WorldWideScience

Sample records for maximum parsimony neighbor-joining

  1. Maximum Parsimony on Phylogenetic networks

    Science.gov (United States)

    2012-01-01

    Background Phylogenetic networks are generalizations of phylogenetic trees, that are used to model evolutionary events in various contexts. Several different methods and criteria have been introduced for reconstructing phylogenetic trees. Maximum Parsimony is a character-based approach that infers a phylogenetic tree by minimizing the total number of evolutionary steps required to explain a given set of data assigned on the leaves. Exact solutions for optimizing parsimony scores on phylogenetic trees have been introduced in the past. Results In this paper, we define the parsimony score on networks as the sum of the substitution costs along all the edges of the network; and show that certain well-known algorithms that calculate the optimum parsimony score on trees, such as Sankoff and Fitch algorithms extend naturally for networks, barring conflicting assignments at the reticulate vertices. We provide heuristics for finding the optimum parsimony scores on networks. Our algorithms can be applied for any cost matrix that may contain unequal substitution costs of transforming between different characters along different edges of the network. We analyzed this for experimental data on 10 leaves or fewer with at most 2 reticulations and found that for almost all networks, the bounds returned by the heuristics matched with the exhaustively determined optimum parsimony scores. Conclusion The parsimony score we define here does not directly reflect the cost of the best tree in the network that displays the evolution of the character. However, when searching for the most parsimonious network that describes a collection of characters, it becomes necessary to add additional cost considerations to prefer simpler structures, such as trees over networks. The parsimony score on a network that we describe here takes into account the substitution costs along the additional edges incident on each reticulate vertex, in addition to the substitution costs along the other edges which are

  2. Approximate maximum parsimony and ancestral maximum likelihood.

    Science.gov (United States)

    Alon, Noga; Chor, Benny; Pardi, Fabio; Rapoport, Anat

    2010-01-01

    We explore the maximum parsimony (MP) and ancestral maximum likelihood (AML) criteria in phylogenetic tree reconstruction. Both problems are NP-hard, so we seek approximate solutions. We formulate the two problems as Steiner tree problems under appropriate distances. The gist of our approach is the succinct characterization of Steiner trees for a small number of leaves for the two distances. This enables the use of known Steiner tree approximation algorithms. The approach leads to a 16/9 approximation ratio for AML and asymptotically to a 1.55 approximation ratio for MP.

  3. Improved Maximum Parsimony Models for Phylogenetic Networks.

    Science.gov (United States)

    Van Iersel, Leo; Jones, Mark; Scornavacca, Celine

    2018-05-01

    Phylogenetic networks are well suited to represent evolutionary histories comprising reticulate evolution. Several methods aiming at reconstructing explicit phylogenetic networks have been developed in the last two decades. In this article, we propose a new definition of maximum parsimony for phylogenetic networks that permits to model biological scenarios that cannot be modeled by the definitions currently present in the literature (namely, the "hardwired" and "softwired" parsimony). Building on this new definition, we provide several algorithmic results that lay the foundations for new parsimony-based methods for phylogenetic network reconstruction.

  4. Maximum parsimony on subsets of taxa.

    Science.gov (United States)

    Fischer, Mareike; Thatte, Bhalchandra D

    2009-09-21

    In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular, we consider the question whether the maximum parsimony method applied to a subset of taxa can reconstruct the ancestral state of the root more accurately than when applied to all taxa, and we give an example showing that this indeed is possible. A surprising feature of our example is that ignoring a taxon closer to the root improves the reliability of the method. On the other hand, in the case of the two-state symmetric substitution model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that under a molecular clock the probability that the state at a single taxon is a correct guess of the ancestral state is a lower bound on the reconstruction accuracy of Fitch's method applied to all taxa.

  5. The worst case complexity of maximum parsimony.

    Science.gov (United States)

    Carmel, Amir; Musa-Lempel, Noa; Tsur, Dekel; Ziv-Ukelson, Michal

    2014-11-01

    One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related organisms. We reexamine the classical maximum parsimony (MP) optimization problem for the general (asymmetric) scoring matrix case, where rooted phylogenies are implied, and analyze the worst case bounds of three approaches to MP: The approach of Cavalli-Sforza and Edwards, the approach of Hendy and Penny, and a new agglomerative, "bottom-up" approach we present in this article. We show that the second and third approaches are faster than the first one by a factor of Θ(√n) and Θ(n), respectively, where n is the number of species.

  6. Ancestral sequence reconstruction with Maximum Parsimony

    OpenAIRE

    Herbst, Lina; Fischer, Mareike

    2017-01-01

    One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference as well as for ancestral sequence inference is Maximum Parsimony (...

  7. Recrafting the Neighbor-Joining Method

    DEFF Research Database (Denmark)

    Mailund; Brodal, Gerth Stølting; Fagerberg, Rolf

    2006-01-01

    Background: The neighbor-joining method by Saitou and Nei is a widely used method for constructing phylogenetic trees. The formulation of the method gives rise to a canonical Θ(n3) algorithm upon which all existing implementations are based. Methods: In this paper we present techniques for speeding...... up the canonical neighbor-joining method. Our algorithms construct the same phylogenetic trees as the canonical neighbor-joining method. The best-case running time of our algorithms are O(n2) but the worst-case remains O(n3). We empirically evaluate the performance of our algoritms on distance...... matrices obtained from the Pfam collection of alignments. Results: The experiments indicate that the running time of our algorithms evolve as Θ(n2) on the examined instance collection. We also compare the running time with that of the QuickTree tool, a widely used efficient implementation of the canonical...

  8. Recrafting the neighbor-joining method

    Directory of Open Access Journals (Sweden)

    Pedersen Christian NS

    2006-01-01

    Full Text Available Abstract Background The neighbor-joining method by Saitou and Nei is a widely used method for constructing phylogenetic trees. The formulation of the method gives rise to a canonical Θ(n3 algorithm upon which all existing implementations are based. Results In this paper we present techniques for speeding up the canonical neighbor-joining method. Our algorithms construct the same phylogenetic trees as the canonical neighbor-joining method. The best-case running time of our algorithms are O(n2 but the worst-case remains O(n3. We empirically evaluate the performance of our algoritms on distance matrices obtained from the Pfam collection of alignments. The experiments indicate that the running time of our algorithms evolve as Θ(n2 on the examined instance collection. We also compare the running time with that of the QuickTree tool, a widely used efficient implementation of the canonical neighbor-joining method. Conclusion The experiments show that our algorithms also yield a significant speed-up, already for medium sized instances.

  9. Ancestral Sequence Reconstruction with Maximum Parsimony.

    Science.gov (United States)

    Herbst, Lina; Fischer, Mareike

    2017-12-01

    One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference and for ancestral sequence inference is Maximum Parsimony (MP). In this manuscript, we focus on this method and on ancestral state inference for fully bifurcating trees. In particular, we investigate a conjecture published by Charleston and Steel in 1995 concerning the number of species which need to have a particular state, say a, at a particular site in order for MP to unambiguously return a as an estimate for the state of the last common ancestor. We prove the conjecture for all even numbers of character states, which is the most relevant case in biology. We also show that the conjecture does not hold in general for odd numbers of character states, but also present some positive results for this case.

  10. Reconstructing phylogenetic networks using maximum parsimony.

    Science.gov (United States)

    Nakhleh, Luay; Jin, Guohua; Zhao, Fengmei; Mellor-Crummey, John

    2005-01-01

    Phylogenies - the evolutionary histories of groups of organisms - are one of the most widely used tools throughout the life sciences, as well as objects of research within systematics, evolutionary biology, epidemiology, etc. Almost every tool devised to date to reconstruct phylogenies produces trees; yet it is widely understood and accepted that trees oversimplify the evolutionary histories of many groups of organims, most prominently bacteria (because of horizontal gene transfer) and plants (because of hybrid speciation). Various methods and criteria have been introduced for phylogenetic tree reconstruction. Parsimony is one of the most widely used and studied criteria, and various accurate and efficient heuristics for reconstructing trees based on parsimony have been devised. Jotun Hein suggested a straightforward extension of the parsimony criterion to phylogenetic networks. In this paper we formalize this concept, and provide the first experimental study of the quality of parsimony as a criterion for constructing and evaluating phylogenetic networks. Our results show that, when extended to phylogenetic networks, the parsimony criterion produces promising results. In a great majority of the cases in our experiments, the parsimony criterion accurately predicts the numbers and placements of non-tree events.

  11. Direct maximum parsimony phylogeny reconstruction from genotype data

    OpenAIRE

    Sridhar, Srinath; Lam, Fumei; Blelloch, Guy E; Ravi, R; Schwartz, Russell

    2007-01-01

    Abstract Background Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of ge...

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

    OpenAIRE

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

    2013-01-01

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

  13. Direct maximum parsimony phylogeny reconstruction from genotype data.

    Science.gov (United States)

    Sridhar, Srinath; Lam, Fumei; Blelloch, Guy E; Ravi, R; Schwartz, Russell

    2007-12-05

    Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes. In this work, we develop the first practical method for computing maximum parsimony phylogenies directly from genotype data. We show that the standard practice of first inferring haplotypes from genotypes and then reconstructing a phylogeny on the haplotypes often substantially overestimates phylogeny size. As an immediate application, our method can be used to determine the minimum number of mutations required to explain a given set of observed genotypes. Phylogeny reconstruction directly from unphased data is computationally feasible for moderate-sized problem instances and can lead to substantially more accurate tree size inferences than the standard practice of treating phasing and phylogeny construction as two separate analysis stages. The difference between the approaches is particularly important for downstream applications that require a lower-bound on the number of mutations that the genetic region has undergone.

  14. MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation.

    Science.gov (United States)

    Hoang, Diep Thi; Vinh, Le Sy; Flouri, Tomáš; Stamatakis, Alexandros; von Haeseler, Arndt; Minh, Bui Quang

    2018-02-02

    The nonparametric bootstrap is widely used to measure the branch support of phylogenetic trees. However, bootstrapping is computationally expensive and remains a bottleneck in phylogenetic analyses. Recently, an ultrafast bootstrap approximation (UFBoot) approach was proposed for maximum likelihood analyses. However, such an approach is still missing for maximum parsimony. To close this gap we present MPBoot, an adaptation and extension of UFBoot to compute branch supports under the maximum parsimony principle. MPBoot works for both uniform and non-uniform cost matrices. Our analyses on biological DNA and protein showed that under uniform cost matrices, MPBoot runs on average 4.7 (DNA) to 7 times (protein data) (range: 1.2-20.7) faster than the standard parsimony bootstrap implemented in PAUP*; but 1.6 (DNA) to 4.1 times (protein data) slower than the standard bootstrap with a fast search routine in TNT (fast-TNT). However, for non-uniform cost matrices MPBoot is 5 (DNA) to 13 times (protein data) (range:0.3-63.9) faster than fast-TNT. We note that MPBoot achieves better scores more frequently than PAUP* and fast-TNT. However, this effect is less pronounced if an intensive but slower search in TNT is invoked. Moreover, experiments on large-scale simulated data show that while both PAUP* and TNT bootstrap estimates are too conservative, MPBoot bootstrap estimates appear more unbiased. MPBoot provides an efficient alternative to the standard maximum parsimony bootstrap procedure. It shows favorable performance in terms of run time, the capability of finding a maximum parsimony tree, and high bootstrap accuracy on simulated as well as empirical data sets. MPBoot is easy-to-use, open-source and available at http://www.cibiv.at/software/mpboot .

  15. Direct maximum parsimony phylogeny reconstruction from genotype data

    Directory of Open Access Journals (Sweden)

    Ravi R

    2007-12-01

    Full Text Available Abstract Background Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes. Results In this work, we develop the first practical method for computing maximum parsimony phylogenies directly from genotype data. We show that the standard practice of first inferring haplotypes from genotypes and then reconstructing a phylogeny on the haplotypes often substantially overestimates phylogeny size. As an immediate application, our method can be used to determine the minimum number of mutations required to explain a given set of observed genotypes. Conclusion Phylogeny reconstruction directly from unphased data is computationally feasible for moderate-sized problem instances and can lead to substantially more accurate tree size inferences than the standard practice of treating phasing and phylogeny construction as two separate analysis stages. The difference between the approaches is particularly important for downstream applications that require a lower-bound on the number of mutations that the genetic region has undergone.

  16. Bootstrap-based Support of HGT Inferred by Maximum Parsimony

    Directory of Open Access Journals (Sweden)

    Nakhleh Luay

    2010-05-01

    Full Text Available Abstract Background Maximum parsimony is one of the most commonly used criteria for reconstructing phylogenetic trees. Recently, Nakhleh and co-workers extended this criterion to enable reconstruction of phylogenetic networks, and demonstrated its application to detecting reticulate evolutionary relationships. However, one of the major problems with this extension has been that it favors more complex evolutionary relationships over simpler ones, thus having the potential for overestimating the amount of reticulation in the data. An ad hoc solution to this problem that has been used entails inspecting the improvement in the parsimony length as more reticulation events are added to the model, and stopping when the improvement is below a certain threshold. Results In this paper, we address this problem in a more systematic way, by proposing a nonparametric bootstrap-based measure of support of inferred reticulation events, and using it to determine the number of those events, as well as their placements. A number of samples is generated from the given sequence alignment, and reticulation events are inferred based on each sample. Finally, the support of each reticulation event is quantified based on the inferences made over all samples. Conclusions We have implemented our method in the NEPAL software tool (available publicly at http://bioinfo.cs.rice.edu/, and studied its performance on both biological and simulated data sets. While our studies show very promising results, they also highlight issues that are inherently challenging when applying the maximum parsimony criterion to detect reticulate evolution.

  17. Bootstrap-based support of HGT inferred by maximum parsimony.

    Science.gov (United States)

    Park, Hyun Jung; Jin, Guohua; Nakhleh, Luay

    2010-05-05

    Maximum parsimony is one of the most commonly used criteria for reconstructing phylogenetic trees. Recently, Nakhleh and co-workers extended this criterion to enable reconstruction of phylogenetic networks, and demonstrated its application to detecting reticulate evolutionary relationships. However, one of the major problems with this extension has been that it favors more complex evolutionary relationships over simpler ones, thus having the potential for overestimating the amount of reticulation in the data. An ad hoc solution to this problem that has been used entails inspecting the improvement in the parsimony length as more reticulation events are added to the model, and stopping when the improvement is below a certain threshold. In this paper, we address this problem in a more systematic way, by proposing a nonparametric bootstrap-based measure of support of inferred reticulation events, and using it to determine the number of those events, as well as their placements. A number of samples is generated from the given sequence alignment, and reticulation events are inferred based on each sample. Finally, the support of each reticulation event is quantified based on the inferences made over all samples. We have implemented our method in the NEPAL software tool (available publicly at http://bioinfo.cs.rice.edu/), and studied its performance on both biological and simulated data sets. While our studies show very promising results, they also highlight issues that are inherently challenging when applying the maximum parsimony criterion to detect reticulate evolution.

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

    Directory of Open Access Journals (Sweden)

    Ivan Gregor

    2013-06-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

  20. Mixed integer linear programming for maximum-parsimony phylogeny inference.

    Science.gov (United States)

    Sridhar, Srinath; Lam, Fumei; Blelloch, Guy E; Ravi, R; Schwartz, Russell

    2008-01-01

    Reconstruction of phylogenetic trees is a fundamental problem in computational biology. While excellent heuristic methods are available for many variants of this problem, new advances in phylogeny inference will be required if we are to be able to continue to make effective use of the rapidly growing stores of variation data now being gathered. In this paper, we present two integer linear programming (ILP) formulations to find the most parsimonious phylogenetic tree from a set of binary variation data. One method uses a flow-based formulation that can produce exponential numbers of variables and constraints in the worst case. The method has, however, proven extremely efficient in practice on datasets that are well beyond the reach of the available provably efficient methods, solving several large mtDNA and Y-chromosome instances within a few seconds and giving provably optimal results in times competitive with fast heuristics than cannot guarantee optimality. An alternative formulation establishes that the problem can be solved with a polynomial-sized ILP. We further present a web server developed based on the exponential-sized ILP that performs fast maximum parsimony inferences and serves as a front end to a database of precomputed phylogenies spanning the human genome.

