, Christian

    In this work we present runtime analyses of randomized search heuristics (RSH) in various settings that are determined by parameters of the problems, the algorithms and also exogenous parameters like noise. In the process we provide new techniques for the theoretical analysis of RSH as well as new...... optimization algorithms. We consider the following topics. Escaping local optima using local search. We analyze memetic algorithms, i.e. evolutionary algorithms equipped with a local search after mutation. To this end we consider the (1+1) EA equipped with Standard Local Search (SLS) and Variable-Depth Search...... (VDS) on an artificial test function. We determine features of the fitness landscape that lead to the (1+1) EA using SLS outperforming the (1+1) EA using VDS with an exponential performance gap. Moreover, we present a new local search operator, Opportunistic Local Search (OLS), that can deal...

  7. Diphoton searches in ATLAS

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00213273; The ATLAS collaboration

    2016-01-01

    Searches for new resonances decaying into two photons in the ATLAS experiment at the LHC are described. The analysis is based on $pp$ collision data corresponding to an integrated luminosity of 3.2 fb$^{-1}$ at $\\sqrt{s}$ = 13 TeV recorded in 2015. Two different searches are performed, one targeted for a spin-2 particle, using Randall-Sundrum graviton states as a benchmark model, and one optimized for a spin-0 particle. The most significant deviation from the background predictions is observed at a diphoton invariant mass around 750 GeV with local significances of 3.6 and 3.9 standard deviations in the searches optimized for a spin-2 and spin-0 particle, respectively. The global significances are estimated to be 1.8 and 2.0 standard deviations. The consistency between the data collected at 13 TeV and 8 TeV is also evaluated. Limits on the production cross-section for the two benchmark resonances are reported.

  8. Application of Genetic Control with Adaptive Scaling Scheme to Signal Acquisition in Global Navigation Satellite System Receiver

    Directory of Open Access Journals (Sweden)

    Ho-Nien Shou

    2012-02-01

    Full Text Available This paper presents a genetic-based control scheme that not only utilizes evolutionary characteristics to find the signal acquisition parameters, but also employs an adaptive scheme to control the search space and avoid the genetic control converging to local optimal value so as to acquire the desired signal precisely and rapidly. Simulations and experiment results show that the proposed method can improve the precision of signal parameters and take less signal acquisition time than traditional serial search methods for global navigation satellite system (GNSS signals.

  9. SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.

    Directory of Open Access Journals (Sweden)

    Steven N Hart

    Full Text Available BACKGROUND: Structural variation (SV represents a significant, yet poorly understood contribution to an individual's genetic makeup. Advanced next-generation sequencing technologies are widely used to discover such variations, but there is no single detection tool that is considered a community standard. In an attempt to fulfil this need, we developed an algorithm, SoftSearch, for discovering structural variant breakpoints in Illumina paired-end next-generation sequencing data. SoftSearch combines multiple strategies for detecting SV including split-read, discordant read-pair, and unmated pairs. Co-localized split-reads and discordant read pairs are used to refine the breakpoints. RESULTS: We developed and validated SoftSearch using real and synthetic datasets. SoftSearch's key features are 1 not requiring secondary (or exhaustive primary alignment, 2 portability into established sequencing workflows, and 3 is applicable to any DNA-sequencing experiment (e.g. whole genome, exome, custom capture, etc.. SoftSearch identifies breakpoints from a small number of soft-clipped bases from split reads and a few discordant read-pairs which on their own would not be sufficient to make an SV call. CONCLUSIONS: We show that SoftSearch can identify more true SVs by combining multiple sequence features. SoftSearch was able to call clinically relevant SVs in the BRCA2 gene not reported by other tools while offering significantly improved overall performance.

  10. Genetics in eating disorders: extending the boundaries of research

    Directory of Open Access Journals (Sweden)

    Andréa Poyastro Pinheiro

    2006-09-01

    Full Text Available OBJECTIVE: To review the recent literature relevant to genetic research in eating disorders and to discuss unique issues which are crucial for the development of a genetic research project in eating disorders in Brazil. METHOD: A computer literature review was conducted in the Medline database between 1984 and may 2005 with the search terms "eating disorders", "anorexia nervosa", "bulimia nervosa", "binge eating disorder", "family", "twin" and "molecular genetic" studies. RESULTS: Current research findings suggest a substantial influence of genetic factors on the liability to anorexia nervosa and bulimia nervosa. Genetic research with admixed populations should take into consideration sample size, density of genotyping and population stratification. Through admixture mapping it is possible to study the genetic structure of admixed human populations to localize genes that underlie ethnic variation in diseases or traits of interest. CONCLUSIONS: The development of a major collaborative genetics initiative of eating disorders in Brazil and South America would represent a realistic possibility of studying the genetics of eating disorders in the context of inter ethnic groups, and also integrate a new perspective on the biological etiology of eating disorders.

  11. On Local Regret

    OpenAIRE

    Bowling, Michael; Zinkevich, Martin

    2012-01-01

    Online learning aims to perform nearly as well as the best hypothesis in hindsight. For some hypothesis classes, though, even finding the best hypothesis offline is challenging. In such offline cases, local search techniques are often employed and only local optimality guaranteed. For online decision-making with such hypothesis classes, we introduce local regret, a generalization of regret that aims to perform nearly as well as only nearby hypotheses. We then present a general algorithm to mi...

  12. Genetic algorithm optimization of atomic clusters

    International Nuclear Information System (INIS)

    Morris, J.R.; Deaven, D.M.; Ho, K.M.; Wang, C.Z.; Pan, B.C.; Wacker, J.G.; Turner, D.E.; Iowa State Univ., Ames, IA

    1996-01-01

    The authors have been using genetic algorithms to study the structures of atomic clusters and related problems. This is a problem where local minima are easy to locate, but barriers between the many minima are large, and the number of minima prohibit a systematic search. They use a novel mating algorithm that preserves some of the geometrical relationship between atoms, in order to ensure that the resultant structures are likely to inherit the best features of the parent clusters. Using this approach, they have been able to find lower energy structures than had been previously obtained. Most recently, they have been able to turn around the building block idea, using optimized structures from the GA to learn about systematic structural trends. They believe that an effective GA can help provide such heuristic information, and (conversely) that such information can be introduced back into the algorithm to assist in the search process

  13. Genetic diversity and structure of wild populations of the tropical dry forest tree Jacaratia Mexicana (Brassicales: Caricaceae at a local scale in Mexico

    Directory of Open Access Journals (Sweden)

    Dulce M. Arias

    2012-03-01

    Full Text Available The tropical dry forest is a greatly endangered ecosystem, from which Jacaratia mexicana is a native tree. With the aim to assess the levels of genetic variation and population structure, four wild populations of J. mexicana were studied in the Sierra de Huautla Biosphere Reserve, Morelos, Mexico. For this, DNA was extracted from 159 individuals and were amplified with six random primers using the Random Amplified Polymorphic DNA (RAPD. A total of 54 bands were obtained, of which 50 (92.6% were polymorphic. The total genetic diversity found within the four populations was 0.451 when estimated by Shannon’s index. An AMOVA analysis showed that 84% of the total genetic variation was found within populations and 16% was among populations. The UPGMA dendrogram showed that all individuals from one of the populations (Huaxtla formed one distinct genetic group, while the rest of the individuals did not cluster according to population. A Mantel test did not show an association between genetic and geographical distances among populations (r=0.893, p=0.20. A Bayesian cluster analysis performed with STRUCTURE, showed that the most probable number of genetic groups in the data was four (K=4, and confirmed the distinctness of Huaxtla population. Our results showed that important genetic differentiation among populations can occur even at this small geographic scale and this has to be considered in conservation actions for this genetic resource.Jacaratia mexicana es un árbol nativo del bosque tropical seco, que es considerado el tipo de vegetación en mayor riesgo de desaparecer completamente. Se utilizaron polimorfismos de ADN amplificados al azar (RAPD, Random Amplified Polymorphic DNA, para evaluar los niveles de variación y estructura genética en cuatro poblaciones silvestres de J. mexicana en la Reserva de la Biósfera Sierra de Huautla (Morelos, México. Se amplificó el ADN de 159 individuos utilizando seis oligonucleótidos (

  14. Long-term effective population sizes, temporal stability of genetic composition and potential for local adaptation in anadromous brown trout ( Salmo trutta ) populations

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Ruzzante, D.E.; Eg Nielsen, Einar

    2002-01-01

    We examined the long-term temporal (1910s to 1990s) genetic variation at eight microsatellite DNA loci in brown trout (Salmo trutta L) collected from five anadromous populations in Denmark to assess the long-term stability of genetic composition and to estimate effective population sizes (N...... temporal samples from the same populations than among samples from different populations. Estimates of N-e, using a likelihood-based implementation of the temporal method, revealed N-e greater than or equal to 500 in two of three populations for which we have historical data. A third population in a small...... adaptations resulting from strong selection were expected to occur at the level of individual populations. Adaptations resulting from weak selection were more likely to occur on a regional basis, i.e. encompassing several populations. N-e appears to have declined recently in at least one of the studied...

  15. Unlocking the potential of tropical root crop biotechnology in east Africa by establishing a genetic transformation platform for local farmer-preferred cassava cultivars

    Directory of Open Access Journals (Sweden)

    Evans eNyaboga

    2013-12-01

    Full Text Available Cassava genetic transformation capacity is still mostly restricted to advanced laboratories in the USA, Europe and China; and its implementation and maintainance in African laboratories has remained scarce. The impact of transgenic technologies for genetic improvement of cassava will depend largely on the transfer of such capabilities to researchers in Africa, where cassava has an important socioeconomic niche. A major constraint to the development of genetic transformation technologies for cassava improvement has been the lack of an efficient and robust transformation and regeneration system. Despite the success achieved in genetic modification of few cassava cultivars, including the model cultivar 60444, transgenic cassava production remains difficult for farmer-preferred cultivars. In this study, a protocol for cultivar 60444 developed at ETH Zurich was successfully implemented and optimized to establish transformation of farmer-preferred cassava cultivars popular in east Africa. The conditions for production and proliferation of friable embryogenic calli (FEC and Agrobacterium-mediated transformation were optimized for three east African farmer-preferred cultivars (Ebwanatereka, Kibandameno and Serere. Our results demonstrated transformation efficiencies of about 14-22 independent transgenic lines per 100 mg of FEC for farmer-preferred cultivars in comparison to 28 lines per 100 mg of the model cultivar 60444. The presence, integration and expression of the transgenes were confirmed by PCR, Southern blot analysis and histochemical GUS assay. This study reports the establishment of a cassava transformation platform at International Institute of Tropical Agriculture (IITA hosted by Biosciences eastern and central Africa (BecA hub in Kenya and provides the basis for transferring important traits such as virus resistance and prolonged shelf-life to farmer-preferred cultivars in east Africa. We anticipate that such platform will also be

  16. Habitat-specific natural selection at a flowering time QTL is a main driver of local adaptation in two wild barley populations

    NARCIS (Netherlands)

    Verhoeven, K.J.F.; Poorter, H.; Nevo, E.; Biere, A.

    2008-01-01

    Understanding the genetic basis of local adaptation requires insight in the fitness effects of individual loci under natural field conditions. While rapid progress is made in the search for genes that control differences between plant populations, it is typically unknown whether the genes under

  17. Interactive searching of facial image databases

    Science.gov (United States)

    Nicholls, Robert A.; Shepherd, John W.; Shepherd, Jean

    1995-09-01

    A set of psychological facial descriptors has been devised to enable computerized searching of criminal photograph albums. The descriptors have been used to encode image databased of up to twelve thousand images. Using a system called FACES, the databases are searched by translating a witness' verbal description into corresponding facial descriptors. Trials of FACES have shown that this coding scheme is more productive and efficient than searching traditional photograph albums. An alternative method of searching the encoded database using a genetic algorithm is currenly being tested. The genetic search method does not require the witness to verbalize a description of the target but merely to indicate a degree of similarity between the target and a limited selection of images from the database. The major drawback of FACES is that is requires a manual encoding of images. Research is being undertaken to automate the process, however, it will require an algorithm which can predict human descriptive values. Alternatives to human derived coding schemes exist using statistical classifications of images. Since databases encoded using statistical classifiers do not have an obvious direct mapping to human derived descriptors, a search method which does not require the entry of human descriptors is required. A genetic search algorithm is being tested for such a purpose.