  1. Maximum parsimony, substitution model, and probability phylogenetic trees.

    Science.gov (United States)

    Weng, J F; Thomas, D A; Mareels, I

    2011-01-01

    The problem of inferring phylogenies (phylogenetic trees) is one of the main problems in computational biology. There are three main methods for inferring phylogenies-Maximum Parsimony (MP), Distance Matrix (DM) and Maximum Likelihood (ML), of which the MP method is the most well-studied and popular method. In the MP method the optimization criterion is the number of substitutions of the nucleotides computed by the differences in the investigated nucleotide sequences. However, the MP method is often criticized as it only counts the substitutions observable at the current time and all the unobservable substitutions that really occur in the evolutionary history are omitted. In order to take into account the unobservable substitutions, some substitution models have been established and they are now widely used in the DM and ML methods but these substitution models cannot be used within the classical MP method. Recently the authors proposed a probability representation model for phylogenetic trees and the reconstructed trees in this model are called probability phylogenetic trees. One of the advantages of the probability representation model is that it can include a substitution model to infer phylogenetic trees based on the MP principle. In this paper we explain how to use a substitution model in the reconstruction of probability phylogenetic trees and show the advantage of this approach with examples.

  2. On the quirks of maximum parsimony and likelihood on phylogenetic networks.

    Science.gov (United States)

    Bryant, Christopher; Fischer, Mareike; Linz, Simone; Semple, Charles

    2017-03-21

    Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe evolution accurately. For instance, processes like hybridization or lateral gene transfer that are commonplace in many groups of organisms and result in mosaic patterns of relationships cannot be represented by a single phylogenetic tree. This is why phylogenetic networks, which can display such events, are becoming of more and more interest in phylogenetic research. It is therefore necessary to extend concepts like maximum parsimony from phylogenetic trees to networks. Several suggestions for possible extensions can be found in recent literature, for instance the softwired and the hardwired parsimony concepts. In this paper, we analyze the so-called big parsimony problem under these two concepts, i.e. we investigate maximum parsimonious networks and analyze their properties. In particular, we show that finding a softwired maximum parsimony network is possible in polynomial time. We also show that the set of maximum parsimony networks for the hardwired definition always contains at least one phylogenetic tree. Lastly, we investigate some parallels of parsimony to different likelihood concepts on phylogenetic networks. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Bayesian, Maximum Parsimony and UPGMA Models for Inferring the Phylogenies of Antelopes Using Mitochondrial Markers

    OpenAIRE

    Khan, Haseeb A.; Arif, Ibrahim A.; Bahkali, Ali H.; Al Farhan, Ahmad H.; Al Homaidan, Ali A.

    2008-01-01

    This investigation was aimed to compare the inference of antelope phylogenies resulting from the 16S rRNA, cytochrome-b (cyt-b) and d-loop segments of mitochondrial DNA using three different computational models including Bayesian (BA), maximum parsimony (MP) and unweighted pair group method with arithmetic mean (UPGMA). The respective nucleotide sequences of three Oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) and an out-group (Addax nasomaculatus) were aligned and subjected to B...

  4. On the Quirks of Maximum Parsimony and Likelihood on Phylogenetic Networks

    OpenAIRE

    Bryant, Christopher; Fischer, Mareike; Linz, Simone; Semple, Charles

    2015-01-01

    Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe evolution accurately. For instance, processes like hybridization or lateral gene transfer that are commonplace in many groups of organisms and result in mosaic patterns of relationships cannot be represented by a single phylogenetic tree. This is why phylogene...

  5. FPGA Hardware Acceleration of a Phylogenetic Tree Reconstruction with Maximum Parsimony Algorithm

    OpenAIRE

    BLOCK, Henry; MARUYAMA, Tsutomu

    2017-01-01

    In this paper, we present an FPGA hardware implementation for a phylogenetic tree reconstruction with a maximum parsimony algorithm. We base our approach on a particular stochastic local search algorithm that uses the Progressive Neighborhood and the Indirect Calculation of Tree Lengths method. This method is widely used for the acceleration of the phylogenetic tree reconstruction algorithm in software. In our implementation, we define a tree structure and accelerate the search by parallel an...

  6. MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

    Science.gov (United States)

    Tamura, Koichiro; Peterson, Daniel; Peterson, Nicholas; Stecher, Glen; Nei, Masatoshi; Kumar, Sudhir

    2011-01-01

    Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net. PMID:21546353

  7. Bayesian, maximum parsimony and UPGMA models for inferring the phylogenies of antelopes using mitochondrial markers.

    Science.gov (United States)

    Khan, Haseeb A; Arif, Ibrahim A; Bahkali, Ali H; Al Farhan, Ahmad H; Al Homaidan, Ali A

    2008-10-06

    This investigation was aimed to compare the inference of antelope phylogenies resulting from the 16S rRNA, cytochrome-b (cyt-b) and d-loop segments of mitochondrial DNA using three different computational models including Bayesian (BA), maximum parsimony (MP) and unweighted pair group method with arithmetic mean (UPGMA). The respective nucleotide sequences of three Oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) and an out-group (Addax nasomaculatus) were aligned and subjected to BA, MP and UPGMA models for comparing the topologies of respective phylogenetic trees. The 16S rRNA region possessed the highest frequency of conserved sequences (97.65%) followed by cyt-b (94.22%) and d-loop (87.29%). There were few transitions (2.35%) and none transversions in 16S rRNA as compared to cyt-b (5.61% transitions and 0.17% transversions) and d-loop (11.57% transitions and 1.14% transversions) while comparing the four taxa. All the three mitochondrial segments clearly differentiated the genus Addax from Oryx using the BA or UPGMA models. The topologies of all the gamma-corrected Bayesian trees were identical irrespective of the marker type. The UPGMA trees resulting from 16S rRNA and d-loop sequences were also identical (Oryx dammah grouped with Oryx leucoryx) to Bayesian trees except that the UPGMA tree based on cyt-b showed a slightly different phylogeny (Oryx dammah grouped with Oryx gazella) with a low bootstrap support. However, the MP model failed to differentiate the genus Addax from Oryx. These findings demonstrate the efficiency and robustness of BA and UPGMA methods for phylogenetic analysis of antelopes using mitochondrial markers.

  8. Inferring phylogenetic networks by the maximum parsimony criterion: a case study.

    Science.gov (United States)

    Jin, Guohua; Nakhleh, Luay; Snir, Sagi; Tuller, Tamir

    2007-01-01

    Horizontal gene transfer (HGT) may result in genes whose evolutionary histories disagree with each other, as well as with the species tree. In this case, reconciling the species and gene trees results in a network of relationships, known as the "phylogenetic network" of the set of species. A phylogenetic network that incorporates HGT consists of an underlying species tree that captures vertical inheritance and a set of edges which model the "horizontal" transfer of genetic material. In a series of papers, Nakhleh and colleagues have recently formulated a maximum parsimony (MP) criterion for phylogenetic networks, provided an array of computationally efficient algorithms and heuristics for computing it, and demonstrated its plausibility on simulated data. In this article, we study the performance and robustness of this criterion on biological data. Our findings indicate that MP is very promising when its application is extended to the domain of phylogenetic network reconstruction and HGT detection. In all cases we investigated, the MP criterion detected the correct number of HGT events required to map the evolutionary history of a gene data set onto the species phylogeny. Furthermore, our results indicate that the criterion is robust with respect to both incomplete taxon sampling and the use of different site substitution matrices. Finally, our results show that the MP criterion is very promising in detecting HGT in chimeric genes, whose evolutionary histories are a mix of vertical and horizontal evolution. Besides the performance analysis of MP, our findings offer new insights into the evolution of 4 biological data sets and new possible explanations of HGT scenarios in their evolutionary history.

  9. A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion

    Science.gov (United States)

    2013-01-01

    Background Phylogeny estimation from aligned haplotype sequences has attracted more and more attention in the recent years due to its importance in analysis of many fine-scale genetic data. Its application fields range from medical research, to drug discovery, to epidemiology, to population dynamics. The literature on molecular phylogenetics proposes a number of criteria for selecting a phylogeny from among plausible alternatives. Usually, such criteria can be expressed by means of objective functions, and the phylogenies that optimize them are referred to as optimal. One of the most important estimation criteria is the parsimony which states that the optimal phylogeny T∗for a set H of n haplotype sequences over a common set of variable loci is the one that satisfies the following requirements: (i) it has the shortest length and (ii) it is such that, for each pair of distinct haplotypes hi,hj∈H, the sum of the edge weights belonging to the path from hi to hj in T∗ is not smaller than the observed number of changes between hi and hj. Finding the most parsimonious phylogeny for H involves solving an optimization problem, called the Most Parsimonious Phylogeny Estimation Problem (MPPEP), which is NP-hard in many of its versions. Results In this article we investigate a recent version of the MPPEP that arises when input data consist of single nucleotide polymorphism haplotypes extracted from a population of individuals on a common genomic region. Specifically, we explore the prospects for improving on the implicit enumeration strategy of implicit enumeration strategy used in previous work using a novel problem formulation and a series of strengthening valid inequalities and preliminary symmetry breaking constraints to more precisely bound the solution space and accelerate implicit enumeration of possible optimal phylogenies. We present the basic formulation and then introduce a series of provable valid constraints to reduce the solution space. We then prove

  10. Dirichlet Process Parsimonious Mixtures for clustering

    OpenAIRE

    Chamroukhi, Faicel; Bartcus, Marius; Glotin, Hervé

    2015-01-01

    The parsimonious Gaussian mixture models, which exploit an eigenvalue decomposition of the group covariance matrices of the Gaussian mixture, have shown their success in particular in cluster analysis. Their estimation is in general performed by maximum likelihood estimation and has also been considered from a parametric Bayesian prospective. We propose new Dirichlet Process Parsimonious mixtures (DPPM) which represent a Bayesian nonparametric formulation of these parsimonious Gaussian mixtur...

  11. Maximum Gene-Support Tree

    Directory of Open Access Journals (Sweden)

    Yunfeng Shan

    2008-01-01

    Full Text Available Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced as well as plants that have the fossil-supported true phylogenetic trees available. In this study, we generated single gene trees of seven yeast species as well as single gene trees of nine baculovirus species using all the orthologous genes among the species compared. Homologous genes among seven known plants were used for validation of the finding. Four algorithms—maximum parsimony (MP, minimum evolution (ME, maximum likelihood (ML, and neighbor-joining (NJ—were used. Trees were reconstructed before and after weighting the DNA and protein sequence lengths among genes. Rarely a gene can always generate the “true tree” by all the four algorithms. However, the most frequent gene tree, termed “maximum gene-support tree” (MGS tree, or WMGS tree for the weighted one, in yeasts, baculoviruses, or plants was consistently found to be the “true tree” among the species. The results provide insights into the overall degree of divergence of orthologous genes of the genomes analyzed and suggest the following: 1 The true tree relationship among the species studied is still maintained by the largest group of orthologous genes; 2 There are usually more orthologous genes with higher similarities between genetically closer species than between genetically more distant ones; and 3 The maximum gene-support tree reflects the phylogenetic relationship among species in comparison.

  12. Parsimonious relevance models

    NARCIS (Netherlands)

    Meij, E.; Weerkamp, W.; Balog, K.; de Rijke, M.; Myang, S.-H.; Oard, D.W.; Sebastiani, F.; Chua, T.-S.; Leong, M.-K.

    2008-01-01

    We describe a method for applying parsimonious language models to re-estimate the term probabilities assigned by relevance models. We apply our method to six topic sets from test collections in five different genres. Our parsimonious relevance models (i) improve retrieval effectiveness in terms of

  13. Parsimonious Surface Wave Interferometry

    KAUST Repository

    Li, Jing

    2017-10-24

    To decrease the recording time of a 2D seismic survey from a few days to one hour or less, we present a parsimonious surface-wave interferometry method. Interferometry allows for the creation of a large number of virtual shot gathers from just two reciprocal shot gathers by crosscoherence of trace pairs, where the virtual surface waves can be inverted for the S-wave velocity model by wave-equation dispersion inversion (WD). Synthetic and field data tests suggest that parsimonious wave-equation dispersion inversion (PWD) gives S-velocity tomograms that are comparable to those obtained from a full survey with a shot at each receiver. The limitation of PWD is that the virtual data lose some information so that the resolution of the S-velocity tomogram can be modestly lower than that of the S-velocity tomogram inverted from a conventional survey.

  14. Parsimonious Surface Wave Interferometry

    KAUST Repository

    Li, Jing; Hanafy, Sherif; Schuster, Gerard T.

    2017-01-01

    To decrease the recording time of a 2D seismic survey from a few days to one hour or less, we present a parsimonious surface-wave interferometry method. Interferometry allows for the creation of a large number of virtual shot gathers from just two reciprocal shot gathers by crosscoherence of trace pairs, where the virtual surface waves can be inverted for the S-wave velocity model by wave-equation dispersion inversion (WD). Synthetic and field data tests suggest that parsimonious wave-equation dispersion inversion (PWD) gives S-velocity tomograms that are comparable to those obtained from a full survey with a shot at each receiver. The limitation of PWD is that the virtual data lose some information so that the resolution of the S-velocity tomogram can be modestly lower than that of the S-velocity tomogram inverted from a conventional survey.

  15. Parsimonious refraction interferometry

    KAUST Repository

    Hanafy, Sherif

    2016-09-06

    We present parsimonious refraction interferometry where a densely populated refraction data set can be obtained from just two shot gathers. The assumptions are that the first arrivals are comprised of head waves and direct waves, and a pair of reciprocal shot gathers is recorded over the line of interest. The refraction traveltimes from these reciprocal shot gathers can be picked and decomposed into O(N2) refraction traveltimes generated by N virtual sources, where N is the number of geophones in the 2D survey. This enormous increase in the number of virtual traveltime picks and associated rays, compared to the 2N traveltimes from the two reciprocal shot gathers, allows for increased model resolution and better condition numbers in the normal equations. Also, a reciprocal survey is far less time consuming than a standard refraction survey with a dense distribution of sources.

  16. Parsimonious refraction interferometry

    KAUST Repository

    Hanafy, Sherif; Schuster, Gerard T.

    2016-01-01

    We present parsimonious refraction interferometry where a densely populated refraction data set can be obtained from just two shot gathers. The assumptions are that the first arrivals are comprised of head waves and direct waves, and a pair of reciprocal shot gathers is recorded over the line of interest. The refraction traveltimes from these reciprocal shot gathers can be picked and decomposed into O(N2) refraction traveltimes generated by N virtual sources, where N is the number of geophones in the 2D survey. This enormous increase in the number of virtual traveltime picks and associated rays, compared to the 2N traveltimes from the two reciprocal shot gathers, allows for increased model resolution and better condition numbers in the normal equations. Also, a reciprocal survey is far less time consuming than a standard refraction survey with a dense distribution of sources.

  17. A unifying model of genome evolution under parsimony.

    Science.gov (United States)

    Paten, Benedict; Zerbino, Daniel R; Hickey, Glenn; Haussler, David

    2014-06-19

    Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation. We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double cut and join (DCJ) rearrangements in the presence of duplications. The problem of constructing parsimonious history graphs thus subsumes related maximum parsimony problems in the fields of phylogenetic reconstruction and genome rearrangement. We show that tractable functions can be used to define upper and lower bounds on the minimum number of substitutions and DCJ rearrangements needed to explain any history graph. These bounds become tight for a special type of unambiguous history graph called an ancestral variation graph (AVG), which constrains in its combinatorial structure the number of operations required. We finally demonstrate that for a given history graph G, a finite set of AVGs describe all parsimonious interpretations of G, and this set can be explored with a few sampling moves. This theoretical study describes a model in which the inference of genome rearrangements and phylogeny can be unified under parsimony.

  18. Parsimonious Refraction Interferometry and Tomography

    KAUST Repository

    Hanafy, Sherif; Schuster, Gerard T.