  18. Genetics Home Reference: Graves disease

    Science.gov (United States)

    ... Tomer Y. Cutting edge: the etiology of autoimmune thyroid diseases. Clin Rev Allergy Immunol. 2011 Oct;41(2): ... The search for the genetic contribution to autoimmune thyroid disease: the never ending story? Brief Funct Genomics. 2011 ...

  19. Genetics Home Reference: Peters anomaly

    Science.gov (United States)

    ... navigation Home Page Search Home Health Conditions Genes Chromosomes & mtDNA Resources Help Me Understand Genetics Share: Email Facebook Twitter Home Health Conditions Peters anomaly Peters anomaly Printable PDF Open All Close All ...

  20. Genetics Home Reference: Fraser syndrome

    Science.gov (United States)

    ... navigation Home Page Search Home Health Conditions Genes Chromosomes & mtDNA Resources Help Me Understand Genetics Share: Email ... of the genitalia and the urinary tract (genitourinary anomalies). Other tissues and organs can also be affected. ...

  1. Genetics Home Reference: Greenberg dysplasia

    Science.gov (United States)

    ... navigation Home Page Search Home Health Conditions Genes Chromosomes & mtDNA Resources Help Me Understand Genetics Share: Email ... K. Mutations causing Greenberg dysplasia but not Pelger anomaly uncouple enzymatic from structural functions of a nuclear ...

  2. Genetics Home Reference: RAPADILINO syndrome

    Science.gov (United States)

    ... navigation Home Page Search Home Health Conditions Genes Chromosomes & mtDNA Resources Help Me Understand Genetics Share: Email ... Rapadilino syndrome Hospital for Sick Children: Radial Ray Anomaly MalaCards: rapadilino syndrome March of Dimes: Cleft Lip ...

  3. Genetics, Disease Prevention and Treatment

    Science.gov (United States)

    Skip to main content FAQ About Genetics, Disease Prevention and Treatment Enter Search Term(s): Español Research Funding An Overview Bioinformatics Current Grants Education and Training Funding Extramural Research News ...

  4. Dark matter searches at the Canfranc tunnel

    International Nuclear Information System (INIS)

    Sarsa, M.L.; Avignone, F.T.; Brodzinski, R.L.; Cerezo, E.; Collar, J.I.; Garcia, E.; Reeves, J.H.; Miley, H.S.; Morales, A.; Morales, J.; Nunez-Lagos, R.; Ortiz de Solorzano, A.; Puimedon, J.; Saenz, C.; Salinas, A.; Villar, J.A.

    1994-01-01

    Results of an on-going search for particle dark matter with a germanium detector at the Canfranc tunnel are reported. Contour limits for cross-sections, masses and local halo densities of particles interacting through spin-independent interactions are presented. Preliminary results and prospects of a search for timing modulation of the signal are also reported. ((orig.))

  5. SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

    Directory of Open Access Journals (Sweden)

    Lefkowitz Elliot J

    2004-10-01

    Full Text Available Abstract Background Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results We describe the implementation of SS-Wrapper (Similarity Search Wrapper, a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST that provides a complementary solution for BLAST searches when the database is too large to fit into

  6. SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.

    Science.gov (United States)

    Wang, Chunlin; Lefkowitz, Elliot J

    2004-10-28

    Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Used together

  7. Search Term Reports

    Science.gov (United States)

    Learn what search terms brought users to choose your page in their search results, and what terms they entered in the EPA search box after visiting your page. Use this information to improve links and content on the page.

  8. FARMERS' SEED SYSTEM AND THE INSTITUTIONALISATION OF GENETIC RESOURCE USE AND MANAGEMENT IN AGRICULTURE: A CASE OF SEED SUPPLY FOR LOCAL TRADITIONAL VEGETABLES IN JAPAN

    OpenAIRE

    Imaizumi, Aki; Hisano, Shuji

    2010-01-01

    N° ISBN - 978-2-7380-1284-5; International audience; Nearly all countries have seed laws and technical regulations to govern their formal seed system, run by formal public organisations and private seed companies, while the role of the farmers' seed system has been marginalised especially in developed countries. Local traditional varieties that are largely taken care of and nurtured by farmers' seed system have also been excluded from the formal seed system. Nowadays, however, it is quite com...

  9. A novel pseudoderivative-based mutation operator for real-coded adaptive genetic algorithms

    Science.gov (United States)

    Kanwal, Maxinder S; Ramesh, Avinash S; Huang, Lauren A

    2013-01-01

    Recent development of large databases, especially those in genetics and proteomics, is pushing the development of novel computational algorithms that implement rapid and accurate search strategies. One successful approach has been to use artificial intelligence and methods, including pattern recognition (e.g. neural networks) and optimization techniques (e.g. genetic algorithms). The focus of this paper is on optimizing the design of genetic algorithms by using an adaptive mutation rate that is derived from comparing the fitness values of successive generations. We propose a novel pseudoderivative-based mutation rate operator designed to allow a genetic algorithm to escape local optima and successfully continue to the global optimum. Once proven successful, this algorithm can be implemented to solve real problems in neurology and bioinformatics. As a first step towards this goal, we tested our algorithm on two 3-dimensional surfaces with multiple local optima, but only one global optimum, as well as on the N-queens problem, an applied problem in which the function that maps the curve is implicit. For all tests, the adaptive mutation rate allowed the genetic algorithm to find the global optimal solution, performing significantly better than other search methods, including genetic algorithms that implement fixed mutation rates. PMID:24627784

  10. Combining Tpi and CO1 Genetic Markers to Discriminate Invasive Helicoverpa armigera From Local Helicoverpa zea (Lepidoptera: Noctuidae) Populations in the Southeastern United States.

    Science.gov (United States)

    Nagoshi, Rodney N; Gilligan, Todd M; Brambila, Julieta

    2016-10-01

    The recent establishment of the Old World pest Helicoverpa armigera (Hübner) into South America has had significant economic consequences and places the rest of the hemisphere at risk, emphasizing the need for improved methods of monitoring. A major complication is that a sibling species endemic to the New World, Helicoverpa zea (Boddie), is morphologically very similar, with the two species capable of producing fertile hybrids in the laboratory. The consequences of such hybridization in the field are uncertain, but could result in significant and unpredictable changes in the timing, range, and pesticide susceptibilities of Helicoverpa infestations. The objective here is to provide new genetic resources applicable to Helicoverpa populations in northern Florida and neighboring states (a region at risk for H. armigera) that can distinguish the two species and possible hybrids. The genetic variability in segments of the mitochondrial cytochrome oxidase 1 (CO1) and the Z-linked triosephosphate isomerase (Tpi) genes were determined for H. zea from the southeastern United States. These were compared to DNA sequences from H. armigera specimens from Morocco, Australia, and Europe. Phylogenetic network analysis showed a clear demarcation between the two species for all gene segments. These results extend earlier studies establishing CO1 as marker for discriminating the Helicoverpa species complex and introduce a new sex-linked genomic marker. The CO1 and Tpi markers in combination provide a more accurate and sensitive method than existing techniques for identifying hybridization between H. zea and H. armigera and could potentially be used to extrapolate the likely source of invasive H. armigera populations. Published by Oxford University Press on behalf of Entomological Society of America 2016. This work is written by US Government employees and is in the public domain in the US.

  11. MiRNA-Related Genetic Variations Associated with Radiotherapy-Induced Toxicities in Patients with Locally Advanced Non-Small Cell Lung Cancer.

    Science.gov (United States)

    Li, Rong; Pu, Xia; Chang, Joe Y; Ye, Yuanqing; Komaki, Ritsuko; Minna, John D; Roth, Jack A; Han, Baohui; Wu, Xifeng

    2016-01-01

    Severe radiation-induced toxicities limit treatment efficacy and compromise outcomes of lung cancer. We aimed to identify microRNA-related genetic variations as biomarkers for the prediction of radiotherapy-induced acute toxicities. We genotyped 233 SNPs (161 in microRNA binding site and 72 in processing gene) and analyzed their associations with pneumonitis and esophagitis in 167 stage III NSCLC patients received definitive radiation therapy. Sixteen and 11 SNPs were associated with esophagitis and pneumonitis, respectively. After multiple comparison correction, RPS6KB2:rs10274, SMO:rs1061280, SMO:rs1061285 remained significantly associated with esophagitis, while processing gene DGCR8:rs720014, DGCR8:rs3757, DGCR8:rs1633445 remained significantly associated with pneumonitis. Patients with the AA genotype of RPS6KB2:rs10274 had an 81% reduced risk of developing esophagitis (OR: 0.19, 95% CI: 0.07-0.51, p = 0.001, q = 0.06). Patients with the AG+GG genotype of SMO:rs1061280 had an 81% reduced risk of developing esophagitis (OR: 0.19, 95% CI: 0.07-0.53, p = 0.001, q = 0.06). Patients with the GG+GA genotype of DGCR8:rs720014 had a 3.54-fold increased risk of pneumonitis (OR: 3.54, 95% CI: 1.65-7.61, p pneumonitis. Our results provide strong evidence that microRNA-related genetic variations contribute to the development of radiotherapy-induced acute esophagitis and pneumonitis and could thus serve as biomarkers to help accurately predict radiotherapy-induced toxicity in NSCLC patients.

  12. MiRNA-Related Genetic Variations Associated with Radiotherapy-Induced Toxicities in Patients with Locally Advanced Non–Small Cell Lung Cancer

    Science.gov (United States)

    Li, Rong; Pu, Xia; Chang, Joe Y.; Ye, Yuanqing; Komaki, Ritsuko; Minna, John D.; Roth, Jack A.

    2016-01-01

    Severe radiation-induced toxicities limit treatment efficacy and compromise outcomes of lung cancer. We aimed to identify microRNA-related genetic variations as biomarkers for the prediction of radiotherapy-induced acute toxicities. We genotyped 233 SNPs (161 in microRNA binding site and 72 in processing gene) and analyzed their associations with pneumonitis and esophagitis in 167 stage III NSCLC patients received definitive radiation therapy. Sixteen and 11 SNPs were associated with esophagitis and pneumonitis, respectively. After multiple comparison correction, RPS6KB2:rs10274, SMO:rs1061280, SMO:rs1061285 remained significantly associated with esophagitis, while processing gene DGCR8:rs720014, DGCR8:rs3757, DGCR8:rs1633445 remained significantly associated with pneumonitis. Patients with the AA genotype of RPS6KB2:rs10274 had an 81% reduced risk of developing esophagitis (OR: 0.19, 95% CI: 0.07–0.51, p = 0.001, q = 0.06). Patients with the AG+GG genotype of SMO:rs1061280 had an 81% reduced risk of developing esophagitis (OR: 0.19, 95% CI: 0.07–0.53, p = 0.001, q = 0.06). Patients with the GG+GA genotype of DGCR8:rs720014 had a 3.54-fold increased risk of pneumonitis (OR: 3.54, 95% CI: 1.65–7.61, p pneumonitis. Our results provide strong evidence that microRNA-related genetic variations contribute to the development of radiotherapy-induced acute esophagitis and pneumonitis and could thus serve as biomarkers to help accurately predict radiotherapy-induced toxicity in NSCLC patients. PMID:26991123

  13. Optimization and Improvement in Robot-Based Assembly Line System by Hybrid Genetic Algorithm

    Science.gov (United States)

    Lin, Lin; Gen, Mitsuo; Gao, Jie

    In the real world, there are a lot of scenes from which the product is made by using the robot, which needs different assembly times to perform a given task, because of its capabilities and specialization. For a robotic assembly line balancing (rALB) problem, a set of tasks have to be assigned to stations, and each station needs to select one robot to process the assigned tasks. In this paper, we propose a hybrid genetic algorithm (hGA) for solving this problem. In the hGA, we use new representation method. Advanced genetic operators adapted to the specific chromosome structure and the characteristics of the rALB problem are used. In order to strengthen the search ability, a local search procedure is integrated under the framework the genetic algorithm. Some practical test instances demonstrate the effectiveness and efficiency of the proposed algorithm.