    2017-01-01

    We present parsimonious refraction interferometry and tomography where a densely populated refraction data set can be obtained from two reciprocal and several infill shot gathers. The assumptions are that the refraction arrivals are head waves

  19. Parsimonious Language Models for Information Retrieval

    NARCIS (Netherlands)

    Hiemstra, Djoerd; Robertson, Stephen; Zaragoza, Hugo

    We systematically investigate a new approach to estimating the parameters of language models for information retrieval, called parsimonious language models. Parsimonious language models explicitly address the relation between levels of language models that are typically used for smoothing. As such,

  20. Phylogenetic analysis using parsimony and likelihood methods.

    Science.gov (United States)

    Yang, Z

    1996-02-01

    The assumptions underlying the maximum-parsimony (MP) method of phylogenetic tree reconstruction were intuitively examined by studying the way the method works. Computer simulations were performed to corroborate the intuitive examination. Parsimony appears to involve very stringent assumptions concerning the process of sequence evolution, such as constancy of substitution rates between nucleotides, constancy of rates across nucleotide sites, and equal branch lengths in the tree. For practical data analysis, the requirement of equal branch lengths means similar substitution rates among lineages (the existence of an approximate molecular clock), relatively long interior branches, and also few species in the data. However, a small amount of evolution is neither a necessary nor a sufficient requirement of the method. The difficulties involved in the application of current statistical estimation theory to tree reconstruction were discussed, and it was suggested that the approach proposed by Felsenstein (1981, J. Mol. Evol. 17: 368-376) for topology estimation, as well as its many variations and extensions, differs fundamentally from the maximum likelihood estimation of a conventional statistical parameter. Evidence was presented showing that the Felsenstein approach does not share the asymptotic efficiency of the maximum likelihood estimator of a statistical parameter. Computer simulations were performed to study the probability that MP recovers the true tree under a hierarchy of models of nucleotide substitution; its performance relative to the likelihood method was especially noted. The results appeared to support the intuitive examination of the assumptions underlying MP. When a simple model of nucleotide substitution was assumed to generate data, the probability that MP recovers the true topology could be as high as, or even higher than, that for the likelihood method. When the assumed model became more complex and realistic, e.g., when substitution rates were

  1. Parsimonious Refraction Interferometry and Tomography

    KAUST Repository

    Hanafy, Sherif

    2017-02-04

    We present parsimonious refraction interferometry and tomography where a densely populated refraction data set can be obtained from two reciprocal and several infill shot gathers. The assumptions are that the refraction arrivals are head waves, and a pair of reciprocal shot gathers and several infill shot gathers are recorded over the line of interest. Refraction traveltimes from these shot gathers are picked and spawned into O(N2) virtual refraction traveltimes generated by N virtual sources, where N is the number of geophones in the 2D survey. The virtual traveltimes can be inverted to give the velocity tomogram. This enormous increase in the number of traveltime picks and associated rays, compared to the many fewer traveltimes from the reciprocal and infill shot gathers, allows for increased model resolution and a better condition number with the system of normal equations. A significant benefit is that the parsimonious survey and the associated traveltime picking is far less time consuming than that for a standard refraction survey with a dense distribution of sources.

  2. Seeking parsimony in hydrology and water resources technology

    Science.gov (United States)

    Koutsoyiannis, D.

    2009-04-01

    systems to single numbers (a probability or an expected value), and statistics provides the empirical basis of summarizing data, making inference from them, and supporting decision making in water resource management. Unfortunately, the current state of the art in probability, statistics and their union, often called stochastics, is not fully satisfactory for the needs of modelling of hydrological and water resource systems. A first problem is that stochastic modelling has traditionally relied on classical statistics, which is based on the independent "coin-tossing" prototype, rather than on the study of real-world systems whose behaviour is very different from the classical prototype. A second problem is that the stochastic models (particularly the multivariate ones) are often not parsimonious themselves. Therefore, substantial advancement of stochastics is necessary in a new paradigm of parsimonious hydrological modelling. These ideas are illustrated using several examples, namely: (a) hydrological modelling of a karst system in Bosnia and Herzegovina using three different approaches ranging from parsimonious to detailed "physically-based"; (b) parsimonious modelling of a peculiar modified catchment in Greece; (c) a stochastic approach that can replace parameter-excessive ARMA-type models with a generalized algorithm that produces any shape of autocorrelation function (consistent with the accuracy provided by the data) using a couple of parameters; (d) a multivariate stochastic approach which replaces a huge number of parameters estimated from data with coefficients estimated by the principle of maximum entropy; and (e) a parsimonious approach for decision making in multi-reservoir systems using a handful of parameters instead of thousands of decision variables.

  3. Parsimonious Wavelet Kernel Extreme Learning Machine

    Directory of Open Access Journals (Sweden)

    Wang Qin

    2015-11-01

    Full Text Available In this study, a parsimonious scheme for wavelet kernel extreme learning machine (named PWKELM was introduced by combining wavelet theory and a parsimonious algorithm into kernel extreme learning machine (KELM. In the wavelet analysis, bases that were localized in time and frequency to represent various signals effectively were used. Wavelet kernel extreme learning machine (WELM maximized its capability to capture the essential features in “frequency-rich” signals. The proposed parsimonious algorithm also incorporated significant wavelet kernel functions via iteration in virtue of Householder matrix, thus producing a sparse solution that eased the computational burden and improved numerical stability. The experimental results achieved from the synthetic dataset and a gas furnace instance demonstrated that the proposed PWKELM is efficient and feasible in terms of improving generalization accuracy and real time performance.

  4. Efficient parsimony-based methods for phylogenetic network reconstruction.

    Science.gov (United States)

    Jin, Guohua; Nakhleh, Luay; Snir, Sagi; Tuller, Tamir

    2007-01-15

    Phylogenies--the evolutionary histories of groups of organisms-play a major role in representing relationships among biological entities. Although many biological processes can be effectively modeled as tree-like relationships, others, such as hybrid speciation and horizontal gene transfer (HGT), result in networks, rather than trees, of relationships. Hybrid speciation is a significant evolutionary mechanism in plants, fish and other groups of species. HGT plays a major role in bacterial genome diversification and is a significant mechanism by which bacteria develop resistance to antibiotics. Maximum parsimony is one of the most commonly used criteria for phylogenetic tree inference. Roughly speaking, inference based on this criterion seeks the tree that minimizes the amount of evolution. In 1990, Jotun Hein proposed using this criterion for inferring the evolution of sequences subject to recombination. Preliminary results on small synthetic datasets. Nakhleh et al. (2005) demonstrated the criterion's application to phylogenetic network reconstruction in general and HGT detection in particular. However, the naive algorithms used by the authors are inapplicable to large datasets due to their demanding computational requirements. Further, no rigorous theoretical analysis of computing the criterion was given, nor was it tested on biological data. In the present work we prove that the problem of scoring the parsimony of a phylogenetic network is NP-hard and provide an improved fixed parameter tractable algorithm for it. Further, we devise efficient heuristics for parsimony-based reconstruction of phylogenetic networks. We test our methods on both synthetic and biological data (rbcL gene in bacteria) and obtain very promising results.

  5. Principle of Parsimony, Fake Science, and Scales

    Science.gov (United States)

    Yeh, T. C. J.; Wan, L.; Wang, X. S.

    2017-12-01

    Considering difficulties in predicting exact motions of water molecules, and the scale of our interests (bulk behaviors of many molecules), Fick's law (diffusion concept) has been created to predict solute diffusion process in space and time. G.I. Taylor (1921) demonstrated that random motion of the molecules reach the Fickian regime in less a second if our sampling scale is large enough to reach ergodic condition. Fick's law is widely accepted for describing molecular diffusion as such. This fits the definition of the parsimony principle at the scale of our concern. Similarly, advection-dispersion or convection-dispersion equation (ADE or CDE) has been found quite satisfactory for analysis of concentration breakthroughs of solute transport in uniformly packed soil columns. This is attributed to the solute is often released over the entire cross-section of the column, which has sampled many pore-scale heterogeneities and met the ergodicity assumption. Further, the uniformly packed column contains a large number of stationary pore-size heterogeneity. The solute thus reaches the Fickian regime after traveling a short distance along the column. Moreover, breakthrough curves are concentrations integrated over the column cross-section (the scale of our interest), and they meet the ergodicity assumption embedded in the ADE and CDE. To the contrary, scales of heterogeneity in most groundwater pollution problems evolve as contaminants travel. They are much larger than the scale of our observations and our interests so that the ergodic and the Fickian conditions are difficult. Upscaling the Fick's law for solution dispersion, and deriving universal rules of the dispersion to the field- or basin-scale pollution migrations are merely misuse of the parsimony principle and lead to a fake science ( i.e., the development of theories for predicting processes that can not be observed.) The appropriate principle of parsimony for these situations dictates mapping of large

  6. Parsimonious Ways to Use Vision for Navigation

    Directory of Open Access Journals (Sweden)

    Paul Graham

    2012-05-01

    Full Text Available The use of visual information for navigation appears to be a universal strategy for sighted animals, amongst which, one particular group of expert navigators are the ants. The broad interest in studies of ant navigation is in part due to their small brains, thus biomimetic engineers expect to be impressed by elegant control solutions, and psychologists might hope for a description of the minimal cognitive requirements for complex spatial behaviours. In this spirit, we have been taking an interdisciplinary approach to the visual guided navigation of ants in their natural habitat. Behavioural experiments and natural image statistics show that visual navigation need not depend on the remembering or recognition of objects. Further modelling work suggests how simple behavioural routines might enable navigation using familiarity detection rather than explicit recall, and we present a proof of concept that visual navigation using familiarity can be achieved without specifying when or what to learn, nor separating routes into sequences of waypoints. We suggest that our current model represents the only detailed and complete model of insect route guidance to date. What's more, we believe the suggested mechanisms represent useful parsimonious hypotheses for the visually guided navigation in larger-brain animals.

  7. Quality Quandaries- Time Series Model Selection and Parsimony

    DEFF Research Database (Denmark)

    Bisgaard, Søren; Kulahci, Murat

    2009-01-01

    Some of the issues involved in selecting adequate models for time series data are discussed using an example concerning the number of users of an Internet server. The process of selecting an appropriate model is subjective and requires experience and judgment. The authors believe an important...... consideration in model selection should be parameter parsimony. They favor the use of parsimonious mixed ARMA models, noting that research has shown that a model building strategy that considers only autoregressive representations will lead to non-parsimonious models and to loss of forecasting accuracy....

  8. A simplified parsimonious higher order multivariate Markov chain model

    Science.gov (United States)

    Wang, Chao; Yang, Chuan-sheng

    2017-09-01

    In this paper, a simplified parsimonious higher-order multivariate Markov chain model (SPHOMMCM) is presented. Moreover, parameter estimation method of TPHOMMCM is give. Numerical experiments shows the effectiveness of TPHOMMCM.

  9. A tridiagonal parsimonious higher order multivariate Markov chain model

    Science.gov (United States)

    Wang, Chao; Yang, Chuan-sheng

    2017-09-01

    In this paper, we present a tridiagonal parsimonious higher-order multivariate Markov chain model (TPHOMMCM). Moreover, estimation method of the parameters in TPHOMMCM is give. Numerical experiments illustrate the effectiveness of TPHOMMCM.

  10. Time-Dependent-Asymmetric-Linear-Parsimonious Ancestral State Reconstruction.

    Science.gov (United States)

    Didier, Gilles

    2017-10-01

    The time-dependent-asymmetric-linear parsimony is an ancestral state reconstruction method which extends the standard linear parsimony (a.k.a. Wagner parsimony) approach by taking into account both branch lengths and asymmetric evolutionary costs for reconstructing quantitative characters (asymmetric costs amount to assuming an evolutionary trend toward the direction with the lowest cost). A formal study of the influence of the asymmetry parameter shows that the time-dependent-asymmetric-linear parsimony infers states which are all taken among the known states, except for some degenerate cases corresponding to special values of the asymmetry parameter. This remarkable property holds in particular for the Wagner parsimony. This study leads to a polynomial algorithm which determines, and provides a compact representation of, the parametric reconstruction of a phylogenetic tree, that is for all the unknown nodes, the set of all the possible reconstructed states associated with the asymmetry parameters leading to them. The time-dependent-asymmetric-linear parsimony is finally illustrated with the parametric reconstruction of the body size of cetaceans.

  11. Parsimonious Charge Deconvolution for Native Mass Spectrometry

    Science.gov (United States)

    2018-01-01

    Charge deconvolution infers the mass from mass over charge (m/z) measurements in electrospray ionization mass spectra. When applied over a wide input m/z or broad target mass range, charge-deconvolution algorithms can produce artifacts, such as false masses at one-half or one-third of the correct mass. Indeed, a maximum entropy term in the objective function of MaxEnt, the most commonly used charge deconvolution algorithm, favors a deconvolved spectrum with many peaks over one with fewer peaks. Here we describe a new “parsimonious” charge deconvolution algorithm that produces fewer artifacts. The algorithm is especially well-suited to high-resolution native mass spectrometry of intact glycoproteins and protein complexes. Deconvolution of native mass spectra poses special challenges due to salt and small molecule adducts, multimers, wide mass ranges, and fewer and lower charge states. We demonstrate the performance of the new deconvolution algorithm on a range of samples. On the heavily glycosylated plasma properdin glycoprotein, the new algorithm could deconvolve monomer and dimer simultaneously and, when focused on the m/z range of the monomer, gave accurate and interpretable masses for glycoforms that had previously been analyzed manually using m/z peaks rather than deconvolved masses. On therapeutic antibodies, the new algorithm facilitated the analysis of extensions, truncations, and Fab glycosylation. The algorithm facilitates the use of native mass spectrometry for the qualitative and quantitative analysis of protein and protein assemblies. PMID:29376659

  12. A Maximum Parsimony Model to Reconstruct Phylogenetic Network in Honey Bee Evolution

    OpenAIRE

    Usha Chouhan; K. R. Pardasani

    2007-01-01

    Phylogenies ; The evolutionary histories of groups of species are one of the most widely used tools throughout the life sciences, as well as objects of research with in systematic, evolutionary biology. In every phylogenetic analysis reconstruction produces trees. These trees represent the evolutionary histories of many groups of organisms, bacteria due to horizontal gene transfer and plants due to process of hybridization. The process of gene transfer in bacteria and hyb...

  13. Live phylogeny with polytomies: Finding the most compact parsimonious trees.

    Science.gov (United States)

    Papamichail, D; Huang, A; Kennedy, E; Ott, J-L; Miller, A; Papamichail, G

    2017-08-01

    Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral evolution and transmission, paleontology, linguistics, and phylogenetic stemmatics, often require phylogeny inference that involves placing input species on ancestral tree nodes (live phylogeny), and polytomies. These requirements, despite their prevalence, lead to computationally harder algorithmic solutions and have been sparsely examined in the literature to date. In this article we prove some unique properties of most parsimonious live phylogenetic trees with polytomies, and their mapping to traditional binary phylogenetic trees. We show that our problem reduces to finding the most compact parsimonious tree for n species, and describe a novel efficient algorithm to find such trees without resorting to exhaustive enumeration of all possible tree topologies. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Molecular phylogeny of ateline new world monkeys (Platyrrhini, atelinae) based on gamma-globin gene sequences: evidence that brachyteles is the sister group of lagothrix.

    Science.gov (United States)

    Meireles, C M; Czelusniak, J; Schneider, M P; Muniz, J A; Brigido, M C; Ferreira, H S; Goodman, M

    1999-06-01

    Nucleotide sequences, each spanning approximately 7 kb of the contiguous gamma1 and gamma2 globin genomic loci, were determined for seven species representing all extant genera (Ateles, Lagothrix, Brachyteles, and Alouatta) of the New World monkey subfamily Atelinae. After aligning these seven ateline sequences with outgroup sequences from several other primate (non-ateline) genera, they were analyzed by maximum parsimony, maximum likelihood, and neighbor-joining algorithms. All three analyzes estimated the same phylogenetic relationships: [Alouatta [Ateles (Brachyteles, Lagothrix)

  15. Quality Assurance Based on Descriptive and Parsimonious Appearance Models

    DEFF Research Database (Denmark)

    Nielsen, Jannik Boll; Eiríksson, Eyþór Rúnar; Kristensen, Rasmus Lyngby

    2015-01-01

    In this positional paper, we discuss the potential benefits of using appearance models in additive manufacturing, metal casting, wind turbine blade production, and 3D content acquisition. Current state of the art in acquisition and rendering of appearance cannot easily be used for quality assurance...... in these areas. The common denominator is the need for descriptive and parsimonious appearance models. By ‘parsimonious’ we mean with few parameters so that a model is useful both for fast acquisition, robust fitting, and fast rendering of appearance. The word ‘descriptive’ refers to the fact that a model should...

  16. A Parsimonious Bootstrap Method to Model Natural Inflow Energy Series

    Directory of Open Access Journals (Sweden)

    Fernando Luiz Cyrino Oliveira

    2014-01-01

    Full Text Available The Brazilian energy generation and transmission system is quite peculiar in its dimension and characteristics. As such, it can be considered unique in the world. It is a high dimension hydrothermal system with huge participation of hydro plants. Such strong dependency on hydrological regimes implies uncertainties related to the energetic planning, requiring adequate modeling of the hydrological time series. This is carried out via stochastic simulations of monthly inflow series using the family of Periodic Autoregressive models, PAR(p, one for each period (month of the year. In this paper it is shown the problems in fitting these models by the current system, particularly the identification of the autoregressive order “p” and the corresponding parameter estimation. It is followed by a proposal of a new approach to set both the model order and the parameters estimation of the PAR(p models, using a nonparametric computational technique, known as Bootstrap. This technique allows the estimation of reliable confidence intervals for the model parameters. The obtained results using the Parsimonious Bootstrap Method of Moments (PBMOM produced not only more parsimonious model orders but also adherent stochastic scenarios and, in the long range, lead to a better use of water resources in the energy operation planning.

  17. A large version of the small parsimony problem

    DEFF Research Database (Denmark)

    Fredslund, Jakob; Hein, Jotun; Scharling, Tejs

    2003-01-01

    the most parsimonious assignment of nucleotides. The gaps of the alignment are represented in a so-called gap graph, and through theoretically sound preprocessing the graph is reduced to pave the way for a running time which in all but the most pathological examples is far better than the exponential worst......Given a multiple alignment over $k$ sequences, an evolutionary tree relating the sequences, and a subadditive gap penalty function (e.g. an affine function), we reconstruct the internal nodes of the tree optimally: we find the optimal explanation in terms of indels of the observed gaps and find...... case time. E.g. for a tree with nine leaves and a random alignment of length 10.000 with 60% gaps, the running time is on average around 45 seconds. For a real alignment of length 9868 of nine HIV-1 sequences, the running time is less than one second....

  18. A Practical pedestrian approach to parsimonious regression with inaccurate inputs

    Directory of Open Access Journals (Sweden)

    Seppo Karrila

    2014-04-01

    Full Text Available A measurement result often dictates an interval containing the correct value. Interval data is also created by roundoff, truncation, and binning. We focus on such common interval uncertainty in data. Inaccuracy in model inputs is typically ignored on model fitting. We provide a practical approach for regression with inaccurate data: the mathematics is easy, and the linear programming formulations simple to use even in a spreadsheet. This self-contained elementary presentation introduces interval linear systems and requires only basic knowledge of algebra. Feature selection is automatic; but can be controlled to find only a few most relevant inputs; and joint feature selection is enabled for multiple modeled outputs. With more features than cases, a novel connection to compressed sensing emerges: robustness against interval errors-in-variables implies model parsimony, and the input inaccuracies determine the regularization term. A small numerical example highlights counterintuitive results and a dramatic difference to total least squares.

  19. Things fall apart: biological species form unconnected parsimony networks.

    Science.gov (United States)

    Hart, Michael W; Sunday, Jennifer

    2007-10-22

    The generality of operational species definitions is limited by problematic definitions of between-species divergence. A recent phylogenetic species concept based on a simple objective measure of statistically significant genetic differentiation uses between-species application of statistical parsimony networks that are typically used for population genetic analysis within species. Here we review recent phylogeographic studies and reanalyse several mtDNA barcoding studies using this method. We found that (i) alignments of DNA sequences typically fall apart into a separate subnetwork for each Linnean species (but with a higher rate of true positives for mtDNA data) and (ii) DNA sequences from single species typically stick together in a single haplotype network. Departures from these patterns are usually consistent with hybridization or cryptic species diversity.

  20. A parsimonious dynamic model for river water quality assessment.

    Science.gov (United States)

    Mannina, Giorgio; Viviani, Gaspare

    2010-01-01

    Water quality modelling is of crucial importance for the assessment of physical, chemical, and biological changes in water bodies. Mathematical approaches to water modelling have become more prevalent over recent years. Different model types ranging from detailed physical models to simplified conceptual models are available. Actually, a possible middle ground between detailed and simplified models may be parsimonious models that represent the simplest approach that fits the application. The appropriate modelling approach depends on the research goal as well as on data available for correct model application. When there is inadequate data, it is mandatory to focus on a simple river water quality model rather than detailed ones. The study presents a parsimonious river water quality model to evaluate the propagation of pollutants in natural rivers. The model is made up of two sub-models: a quantity one and a quality one. The model employs a river schematisation that considers different stretches according to the geometric characteristics and to the gradient of the river bed. Each stretch is represented with a conceptual model of a series of linear channels and reservoirs. The channels determine the delay in the pollution wave and the reservoirs cause its dispersion. To assess the river water quality, the model employs four state variables: DO, BOD, NH(4), and NO. The model was applied to the Savena River (Italy), which is the focus of a European-financed project in which quantity and quality data were gathered. A sensitivity analysis of the model output to the model input or parameters was done based on the Generalised Likelihood Uncertainty Estimation methodology. The results demonstrate the suitability of such a model as a tool for river water quality management.

  1. Phylogenetic inferences of Nepenthes species in Peninsular Malaysia revealed by chloroplast (trnL intron) and nuclear (ITS) DNA sequences

    OpenAIRE

    Bunawan, Hamidun; Yen, Choong Chee; Yaakop, Salmah; Noor, Normah Mohd

    2017-01-01

    Background The chloroplastic trnL intron and the nuclear internal transcribed spacer (ITS) region were sequenced for 11 Nepenthes species recorded in Peninsular Malaysia to examine their phylogenetic relationship and to evaluate the usage of trnL intron and ITS sequences for phylogenetic reconstruction of this genus. Results Phylogeny reconstruction was carried out using neighbor-joining, maximum parsimony and Bayesian analyses. All the trees revealed two major clusters, a lowland group consi...

  2. A new mathematical modeling for pure parsimony haplotyping problem.

    Science.gov (United States)

    Feizabadi, R; Bagherian, M; Vaziri, H R; Salahi, M

    2016-11-01

    Pure parsimony haplotyping (PPH) problem is important in bioinformatics because rational haplotyping inference plays important roles in analysis of genetic data, mapping complex genetic diseases such as Alzheimer's disease, heart disorders and etc. Haplotypes and genotypes are m-length sequences. Although several integer programing models have already been presented for PPH problem, its NP-hardness characteristic resulted in ineffectiveness of those models facing the real instances especially instances with many heterozygous sites. In this paper, we assign a corresponding number to each haplotype and genotype and based on those numbers, we set a mixed integer programing model. Using numbers, instead of sequences, would lead to less complexity of the new model in comparison with previous models in a way that there are neither constraints nor variables corresponding to heterozygous nucleotide sites in it. Experimental results approve the efficiency of the new model in producing better solution in comparison to two state-of-the art haplotyping approaches. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Pengintegrasian Model Leadership Menuju Model yang Lebih Komprhensip dan Parsimoni

    Directory of Open Access Journals (Sweden)

    Miswanto Miswanti

    2016-06-01

    Full Text Available ABTSRACT Through leadership models offered by Locke et. al (1991 we can say that whether good or not the vision of leaders in the organization is highly dependent on whether good or not the motives and traits, knowledge, skill, and abilities owned leaders. Then, good or not the implementation of the vision by the leader depends on whether good or not the motives and traits, knowledge, skills, abilities, and the vision of the leaders. Strategic Leadership written by Davies (1991 states that the implementation of the vision by using strategic leadership, the meaning is much more complete than what has been written by Locke et. al. in the fourth stage of leadership. Thus, aspects of the implementation of the vision by Locke et al (1991 it is not complete implementation of the vision according to Davies (1991. With the considerations mentioned above, this article attempts to combine the leadership model of the Locke et. al and strategic leadership of the Davies. With this modification is expected to be an improvement model of leadership is more comprehensive and parsimony.

  4. SEAPODYM-LTL: a parsimonious zooplankton dynamic biomass model

    Science.gov (United States)

    Conchon, Anna; Lehodey, Patrick; Gehlen, Marion; Titaud, Olivier; Senina, Inna; Séférian, Roland

    2017-04-01

    Mesozooplankton organisms are of critical importance for the understanding of early life history of most fish stocks, as well as the nutrient cycles in the ocean. Ongoing climate change and the need for improved approaches to the management of living marine resources has driven recent advances in zooplankton modelling. The classical modeling approach tends to describe the whole biogeochemical and plankton cycle with increasing complexity. We propose here a different and parsimonious zooplankton dynamic biomass model (SEAPODYM-LTL) that is cost efficient and can be advantageously coupled with primary production estimated either from satellite derived ocean color data or biogeochemical models. In addition, the adjoint code of the model is developed allowing a robust optimization approach for estimating the few parameters of the model. In this study, we run the first optimization experiments using a global database of climatological zooplankton biomass data and we make a comparative analysis to assess the importance of resolution and primary production inputs on model fit to observations. We also compare SEAPODYM-LTL outputs to those produced by a more complex biogeochemical model (PISCES) but sharing the same physical forcings.

  5. Systematics and morphological evolution within the moss family Bryaceae: a comparison between parsimony and Bayesian methods for reconstruction of ancestral character states.

    Science.gov (United States)

    Pedersen, Niklas; Holyoak, David T; Newton, Angela E

    2007-06-01

    The Bryaceae are a large cosmopolitan moss family including genera of significant morphological and taxonomic complexity. Phylogenetic relationships within the Bryaceae were reconstructed based on DNA sequence data from all three genomic compartments. In addition, maximum parsimony and Bayesian inference were employed to reconstruct ancestral character states of 38 morphological plus four habitat characters and eight insertion/deletion events. The recovered phylogenetic patterns are generally in accord with previous phylogenies based on chloroplast DNA sequence data and three major clades are identified. The first clade comprises Bryum bornholmense, B. rubens, B. caespiticium, and Plagiobryum. This corroborates the hypothesis suggested by previous studies that several Bryum species are more closely related to Plagiobryum than to the core Bryum species. The second clade includes Acidodontium, Anomobryum, and Haplodontium, while the third clade contains the core Bryum species plus Imbribryum. Within the latter clade, B. subapiculatum and B. tenuisetum form the sister clade to Imbribryum. Reconstructions of ancestral character states under maximum parsimony and Bayesian inference suggest fourteen morphological synapomorphies for the ingroup and synapomorphies are detected for most clades within the ingroup. Maximum parsimony and Bayesian reconstructions of ancestral character states are mostly congruent although Bayesian inference shows that the posterior probability of ancestral character states may decrease dramatically when node support is taken into account. Bayesian inference also indicates that reconstructions may be ambiguous at internal nodes for highly polymorphic characters.

  6. Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta

    Directory of Open Access Journals (Sweden)

    Rahmann Sven

    2004-06-01

    Full Text Available Abstract Background In phylogenetic analysis we face the problem that several subclade topologies are known or easily inferred and well supported by bootstrap analysis, but basal branching patterns cannot be unambiguously estimated by the usual methods (maximum parsimony (MP, neighbor-joining (NJ, or maximum likelihood (ML, nor are they well supported. We represent each subclade by a sequence profile and estimate evolutionary distances between profiles to obtain a matrix of distances between subclades. Results Our estimator of profile distances generalizes the maximum likelihood estimator of sequence distances. The basal branching pattern can be estimated by any distance-based method, such as neighbor-joining. Our method (profile neighbor-joining, PNJ then inherits the accuracy and robustness of profiles and the time efficiency of neighbor-joining. Conclusions Phylogenetic analysis of Chlorophyceae with traditional methods (MP, NJ, ML and MrBayes reveals seven well supported subclades, but the methods disagree on the basal branching pattern. The tree reconstructed by our method is better supported and can be confirmed by known morphological characters. Moreover the accuracy is significantly improved as shown by parametric bootstrap.

  7. Parsimonious Hydrologic and Nitrate Response Models For Silver Springs, Florida

    Science.gov (United States)

    Klammler, Harald; Yaquian-Luna, Jose Antonio; Jawitz, James W.; Annable, Michael D.; Hatfield, Kirk

    2014-05-01

    Silver Springs with an approximate discharge of 25 m3/sec is one of Florida's first magnitude springs and among the largest springs worldwide. Its 2500-km2 springshed overlies the mostly unconfined Upper Floridan Aquifer. The aquifer is approximately 100 m thick and predominantly consists of porous, fractured and cavernous limestone, which leads to excellent surface drainage properties (no major stream network other than Silver Springs run) and complex groundwater flow patterns through both rock matrix and fast conduits. Over the past few decades, discharge from Silver Springs has been observed to slowly but continuously decline, while nitrate concentrations in the spring water have enormously increased from a background level of 0.05 mg/l to over 1 mg/l. In combination with concurrent increases in algae growth and turbidity, for example, and despite an otherwise relatively stable water quality, this has given rise to concerns about the ecological equilibrium in and near the spring run as well as possible impacts on tourism. The purpose of the present work is to elaborate parsimonious lumped parameter models that may be used by resource managers for evaluating the springshed's hydrologic and nitrate transport responses. Instead of attempting to explicitly consider the complex hydrogeologic features of the aquifer in a typically numerical and / or stochastic approach, we use a transfer function approach wherein input signals (i.e., time series of groundwater recharge and nitrate loading) are transformed into output signals (i.e., time series of spring discharge and spring nitrate concentrations) by some linear and time-invariant law. The dynamic response types and parameters are inferred from comparing input and output time series in frequency domain (e.g., after Fourier transformation). Results are converted into impulse (or step) response functions, which describe at what time and to what magnitude a unitary change in input manifests at the output. For the

  8. A short proof that phylogenetic tree reconstruction by maximum likelihood is hard.

    Science.gov (United States)

    Roch, Sebastien

    2006-01-01

    Maximum likelihood is one of the most widely used techniques to infer evolutionary histories. Although it is thought to be intractable, a proof of its hardness has been lacking. Here, we give a short proof that computing the maximum likelihood tree is NP-hard by exploiting a connection between likelihood and parsimony observed by Tuffley and Steel.

  9. A Short Proof that Phylogenetic Tree Reconstruction by Maximum Likelihood is Hard

    OpenAIRE

    Roch, S.

    2005-01-01

    Maximum likelihood is one of the most widely used techniques to infer evolutionary histories. Although it is thought to be intractable, a proof of its hardness has been lacking. Here, we give a short proof that computing the maximum likelihood tree is NP-hard by exploiting a connection between likelihood and parsimony observed by Tuffley and Steel.

  10. Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees.

    Science.gov (United States)

    Mirzaei, Sajad; Wu, Yufeng

    2016-01-01

    Hybridization networks represent plausible evolutionary histories of species that are affected by reticulate evolutionary processes. An established computational problem on hybridization networks is constructing the most parsimonious hybridization network such that each of the given phylogenetic trees (called gene trees) is "displayed" in the network. There have been several previous approaches, including an exact method and several heuristics, for this NP-hard problem. However, the exact method is only applicable to a limited range of data, and heuristic methods can be less accurate and also slow sometimes. In this paper, we develop a new algorithm for constructing near parsimonious networks for multiple binary gene trees. This method is more efficient for large numbers of gene trees than previous heuristics. This new method also produces more parsimonious results on many simulated datasets as well as a real biological dataset than a previous method. We also show that our method produces topologically more accurate networks for many datasets.

  11. Seeing the elephant: Parsimony, functionalism, and the emergent design of contempt and other sentiments.

    Science.gov (United States)

    Gervais, Matthew M; Fessler, Daniel M T

    2017-01-01

    The target article argues that contempt is a sentiment, and that sentiments are the deep structure of social affect. The 26 commentaries meet these claims with a range of exciting extensions and applications, as well as critiques. Most significantly, we reply that construction and emergence are necessary for, not incompatible with, evolved design, while parsimony requires explanatory adequacy and predictive accuracy, not mere simplicity.