  14. Genetic susceptibility of periodontitis

    NARCIS (Netherlands)

    Laine, M.L.; Crielaard, W.; Loos, B.G.

    2012-01-01

    In this systematic review, we explore and summarize the peer-reviewed literature on putative genetic risk factors for susceptibility to aggressive and chronic periodontitis. A comprehensive literature search on the PubMed database was performed using the keywords ‘periodontitis’ or ‘periodontal

  15. The genetic background to PTSD

    NARCIS (Netherlands)

    Broekman, B. F. P.; Olff, M.; Boer, F.

    2007-01-01

    Although extensive research has already been done on the genetic bases of psychiatric disorders, little is known about polygenetic influences in posttraumatic stress disorder (PTSD). This article reviews molecular genetic studies relating to PTSD that were found in a literature search in Medline,

  16. Search Results | Page 151 | IDRC - International Development ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Fair Access to and Benefit Sharing of Genetic Resources : National Policy Development (China, Jordan, Nepal, Peru). Local practices pertaining to biodiversity conservation, crop improvement and natural resource management are under stress. Project ...

  17. MiRNA-Related Genetic Variations Associated with Radiotherapy-Induced Toxicities in Patients with Locally Advanced Non-Small Cell Lung Cancer.

    Directory of Open Access Journals (Sweden)

    Rong Li

    Full Text Available Severe radiation-induced toxicities limit treatment efficacy and compromise outcomes of lung cancer. We aimed to identify microRNA-related genetic variations as biomarkers for the prediction of radiotherapy-induced acute toxicities. We genotyped 233 SNPs (161 in microRNA binding site and 72 in processing gene and analyzed their associations with pneumonitis and esophagitis in 167 stage III NSCLC patients received definitive radiation therapy. Sixteen and 11 SNPs were associated with esophagitis and pneumonitis, respectively. After multiple comparison correction, RPS6KB2:rs10274, SMO:rs1061280, SMO:rs1061285 remained significantly associated with esophagitis, while processing gene DGCR8:rs720014, DGCR8:rs3757, DGCR8:rs1633445 remained significantly associated with pneumonitis. Patients with the AA genotype of RPS6KB2:rs10274 had an 81% reduced risk of developing esophagitis (OR: 0.19, 95% CI: 0.07-0.51, p = 0.001, q = 0.06. Patients with the AG+GG genotype of SMO:rs1061280 had an 81% reduced risk of developing esophagitis (OR: 0.19, 95% CI: 0.07-0.53, p = 0.001, q = 0.06. Patients with the GG+GA genotype of DGCR8:rs720014 had a 3.54-fold increased risk of pneumonitis (OR: 3.54, 95% CI: 1.65-7.61, p <0.05, q <0.1. Significantly cumulative effects of the top SNPs were observed for both toxicities (P-trend <0.001. Using bioinformatics tools, we found that the genotype of rs10274 was associated with altered expression of the RPS6KB2 gene. Gene-based analysis showed DGCR8 (p = 0.010 and GEMIN4 (p = 0.039 were the top genes associated with the risk of developing pneumonitis. Our results provide strong evidence that microRNA-related genetic variations contribute to the development of radiotherapy-induced acute esophagitis and pneumonitis and could thus serve as biomarkers to help accurately predict radiotherapy-induced toxicity in NSCLC patients.

  18. submitter Searches at LEP

    CERN Document Server

    Kawagoe, Kiyotomo

    2001-01-01

    Searches for new particles and new physics were extensively performed at LEP. Although no evidence for new particle/physics was discovered, the null results set very stringent limits to theories beyond the standard model. In this paper, searches at LEP and anomalies observed in the searches are presented. Future prospect of searches at the new energy frontier machines is also discussed.

  19. Web Search Engines

    OpenAIRE

    Rajashekar, TB

    1998-01-01

    The World Wide Web is emerging as an all-in-one information source. Tools for searching Web-based information include search engines, subject directories and meta search tools. We take a look at key features of these tools and suggest practical hints for effective Web searching.

  20. Sound Search Engine Concept

    DEFF Research Database (Denmark)

    2006-01-01

    Sound search is provided by the major search engines, however, indexing is text based, not sound based. We will establish a dedicated sound search services with based on sound feature indexing. The current demo shows the concept of the sound search engine. The first engine will be realased June...

  1. How doctors search

    DEFF Research Database (Denmark)

    Lykke, Marianne; Price, Susan; Delcambre, Lois

    2012-01-01

    Professional, workplace searching is different from general searching, because it is typically limited to specific facets and targeted to a single answer. We have developed the semantic component (SC) model, which is a search feature that allows searchers to structure and specify the search...

  2. Superclone Expansion, Long-Distance Clonal Dispersal and Local Genetic Structuring in the Coral Pocillopora damicornis Type β in Reunion Island, South Western Indian Ocean.

    Directory of Open Access Journals (Sweden)

    Pauline Gélin

    Full Text Available The scleractinian coral Pocillopora damicornis type β is known to present a mixed reproduction mode: through sexual reproduction, new genotypes are created, while asexual reproduction insures their propagation. In order to investigate the relative proportion of each reproduction mode in P. damicornis type β populations from Reunion Island, Indian Ocean, clonal propagation along the west coast was assessed through four sampling sites with increasing geographical distance between sites. Coral colonies were sampled either exhaustively, randomly or haphazardly within each site, and genotypic diversity was assessed using 13 microsatellite loci over a total of 510 P. damicornis type β determined a posteriori from their mtDNA haplotype (a 840 bp sequenced fragment of the Open Reading Frame. Overall, 47% of all the sampled colonies presented the same multi-locus genotype (MLG, a superclone, suggesting that asexual propagation is extremely important in Reunion Island. Within each site, numerous MLGs were shared by several colonies, suggesting local clonal propagation through fragmentation. Moreover, some of these MLGs were found to be shared among several sites located 40 km apart. While asexual reproduction by fragmentation seems unlikely over long distances, our results suggest a production of parthenogenetic larvae. Despite shared MLGs, two differentiated clusters were enclosed among populations of the west coast of Reunion Island, revealing the necessity to set up appropriate managing strategies at a local scale.

  3. Large Neighborhood Search

    DEFF Research Database (Denmark)

    Pisinger, David; Røpke, Stefan

    2010-01-01

    Heuristics based on large neighborhood search have recently shown outstanding results in solving various transportation and scheduling problems. Large neighborhood search methods explore a complex neighborhood by use of heuristics. Using large neighborhoods makes it possible to find better...... candidate solutions in each iteration and hence traverse a more promising search path. Starting from the large neighborhood search method,we give an overview of very large scale neighborhood search methods and discuss recent variants and extensions like variable depth search and adaptive large neighborhood...... search....

  4. Myanmar Language Search Engine

    OpenAIRE

    Pann Yu Mon; Yoshiki Mikami

    2011-01-01

    With the enormous growth of the World Wide Web, search engines play a critical role in retrieving information from the borderless Web. Although many search engines are available for the major languages, but they are not much proficient for the less computerized languages including Myanmar. The main reason is that those search engines are not considering the specific features of those languages. A search engine which capable of searching the Web documents written in those languages is highly n...

  5. An investigation of genetic algorithms

    International Nuclear Information System (INIS)

    Douglas, S.R.

    1995-04-01

    Genetic algorithms mimic biological evolution by natural selection in their search for better individuals within a changing population. they can be used as efficient optimizers. This report discusses the developing field of genetic algorithms. It gives a simple example of the search process and introduces the concept of schema. It also discusses modifications to the basic genetic algorithm that result in species and niche formation, in machine learning and artificial evolution of computer programs, and in the streamlining of human-computer interaction. (author). 3 refs., 1 tab., 2 figs

  6. Bioinformatics: searching the Net.

    Science.gov (United States)

    Kastin, S; Wexler, J

    1998-04-01

    During the past 30 years, there has been an explosion in the volume of published medical information. As this volume has increased, so has the need for efficient methods for searching the data. MEDLINE, the primary medical database, is currently limited to abstracts of the medical literature. MEDLINE searches use AND/OR/NOT logical searching for keywords that have been assigned to each article and for textwords included in article abstracts. Recently, the complete text of some scientific journals, including figures and tables, has become accessible electronically. Keyword and textword searches can provide an overwhelming number of results. Search engines that use phrase searching, or searches that limit the number of words between two finds, improve the precision of search engines. The development of the Internet as a vehicle for worldwide communication, and the emergence of the World Wide Web (WWW) as a common vehicle for communication have made instantaneous access to much of the entire body of medical information an exciting possibility. There is more than one way to search the WWW for information. At the present time, two broad strategies have emerged for cataloging the WWW: directories and search engines. These allow more efficient searching of the WWW. Directories catalog WWW information by creating categories and subcategories of information and then publishing pointers to information within the category listings. Directories are analogous to yellow pages of the phone book. Search engines make no attempt to categorize information. They automatically scour the WWW looking for words and then automatically create an index of those words. When a specific search engine is used, its index is searched for a particular word. Usually, search engines are nonspecific and produce voluminous results. Use of AND/OR/NOT and "near" and "adjacent" search refinements greatly improve the results of a search. Search engines that limit their scope to specific sites, and

  7. To Search or Not to Search!

    Science.gov (United States)

    Taylor, J. Rodney

    Constitutional guarantees, as provided by the Bill of Rights, are enjoyed by all citizens. This principle applies no less to students with respect to their college or university domicile. Case law on this subject suggests that three questions must be answered to determine the reasonableness of residence searching: (1) by whom the search is…

  8. Genetic engineering compared to natural genetic variations.

    Science.gov (United States)

    Arber, Werner

    2010-11-30

    By comparing strategies of genetic alterations introduced in genetic engineering with spontaneously occurring genetic variation, we have come to conclude that both processes depend on several distinct and specific molecular mechanisms. These mechanisms can be attributed, with regard to their evolutionary impact, to three different strategies of genetic variation. These are local nucleotide sequence changes, intragenomic rearrangement of DNA segments and the acquisition of a foreign DNA segment by horizontal gene transfer. Both the strategies followed in genetic engineering and the amounts of DNA sequences thereby involved are identical to, or at least very comparable with, those involved in natural genetic variation. Therefore, conjectural risks of genetic engineering must be of the same order as those for natural biological evolution and for conventional breeding methods. These risks are known to be quite low. There is no scientific reason to assume special long-term risks for GM crops. For future agricultural developments, a road map is designed that can be expected to lead, by a combination of genetic engineering and conventional plant breeding, to crops that can insure food security and eliminate malnutrition and hunger for the entire human population on our planet. Public-private partnerships should be formed with the mission to reach the set goals in the coming decades. Copyright © 2010 Elsevier B.V. All rights reserved.

  9. Nonlinear inversion of potential-field data using a hybrid-encoding genetic algorithm

    Science.gov (United States)

    Chen, C.; Xia, J.; Liu, J.; Feng, G.