  12. Consequence Valuing as Operation and Process: A Parsimonious Analysis of Motivation

    Science.gov (United States)

    Whelan, Robert; Barnes-Holmes, Dermot

    2010-01-01

    The concept of the motivating operation (MO) has been subject to 3 criticisms: (a) the terms and concepts employed do not always overlap with traditional behavior-analytic verbal practices; (b) the dual nature of the MO is unclear; and (c) there is a lack of adequate contact with empirical data. We offer a more parsimonious approach to motivation,…

  13. A Parsimonious Instrument for Predicting Students' Intent to Pursue a Sales Career: Scale Development and Validation

    Science.gov (United States)

    Peltier, James W.; Cummins, Shannon; Pomirleanu, Nadia; Cross, James; Simon, Rob

    2014-01-01

    Students' desire and intention to pursue a career in sales continue to lag behind industry demand for sales professionals. This article develops and validates a reliable and parsimonious scale for measuring and predicting student intention to pursue a selling career. The instrument advances previous scales in three ways. The instrument is…

  14. A simplified parsimonious higher order multivariate Markov chain model with new convergence condition

    Science.gov (United States)

    Wang, Chao; Yang, Chuan-sheng

    2017-09-01

    In this paper, we present a simplified parsimonious higher-order multivariate Markov chain model with new convergence condition. (TPHOMMCM-NCC). Moreover, estimation method of the parameters in TPHOMMCM-NCC is give. Numerical experiments illustrate the effectiveness of TPHOMMCM-NCC.

  15. Vector Autoregressions with Parsimoniously Time Varying Parameters and an Application to Monetary Policy

    DEFF Research Database (Denmark)

    Callot, Laurent; Kristensen, Johannes Tang

    the monetary policy response to inflation and business cycle fluctuations in the US by estimating a parsimoniously time varying parameter Taylor rule.We document substantial changes in the policy response of the Fed in the 1970s and 1980s, and since 2007, but also document the stability of this response...

  16. Time-Lapse Monitoring of Subsurface Fluid Flow using Parsimonious Seismic Interferometry

    KAUST Repository

    Hanafy, Sherif; Li, Jing; Schuster, Gerard T.

    2017-01-01

    of parsimonious seismic interferometry with the time-lapse mentoring idea with field examples, where we were able to record 30 different data sets within a 2-hour period. The recorded data are then processed to generate 30 snapshots that shows the spread of water

  17. Parsimonious wave-equation travel-time inversion for refraction waves

    KAUST Repository

    Fu, Lei; Hanafy, Sherif M.; Schuster, Gerard T.

    2017-01-01

    We present a parsimonious wave-equation travel-time inversion technique for refraction waves. A dense virtual refraction dataset can be generated from just two reciprocal shot gathers for the sources at the endpoints of the survey line, with N

  18. Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data.

    Science.gov (United States)

    O'Reilly, Joseph E; Puttick, Mark N; Parry, Luke; Tanner, Alastair R; Tarver, James E; Fleming, James; Pisani, Davide; Donoghue, Philip C J

    2016-04-01

    Different analytical methods can yield competing interpretations of evolutionary history and, currently, there is no definitive method for phylogenetic reconstruction using morphological data. Parsimony has been the primary method for analysing morphological data, but there has been a resurgence of interest in the likelihood-based Mk-model. Here, we test the performance of the Bayesian implementation of the Mk-model relative to both equal and implied-weight implementations of parsimony. Using simulated morphological data, we demonstrate that the Mk-model outperforms equal-weights parsimony in terms of topological accuracy, and implied-weights performs the most poorly. However, the Mk-model produces phylogenies that have less resolution than parsimony methods. This difference in the accuracy and precision of parsimony and Bayesian approaches to topology estimation needs to be considered when selecting a method for phylogeny reconstruction. © 2016 The Authors.

  19. IRT Item Parameter Recovery with Marginal Maximum Likelihood Estimation Using Loglinear Smoothing Models

    Science.gov (United States)

    Casabianca, Jodi M.; Lewis, Charles

    2015-01-01

    Loglinear smoothing (LLS) estimates the latent trait distribution while making fewer assumptions about its form and maintaining parsimony, thus leading to more precise item response theory (IRT) item parameter estimates than standard marginal maximum likelihood (MML). This article provides the expectation-maximization algorithm for MML estimation…

  20. DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

    Science.gov (United States)

    Wehe, André; Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver

    2008-07-01

    DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++. DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree

  1. Parsimonious data

    DEFF Research Database (Denmark)

    Kristensen, Jakob Baek; Albrechtsen, Thomas; Dahl-Nielsen, Emil

    2017-01-01

    This study shows how liking politicians’ public Facebook posts can be used as an accurate measure for predicting present-day voter intention in a multiparty system. We highlight that a few, but selective digital traces produce prediction accuracies that are on par or even greater than most curren...

  2. Assessing Internet addiction using the parsimonious Internet addiction components model - a preliminary study [forthcoming

    OpenAIRE

    Kuss, DJ; Shorter, GW; Van Rooij, AJ; Griffiths, MD; Schoenmakers, T

    2014-01-01

    Internet usage has grown exponentially over the last decade. Research indicates that excessive Internet use can lead to symptoms associated with addiction. To date, assessment of potential Internet addiction has varied regarding populations studied and instruments used, making reliable prevalence estimations difficult. To overcome the present problems a preliminary study was conducted testing a parsimonious Internet addiction components model based on Griffiths’ addiction components (2005), i...

  3. Assessing internet addiction using the parsimonious internet addiction components model—A preliminary study.

    OpenAIRE

    Kuss, D.J.; Shorter, G.W.; Rooij, A.J. van; Griffiths, M.D.; Schoenmakers, T.M.

    2014-01-01

    Internet usage has grown exponentially over the last decade. Research indicates that excessive Internet use can lead to symptoms associated with addiction. To date, assessment of potential Internet addiction has varied regarding populations studied and instruments used, making reliable prevalence estimations difficult. To overcome the present problems a preliminary study was conducted testing a parsimonious Internet addiction components model based on Griffiths’ addiction components (Journal ...

  4. A class representative model for Pure Parsimony Haplotyping under uncertain data.

    Directory of Open Access Journals (Sweden)

    Daniele Catanzaro

    Full Text Available The Pure Parsimony Haplotyping (PPH problem is a NP-hard combinatorial optimization problem that consists of finding the minimum number of haplotypes necessary to explain a given set of genotypes. PPH has attracted more and more attention in recent years due to its importance in analysis of many fine-scale genetic data. Its application fields range from mapping complex disease genes to inferring population histories, passing through designing drugs, functional genomics and pharmacogenetics. In this article we investigate, for the first time, a recent version of PPH called the Pure Parsimony Haplotype problem under Uncertain Data (PPH-UD. This version mainly arises when the input genotypes are not accurate, i.e., when some single nucleotide polymorphisms are missing or affected by errors. We propose an exact approach to solution of PPH-UD based on an extended version of Catanzaro et al.[1] class representative model for PPH, currently the state-of-the-art integer programming model for PPH. The model is efficient, accurate, compact, polynomial-sized, easy to implement, solvable with any solver for mixed integer programming, and usable in all those cases for which the parsimony criterion is well suited for haplotype estimation.

  5. The plunge in German electricity futures prices – Analysis using a parsimonious fundamental model

    International Nuclear Information System (INIS)

    Kallabis, Thomas; Pape, Christian; Weber, Christoph

    2016-01-01

    The German market has seen a plunge in wholesale electricity prices from 2007 until 2014, with base futures prices dropping by more than 40%. This is frequently attributed to the unexpected high increase in renewable power generation. Using a parsimonious fundamental model, we determine the respective impact of supply and demand shocks on electricity futures prices. The used methodology is based on a piecewise linear approximation of the supply stack and time-varying price-inelastic demand. This parsimonious model is able to replicate electricity futures prices and discover non-linear dependencies in futures price formation. We show that emission prices have a higher impact on power prices than renewable penetration. Changes in renewables, demand and installed capacities turn out to be similarly important for explaining the decrease in operation margins of conventional power plants. We thus argue for the establishment of an independent authority to stabilize emission prices. - Highlights: •We build a parsimonious fundamental model based on a piecewise linear bid stack. •We use the model to investigate impact factors for the plunge in German futures prices. •Largest impact by CO_2 price developments followed by demand and renewable feed-in. •Power plant operating profits strongly affected by demand and renewables. •We argue that stabilizing CO_2 emission prices could provide better market signals.

  6. Composite scores in comparative effectiveness research: counterbalancing parsimony and dimensionality in patient-reported outcomes.

    Science.gov (United States)

    Schwartz, Carolyn E; Patrick, Donald L

    2014-07-01

    When planning a comparative effectiveness study comparing disease-modifying treatments, competing demands influence choice of outcomes. Current practice emphasizes parsimony, although understanding multidimensional treatment impact can help to personalize medical decision-making. We discuss both sides of this 'tug of war'. We discuss the assumptions, advantages and drawbacks of composite scores and multidimensional outcomes. We describe possible solutions to the multiple comparison problem, including conceptual hierarchy distinctions, statistical approaches, 'real-world' benchmarks of effectiveness and subgroup analysis. We conclude that comparative effectiveness research should consider multiple outcome dimensions and compare different approaches that fit the individual context of study objectives.

  7. Parsimonious wave-equation travel-time inversion for refraction waves

    KAUST Repository

    Fu, Lei

    2017-02-14

    We present a parsimonious wave-equation travel-time inversion technique for refraction waves. A dense virtual refraction dataset can be generated from just two reciprocal shot gathers for the sources at the endpoints of the survey line, with N geophones evenly deployed along the line. These two reciprocal shots contain approximately 2N refraction travel times, which can be spawned into O(N2) refraction travel times by an interferometric transformation. Then, these virtual refraction travel times are used with a source wavelet to create N virtual refraction shot gathers, which are the input data for wave-equation travel-time inversion. Numerical results show that the parsimonious wave-equation travel-time tomogram has about the same accuracy as the tomogram computed by standard wave-equation travel-time inversion. The most significant benefit is that a reciprocal survey is far less time consuming than the standard refraction survey where a source is excited at each geophone location.

  8. Beyond technology acceptance to effective technology use: a parsimonious and actionable model.

    Science.gov (United States)

    Holahan, Patricia J; Lesselroth, Blake J; Adams, Kathleen; Wang, Kai; Church, Victoria

    2015-05-01

    To develop and test a parsimonious and actionable model of effective technology use (ETU). Cross-sectional survey of primary care providers (n = 53) in a large integrated health care organization that recently implemented new medication reconciliation technology. Surveys assessed 5 technology-related perceptions (compatibility with work values, implementation climate, compatibility with work processes, perceived usefulness, and ease of use) and 1 outcome variable, ETU. ETU was measured as both consistency and quality of technology use. Compatibility with work values and implementation climate were found to have differential effects on consistency and quality of use. When implementation climate was strong, consistency of technology use was high. However, quality of technology use was high only when implementation climate was strong and values compatibility was high. This is an important finding and highlights the importance of users' workplace values as a key determinant of quality of use. To extend our effectiveness in implementing new health care information technology, we need parsimonious models that include actionable determinants of ETU and account for the differential effects of these determinants on the multiple dimensions of ETU. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  9. The scenario on the origin of translation in the RNA world: in principle of replication parsimony

    Directory of Open Access Journals (Sweden)

    Ma Wentao

    2010-11-01

    Full Text Available Abstract Background It is now believed that in the origin of life, proteins should have been "invented" in an RNA world. However, due to the complexity of a possible RNA-based proto-translation system, this evolving process seems quite complicated and the associated scenario remains very blurry. Considering that RNA can bind amino acids with specificity, it has been reasonably supposed that initial peptides might have been synthesized on "RNA templates" containing multiple amino acid binding sites. This "Direct RNA Template (DRT" mechanism is attractive because it should be the simplest mechanism for RNA to synthesize peptides, thus very likely to have been adopted initially in the RNA world. Then, how this mechanism could develop into a proto-translation system mechanism is an interesting problem. Presentation of the hypothesis Here an explanation to this problem is shown considering the principle of "replication parsimony" --- genetic information tends to be utilized in a parsimonious way under selection pressure, due to its replication cost (e.g., in the RNA world, nucleotides and ribozymes for RNA replication. Because a DRT would be quite long even for a short peptide, its replication cost would be great. Thus the diversity and the length of functional peptides synthesized by the DRT mechanism would be seriously limited. Adaptors (proto-tRNAs would arise to allow a DRT's complementary strand (called "C-DRT" here to direct the synthesis of the same peptide synthesized by the DRT itself. Because the C-DRT is a necessary part in the DRT's replication, fewer turns of the DRT's replication would be needed to synthesize definite copies of the functional peptide, thus saving the replication cost. Acting through adaptors, C-DRTs could transform into much shorter templates (called "proto-mRNAs" here and substitute the role of DRTs, thus significantly saving the replication cost. A proto-rRNA corresponding to the small subunit rRNA would then emerge

  10. Catchment legacies and time lags: a parsimonious watershed model to predict the effects of legacy storage on nitrogen export.

    Directory of Open Access Journals (Sweden)

    Kimberly J Van Meter

    Full Text Available Nutrient legacies in anthropogenic landscapes, accumulated over decades of fertilizer application, lead to time lags between implementation of conservation measures and improvements in water quality. Quantification of such time lags has remained difficult, however, due to an incomplete understanding of controls on nutrient depletion trajectories after changes in land-use or management practices. In this study, we have developed a parsimonious watershed model for quantifying catchment-scale time lags based on both soil nutrient accumulations (biogeochemical legacy and groundwater travel time distributions (hydrologic legacy. The model accurately predicted the time lags observed in an Iowa watershed that had undergone a 41% conversion of area from row crop to native prairie. We explored the time scales of change for stream nutrient concentrations as a function of both natural and anthropogenic controls, from topography to spatial patterns of land-use change. Our results demonstrate that the existence of biogeochemical nutrient legacies increases time lags beyond those due to hydrologic legacy alone. In addition, we show that the maximum concentration reduction benefits vary according to the spatial pattern of intervention, with preferential conversion of land parcels having the shortest catchment-scale travel times providing proportionally greater concentration reductions as well as faster response times. In contrast, a random pattern of conversion results in a 1:1 relationship between percent land conversion and percent concentration reduction, irrespective of denitrification rates within the landscape. Our modeling framework allows for the quantification of tradeoffs between costs associated with implementation of conservation measures and the time needed to see the desired concentration reductions, making it of great value to decision makers regarding optimal implementation of watershed conservation measures.

  11. Cases in which ancestral maximum likelihood will be confusingly misleading.

    Science.gov (United States)

    Handelman, Tomer; Chor, Benny

    2017-05-07

    Ancestral maximum likelihood (AML) is a phylogenetic tree reconstruction criteria that "lies between" maximum parsimony (MP) and maximum likelihood (ML). ML has long been known to be statistically consistent. On the other hand, Felsenstein (1978) showed that MP is statistically inconsistent, and even positively misleading: There are cases where the parsimony criteria, applied to data generated according to one tree topology, will be optimized on a different tree topology. The question of weather AML is statistically consistent or not has been open for a long time. Mossel et al. (2009) have shown that AML can "shrink" short tree edges, resulting in a star tree with no internal resolution, which yields a better AML score than the original (resolved) model. This result implies that AML is statistically inconsistent, but not that it is positively misleading, because the star tree is compatible with any other topology. We show that AML is confusingly misleading: For some simple, four taxa (resolved) tree, the ancestral likelihood optimization criteria is maximized on an incorrect (resolved) tree topology, as well as on a star tree (both with specific edge lengths), while the tree with the original, correct topology, has strictly lower ancestral likelihood. Interestingly, the two short edges in the incorrect, resolved tree topology are of length zero, and are not adjacent, so this resolved tree is in fact a simple path. While for MP, the underlying phenomenon can be described as long edge attraction, it turns out that here we have long edge repulsion. Copyright © 2017. Published by Elsevier Ltd.

  12. Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration.