    2006-01-01

    Using a genetic algorithm to solve an inverse problem of complex nonlinear geophysical equations is advantageous because it does not require computer gradients of models or "good" initial models. The multi-point search of a genetic algorithm makes it easier to find the globally optimal solution while avoiding falling into a local extremum. As is the case in other optimization approaches, the search efficiency for a genetic algorithm is vital in finding desired solutions successfully in a multi-dimensional model space. A binary-encoding genetic algorithm is hardly ever used to resolve an optimization problem such as a simple geophysical inversion with only three unknowns. The encoding mechanism, genetic operators, and population size of the genetic algorithm greatly affect search processes in the evolution. It is clear that improved operators and proper population size promote the convergence. Nevertheless, not all genetic operations perform perfectly while searching under either a uniform binary or a decimal encoding system. With the binary encoding mechanism, the crossover scheme may produce more new individuals than with the decimal encoding. On the other hand, the mutation scheme in a decimal encoding system will create new genes larger in scope than those in the binary encoding. This paper discusses approaches of exploiting the search potential of genetic operations in the two encoding systems and presents an approach with a hybrid-encoding mechanism, multi-point crossover, and dynamic population size for geophysical inversion. We present a method that is based on the routine in which the mutation operation is conducted in the decimal code and multi-point crossover operation in the binary code. The mix-encoding algorithm is called the hybrid-encoding genetic algorithm (HEGA). HEGA provides better genes with a higher probability by a mutation operator and improves genetic algorithms in resolving complicated geophysical inverse problems. Another significant

  10. Searching for preeclampsia genes : the current position

    NARCIS (Netherlands)

    Lachmeijer, AMA; Dekker, GA; Pals, G; Aarnoudse, JG; ten Kate, LP; Arngrimsson, R

    2002-01-01

    Although there is substantial evidence that preeclampsia has a genetic background, the complexity of the processes involved and the fact that preeclampsia is a maternal-fetal phenomenon does not make the search for the molecular basis of preeclampsia genes easy. It is possible that the single

  11. Search for new breast cancer susceptibility genes

    NARCIS (Netherlands)

    Oldenburg, Rogier Abel

    2008-01-01

    This thesis describes the search for new high-risk breast cancer susceptibility genes by linkage analysis. To date 20-25% of familial breast cancer is explained by mutations in the high-risk BRCA1 and BRCA2 breast cancer susceptibility genes. For the remaining families the genetic etiology is

  12. The Search Performance Evaluation and Prediction in Exploratory Search

    OpenAIRE

    LIU, FEI

    2016-01-01

    The exploratory search for complex search tasks requires an effective search behavior model to evaluate and predict user search performance. Few studies have investigated the relationship between user search behavior and search performance in exploratory search. This research adopts a mixed approach combining search system development, user search experiment, search query log analysis, and multivariate regression analysis to resolve the knowledge gap. Through this study, it is shown that expl...

  13. Multivariate analysis in a genetic divergence study of Psidium guajava.

    Science.gov (United States)

    Nogueira, A M; Ferreira, M F S; Guilhen, J H S; Ferreira, A

    2014-12-18

    The family Myrtaceae is widespread in the Atlantic Forest and is well-represented in the Espírito Santo State in Brazil. In the genus Psidium of this family, guava (Psidium guajava L.) is the most economically important species. Guava is widely cultivated in tropical and subtropical countries; however, the widespread cultivation of only a small number of guava tree cultivars may cause the genetic vulnerability of this crop, making the search for promising genotypes in natural populations important for breeding programs and conservation. In this study, the genetic diversity of 66 guava trees sampled in the southern region of Espírito Santo and in Caparaó, MG, Brazil were evaluated. A total of 28 morphological descriptors (11 quantitative and 17 multicategorical) and 18 microsatellite markers were used. Principal component, discriminant and cluster analyses, descriptive analyses, and genetic diversity analyses using simple sequence repeats were performed. Discrimination of accessions using molecular markers resulted in clustering of genotypes of the same origin, which was not observed using morphological data. Genetic diversity was detected between and within the localities evaluated, regardless of the methodology used. Genetic differentiation among the populations using morphological and molecular data indicated the importance of the study area for species conservation, genetic erosion estimation, and exploitation in breeding programs.

  14. Worldwide Genetic Features of HIV-1 Env α4β7 Binding Motif: The Local Dissemination Impact of the LDI Tripeptide.

    Science.gov (United States)

    Hait, Sabrina H; Soares, Esmeralda A; Sprinz, Eduardo; Arthos, James; Machado, Elizabeth S; Soares, Marcelo A

    2015-12-15

    HIV-1 gp120 binds to integrin α4β7, a homing receptor of lymphocytes to gut-associated lymphoid tissues. This interaction is mediated by the LDI/V tripeptide encoded in the V2-loop. This tripeptide mimics similar motifs in mucosal addressin cellular adhesion molecule (MAdCAM) and vascular CAM (VCAM), the natural ligands of α4β7. In this study, we explored the association of V2-loop LDI/V mimotopes with transmission routes and patterns of disease progression in HIV-infected adult and pediatric patients. HIV-1 env sequences available in the Los Alamos HIV Sequence database were included in the analyses. HIV-1 V2-loop sequences generated from infected adults and infants from South and Southeast Brazil, and also retrieved from the Los Alamos database, were assessed for α4β7 binding tripeptide composition. Chi-Square/Fisher Exact test and Mann Whitney U test were used for tripeptide comparisons. Shannon entropy was assessed for conservancy of the α4β7 tripeptide mimotope. We observed no association between the tripeptide composition or conservation and virus transmission route or disease progression. However, LDI was linked to successful epidemic dissemination of HIV-1 subtype C in South America, and further to other expanding non-B subtypes in Europe and Asia. In Africa, subtypes showing increased LDV prevalence evidenced an ongoing process of selection toward LDI expansion, an observation also extended to subtype B in the Americas and Western Europe. The V2-loop LDI mimotope was conserved in HIV-1C from South America and other expanding subtypes across the globe, which suggests that LDI may promote successful dissemination of HIV at local geographic levels by means of increased transmission fitness.

  15. Collective search by ants in microgravity

    Directory of Open Access Journals (Sweden)

    Stefanie M. Countryman

    2015-03-01

    Full Text Available The problem of collective search is a tradeoff between searching thoroughly and covering as much area as possible. This tradeoff depends on the density of searchers. Solutions to the problem of collective search are currently of much interest in robotics and in the study of distributed algorithms, for example to design ways that without central control robots can use local information to perform search and rescue operations. Ant colonies operate without central control. Because they can perceive only local, mostly chemical and tactile cues, they must search collectively to find resources and to monitor the colony's environment. Examining how ants in diverse environments solve the problem of collective search can elucidate how evolution has led to diverse forms of collective behavior. An experiment on the International Space Station in January 2014 examined how ants (Tetramorium caespitum perform collective search in microgravity. In the ISS experiment, the ants explored a small arena in which a barrier was lowered to increase the area and thus lower ant density. In microgravity, relative to ground controls, ants explored the area less thoroughly and took more convoluted paths. It appears that the difficulty of holding on to the surface interfered with the ants’ ability to search collectively. Ants frequently lost contact with the surface, but showed a remarkable ability to regain contact with the surface.

  16. Cube search, revisited

    Science.gov (United States)

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

    2015-01-01

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

  17. Molecular genetics

    International Nuclear Information System (INIS)

    Kubitschek, H.E.

    1975-01-01

    Progress is reported on studies on the nature and action of lethal and mutagenic lesions in DNA and the mechanisms by which these are produced in bacteria by ionizing radiation or by decay of radioisotopes incorporated in DNA. Studies of radioisotope decay provide the advantages that the original lesion is localized in the genetic material and the immediate physical and chemical changes that occur at decay are known. Specific types of DNA damage were related to characteristic decay properties of several radioisotopes. Incorporated 125 I, for example, induces a double-stranded break in DNA with almost every decay, but causes remarkably little damage of any other kind to the DNA. (U.S.)

  18. Integrated vs. Federated Search

    DEFF Research Database (Denmark)

    Løvschall, Kasper

    2009-01-01

    Oplæg om forskelle og ligheder mellem integrated og federated search i bibliotekskontekst. Holdt ved temadag om "Integrated Search - samsøgning i alle kilder" på Danmarks Biblioteksskole den 22. januar 2009.......Oplæg om forskelle og ligheder mellem integrated og federated search i bibliotekskontekst. Holdt ved temadag om "Integrated Search - samsøgning i alle kilder" på Danmarks Biblioteksskole den 22. januar 2009....

  19. The Information Search

    Science.gov (United States)

    Doraiswamy, Uma

    2011-01-01

    This paper in the form of story discusses a college student's information search process. In this story we see Kuhlthau's information search process: initiation, selection, exploration, formulation, collection, and presentation. Katie is a student who goes in search of information for her class research paper. Katie's class readings, her interest…

  20. Inversion for Refractivity Parameters Using a Dynamic Adaptive Cuckoo Search with Crossover Operator Algorithm

    Directory of Open Access Journals (Sweden)

    Zhihua Zhang

    2016-01-01

    Full Text Available Using the RFC technique to estimate refractivity parameters is a complex nonlinear optimization problem. In this paper, an improved cuckoo search (CS algorithm is proposed to deal with this problem. To enhance the performance of the CS algorithm, a parameter dynamic adaptive operation and crossover operation were integrated into the standard CS (DACS-CO. Rechenberg’s 1/5 criteria combined with learning factor were used to control the parameter dynamic adaptive adjusting process. The crossover operation of genetic algorithm was utilized to guarantee the population diversity. The new hybrid algorithm has better local search ability and contributes to superior performance. To verify the ability of the DACS-CO algorithm to estimate atmospheric refractivity parameters, the simulation data and real radar clutter data are both implemented. The numerical experiments demonstrate that the DACS-CO algorithm can provide an effective method for near-real-time estimation of the atmospheric refractivity profile from radar clutter.

  1. Stochastic search techniques for post-fault restoration of electrical ...

    Indian Academy of Sciences (India)

    Three stochastic search techniques have been used to find the optimal sequence of operations required to restore supply in an electrical distribution system on the occurrence of a fault. The three techniques are the genetic algorithm,simulated annealing and the tabu search. The performance of these techniques has been ...

  2. Keyword Search in Databases

    CERN Document Server

    Yu, Jeffrey Xu; Chang, Lijun

    2009-01-01

    It has become highly desirable to provide users with flexible ways to query/search information over databases as simple as keyword search like Google search. This book surveys the recent developments on keyword search over databases, and focuses on finding structural information among objects in a database using a set of keywords. Such structural information to be returned can be either trees or subgraphs representing how the objects, that contain the required keywords, are interconnected in a relational database or in an XML database. The structural keyword search is completely different from

  3. Adiabatic quantum search algorithm for structured problems

    International Nuclear Information System (INIS)

    Roland, Jeremie; Cerf, Nicolas J.

    2003-01-01

    The study of quantum computation has been motivated by the hope of finding efficient quantum algorithms for solving classically hard problems. In this context, quantum algorithms by local adiabatic evolution have been shown to solve an unstructured search problem with a quadratic speedup over a classical search, just as Grover's algorithm. In this paper, we study how the structure of the search problem may be exploited to further improve the efficiency of these quantum adiabatic algorithms. We show that by nesting a partial search over a reduced set of variables into a global search, it is possible to devise quantum adiabatic algorithms with a complexity that, although still exponential, grows with a reduced order in the problem size

  4. Relevance ranking for vertical search engines

    CERN Document Server

    Chang, Yi

    2014-01-01

    In plain, uncomplicated language, and using detailed examples to explain the key concepts, models, and algorithms in vertical search ranking, Relevance Ranking for Vertical Search Engines teaches readers how to manipulate ranking algorithms to achieve better results in real-world applications. This reference book for professionals covers concepts and theories from the fundamental to the advanced, such as relevance, query intention, location-based relevance ranking, and cross-property ranking. It covers the most recent developments in vertical search ranking applications, such as freshness-based relevance theory for new search applications, location-based relevance theory for local search applications, and cross-property ranking theory for applications involving multiple verticals. It introduces ranking algorithms and teaches readers how to manipulate ranking algorithms for the best results. It covers concepts and theories from the fundamental to the advanced. It discusses the state of the art: development of ...

  5. A genetic algorithm approach to optimization for the radiological worker allocation problem

    International Nuclear Information System (INIS)

    Yan Chen; Masakuni Narita; Masashi Tsuji; Sangduk Sa

    1996-01-01

    The worker allocation optimization problem in radiological facilities inevitably involves various types of requirements and constraints relevant to radiological protection and labor management. Some of these goals and constraints are not amenable to a rigorous mathematical formulation. Conventional methods for this problem rely heavily on sophisticated algebraic or numerical algorithms, which cause difficulties in the search for optimal solutions in the search space of worker allocation optimization problems. Genetic algorithms (GAB) are stochastic search algorithms introduced by J. Holland in the 1970s based on ideas and techniques from genetic and evolutionary theories. The most striking characteristic of GAs is the large flexibility allowed in the formulation of the optimal problem and the process of the search for the optimal solution. In the formulation, it is not necessary to define the optimal problem in rigorous mathematical terms, as required in the conventional methods. Furthermore, by designing a model of evolution for the optimal search problem, the optimal solution can be sought efficiently with computational simple manipulations without highly complex mathematical algorithms. We reported a GA approach to the worker allocation problem in radiological facilities in the previous study. In this study, two types of hard constraints were employed to reduce the huge search space, where the optimal solution is sought in such a way as to satisfy as many of soft constraints as possible. It was demonstrated that the proposed evolutionary method could provide the optimal solution efficiently compared with conventional methods. However, although the employed hard constraints could localize the search space into a very small region, it brought some complexities in the designed genetic operators and demanded additional computational burdens. In this paper, we propose a simplified evolutionary model with less restrictive hard constraints and make comparisons between

  6. Genetics in endocrinology: genetic variation in deiodinases: a systematic review of potential clinical effects in humans.

    Science.gov (United States)

    Verloop, Herman; Dekkers, Olaf M; Peeters, Robin P; Schoones, Jan W; Smit, Johannes W A

    2014-09-01

    Iodothyronine deiodinases represent a family of selenoproteins involved in peripheral and local homeostasis of thyroid hormone action. Deiodinases are expressed in multiple organs and thyroid hormone affects numerous biological systems, thus genetic variation in deiodinases may affect multiple clinical endpoints. Interest in clinical effects of genetic variation in deiodinases has clearly increased. We aimed to provide an overview for the role of deiodinase polymorphisms in human physiology and morbidity. In this systematic review, studies evaluating the relationship between deiodinase polymorphisms and clinical parameters in humans were eligible. No restrictions on publication date were imposed. The following databases were searched up to August 2013: Pubmed, EMBASE (OVID-version), Web of Science, COCHRANE Library, CINAHL (EbscoHOST-version), Academic Search Premier (EbscoHOST-version), and ScienceDirect. Deiodinase physiology at molecular and tissue level is described, and finally the role of these polymorphisms in pathophysiological conditions is reviewed. Deiodinase type 1 (D1) polymorphisms particularly show moderate-to-strong relationships with thyroid hormone parameters, IGF1 production, and risk for depression. D2 variants correlate with thyroid hormone levels, insulin resistance, bipolar mood disorder, psychological well-being, mental retardation, hypertension, and risk for osteoarthritis. D3 polymorphisms showed no relationship with inter-individual variation in serum thyroid hormone parameters. One D3 polymorphism was associated with risk for osteoarthritis. Genetic deiodinase profiles only explain a small proportion of inter-individual variations in serum thyroid hormone levels. Evidence suggests a role of genetic deiodinase variants in certain pathophysiological conditions. The value for determination of deiodinase polymorphism in clinical practice needs further investigation. © 2014 European Society of Endocrinology.

  7. Adaptive Large Neighbourhood Search

    DEFF Research Database (Denmark)

    Røpke, Stefan

    Large neighborhood search is a metaheuristic that has gained popularity in recent years. The heuristic repeatedly moves from solution to solution by first partially destroying the solution and then repairing it. The best solution observed during this search is presented as the final solution....... This tutorial introduces the large neighborhood search metaheuristic and the variant adaptive large neighborhood search that dynamically tunes parameters of the heuristic while it is running. Both heuristics belong to a broader class of heuristics that are searching a solution space using very large...... neighborhoods. The tutorial also present applications of the adaptive large neighborhood search, mostly related to vehicle routing problems for which the heuristic has been extremely successful. We discuss how the heuristic can be parallelized and thereby take advantage of modern desktop computers...

  8. A parallel genetic algorithm for the set partitioning problem

    Energy Technology Data Exchange (ETDEWEB)

    Levine, D. [Argonne National Lab., IL (United States). Mathematics and Computer Science Division.

    1994-05-01

    In this dissertation the author reports on his efforts to develop a parallel genetic algorithm and apply it to the solution of set partitioning problem -- a difficult combinatorial optimization problem used by many airlines as a mathematical model for flight crew scheduling. He developed a distributed steady-state genetic algorithm in conjunction with a specialized local search heuristic for solving the set partitioning problem. The genetic algorithm is based on an island model where multiple independent subpopulations each run a steady-state genetic algorithm on their subpopulation and occasionally fit strings migrate between the subpopulations. Tests on forty real-world set partitioning problems were carried out on up to 128 nodes of an IBM SP1 parallel computer. The authors found that performance, as measured by the quality of the solution found and the iteration on which it was found, improved as additional subpopulation found and the iteration on which it was found, improved as additional subpopulations were added to the computation. With larger numbers of subpopulations the genetic algorithm was regularly able to find the optimal solution to problems having up to a few thousand integer variables. In two cases, high-quality integer feasible solutions were found for problems with 36,699 and 43,749 integer variables, respectively. A notable limitation they found was the difficulty solving problems with many constraints.

  9. Intrinsic position uncertainty impairs overt search performance.

    Science.gov (United States)

    Semizer, Yelda; Michel, Melchi M

    2017-08-01

    Uncertainty regarding the position of the search target is a fundamental component of visual search. However, due to perceptual limitations of the human visual system, this uncertainty can arise from intrinsic, as well as extrinsic, sources. The current study sought to characterize the role of intrinsic position uncertainty (IPU) in overt visual search and to determine whether it significantly limits human search performance. After completing a preliminary detection experiment to characterize sensitivity as a function of visual field position, observers completed a search task that required localizing a Gabor target within a field of synthetic luminance noise. The search experiment included two clutter conditions designed to modulate the effect of IPU across search displays of varying set size. In the Cluttered condition, the display was tiled uniformly with feature clutter to maximize the effects of IPU. In the Uncluttered condition, the clutter at irrelevant locations was removed to attenuate the effects of IPU. Finally, we derived an IPU-constrained ideal searcher model, limited by the IPU measured in human observers. Ideal searchers were simulated based on the detection sensitivity and fixation sequences measured for individual human observers. The IPU-constrained ideal searcher predicted performance trends similar to those exhibited by the human observers. In the Uncluttered condition, performance decreased steeply as a function of increasing set size. However, in the Cluttered condition, the effect of IPU dominated and performance was approximately constant as a function of set size. Our findings suggest that IPU substantially limits overt search performance, especially in crowded displays.

  10. University Students' Online Information Searching Strategies in Different Search Contexts

    Science.gov (United States)

    Tsai, Meng-Jung; Liang, Jyh-Chong; Hou, Huei-Tse; Tsai, Chin-Chung

    2012-01-01

    This study investigates the role of search context played in university students' online information searching strategies. A total of 304 university students in Taiwan were surveyed with questionnaires in which two search contexts were defined as searching for learning, and searching for daily life information. Students' online search strategies…

  11. [Advanced online search techniques and dedicated search engines for physicians].

    Science.gov (United States)

    Nahum, Yoav

    2008-02-01

    In recent years search engines have become an essential tool in the work of physicians. This article will review advanced search techniques from the world of information specialists, as well as some advanced search engine operators that may help physicians improve their online search capabilities, and maximize the yield of their searches. This article also reviews popular dedicated scientific and biomedical literature search engines.

  12. Research on rolling element bearing fault diagnosis based on genetic algorithm matching pursuit

    Science.gov (United States)

    Rong, R. W.; Ming, T. F.

    2017-12-01

    In order to solve the problem of slow computation speed, matching pursuit algorithm is applied to rolling bearing fault diagnosis, and the improvement are conducted from two aspects that are the construction of dictionary and the way to search for atoms. To be specific, Gabor function which can reflect time-frequency localization characteristic well is used to construct the dictionary, and the genetic algorithm to improve the searching speed. A time-frequency analysis method based on genetic algorithm matching pursuit (GAMP) algorithm is proposed. The way to set property parameters for the improvement of the decomposition results is studied. Simulation and experimental results illustrate that the weak fault feature of rolling bearing can be extracted effectively by this proposed method, at the same time, the computation speed increases obviously.

  13. Mobile Search and Advertising

    OpenAIRE

    Lovitskii, Vladimir; McCaffery, Colin; Thrasher, Michael; Traynor, David; Wright, Peter

    2009-01-01

    Mobile advertising is a rapidly growing sector providing brands and marketing agencies the opportunity to connect with consumers beyond traditional and digital media and instead communicate directly on their mobile phones. Mobile advertising will be intrinsically linked with mobile search, which has transported from the internet to the mobile and is identified as an area of potential growth. The result of mobile searching show that as a general rule such search result exceed 1...

  14. Mastering ElasticSearch

    CERN Document Server

    Kuc, Rafal

    2013-01-01

    A practical tutorial that covers the difficult design, implementation, and management of search solutions.Mastering ElasticSearch is aimed at to intermediate users who want to extend their knowledge about ElasticSearch. The topics that are described in the book are detailed, but we assume that you already know the basics, like the query DSL or data indexing. Advanced users will also find this book useful, as the examples are getting deep into the internals where it is needed.

  15. ElasticSearch cookbook

    CERN Document Server

    Paro, Alberto

    2013-01-01

    Written in an engaging, easy-to-follow style, the recipes will help you to extend the capabilities of ElasticSearch to manage your data effectively.If you are a developer who implements ElasticSearch in your web applications, manage data, or have decided to start using ElasticSearch, this book is ideal for you. This book assumes that you've got working knowledge of JSON and Java

  16. Genetics Home Reference: primary localized cutaneous amyloidosis

    Science.gov (United States)

    ... are mildly itchy. Nodular amyloidosis is characterized by firm, raised bumps (nodules) that are pink, red, or ... 31: Cytokines, receptors, signal transduction and physiology. Cytokine Growth Factor Rev. 2015 Oct;26(5):545-58. ...

  17. Common Genetic Components of Obesity Traits and Serum Leptin

    DEFF Research Database (Denmark)

    Hasselbalch, Ann L; Benyamin, Beben; Visscher, Peter M

    2008-01-01

    To estimate common and distinct genetic influences on a panel of obesity-related traits and serum leptin level in adults. In a cross-sectional study of 625 Danish, adult, healthy, monozygotic, and same-sex dizygotic twin pairs of both genders, we carried out detailed anthropometry (height, weight...... components, which suggests that it is important to distinguish between the different phenotypes in the search for genes involved in the development of obesity.Obesity (2008) doi:10.1038/oby.2008.440........ For leptin vs. the various measures of overall and local fatness the correlations ranged from 0.54 to 0.74 in men and from 0.48 to 0.75 in women. All correlations were significantly different genetic...