    Science.gov (United States)

    de Queiroz, K; Poe, S

    2001-06-01

    Advocates of cladistic parsimony methods have invoked the philosophy of Karl Popper in an attempt to argue for the superiority of those methods over phylogenetic methods based on Ronald Fisher's statistical principle of likelihood. We argue that the concept of likelihood in general, and its application to problems of phylogenetic inference in particular, are highly compatible with Popper's philosophy. Examination of Popper's writings reveals that his concept of corroboration is, in fact, based on likelihood. Moreover, because probabilistic assumptions are necessary for calculating the probabilities that define Popper's corroboration, likelihood methods of phylogenetic inference--with their explicit probabilistic basis--are easily reconciled with his concept. In contrast, cladistic parsimony methods, at least as described by certain advocates of those methods, are less easily reconciled with Popper's concept of corroboration. If those methods are interpreted as lacking probabilistic assumptions, then they are incompatible with corroboration. Conversely, if parsimony methods are to be considered compatible with corroboration, then they must be interpreted as carrying implicit probabilistic assumptions. Thus, the non-probabilistic interpretation of cladistic parsimony favored by some advocates of those methods is contradicted by an attempt by the same authors to justify parsimony methods in terms of Popper's concept of corroboration. In addition to being compatible with Popperian corroboration, the likelihood approach to phylogenetic inference permits researchers to test the assumptions of their analytical methods (models) in a way that is consistent with Popper's ideas about the provisional nature of background knowledge.

  13. Maximum permissible dose

    International Nuclear Information System (INIS)

    Anon.

    1979-01-01

    This chapter presents a historic overview of the establishment of radiation guidelines by various national and international agencies. The use of maximum permissible dose and maximum permissible body burden limits to derive working standards is discussed

  14. More quality measures versus measuring what matters: a call for balance and parsimony.

    Science.gov (United States)

    Meyer, Gregg S; Nelson, Eugene C; Pryor, David B; James, Brent; Swensen, Stephen J; Kaplan, Gary S; Weissberg, Jed I; Bisognano, Maureen; Yates, Gary R; Hunt, Gordon C

    2012-11-01

    External groups requiring measures now include public and private payers, regulators, accreditors and others that certify performance levels for consumers, patients and payers. Although benefits have accrued from the growth in quality measurement, the recent explosion in the number of measures threatens to shift resources from improving quality to cover a plethora of quality-performance metrics that may have a limited impact on the things that patients and payers want and need (ie, better outcomes, better care, and lower per capita costs). Here we propose a policy that quality measurement should be: balanced to meet the need of end users to judge quality and cost performance and the need of providers to continuously improve the quality, outcomes and costs of their services; and parsimonious to measure quality, outcomes and costs with appropriate metrics that are selected based on end-user needs.

  15. Time-Lapse Monitoring of Subsurface Fluid Flow using Parsimonious Seismic Interferometry

    KAUST Repository

    Hanafy, Sherif

    2017-04-21

    A typical small-scale seismic survey (such as 240 shot gathers) takes at least 16 working hours to be completed, which is a major obstacle in case of time-lapse monitoring experiments. This is especially true if the subject that needs to be monitored is rapidly changing. In this work, we will discuss how to decrease the recording time from 16 working hours to less than one hour of recording. Here, the virtual data has the same accuracy as the conventional data. We validate the efficacy of parsimonious seismic interferometry with the time-lapse mentoring idea with field examples, where we were able to record 30 different data sets within a 2-hour period. The recorded data are then processed to generate 30 snapshots that shows the spread of water from the ground surface down to a few meters.

  16. Singular Spectrum Analysis for Astronomical Time Series: Constructing a Parsimonious Hypothesis Test

    Science.gov (United States)

    Greco, G.; Kondrashov, D.; Kobayashi, S.; Ghil, M.; Branchesi, M.; Guidorzi, C.; Stratta, G.; Ciszak, M.; Marino, F.; Ortolan, A.

    We present a data-adaptive spectral method - Monte Carlo Singular Spectrum Analysis (MC-SSA) - and its modification to tackle astrophysical problems. Through numerical simulations we show the ability of the MC-SSA in dealing with 1/f β power-law noise affected by photon counting statistics. Such noise process is simulated by a first-order autoregressive, AR(1) process corrupted by intrinsic Poisson noise. In doing so, we statistically estimate a basic stochastic variation of the source and the corresponding fluctuations due to the quantum nature of light. In addition, MC-SSA test retains its effectiveness even when a significant percentage of the signal falls below a certain level of detection, e.g., caused by the instrument sensitivity. The parsimonious approach presented here may be broadly applied, from the search for extrasolar planets to the extraction of low-intensity coherent phenomena probably hidden in high energy transients.

  17. On the Accuracy of Ancestral Sequence Reconstruction for Ultrametric Trees with Parsimony.

    Science.gov (United States)

    Herbst, Lina; Fischer, Mareike

    2018-04-01

    We examine a mathematical question concerning the reconstruction accuracy of the Fitch algorithm for reconstructing the ancestral sequence of the most recent common ancestor given a phylogenetic tree and sequence data for all taxa under consideration. In particular, for the symmetric four-state substitution model which is also known as Jukes-Cantor model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that for any ultrametric phylogenetic tree and a symmetric model, the Fitch parsimony method using all terminal taxa is more accurate, or at least as accurate, for ancestral state reconstruction than using any particular terminal taxon or any particular pair of taxa. This conjecture had so far only been answered for two-state data by Fischer and Thatte. Here, we focus on answering the biologically more relevant case with four states, which corresponds to ancestral sequence reconstruction from DNA or RNA data.

  18. Hypothesis of the Disappearance of the Limits of Improvidence and Parsimony in the Function of Consumption in an Islamic Economy

    Directory of Open Access Journals (Sweden)

    محمد أحمد حسن الأفندي

    2018-04-01

    Full Text Available There is a rich literature about the analysis of consumption behavior from the perspective of Islamic economy. The focus of such literature has been on the incorporation of the effect of moral values on individuals’ consumption behavior. However, studies on consumption did not pay enough heed to the analysis of the ultimate effect of faith values on the track of consumption behavior over time. This desired track of consumption involves showing certain hypotheses and probabilities. This study suggests a normative statement which includes the gradual disappearance of parsimony and improvidence over time. This disappearance would correct the deviation of actual consumption of society members from the desired moderate consumption level, so as to make households’ consumption behavior at the desired level which is consistent with Islamic Sharia. The study emphasizes the need to develop analysis and research in two integrated directions: i conducting more empirical studies to examine the consistency of the normative statement with evidence from real situations, and ii conducting more analysis to develop a specific measure for the desired consumption levels as well as the limits of parsimony and improvidence. Keywords: Disappearance of improvidence and parsimony limits, Desired moderate consumption level, Actual consumption, Improvidence and parsimony consumption levels, Track of households’ consumption behavior.

  19. Phylogenetic relationships of click beetles (Coleoptera: Elateridae) inferred from 28S ribosomal DNA: insights into the evolution of bioluminescence in Elateridae.

    Science.gov (United States)

    Sagegami-Oba, Reiko; Oba, Yuichi; Ohira, Hitoo

    2007-02-01

    Although the taxonomy of click beetles (family Elateridae) has been studied extensively, inconsistencies remain. We examine here the relationships between species of Elateridae based on partial sequences of nuclear 28S ribosomal DNA. Specimens were collected primarily from Japan, while luminous click beetles were also sampled from Central and South America to investigate the origins of bioluminescence in Elateridae. Neighbor-joining, maximum-parsimony, and maximum-likelihood analyses produced a consistent basal topology with high statistical support that is partially congruent with the results of previous investigations based on the morphological characteristics of larvae and adults. The most parsimonious reconstruction of the "luminous" and "nonluminous" states, based on the present molecular phylogeny, indicates that the ancestral state of Elateridae was nonluminous. This suggests that the bioluminescence in click beetle evolved independent of that of other luminous beetles, such as Lampyridae, despite their common mechanisms of bioluminescence.

  20. The efficiency of different search strategies in estimating parsimony jackknife, bootstrap, and Bremer support

    Directory of Open Access Journals (Sweden)

    Müller Kai F

    2005-10-01

    Full Text Available Abstract Background For parsimony analyses, the most common way to estimate confidence is by resampling plans (nonparametric bootstrap, jackknife, and Bremer support (Decay indices. The recent literature reveals that parameter settings that are quite commonly employed are not those that are recommended by theoretical considerations and by previous empirical studies. The optimal search strategy to be applied during resampling was previously addressed solely via standard search strategies available in PAUP*. The question of a compromise between search extensiveness and improved support accuracy for Bremer support received even less attention. A set of experiments was conducted on different datasets to find an empirical cut-off point at which increased search extensiveness does not significantly change Bremer support and jackknife or bootstrap proportions any more. Results For the number of replicates needed for accurate estimates of support in resampling plans, a diagram is provided that helps to address the question whether apparently different support values really differ significantly. It is shown that the use of random addition cycles and parsimony ratchet iterations during bootstrapping does not translate into higher support, nor does any extension of the search extensiveness beyond the rather moderate effort of TBR (tree bisection and reconnection branch swapping plus saving one tree per replicate. Instead, in case of very large matrices, saving more than one shortest tree per iteration and using a strict consensus tree of these yields decreased support compared to saving only one tree. This can be interpreted as a small risk of overestimating support but should be more than compensated by other factors that counteract an enhanced type I error. With regard to Bremer support, a rule of thumb can be derived stating that not much is gained relative to the surplus computational effort when searches are extended beyond 20 ratchet iterations per

  1. Anelastic sensitivity kernels with parsimonious storage for adjoint tomography and full waveform inversion

    KAUST Repository

    Komatitsch, Dimitri

    2016-06-13

    We introduce a technique to compute exact anelastic sensitivity kernels in the time domain using parsimonious disk storage. The method is based on a reordering of the time loop of time-domain forward/adjoint wave propagation solvers combined with the use of a memory buffer. It avoids instabilities that occur when time-reversing dissipative wave propagation simulations. The total number of required time steps is unchanged compared to usual acoustic or elastic approaches. The cost is reduced by a factor of 4/3 compared to the case in which anelasticity is partially accounted for by accommodating the effects of physical dispersion. We validate our technique by performing a test in which we compare the Kα sensitivity kernel to the exact kernel obtained by saving the entire forward calculation. This benchmark confirms that our approach is also exact. We illustrate the importance of including full attenuation in the calculation of sensitivity kernels by showing significant differences with physical-dispersion-only kernels.

  2. Parsimonious data: How a single Facebook like predicts voting behavior in multiparty systems.

    Directory of Open Access Journals (Sweden)

    Jakob Bæk Kristensen

    Full Text Available This study shows how liking politicians' public Facebook posts can be used as an accurate measure for predicting present-day voter intention in a multiparty system. We highlight that a few, but selective digital traces produce prediction accuracies that are on par or even greater than most current approaches based upon bigger and broader datasets. Combining the online and offline, we connect a subsample of surveyed respondents to their public Facebook activity and apply machine learning classifiers to explore the link between their political liking behaviour and actual voting intention. Through this work, we show that even a single selective Facebook like can reveal as much about political voter intention as hundreds of heterogeneous likes. Further, by including the entire political like history of the respondents, our model reaches prediction accuracies above previous multiparty studies (60-70%. The main contribution of this paper is to show how public like-activity on Facebook allows political profiling of individual users in a multiparty system with accuracies above previous studies. Beside increased accuracies, the paper shows how such parsimonious measures allows us to generalize our findings to the entire population of a country and even across national borders, to other political multiparty systems. The approach in this study relies on data that are publicly available, and the simple setup we propose can with some limitations, be generalized to millions of users in other multiparty systems.

  3. An integer programming formulation of the parsimonious loss of heterozygosity problem.

    Science.gov (United States)

    Catanzaro, Daniele; Labbé, Martine; Halldórsson, Bjarni V

    2013-01-01

    A loss of heterozygosity (LOH) event occurs when, by the laws of Mendelian inheritance, an individual should be heterozygote at a given site but, due to a deletion polymorphism, is not. Deletions play an important role in human disease and their detection could provide fundamental insights for the development of new diagnostics and treatments. In this paper, we investigate the parsimonious loss of heterozygosity problem (PLOHP), i.e., the problem of partitioning suspected polymorphisms from a set of individuals into a minimum number of deletion areas. Specifically, we generalize Halldórsson et al.'s work by providing a more general formulation of the PLOHP and by showing how one can incorporate different recombination rates and prior knowledge about the locations of deletions. Moreover, we show that the PLOHP can be formulated as a specific version of the clique partition problem in a particular class of graphs called undirected catch-point interval graphs and we prove its general $({\\cal NP})$-hardness. Finally, we provide a state-of-the-art integer programming (IP) formulation and strengthening valid inequalities to exactly solve real instances of the PLOHP containing up to 9,000 individuals and 3,000 SNPs. Our results give perspectives on the mathematics of the PLOHP and suggest new directions on the development of future efficient exact solution approaches.

  4. Anelastic sensitivity kernels with parsimonious storage for adjoint tomography and full waveform inversion

    KAUST Repository

    Komatitsch, Dimitri; Xie, Zhinan; Bozdağ, Ebru; de Andrade, Elliott Sales; Peter, Daniel; Liu, Qinya; Tromp, Jeroen

    2016-01-01

    We introduce a technique to compute exact anelastic sensitivity kernels in the time domain using parsimonious disk storage. The method is based on a reordering of the time loop of time-domain forward/adjoint wave propagation solvers combined with the use of a memory buffer. It avoids instabilities that occur when time-reversing dissipative wave propagation simulations. The total number of required time steps is unchanged compared to usual acoustic or elastic approaches. The cost is reduced by a factor of 4/3 compared to the case in which anelasticity is partially accounted for by accommodating the effects of physical dispersion. We validate our technique by performing a test in which we compare the Kα sensitivity kernel to the exact kernel obtained by saving the entire forward calculation. This benchmark confirms that our approach is also exact. We illustrate the importance of including full attenuation in the calculation of sensitivity kernels by showing significant differences with physical-dispersion-only kernels.

  5. Stochastic rainfall modeling in West Africa: Parsimonious approaches for domestic rainwater harvesting assessment

    Science.gov (United States)

    Cowden, Joshua R.; Watkins, David W., Jr.; Mihelcic, James R.

    2008-10-01

    SummarySeveral parsimonious stochastic rainfall models are developed and compared for application to domestic rainwater harvesting (DRWH) assessment in West Africa. Worldwide, improved water access rates are lowest for Sub-Saharan Africa, including the West African region, and these low rates have important implications on the health and economy of the region. Domestic rainwater harvesting (DRWH) is proposed as a potential mechanism for water supply enhancement, especially for the poor urban households in the region, which is essential for development planning and poverty alleviation initiatives. The stochastic rainfall models examined are Markov models and LARS-WG, selected due to availability and ease of use for water planners in the developing world. A first-order Markov occurrence model with a mixed exponential amount model is selected as the best option for unconditioned Markov models. However, there is no clear advantage in selecting Markov models over the LARS-WG model for DRWH in West Africa, with each model having distinct strengths and weaknesses. A multi-model approach is used in assessing DRWH in the region to illustrate the variability associated with the rainfall models. It is clear DRWH can be successfully used as a water enhancement mechanism in West Africa for certain times of the year. A 200 L drum storage capacity could potentially optimize these simple, small roof area systems for many locations in the region.

  6. Anelastic sensitivity kernels with parsimonious storage for adjoint tomography and full waveform inversion

    Science.gov (United States)

    Komatitsch, Dimitri; Xie, Zhinan; Bozdaǧ, Ebru; Sales de Andrade, Elliott; Peter, Daniel; Liu, Qinya; Tromp, Jeroen

    2016-09-01

    We introduce a technique to compute exact anelastic sensitivity kernels in the time domain using parsimonious disk storage. The method is based on a reordering of the time loop of time-domain forward/adjoint wave propagation solvers combined with the use of a memory buffer. It avoids instabilities that occur when time-reversing dissipative wave propagation simulations. The total number of required time steps is unchanged compared to usual acoustic or elastic approaches. The cost is reduced by a factor of 4/3 compared to the case in which anelasticity is partially accounted for by accommodating the effects of physical dispersion. We validate our technique by performing a test in which we compare the Kα sensitivity kernel to the exact kernel obtained by saving the entire forward calculation. This benchmark confirms that our approach is also exact. We illustrate the importance of including full attenuation in the calculation of sensitivity kernels by showing significant differences with physical-dispersion-only kernels.

  7. An objective and parsimonious approach for classifying natural flow regimes at a continental scale

    Science.gov (United States)

    Archfield, S. A.; Kennen, J.; Carlisle, D.; Wolock, D.