  18. Local Publications.

    Science.gov (United States)

    Wilson, Yvonne; And Others

    1991-01-01

    Includes annotations for 23 local government publications that reflect the main issues confronting local communities, including AIDS, children at risk, homelessness, human rights, and environmental decline. The shift of local problem solving from the federal and state government levels to the local level is briefly discussed. (LRW)

  19. Google Power Search

    CERN Document Server

    Spencer, Stephan

    2011-01-01

    Behind Google's deceptively simple interface is immense power for both market and competitive research-if you know how to use it well. Sure, basic searches are easy, but complex searches require specialized skills. This concise book takes you through the full range of Google's powerful search-refinement features, so you can quickly find the specific information you need. Learn techniques ranging from simple Boolean logic to URL parameters and other advanced tools, and see how they're applied to real-world market research examples. Incorporate advanced search operators such as filetype:, intit

  20. Supersymmetry searches at CMS

    Directory of Open Access Journals (Sweden)

    Bargassa Pedrame

    2014-04-01

    Full Text Available The accumulation of 19 fb−1 of data at 8 TeV has been a unique window for Supersymmetry searches at the LHC, allowing the CMS collaboration to search for specific supersymmetric particles. This article covers the search for supersymmetric particles in a variety of production-and decay-modes as well as channels. It focuses on the search for the lightest scalar top (stop in the single lepton channel, stop which might be the only observable in the case where Supersymmetry is realized in nature, and which can play a unique role in “naturalness”

  1. Exotic Higgs searches

    CERN Document Server

    Pelliccioni, Mario

    2016-01-01

    Exotic Higgs searches cover a wide range of signatures, thus leading to indications to new physics beyond Standard Model. We report a review on exotic Higgs searches for lepton flavour violating Higgs decays, for "mono-Higgs" searches, for Higgs decays to invisible and for high mass Higgs searches. Both ATLAS and CMS results will be shown, for Run-1 data statistics collected at the energy of $\\sqrt s$ = 7,8 TeV and for the first data collected during Run-2 phase at the energy of $\\sqrt s$ = 13 TeV.

  2. Unstoppable, sbottomless sfermion searches

    Science.gov (United States)

    Trigger, Isabel

    Results are presented from searches by the LEP collaborations for scalar partners of leptons and light quarks in the context of the Minimal Supersymmetric Standard Model (MSSM). Examples shown are searches by OPAL for events with two leptons and significant missing transverse momentum and events with anomalous dE/dx, L3 searches for mass-degenerate squarks and for single electrons, and a DELPHI search for staus of mass less than MZ0/2. No evidence is observed for any signal indicating physics beyond the Standard Model (SM). Limits are shown in the context of a constrained MSSM (CMSSM).

  3. Unstoppable, bottomless sfermion searches

    Energy Technology Data Exchange (ETDEWEB)

    Trigger, Isabel [CERN (Switzerland)

    2004-07-01

    Results are presented from searches by the LEP collaborations for scalar partners of leptons and light quarks in the context of the Minimal Supersymmetric Standard Model (MSSM). Examples shown are searches by OPAL for events with two leptons and significant missing transverse momentum and events with anomalous dE/dx, L3 searches for mass-degenerate squarks and for single electrons, and a DELPHI search for staus of mass less than M{sub Z{sup 0/2}}. No evidence is observed for any signal indicating physics beyond the Standard Model (SM). Limits are shown in the context of a constrained MSSM (CMSSM). (orig.)

  4. Unstoppable, bottomless sfermion searches

    International Nuclear Information System (INIS)

    Trigger, Isabel

    2004-01-01

    Results are presented from searches by the LEP collaborations for scalar partners of leptons and light quarks in the context of the Minimal Supersymmetric Standard Model (MSSM). Examples shown are searches by OPAL for events with two leptons and significant missing transverse momentum and events with anomalous dE/dx, L3 searches for mass-degenerate squarks and for single electrons, and a DELPHI search for staus of mass less than M Z 0 /2. No evidence is observed for any signal indicating physics beyond the Standard Model (SM). Limits are shown in the context of a constrained MSSM (CMSSM). (orig.)

  5. Application of Genetic Algorithms in Seismic Tomography

    Science.gov (United States)

    Soupios, Pantelis; Akca, Irfan; Mpogiatzis, Petros; Basokur, Ahmet; Papazachos, Constantinos

    2010-05-01

    application of hybrid genetic algorithms in seismic tomography is examined and the efficiency of least squares and genetic methods as representative of the local and global optimization, respectively, is presented and evaluated. The robustness of both optimization methods has been tested and compared for the same source-receiver geometry and characteristics of the model structure (anomalies, etc.). A set of seismic refraction synthetic (noise free) data was used for modeling. Specifically, cross-well, down-hole and typical refraction studies using 24 geophones and 5 shoots were used to confirm the applicability of the genetic algorithms in seismic tomography. To solve the forward modeling and estimate the traveltimes, the revisited ray bending method was used supplemented by an approximate computation of the first Fresnel volume. The root mean square (rms) error as the misfit function was used and calculated for the entire random velocity model for each generation. After the end of each generation and based on the misfit of the individuals (velocity models), the selection, crossover and mutation (typical process steps of genetic algorithms) were selected continuing the evolution theory and coding the new generation. To optimize the computation time, since the whole procedure is quite time consuming, the Matlab Distributed Computing Environment (MDCE) was used in a multicore engine. During the tests, we noticed that the fast convergence that the algorithm initially exhibits (first 5 generations) is followed by progressively slower improvements of the reconstructed velocity models. Thus, to improve the final tomographic models, a hybrid genetic algorithm (GA) approach was adopted by combining the GAs with a local optimization method after several generations, on the basis of the convergence of the resulting models. This approach is shown to be efficient, as it directs the solution search towards a model region close to the global minimum solution.

  6. Local formularies

    Science.gov (United States)

    Reynolds, D John M; Fajemisin, Olubunmi; Wilds, Sara

    2012-01-01

    The widespread availability of authoritative guidance on prescribing from a wide variety of international and national bodies calls into question the need for additional local formulary advice. This article describes contemporary local formulary management in the United Kingdom and discusses the areas where local decision making remains valuable. Local formularies can fulfil important roles which justify their continued existence, including ensuring local ownership and acceptance of advice, rapid dissemination of information, responsiveness to local circumstances and service design, sensitivity to local pricing arrangements and close professional links with commissioners, pharmacists and prescribers. PMID:22420709

  7. Nonsequential search equilibrium with search cost heterogeneity

    NARCIS (Netherlands)

    Moraga-Gonzalez, Jose Luis; Sandor, Zsolt; Wildenbeest, Matthijs R.

    We generalize the model of Burdett and Judd (1983) to the case where an arbitrary finite number of firms sells a homogeneous good to buyers who have heterogeneous search costs. We show that a price dispersed symmetric Nash equilibrium always exists. Numerical results show that the behavior of prices

  8. Citation Searching: Search Smarter & Find More

    Science.gov (United States)

    Hammond, Chelsea C.; Brown, Stephanie Willen

    2008-01-01

    The staff at University of Connecticut are participating in Elsevier's Student Ambassador Program (SAmP) in which graduate students train their peers on "citation searching" research using Scopus and Web of Science, two tremendous citation databases. They are in the fourth semester of these training programs, and they are wildly successful: They…

  9. Review- Cancer: Some genetic considerations | Salem | Egyptian ...

    African Journals Online (AJOL)

    Egyptian Journal of Medical Human Genetics. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives · Journal Home > Vol 16, No 1 (2015) >. Log in or Register to get access to full text downloads.

  10. Biological evolution: Some genetic considerations | Salem ...

    African Journals Online (AJOL)

    Egyptian Journal of Medical Human Genetics. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives · Journal Home > Vol 15, No 1 (2014) >. Log in or Register to get access to full text downloads.

  11. Basics on Genes and Genetic Disorders

    Science.gov (United States)

    ... for Educators Search English Español The Basics on Genes and Genetic Disorders KidsHealth / For Teens / The Basics ... such as treating health problems. What Is a Gene? To understand how genes work, let's review some ...

  12. Genetics Home Reference: Holt-Oram syndrome

    Science.gov (United States)

    ... navigation Home Page Search Home Health Conditions Genes Chromosomes & mtDNA Resources Help Me Understand Genetics Share: Email ... from the University of Kansas Medical Center: Limb Anomalies GeneReviews (1 link) Holt-Oram Syndrome Scientific Articles ...

  13. Genetics Home Reference: Klippel-Feil syndrome

    Science.gov (United States)

    ... navigation Home Page Search Home Health Conditions Genes Chromosomes & mtDNA Resources Help Me Understand Genetics Share: Email ... Klimo P Jr, Rao G, Brockmeyer D. Congenital anomalies of the cervical spine. Neurosurg Clin N Am. ...

  14. Genetics Home Reference: enlarged parietal foramina

    Science.gov (United States)

    ... navigation Home Page Search Home Health Conditions Genes Chromosomes & mtDNA Resources Help Me Understand Genetics Share: Email ... parietal foramina: association with cerebral venous and cortical anomalies. Neurology. 2000 Mar 14;54(5):1175-8. ...

  15. Genetics Home Reference: auriculo-condylar syndrome

    Science.gov (United States)

    ... Health Topic: Jaw Injuries and Disorders Health Topic: Temporomandibular Joint Dysfunction Genetic and Rare Diseases Information Center (1 link) Auriculo-condylar syndrome Educational Resources (6 links) American ... InfoSearch: Dysgnathia Complex MalaCards: auriculo-condylar ...

  16. Local formularies

    OpenAIRE

    Reynolds, D John M; Fajemisin, Olubunmi; Wilds, Sara

    2012-01-01

    The widespread availability of authoritative guidance on prescribing from a wide variety of international and national bodies calls into question the need for additional local formulary advice. This article describes contemporary local formulary management in the United Kingdom and discusses the areas where local decision making remains valuable. Local formularies can fulfil important roles which justify their continued existence, including ensuring local ownership and acceptance of advice, r...

  17. A hybrid genetic algorithm for the distributed permutation flowshop scheduling problem

    Directory of Open Access Journals (Sweden)

    Jian Gao

    2011-08-01

    Full Text Available Distributed Permutation Flowshop Scheduling Problem (DPFSP is a newly proposed scheduling problem, which is a generalization of classical permutation flow shop scheduling problem. The DPFSP is NP-hard in general. It is in the early stages of studies on algorithms for solving this problem. In this paper, we propose a GA-based algorithm, denoted by GA_LS, for solving this problem with objective to minimize the maximum completion time. In the proposed GA_LS, crossover and mutation operators are designed to make it suitable for the representation of DPFSP solutions, where the set of partial job sequences is employed. Furthermore, GA_LS utilizes an efficient local search method to explore neighboring solutions. The local search method uses three proposed rules that move jobs within a factory or between two factories. Intensive experiments on the benchmark instances, extended from Taillard instances, are carried out. The results indicate that the proposed hybrid genetic algorithm can obtain better solutions than all the existing algorithms for the DPFSP, since it obtains better relative percentage deviation and differences of the results are also statistically significant. It is also seen that best-known solutions for most instances are updated by our algorithm. Moreover, we also show the efficiency of the GA_LS by comparing with similar genetic algorithms with the existing local search methods.

  18. Graphical models for genetic analyses

    DEFF Research Database (Denmark)

    Lauritzen, Steffen Lilholt; Sheehan, Nuala A.

    2003-01-01

    This paper introduces graphical models as a natural environment in which to formulate and solve problems in genetics and related areas. Particular emphasis is given to the relationships among various local computation algorithms which have been developed within the hitherto mostly separate areas...... of graphical models and genetics. The potential of graphical models is explored and illustrated through a number of example applications where the genetic element is substantial or dominating....

  19. Further investigation on adaptive search

    Directory of Open Access Journals (Sweden)

    Ming Hong Pi

    2014-05-01

    Full Text Available Adaptive search is one of the fastest fractal compression algorithms and has gained great success in many industrial applications. By substituting the luminance offset by the range block mean, the authors create a completely new version for both the encoding and decoding algorithms. In this paper, theoretically, they prove that the proposed decoding algorithm converges at least as fast as the existing decoding algorithms using the luminance offset. In addition, they prove that the attractor of the decoding algorithm can be represented by a linear combination of range-averaged images. These theorems are very important contributions to the theory and applications of fractal image compression. As a result, the decoding image can be represented as the sum of the DC and AC component images, which is similar with discrete cosine transform or wavelet transform. To further speed up this algorithm and reduce the complexity of range and domain blocks matching, they propose two improvements in this paper, that is, employing the post-quantisation and geometric neighbouring local search to replace the currently used pre-quantisation and the global search, respectively. The corresponding experimental results show the proposed encoding and decoding algorithms can provide a better performance compared with the existing algorithms.

  20. Agrosearch: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  1. Africa Development: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  2. African Anthropologist: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  3. Biokemistri: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  4. Acta Structilia: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  5. Measuring Online Search Expertise

    Science.gov (United States)

    Bailey, Earl

    2017-01-01

    Search expertise has long been studied and used extensively in information seeking behavior research, both as a fundamental concept and as a method of comparing groups of users. Unfortunately, while search expertise has been studied for some time, the conceptualization of it has lagged behind its use in categorizing users. This has led to users…

  6. Ergonomics SA: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  7. Agronomie Africaine: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  8. Mathematics Connection: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  9. Critical Arts: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  10. Rwanda Journal: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  11. Kenya Veterinarian: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  12. Supporting complex search tasks

    DEFF Research Database (Denmark)

    Gäde, Maria; Hall, Mark; Huurdeman, Hugo

    2015-01-01

    introductory to specialized, and from authoritative to speculative or opinionated, when to show what sources of information? How does the information seeking process evolve and what are relevant differences between different stages? With complex task and search process management, blending searching, browsing...

  13. Innovation: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  14. Distributed Deep Web Search

    NARCIS (Netherlands)

    Tjin-Kam-Jet, Kien

    2013-01-01

    The World Wide Web contains billions of documents (and counting); hence, it is likely that some document will contain the answer or content you are searching for. While major search engines like Bing and Google often manage to return relevant results to your query, there are plenty of situations in

  15. Search and switching costs

    NARCIS (Netherlands)

    Siekman, Wilhelm Henricus

    2016-01-01

    This thesis analyses markets with search and with switching costs. It provides insights in several important issues in search markets, including how loss aversion may affect consumer behavior and firm conduct, and how prices, welfare, and profits may change when an intermediating platform orders

  16. Human memory search

    NARCIS (Netherlands)

    Davelaar, E.J.; Raaijmakers, J.G.W.; Hills, T.T.; Robbins, T.W.; Todd, P.M.

    2012-01-01

    The importance of understanding human memory search is hard to exaggerate: we build and live our lives based on what whe remember. This chapter explores the characteristics of memory search, with special emphasis on the use of retrieval cues. We introduce the dependent measures that are obtained

  17. ElasticSearch cookbook

    CERN Document Server

    Paro, Alberto

    2015-01-01

    If you are a developer who implements ElasticSearch in your web applications and want to sharpen your understanding of the core elements and applications, this is the book for you. It is assumed that you've got working knowledge of JSON and, if you want to extend ElasticSearch, of Java and related technologies.

  18. Annales Aequatoria: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  19. Searching low and high

    DEFF Research Database (Denmark)

    Laursen, Keld; Salter, Ammon

    2003-01-01

    .The results suggest that firms who adopt `open' search strategies and invest in R&D are morelikely than other firms to draw from universities, indicating that managerial choice matters inshaping the propensity of firms to draw from universities.Key words: University-industry links, innovation, external search...

  20. Lexikos: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  1. Kiswahili: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  2. Philosophical Papers: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  3. Sciences & Nature: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  4. Counsellor (The): Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  5. Nigerian Libraries: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  6. Vulture News: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  7. Afrika Statistika: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  8. Acta Theologica: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  9. Water SA: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  10. Tropical Veterinarian: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  11. African Environment: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  12. Zede Journal: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  13. Africa Insight: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  14. African Zoology: Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  15. Searches for Supersymmetry

    CERN Document Server

    Ventura, Andrea; The ATLAS collaboration

    2017-01-01

    New and recent results on Supersymmetry searches are shown for the ATLAS and the CMS experiments. Analyses with about 36 fb$^{-1}$ are considered for searches concerning light squarks and gluinos, direct pair production of 3$^{rd}$ generation squarks, electroweak production of charginos, neutralinos, sleptons, R-parity violating scenarios and long-lived particles.

  16. Search and Disrupt

    DEFF Research Database (Denmark)

    Ørding Olsen, Anders

    This paper analyzes how external search is affected by strategic interest alignment among knowledge sources. I focus on misalignment arising from the heterogeneous effects of disruptive technologies by analyzing the influence of incumbents on 2,855 non-incumbents? external knowledge search efforts....... The efforts most likely to solve innovation problems obtained funding from the European Commission?s 7th Framework Program (2007-2013). The results show that involving incumbents improves search in complementary technologies, while demoting it when strategic interests are misaligned in disruptive technologies....... However, incumbent sources engaged in capability reconfiguration to accommodate disruption improve search efforts in disruptive technologies. The paper concludes that the value of external sources is contingent on more than their knowledge. Specifically, interdependence of sources in search gives rise...

  17. A Study of Penalty Function Methods for Constraint Handling with Genetic Algorithm

    Science.gov (United States)

    Ortiz, Francisco

    2004-01-01

    COMETBOARDS (Comparative Evaluation Testbed of Optimization and Analysis Routines for Design of Structures) is a design optimization test bed that can evaluate the performance of several different optimization algorithms. A few of these optimization algorithms are the sequence of unconstrained minimization techniques (SUMT), sequential linear programming (SLP) and the sequential quadratic programming techniques (SQP). A genetic algorithm (GA) is a search technique that is based on the principles of natural selection or "survival of the fittest". Instead of using gradient information, the GA uses the objective function directly in the search. The GA searches the solution space by maintaining a population of potential solutions. Then, using evolving operations such as recombination, mutation and selection, the GA creates successive generations of solutions that will evolve and take on the positive characteristics of their parents and thus gradually approach optimal or near-optimal solutions. By using the objective function directly in the search, genetic algorithms can be effectively applied in non-convex, highly nonlinear, complex problems. The genetic algorithm is not guaranteed to find the global optimum, but it is less likely to get trapped at a local optimum than traditional gradient-based search methods when the objective function is not smooth and generally well behaved. The purpose of this research is to assist in the integration of genetic algorithm (GA) into COMETBOARDS. COMETBOARDS cast the design of structures as a constrained nonlinear optimization problem. One method used to solve constrained optimization problem with a GA to convert the constrained optimization problem into an unconstrained optimization problem by developing a penalty function that penalizes infeasible solutions. There have been several suggested penalty function in the literature each with there own strengths and weaknesses. A statistical analysis of some suggested penalty functions

  18. Ringed Seal Search for Global Optimization via a Sensitive Search Model.

    Science.gov (United States)

    Saadi, Younes; Yanto, Iwan Tri Riyadi; Herawan, Tutut; Balakrishnan, Vimala; Chiroma, Haruna; Risnumawan, Anhar

    2016-01-01

    The efficiency of a metaheuristic algorithm for global optimization is based on its ability to search and find the global optimum. However, a good search often requires to be balanced between exploration and exploitation of the search space. In this paper, a new metaheuristic algorithm called Ringed Seal Search (RSS) is introduced. It is inspired by the natural behavior of the seal pup. This algorithm mimics the seal pup movement behavior and its ability to search and choose the best lair to escape predators. The scenario starts once the seal mother gives birth to a new pup in a birthing lair that is constructed for this purpose. The seal pup strategy consists of searching and selecting the best lair by performing a random walk to find a new lair. Affected by the sensitive nature of seals against external noise emitted by predators, the random walk of the seal pup takes two different search states, normal state and urgent state. In the normal state, the pup performs an intensive search between closely adjacent lairs; this movement is modeled via a Brownian walk. In an urgent state, the pup leaves the proximity area and performs an extensive search to find a new lair from sparse targets; this movement is modeled via a Levy walk. The switch between these two states is realized by the random noise emitted by predators. The algorithm keeps switching between normal and urgent states until the global optimum is reached. Tests and validations were performed using fifteen benchmark test functions to compare the performance of RSS with other baseline algorithms. The results show that RSS is more efficient than Genetic Algorithm, Particles Swarm Optimization and Cuckoo Search in terms of convergence rate to the global optimum. The RSS shows an improvement in terms of balance between exploration (extensive) and exploitation (intensive) of the search space. The RSS can efficiently mimic seal pups behavior to find best lair and provide a new algorithm to be used in global

  19. Control of Disease Induced by Tospoviruses in Tomato: An Update of the Genetic Approach

    Directory of Open Access Journals (Sweden)

    J. Cebolla-Cornejo

    2003-12-01

    Full Text Available Advances in the search for genetic resistance to tospoviruses affecting tomato crops are reviewed. The economic losses caused by Tomato spotted wilt tospovirus (TSWV, the great number of hosts it affects and its wide distribution around the world has made TSWV one of the ten most important plant viruses. Other viruses in or related to the same genus also cause severe damage, although their presence in the world is much more localized. Due to the limited effectiveness of physical, chemical and biological control methods, the use of genetic resistance for control is the best management strategy on a medium-long term basis. Given the relative ease with which new TSWV isolates that overcome existing genetic resistance are generated, it is of prime importance to continue the search for new sources of resistance, as well as to promote a better exploitation of available ones. A better understanding of the mechanisms causing resistance and of their genetic control, as well as the identification of molecular markers linked to resistance genes, would enable the pyramiding of different resistance genes. This would be a positive contribution to the development of a greater and more durable resistance. It is also necessary to further the study of genetic resistance to other viruses of the genus Tospovirus, as globalisation can speed up their distribution throughout the world.

  20. Search and rescue in Alaska's national parks.

    Science.gov (United States)

    Heggie, Travis W

    2008-11-01

    Recreational travel to wilderness destinations such as national parks is increasing. The inherent risks present in such destinations can result in injury and illness, have a significant impact on local medical resources, and end with expensive search and rescue operations. In order to increase our understanding of the activities and situations which lead to wilderness search and rescue incidents, this study examines search and rescue operations from National Park Service units in Alaska. A retrospective review of all search and rescue incident reports filed by National Park Service units in Alaska during 2002. During 2002 there were 25 reported search and rescue incidents involving 38 individuals. The majority of incidents (19 of 25) occurred at Denali National Park and Preserve. Thirteen fatalities were reported in six incidents, nine incidents involved traumatic injuries, eight involved illnesses, and two involved both injuries and an illness. Mountain climbing (20) and hiking (8) were the most common subject activities at the time search and rescue assistance was required. Climbing solo (4), uneven and wet terrain (4), falls into crevasses (3), and a lack of experience or ability (3) were the factors most commonly contributing to search and rescue incidents. Nineteen helicopters were utilized in 15 operations and fixed-wing aircraft were utilized in seven operations. Males accounted for 33 of the 38 individuals involved in all search and rescue incidents and United States citizens accounted for 74% of the individuals involved. The mountain environment higher than 4500m was the most common search and rescue environment (11). The average cost was USD $6253. Search and rescue operations in Alaska can be expensive and end with severe health consequences. Preventive education efforts at park visitor centers and at the lower and upper base camps on Mt. McKinley should be continued. In addition, pre-departure travel education efforts via the internet should be expanded

  1. Genetic Mapping

    Science.gov (United States)

    ... Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for Teachers Genomic ... genetic mapping? Among the main goals of the Human Genome Project (HGP) was to develop new, better and cheaper ...

  2. Genetic Disorders

    Science.gov (United States)

    ... This can cause a medical condition called a genetic disorder. You can inherit a gene mutation from ... during your lifetime. There are three types of genetic disorders: Single-gene disorders, where a mutation affects ...

  3. Genetic Testing

    Science.gov (United States)

    ... risk factor for the development of celiac disease, genetic predisposition. Without this factor, it is impossible that the ... with antibody testing in the future. When the genetic predisposition for celiac disease was detected (on Chromosome 6) ...

  4. Genetic counseling

    Science.gov (United States)

    ... have a high risk of having babies with Tay-Sachs or Canavan's disease. African-Americans, who may risk ... yours to make. Images Genetic counseling and prenatal diagnosis References Simpson JL, Holzgreve W, Driscoll DA. Genetic ...

  5. Forecasting nonlinear chaotic time series with function expression method based on an improved genetic-simulated annealing algorithm.