    2013-12-01

    Hydroecological stream classification--the process of grouping streams by similar hydrologic responses and, thereby, similar aquatic habitat--has been widely accepted and is often one of the first steps towards developing ecological flow targets. Despite its importance, the last national classification of streamgauges was completed about 20 years ago. A new classification of 1,534 streamgauges in the contiguous United States is presented using a novel and parsimonious approach to understand similarity in ecological streamflow response. This new classification approach uses seven fundamental daily streamflow statistics (FDSS) rather than winnowing down an uncorrelated subset from 200 or more ecologically relevant streamflow statistics (ERSS) commonly used in hydroecological classification studies. The results of this investigation demonstrate that the distributions of 33 tested ERSS are consistently different among the classes derived from the seven FDSS. It is further shown that classification based solely on the 33 ERSS generally does a poorer job in grouping similar streamgauges than the classification based on the seven FDSS. This new classification approach has the additional advantages of overcoming some of the subjectivity associated with the selection of the classification variables and provides a set of robust continental-scale classes of US streamgauges.

  8. Failed refutations: further comments on parsimony and likelihood methods and their relationship to Popper's degree of corroboration.

    Science.gov (United States)

    de Queiroz, Kevin; Poe, Steven

    2003-06-01

    Kluge's (2001, Syst. Biol. 50:322-330) continued arguments that phylogenetic methods based on the statistical principle of likelihood are incompatible with the philosophy of science described by Karl Popper are based on false premises related to Kluge's misrepresentations of Popper's philosophy. Contrary to Kluge's conjectures, likelihood methods are not inherently verificationist; they do not treat every instance of a hypothesis as confirmation of that hypothesis. The historical nature of phylogeny does not preclude phylogenetic hypotheses from being evaluated using the probability of evidence. The low absolute probabilities of hypotheses are irrelevant to the correct interpretation of Popper's concept termed degree of corroboration, which is defined entirely in terms of relative probabilities. Popper did not advocate minimizing background knowledge; in any case, the background knowledge of both parsimony and likelihood methods consists of the general assumption of descent with modification and additional assumptions that are deterministic, concerning which tree is considered most highly corroborated. Although parsimony methods do not assume (in the sense of entailing) that homoplasy is rare, they do assume (in the sense of requiring to obtain a correct phylogenetic inference) certain things about patterns of homoplasy. Both parsimony and likelihood methods assume (in the sense of implying by the manner in which they operate) various things about evolutionary processes, although violation of those assumptions does not always cause the methods to yield incorrect phylogenetic inferences. Test severity is increased by sampling additional relevant characters rather than by character reanalysis, although either interpretation is compatible with the use of phylogenetic likelihood methods. Neither parsimony nor likelihood methods assess test severity (critical evidence) when used to identify a most highly corroborated tree(s) based on a single method or model and a

  9. Maximum Acceleration Recording Circuit

    Science.gov (United States)

    Bozeman, Richard J., Jr.

    1995-01-01

    Coarsely digitized maximum levels recorded in blown fuses. Circuit feeds power to accelerometer and makes nonvolatile record of maximum level to which output of accelerometer rises during measurement interval. In comparison with inertia-type single-preset-trip-point mechanical maximum-acceleration-recording devices, circuit weighs less, occupies less space, and records accelerations within narrower bands of uncertainty. In comparison with prior electronic data-acquisition systems designed for same purpose, circuit simpler, less bulky, consumes less power, costs and analysis of data recorded in magnetic or electronic memory devices. Circuit used, for example, to record accelerations to which commodities subjected during transportation on trucks.

  10. Maximum Quantum Entropy Method

    OpenAIRE

    Sim, Jae-Hoon; Han, Myung Joon

    2018-01-01

    Maximum entropy method for analytic continuation is extended by introducing quantum relative entropy. This new method is formulated in terms of matrix-valued functions and therefore invariant under arbitrary unitary transformation of input matrix. As a result, the continuation of off-diagonal elements becomes straightforward. Without introducing any further ambiguity, the Bayesian probabilistic interpretation is maintained just as in the conventional maximum entropy method. The applications o...

  11. Maximum power demand cost

    International Nuclear Information System (INIS)

    Biondi, L.

    1998-01-01

    The charging for a service is a supplier's remuneration for the expenses incurred in providing it. There are currently two charges for electricity: consumption and maximum demand. While no problem arises about the former, the issue is more complicated for the latter and the analysis in this article tends to show that the annual charge for maximum demand arbitrarily discriminates among consumer groups, to the disadvantage of some [it

  12. Modeling the isotopic evolution of snowpack and snowmelt: Testing a spatially distributed parsimonious approach.

    Science.gov (United States)

    Ala-Aho, Pertti; Tetzlaff, Doerthe; McNamara, James P; Laudon, Hjalmar; Kormos, Patrick; Soulsby, Chris

    2017-07-01

    Use of stable water isotopes has become increasingly popular in quantifying water flow paths and travel times in hydrological systems using tracer-aided modeling. In snow-influenced catchments, snowmelt produces a traceable isotopic signal, which differs from original snowfall isotopic composition because of isotopic fractionation in the snowpack. These fractionation processes in snow are relatively well understood, but representing their spatiotemporal variability in tracer-aided studies remains a challenge. We present a novel, parsimonious modeling method to account for the snowpack isotope fractionation and estimate isotope ratios in snowmelt water in a fully spatially distributed manner. Our model introduces two calibration parameters that alone account for the isotopic fractionation caused by sublimation from interception and ground snow storage, and snowmelt fractionation progressively enriching the snowmelt runoff. The isotope routines are linked to a generic process-based snow interception-accumulation-melt model facilitating simulation of spatially distributed snowmelt runoff. We use a synthetic modeling experiment to demonstrate the functionality of the model algorithms in different landscape locations and under different canopy characteristics. We also provide a proof-of-concept model test and successfully reproduce isotopic ratios in snowmelt runoff sampled with snowmelt lysimeters in two long-term experimental catchment with contrasting winter conditions. To our knowledge, the method is the first such tool to allow estimation of the spatially distributed nature of isotopic fractionation in snowpacks and the resulting isotope ratios in snowmelt runoff. The method can thus provide a useful tool for tracer-aided modeling to better understand the integrated nature of flow, mixing, and transport processes in snow-influenced catchments.

  13. Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles.

    Directory of Open Access Journals (Sweden)

    Bin Lu

    Full Text Available The phylogenetic position of turtles within the vertebrate tree of life remains controversial. Conflicting conclusions from different studies are likely a consequence of systematic error in the tree construction process, rather than random error from small amounts of data. Using genomic data, we evaluate the phylogenetic position of turtles with both conventional concatenated data analysis and a "genes as characters" approach. Two datasets were constructed, one with seven species (human, opossum, zebra finch, chicken, green anole, Chinese pond turtle, and western clawed frog and 4584 orthologous genes, and the second with four additional species (soft-shelled turtle, Nile crocodile, royal python, and tuatara but only 1638 genes. Our concatenated data analysis strongly supported turtle as the sister-group to archosaurs (the archosaur hypothesis, similar to several recent genomic data based studies using similar methods. When using genes as characters and gene trees as character-state trees with equal weighting for each gene, however, our parsimony analysis suggested that turtles are possibly sister-group to diapsids, archosaurs, or lepidosaurs. None of these resolutions were strongly supported by bootstraps. Furthermore, our incongruence analysis clearly demonstrated that there is a large amount of inconsistency among genes and most of the conflict relates to the placement of turtles. We conclude that the uncertain placement of turtles is a reflection of the true state of nature. Concatenated data analysis of large and heterogeneous datasets likely suffers from systematic error and over-estimates of confidence as a consequence of a large number of characters. Using genes as characters offers an alternative for phylogenomic analysis. It has potential to reduce systematic error, such as data heterogeneity and long-branch attraction, and it can also avoid problems associated with computation time and model selection. Finally, treating genes as

  14. Parsimonious model for blood glucose level monitoring in type 2 diabetes patients.

    Science.gov (United States)

    Zhao, Fang; Ma, Yan Fen; Wen, Jing Xiao; DU, Yan Fang; Li, Chun Lin; Li, Guang Wei

    2014-07-01

    To establish the parsimonious model for blood glucose monitoring in patients with type 2 diabetes receiving oral hypoglycemic agent treatment. One hundred and fifty-nine adult Chinese type 2 diabetes patients were randomized to receive rapid-acting or sustained-release gliclazide therapy for 12 weeks. Their blood glucose levels were measured at 10 time points in a 24 h period before and after treatment, and the 24 h mean blood glucose levels were measured. Contribution of blood glucose levels to the mean blood glucose level and HbA1c was assessed by multiple regression analysis. The correlation coefficients of blood glucose level measured at 10 time points to the daily MBG were 0.58-0.74 and 0.59-0.79, respectively, before and after treatment (Pblood glucose levels measured at 6 of the 10 time points could explain 95% and 97% of the changes in MBG before and after treatment. The three blood glucose levels, which were measured at fasting, 2 h after breakfast and before dinner, of the 10 time points could explain 84% and 86% of the changes in MBG before and after treatment, but could only explain 36% and 26% of the changes in HbA1c before and after treatment, and they had a poorer correlation with the HbA1c than with the 24 h MBG. The blood glucose levels measured at fasting, 2 h after breakfast and before dinner truly reflected the change 24 h blood glucose level, suggesting that they are appropriate for the self-monitoring of blood glucose levels in diabetes patients receiving oral anti-diabetes therapy. Copyright © 2014 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  15. Using Genes as Characters and a Parsimony Analysis to Explore the Phylogenetic Position of Turtles

    Science.gov (United States)

    Lu, Bin; Yang, Weizhao; Dai, Qiang; Fu, Jinzhong

    2013-01-01

    The phylogenetic position of turtles within the vertebrate tree of life remains controversial. Conflicting conclusions from different studies are likely a consequence of systematic error in the tree construction process, rather than random error from small amounts of data. Using genomic data, we evaluate the phylogenetic position of turtles with both conventional concatenated data analysis and a “genes as characters” approach. Two datasets were constructed, one with seven species (human, opossum, zebra finch, chicken, green anole, Chinese pond turtle, and western clawed frog) and 4584 orthologous genes, and the second with four additional species (soft-shelled turtle, Nile crocodile, royal python, and tuatara) but only 1638 genes. Our concatenated data analysis strongly supported turtle as the sister-group to archosaurs (the archosaur hypothesis), similar to several recent genomic data based studies using similar methods. When using genes as characters and gene trees as character-state trees with equal weighting for each gene, however, our parsimony analysis suggested that turtles are possibly sister-group to diapsids, archosaurs, or lepidosaurs. None of these resolutions were strongly supported by bootstraps. Furthermore, our incongruence analysis clearly demonstrated that there is a large amount of inconsistency among genes and most of the conflict relates to the placement of turtles. We conclude that the uncertain placement of turtles is a reflection of the true state of nature. Concatenated data analysis of large and heterogeneous datasets likely suffers from systematic error and over-estimates of confidence as a consequence of a large number of characters. Using genes as characters offers an alternative for phylogenomic analysis. It has potential to reduce systematic error, such as data heterogeneity and long-branch attraction, and it can also avoid problems associated with computation time and model selection. Finally, treating genes as characters

  16. Maximum likely scale estimation

    DEFF Research Database (Denmark)

    Loog, Marco; Pedersen, Kim Steenstrup; Markussen, Bo

    2005-01-01

    A maximum likelihood local scale estimation principle is presented. An actual implementation of the estimation principle uses second order moments of multiple measurements at a fixed location in the image. These measurements consist of Gaussian derivatives possibly taken at several scales and/or ...

  17. Robust Maximum Association Estimators

    NARCIS (Netherlands)

    A. Alfons (Andreas); C. Croux (Christophe); P. Filzmoser (Peter)

    2017-01-01

    textabstractThe maximum association between two multivariate variables X and Y is defined as the maximal value that a bivariate association measure between one-dimensional projections αX and αY can attain. Taking the Pearson correlation as projection index results in the first canonical correlation

  18. Urban micro-scale flood risk estimation with parsimonious hydraulic modelling and census data

    Directory of Open Access Journals (Sweden)

    C. Arrighi

    2013-05-01

    Full Text Available The adoption of 2007/60/EC Directive requires European countries to implement flood hazard and flood risk maps by the end of 2013. Flood risk is the product of flood hazard, vulnerability and exposure, all three to be estimated with comparable level of accuracy. The route to flood risk assessment is consequently much more than hydraulic modelling of inundation, that is hazard mapping. While hazard maps have already been implemented in many countries, quantitative damage and risk maps are still at a preliminary level. A parsimonious quasi-2-D hydraulic model is here adopted, having many advantages in terms of easy set-up. It is here evaluated as being accurate in flood depth estimation in urban areas with a high-resolution and up-to-date Digital Surface Model (DSM. The accuracy, estimated by comparison with marble-plate records of a historic flood in the city of Florence, is characterized in the downtown's most flooded area by a bias of a very few centimetres and a determination coefficient of 0.73. The average risk is found to be about 14 € m−2 yr−1, corresponding to about 8.3% of residents' income. The spatial distribution of estimated risk highlights a complex interaction between the flood pattern and the building characteristics. As a final example application, the estimated risk values have been used to compare different retrofitting measures. Proceeding through the risk estimation steps, a new micro-scale potential damage assessment method is proposed. This is based on the georeferenced census system as the optimal compromise between spatial detail and open availability of socio-economic data. The results of flood risk assessment at the census section scale resolve most of the risk spatial variability, and they can be easily aggregated to whatever upper scale is needed given that they are geographically defined as contiguous polygons. Damage is calculated through stage–damage curves, starting from census data on building type and

  19. Maximum power point tracking

    International Nuclear Information System (INIS)

    Enslin, J.H.R.

    1990-01-01

    A well engineered renewable remote energy system, utilizing the principal of Maximum Power Point Tracking can be m ore cost effective, has a higher reliability and can improve the quality of life in remote areas. This paper reports that a high-efficient power electronic converter, for converting the output voltage of a solar panel, or wind generator, to the required DC battery bus voltage has been realized. The converter is controlled to track the maximum power point of the input source under varying input and output parameters. Maximum power point tracking for relative small systems is achieved by maximization of the output current in a battery charging regulator, using an optimized hill-climbing, inexpensive microprocessor based algorithm. Through practical field measurements it is shown that a minimum input source saving of 15% on 3-5 kWh/day systems can easily be achieved. A total cost saving of at least 10-15% on the capital cost of these systems are achievable for relative small rating Remote Area Power Supply systems. The advantages at larger temperature variations and larger power rated systems are much higher. Other advantages include optimal sizing and system monitor and control

  20. Maximum entropy methods

    International Nuclear Information System (INIS)

    Ponman, T.J.

    1984-01-01

    For some years now two different expressions have been in use for maximum entropy image restoration and there has been some controversy over which one is appropriate for a given problem. Here two further entropies are presented and it is argued that there is no single correct algorithm. The properties of the four different methods are compared using simple 1D simulations with a view to showing how they can be used together to gain as much information as possible about the original object. (orig.)

  1. The last glacial maximum

    Science.gov (United States)

    Clark, P.U.; Dyke, A.S.; Shakun, J.D.; Carlson, A.E.; Clark, J.; Wohlfarth, B.; Mitrovica, J.X.; Hostetler, S.W.; McCabe, A.M.

    2009-01-01

    We used 5704 14C, 10Be, and 3He ages that span the interval from 10,000 to 50,000 years ago (10 to 50 ka) to constrain the timing of the Last Glacial Maximum (LGM) in terms of global ice-sheet and mountain-glacier extent. Growth of the ice sheets to their maximum positions occurred between 33.0 and 26.5 ka in response to climate forcing from decreases in northern summer insolation, tropical Pacific sea surface temperatures, and atmospheric CO2. Nearly all ice sheets were at their LGM positions from 26.5 ka to 19 to 20 ka, corresponding to minima in these forcings. The onset of Northern Hemisphere deglaciation 19 to 20 ka was induced by an increase in northern summer insolation, providing the source for an abrupt rise in sea level. The onset of deglaciation of the West Antarctic Ice Sheet occurred between 14 and 15 ka, consistent with evidence that this was the primary source for an abrupt rise in sea level ???14.5 ka.