    Science.gov (United States)

    Wang, Jun; Zhou, Bi-hua; Zhou, Shu-dao; Sheng, Zheng

    2015-01-01

    The paper proposes a novel function expression method to forecast chaotic time series, using an improved genetic-simulated annealing (IGSA) algorithm to establish the optimum function expression that describes the behavior of time series. In order to deal with the weakness associated with the genetic algorithm, the proposed algorithm incorporates the simulated annealing operation which has the strong local search ability into the genetic algorithm to enhance the performance of optimization; besides, the fitness function and genetic operators are also improved. Finally, the method is applied to the chaotic time series of Quadratic and Rossler maps for validation. The effect of noise in the chaotic time series is also studied numerically. The numerical results verify that the method can forecast chaotic time series with high precision and effectiveness, and the forecasting precision with certain noise is also satisfactory. It can be concluded that the IGSA algorithm is energy-efficient and superior.

  6. Black-Box Search by Unbiased Variation

    DEFF Research Database (Denmark)

    Lehre, Per Kristian; Witt, Carsten

    2012-01-01

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

  7. Genetic risk

    OpenAIRE

    ten Kate, Leo P.

    2012-01-01

    In this paper I will review different aspects of genetic risk in the context of preconception care. I restrict myself to the knowledge of risk which is relevant for care and/or enables reproductive choice. The paper deals with chromosomes, genes and the genetic classification of diseases, and it explains why Mendelian disorders frequently do not show the expected pattern of occurrence in families. Factors that amplify genetic risk are also discussed. Of the two methods of genetic risk assessm...

  8. Imaging Genetics

    Science.gov (United States)

    Munoz, Karen E.; Hyde, Luke W.; Hariri, Ahmad R.

    2009-01-01

    Imaging genetics is an experimental strategy that integrates molecular genetics and neuroimaging technology to examine biological mechanisms that mediate differences in behavior and the risks for psychiatric disorder. The basic principles in imaging genetics and the development of the field are discussed.

  9. Deceptiveness and genetic algorithm dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Liepins, G.E. (Oak Ridge National Lab., TN (USA)); Vose, M.D. (Tennessee Univ., Knoxville, TN (USA))

    1990-01-01

    We address deceptiveness, one of at least four reasons genetic algorithms can fail to converge to function optima. We construct fully deceptive functions and other functions of intermediate deceptiveness. For the fully deceptive functions of our construction, we generate linear transformations that induce changes of representation to render the functions fully easy. We further model genetic algorithm selection recombination as the interleaving of linear and quadratic operators. Spectral analysis of the underlying matrices allows us to draw preliminary conclusions about fixed points and their stability. We also obtain an explicit formula relating the nonuniform Walsh transform to the dynamics of genetic search. 21 refs.

  10. A novel pseudoderivative-based mutation operator for real-coded adaptive genetic algorithms [v2; ref status: indexed, http://f1000r.es/1td

    Directory of Open Access Journals (Sweden)

    Maxinder S Kanwal

    2013-11-01

    Full Text Available Recent development of large databases, especially those in genetics and proteomics, is pushing the development of novel computational algorithms that implement rapid and accurate search strategies. One successful approach has been to use artificial intelligence and methods, including pattern recognition (e.g. neural networks and optimization techniques (e.g. genetic algorithms. The focus of this paper is on optimizing the design of genetic algorithms by using an adaptive mutation rate that is derived from comparing the fitness values of successive generations. We propose a novel pseudoderivative-based mutation rate operator designed to allow a genetic algorithm to escape local optima and successfully continue to the global optimum. Once proven successful, this algorithm can be implemented to solve real problems in neurology and bioinformatics. As a first step towards this goal, we tested our algorithm on two 3-dimensional surfaces with multiple local optima, but only one global optimum, as well as on the N-queens problem, an applied problem in which the function that maps the curve is implicit. For all tests, the adaptive mutation rate allowed the genetic algorithm to find the global optimal solution, performing significantly better than other search methods, including genetic algorithms that implement fixed mutation rates.

  11. Utilization of a radiology-centric search engine.

    Science.gov (United States)

    Sharpe, Richard E; Sharpe, Megan; Siegel, Eliot; Siddiqui, Khan

    2010-04-01

    Internet-based search engines have become a significant component of medical practice. Physicians increasingly rely on information available from search engines as a means to improve patient care, provide better education, and enhance research. Specialized search engines have emerged to more efficiently meet the needs of physicians. Details about the ways in which radiologists utilize search engines have not been documented. The authors categorized every 25th search query in a radiology-centric vertical search engine by radiologic subspecialty, imaging modality, geographic location of access, time of day, use of abbreviations, misspellings, and search language. Musculoskeletal and neurologic imagings were the most frequently searched subspecialties. The least frequently searched were breast imaging, pediatric imaging, and nuclear medicine. Magnetic resonance imaging and computed tomography were the most frequently searched modalities. A majority of searches were initiated in North America, but all continents were represented. Searches occurred 24 h/day in converted local times, with a majority occurring during the normal business day. Misspellings and abbreviations were common. Almost all searches were performed in English. Search engine utilization trends are likely to mirror trends in diagnostic imaging in the region from which searches originate. Internet searching appears to function as a real-time clinical decision-making tool, a research tool, and an educational resource. A more thorough understanding of search utilization patterns can be obtained by analyzing phrases as actually entered as well as the geographic location and time of origination. This knowledge may contribute to the development of more efficient and personalized search engines.

  12. Backtrack Orbit Search Algorithm

    Science.gov (United States)

    Knowles, K.; Swick, R.

    2002-12-01

    A Mathematical Solution to a Mathematical Problem. With the dramatic increase in satellite-born sensor resolution traditional methods of spatially searching for orbital data have become inadequate. As data volumes increase end-users of the data have become increasingly intolerant of false positives. And, as computing power rapidly increases end-users have come to expect equally rapid search speeds. Meanwhile data archives have an interest in delivering the minimum amount of data that meets users' needs. This keeps their costs down and allows them to serve more users in a more timely manner. Many methods of spatial search for orbital data have been tried in the past and found wanting. The ever popular lat/lon bounding box on a flat Earth is highly inaccurate. Spatial search based on nominal "orbits" is somewhat more accurate at much higher implementation cost and slower performance. Spatial search of orbital data based on predict orbit models are very accurate at a much higher maintenance cost and slower performance. This poster describes the Backtrack Orbit Search Algorithm--an alternative spatial search method for orbital data. Backtrack has a degree of accuracy that rivals predict methods while being faster, less costly to implement, and less costly to maintain than other methods.

  13. Skewed Binary Search Trees

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Moruz, Gabriel

    2006-01-01

    It is well-known that to minimize the number of comparisons a binary search tree should be perfectly balanced. Previous work has shown that a dominating factor over the running time for a search is the number of cache faults performed, and that an appropriate memory layout of a binary search tree...... can reduce the number of cache faults by several hundred percent. Motivated by the fact that during a search branching to the left or right at a node does not necessarily have the same cost, e.g. because of branch prediction schemes, we in this paper study the class of skewed binary search trees....... For all nodes in a skewed binary search tree the ratio between the size of the left subtree and the size of the tree is a fixed constant (a ratio of 1/2 gives perfect balanced trees). In this paper we present an experimental study of various memory layouts of static skewed binary search trees, where each...

  14. Generalised Adaptive Harmony Search: A Comparative Analysis of Modern Harmony Search

    Directory of Open Access Journals (Sweden)

    Jaco Fourie

    2013-01-01

    Full Text Available Harmony search (HS was introduced in 2001 as a heuristic population-based optimisation algorithm. Since then HS has become a popular alternative to other heuristic algorithms like simulated annealing and particle swarm optimisation. However, some flaws, like the need for parameter tuning, were identified and have been a topic of study for much research over the last 10 years. Many variants of HS were developed to address some of these flaws, and most of them have made substantial improvements. In this paper we compare the performance of three recent HS variants: exploratory harmony search, self-adaptive harmony search, and dynamic local-best harmony search. We compare the accuracy of these algorithms, using a set of well-known optimisation benchmark functions that include both unimodal and multimodal problems. Observations from this comparison led us to design a novel hybrid that combines the best attributes of these modern variants into a single optimiser called generalised adaptive harmony search.

  15. How Users Search the Library from a Single Search Box

    Science.gov (United States)

    Lown, Cory; Sierra, Tito; Boyer, Josh

    2013-01-01

    Academic libraries are turning increasingly to unified search solutions to simplify search and discovery of library resources. Unfortunately, very little research has been published on library user search behavior in single search box environments. This study examines how users search a large public university library using a prominent, single…

  16. A Hybrid Intelligent Search Algorithm for Automatic Test Data Generation

    Directory of Open Access Journals (Sweden)

    Ying Xing

    2015-01-01

    Full Text Available The increasing complexity of large-scale real-world programs necessitates the automation of software testing. As a basic problem in software testing, the automation of path-wise test data generation is especially important, which is in essence a constraint optimization problem solved by search strategies. Therefore, the constraint processing efficiency of the selected search algorithm is a key factor. Aiming at the increase of search efficiency, a hybrid intelligent algorithm is proposed to efficiently search the solution space of potential test data by making full use of both global and local search methods. Branch and bound is adopted for global search, which gives definite results with relatively less cost. In the search procedure for each variable, hill climbing is adopted for local search, which is enhanced with the initial values selected heuristically based on the monotonicity analysis of branching conditions. They are highly integrated by an efficient ordering method and the backtracking operation. In order to facilitate the search methods, the solution space is represented as state space. Experimental results show that the proposed method outperformed some other methods used in test data generation. The heuristic initial value selection strategy improves the search efficiency greatly and makes the search basically backtrack-free. The results also demonstrate that the proposed method is applicable in engineering.

  17. Entropy, Search, Complexity

    CERN Document Server

    Katona, Gyula O H; Tardos, Gábor

    2007-01-01

    The present volume is a collection of survey papers in the fields of entropy, search and complexity. They summarize the latest developments in their respective areas. More than half of the papers belong to search theory which lies on the borderline of mathematics and computer science, information theory and combinatorics, respectively. Search theory has variegated applications, among others in bioinformatics. Some of these papers also have links to linear statistics and communicational complexity. Further works survey the fundamentals of information theory and quantum source coding. The volume is recommended to experienced researchers as well as young scientists and students both in mathematics and computer science

  18. ElasticSearch server

    CERN Document Server

    Rogozinski, Marek

    2014-01-01

    This book is a detailed, practical, hands-on guide packed with real-life scenarios and examples which will show you how to implement an ElasticSearch search engine on your own websites.If you are a web developer or a user who wants to learn more about ElasticSearch, then this is the book for you. You do not need to know anything about ElastiSeach, Java, or Apache Lucene in order to use this book, though basic knowledge about databases and queries is required.

  19. Search for disappearing tracks

    CERN Document Server

    INSPIRE-00024550

    2015-01-01

    We present a search for long-lived charged particles that decay within the CMS detector and produce the signature of a disappearing track. Disappearing tracks are identified as those with little or no associated calorimeter energy deposits and with missing hits in the outer layers of the tracker. The search uses proton-proton collision data recorded at $\\sqrt{s} = 8$ TeV that corresponds to an integrated luminosity of 19.5 fb$^{-1}$. The results of the search are interpreted in the context of the anomaly-mediated supersymmetry breaking model and in terms of the phenomenological MSSM.

  20. Magnetic monopole search experiments

    International Nuclear Information System (INIS)

    Stone, J.L.

    1986-01-01

    Experimental searches for the elusive magnetic monopole have extended over 50 years -- ever since Dirac showed that the existence of isolated magnetic charges could account for the observation of quantized electric charge. Early searches for Dirac's monopole were hampered since there was no indication of the expected monopole mass, velocity, or origin in the theory. Consequently, numerous experiments searched more or less blindly for relativistic low mass monopoles in the cosmic rays and in particle collisions at high energy accelerators. In this paper, the author reviews briefly the monopole properties which are relevant for their detection and summarize current experimental efforts using induction, ionization/excitation, and catalysis techniques