  2. Maximum Entropy Fundamentals

    Directory of Open Access Journals (Sweden)

    F. Topsøe

    2001-09-01

    Full Text Available Abstract: In its modern formulation, the Maximum Entropy Principle was promoted by E.T. Jaynes, starting in the mid-fifties. The principle dictates that one should look for a distribution, consistent with available information, which maximizes the entropy. However, this principle focuses only on distributions and it appears advantageous to bring information theoretical thinking more prominently into play by also focusing on the "observer" and on coding. This view was brought forward by the second named author in the late seventies and is the view we will follow-up on here. It leads to the consideration of a certain game, the Code Length Game and, via standard game theoretical thinking, to a principle of Game Theoretical Equilibrium. This principle is more basic than the Maximum Entropy Principle in the sense that the search for one type of optimal strategies in the Code Length Game translates directly into the search for distributions with maximum entropy. In the present paper we offer a self-contained and comprehensive treatment of fundamentals of both principles mentioned, based on a study of the Code Length Game. Though new concepts and results are presented, the reading should be instructional and accessible to a rather wide audience, at least if certain mathematical details are left aside at a rst reading. The most frequently studied instance of entropy maximization pertains to the Mean Energy Model which involves a moment constraint related to a given function, here taken to represent "energy". This type of application is very well known from the literature with hundreds of applications pertaining to several different elds and will also here serve as important illustration of the theory. But our approach reaches further, especially regarding the study of continuity properties of the entropy function, and this leads to new results which allow a discussion of models with so-called entropy loss. These results have tempted us to speculate over

  3. Probable maximum flood control

    International Nuclear Information System (INIS)

    DeGabriele, C.E.; Wu, C.L.

    1991-11-01

    This study proposes preliminary design concepts to protect the waste-handling facilities and all shaft and ramp entries to the underground from the probable maximum flood (PMF) in the current design configuration for the proposed Nevada Nuclear Waste Storage Investigation (NNWSI) repository protection provisions were furnished by the United States Bureau of Reclamation (USSR) or developed from USSR data. Proposed flood protection provisions include site grading, drainage channels, and diversion dikes. Figures are provided to show these proposed flood protection provisions at each area investigated. These areas are the central surface facilities (including the waste-handling building and waste treatment building), tuff ramp portal, waste ramp portal, men-and-materials shaft, emplacement exhaust shaft, and exploratory shafts facility

  4. Introduction to maximum entropy

    International Nuclear Information System (INIS)

    Sivia, D.S.

    1988-01-01

    The maximum entropy (MaxEnt) principle has been successfully used in image reconstruction in a wide variety of fields. We review the need for such methods in data analysis and show, by use of a very simple example, why MaxEnt is to be preferred over other regularizing functions. This leads to a more general interpretation of the MaxEnt method, and its use is illustrated with several different examples. Practical difficulties with non-linear problems still remain, this being highlighted by the notorious phase problem in crystallography. We conclude with an example from neutron scattering, using data from a filter difference spectrometer to contrast MaxEnt with a conventional deconvolution. 12 refs., 8 figs., 1 tab

  5. Solar maximum observatory

    International Nuclear Information System (INIS)

    Rust, D.M.

    1984-01-01

    The successful retrieval and repair of the Solar Maximum Mission (SMM) satellite by Shuttle astronauts in April 1984 permitted continuance of solar flare observations that began in 1980. The SMM carries a soft X ray polychromator, gamma ray, UV and hard X ray imaging spectrometers, a coronagraph/polarimeter and particle counters. The data gathered thus far indicated that electrical potentials of 25 MeV develop in flares within 2 sec of onset. X ray data show that flares are composed of compressed magnetic loops that have come too close together. Other data have been taken on mass ejection, impacts of electron beams and conduction fronts with the chromosphere and changes in the solar radiant flux due to sunspots. 13 references

  6. Introduction to maximum entropy

    International Nuclear Information System (INIS)

    Sivia, D.S.

    1989-01-01

    The maximum entropy (MaxEnt) principle has been successfully used in image reconstruction in a wide variety of fields. The author reviews the need for such methods in data analysis and shows, by use of a very simple example, why MaxEnt is to be preferred over other regularizing functions. This leads to a more general interpretation of the MaxEnt method, and its use is illustrated with several different examples. Practical difficulties with non-linear problems still remain, this being highlighted by the notorious phase problem in crystallography. He concludes with an example from neutron scattering, using data from a filter difference spectrometer to contrast MaxEnt with a conventional deconvolution. 12 refs., 8 figs., 1 tab

  7. Functional Maximum Autocorrelation Factors

    DEFF Research Database (Denmark)

    Larsen, Rasmus; Nielsen, Allan Aasbjerg

    2005-01-01

    MAF outperforms the functional PCA in concentrating the interesting' spectra/shape variation in one end of the eigenvalue spectrum and allows for easier interpretation of effects. Conclusions. Functional MAF analysis is a useful methods for extracting low dimensional models of temporally or spatially......Purpose. We aim at data where samples of an underlying function are observed in a spatial or temporal layout. Examples of underlying functions are reflectance spectra and biological shapes. We apply functional models based on smoothing splines and generalize the functional PCA in......\\verb+~+\\$\\backslash\\$cite{ramsay97} to functional maximum autocorrelation factors (MAF)\\verb+~+\\$\\backslash\\$cite{switzer85,larsen2001d}. We apply the method to biological shapes as well as reflectance spectra. {\\$\\backslash\\$bf Methods}. MAF seeks linear combination of the original variables that maximize autocorrelation between...

  8. Regularized maximum correntropy machine

    KAUST Repository

    Wang, Jim Jing-Yan; Wang, Yunji; Jing, Bing-Yi; Gao, Xin

    2015-01-01

    In this paper we investigate the usage of regularized correntropy framework for learning of classifiers from noisy labels. The class label predictors learned by minimizing transitional loss functions are sensitive to the noisy and outlying labels of training samples, because the transitional loss functions are equally applied to all the samples. To solve this problem, we propose to learn the class label predictors by maximizing the correntropy between the predicted labels and the true labels of the training samples, under the regularized Maximum Correntropy Criteria (MCC) framework. Moreover, we regularize the predictor parameter to control the complexity of the predictor. The learning problem is formulated by an objective function considering the parameter regularization and MCC simultaneously. By optimizing the objective function alternately, we develop a novel predictor learning algorithm. The experiments on two challenging pattern classification tasks show that it significantly outperforms the machines with transitional loss functions.

  9. Regularized maximum correntropy machine

    KAUST Repository

    Wang, Jim Jing-Yan

    2015-02-12

    In this paper we investigate the usage of regularized correntropy framework for learning of classifiers from noisy labels. The class label predictors learned by minimizing transitional loss functions are sensitive to the noisy and outlying labels of training samples, because the transitional loss functions are equally applied to all the samples. To solve this problem, we propose to learn the class label predictors by maximizing the correntropy between the predicted labels and the true labels of the training samples, under the regularized Maximum Correntropy Criteria (MCC) framework. Moreover, we regularize the predictor parameter to control the complexity of the predictor. The learning problem is formulated by an objective function considering the parameter regularization and MCC simultaneously. By optimizing the objective function alternately, we develop a novel predictor learning algorithm. The experiments on two challenging pattern classification tasks show that it significantly outperforms the machines with transitional loss functions.

  10. Patterns and effects of GC3 heterogeneity and parsimony informative sites on the phylogenetic tree of genes.

    Science.gov (United States)

    Ma, Shuai; Wu, Qi; Hu, Yibo; Wei, Fuwen

    2018-05-20

    The explosive growth in genomic data has provided novel insights into the conflicting signals hidden in phylogenetic trees. Although some studies have explored the effects of the GC content and parsimony informative sites (PIS) on the phylogenetic tree, the effect of the heterogeneity of the GC content at the first/second/third codon position on parsimony informative sites (GC1/2/3 PIS ) among different species and the effect of PIS on phylogenetic tree construction remain largely unexplored. Here, we used two different mammal genomic datasets to explore the patterns of GC1/2/3 PIS heterogeneity and the effect of PIS on the phylogenetic tree of genes: (i) all GC1/2/3 PIS have obvious heterogeneity between different mammals, and the levels of heterogeneity are GC3 PIS  > GC2 PIS  > GC1 PIS ; (ii) the number of PIS is positively correlated with the metrics of "good" gene tree topologies, and excluding the third codon position (C3) decreases the quality of gene trees by removing too many PIS. These results provide novel insights into the heterogeneity pattern of GC1/2/3 PIS in mammals and the relationship between GC3/PIS and gene trees. Additionally, it is necessary to carefully consider whether to exclude C3 to improve the quality of gene trees, especially in the super-tree method. Copyright © 2018 Elsevier B.V. All rights reserved.

  11. Balancing practicality and hydrologic realism: a parsimonious approach for simulating rapid groundwater recharge via unsaturated-zone preferential flow

    Science.gov (United States)

    Mirus, Benjamin B.; Nimmo, J.R.

    2013-01-01

    The impact of preferential flow on recharge and contaminant transport poses a considerable challenge to water-resources management. Typical hydrologic models require extensive site characterization, but can underestimate fluxes when preferential flow is significant. A recently developed source-responsive model incorporates film-flow theory with conservation of mass to estimate unsaturated-zone preferential fluxes with readily available data. The term source-responsive describes the sensitivity of preferential flow in response to water availability at the source of input. We present the first rigorous tests of a parsimonious formulation for simulating water table fluctuations using two case studies, both in arid regions with thick unsaturated zones of fractured volcanic rock. Diffuse flow theory cannot adequately capture the observed water table responses at both sites; the source-responsive model is a viable alternative. We treat the active area fraction of preferential flow paths as a scaled function of water inputs at the land surface then calibrate the macropore density to fit observed water table rises. Unlike previous applications, we allow the characteristic film-flow velocity to vary, reflecting the lag time between source and deep water table responses. Analysis of model performance and parameter sensitivity for the two case studies underscores the importance of identifying thresholds for initiation of film flow in unsaturated rocks, and suggests that this parsimonious approach is potentially of great practical value.

  12. Solar maximum mission

    International Nuclear Information System (INIS)

    Ryan, J.

    1981-01-01

    By understanding the sun, astrophysicists hope to expand this knowledge to understanding other stars. To study the sun, NASA launched a satellite on February 14, 1980. The project is named the Solar Maximum Mission (SMM). The satellite conducted detailed observations of the sun in collaboration with other satellites and ground-based optical and radio observations until its failure 10 months into the mission. The main objective of the SMM was to investigate one aspect of solar activity: solar flares. A brief description of the flare mechanism is given. The SMM satellite was valuable in providing information on where and how a solar flare occurs. A sequence of photographs of a solar flare taken from SMM satellite shows how a solar flare develops in a particular layer of the solar atmosphere. Two flares especially suitable for detailed observations by a joint effort occurred on April 30 and May 21 of 1980. These flares and observations of the flares are discussed. Also discussed are significant discoveries made by individual experiments

  13. The dynamic effect of exchange-rate volatility on Turkish exports: Parsimonious error-correction model approach

    Directory of Open Access Journals (Sweden)

    Demirhan Erdal

    2015-01-01

    Full Text Available This paper aims to investigate the effect of exchange-rate stability on real export volume in Turkey, using monthly data for the period February 2001 to January 2010. The Johansen multivariate cointegration method and the parsimonious error-correction model are applied to determine long-run and short-run relationships between real export volume and its determinants. In this study, the conditional variance of the GARCH (1, 1 model is taken as a proxy for exchange-rate stability, and generalized impulse-response functions and variance-decomposition analyses are applied to analyze the dynamic effects of variables on real export volume. The empirical findings suggest that exchangerate stability has a significant positive effect on real export volume, both in the short and the long run.

  14. Prediction of dissolved reactive phosphorus losses from small agricultural catchments: calibration and validation of a parsimonious model

    Directory of Open Access Journals (Sweden)

    C. Hahn

    2013-10-01

    Full Text Available Eutrophication of surface waters due to diffuse phosphorus (P losses continues to be a severe water quality problem worldwide, causing the loss of ecosystem functions of the respective water bodies. Phosphorus in runoff often originates from a small fraction of a catchment only. Targeting mitigation measures to these critical source areas (CSAs is expected to be most efficient and cost-effective, but requires suitable tools. Here we investigated the capability of the parsimonious Rainfall-Runoff-Phosphorus (RRP model to identify CSAs in grassland-dominated catchments based on readily available soil and topographic data. After simultaneous calibration on runoff data from four small hilly catchments on the Swiss Plateau, the model was validated on a different catchment in the same region without further calibration. The RRP model adequately simulated the discharge and dissolved reactive P (DRP export from the validation catchment. Sensitivity analysis showed that the model predictions were robust with respect to the classification of soils into "poorly drained" and "well drained", based on the available soil map. Comparing spatial hydrological model predictions with field data from the validation catchment provided further evidence that the assumptions underlying the model are valid and that the model adequately accounts for the dominant P export processes in the target region. Thus, the parsimonious RRP model is a valuable tool that can be used to determine CSAs. Despite the considerable predictive uncertainty regarding the spatial extent of CSAs, the RRP can provide guidance for the implementation of mitigation measures. The model helps to identify those parts of a catchment where high DRP losses are expected or can be excluded with high confidence. Legacy P was predicted to be the dominant source for DRP losses and thus, in combination with hydrologic active areas, a high risk for water quality.

  15. Innovative Bayesian and Parsimony Phylogeny of Dung Beetles (Coleoptera, Scarabaeidae, Scarabaeinae) Enhanced by Ontology-Based Partitioning of Morphological Characters

    Science.gov (United States)

    Tarasov, Sergei; Génier, François

    2015-01-01

    Scarabaeine dung beetles are the dominant dung feeding group of insects and are widely used as model organisms in conservation, ecology and developmental biology. Due to the conflicts among 13 recently published phylogenies dealing with the higher-level relationships of dung beetles, the phylogeny of this lineage remains largely unresolved. In this study, we conduct rigorous phylogenetic analyses of dung beetles, based on an unprecedented taxon sample (110 taxa) and detailed investigation of morphology (205 characters). We provide the description of morphology and thoroughly illustrate the used characters. Along with parsimony, traditionally used in the analysis of morphological data, we also apply the Bayesian method with a novel approach that uses anatomy ontology for matrix partitioning. This approach allows for heterogeneity in evolutionary rates among characters from different anatomical regions. Anatomy ontology generates a number of parameter-partition schemes which we compare using Bayes factor. We also test the effect of inclusion of autapomorphies in the morphological analysis, which hitherto has not been examined. Generally, schemes with more parameters were favored in the Bayesian comparison suggesting that characters located on different body regions evolve at different rates and that partitioning of the data matrix using anatomy ontology is reasonable; however, trees from the parsimony and all the Bayesian analyses were quite consistent. The hypothesized phylogeny reveals many novel clades and provides additional support for some clades recovered in previous analyses. Our results provide a solid basis for a new classification of dung beetles, in which the taxonomic limits of the tribes Dichotomiini, Deltochilini and Coprini are restricted and many new tribes must be described. Based on the consistency of the phylogeny with biogeography, we speculate that dung beetles may have originated in the Mesozoic contrary to the traditional view pointing to a

  16. Evolutionary position of Peruvian land snails (Orthalicidae among Stylommatophora (Mollusca: Gastropoda

    Directory of Open Access Journals (Sweden)

    Jorge Ramirez

    2011-07-01

    Full Text Available The genera Bostryx and Scutalus (Orthalicidae: Bulimulinae are endemics from South America. They are mainly distributed on the western slopes of the Peruvian Andes. The goal of the present work was to assess their evolutionary position among the stylommatophoran gastropods based on the 16S rRNA mitochondrial marker. Four sequences were obtained, and along with 28 sequences of other Stylommatophora retrieved from the GenBank, were aligned with ClustalX. The phylogenetic reconstruction was carried out using the methods of Neighbor-Joining, Maximum Parsimony, Maximum Likelihood and Bayesian inference. The multiple sequence alignment had 371 sites, with indels. The two genera of the family Orthalicidae for the first time included in a molecular phylogeny (Bostryx and Scutalus, formed a monophyletic group along with another member of the superfamily Orthalicoidea (Placostylus, result that is comparable with that obtained with nuclear markers. Their evolutionary relationship with other land snails is also discussed.

  17. Mitochondrial COI and morphological specificity of the mealy aphids (Hyalopterus ssp. collected from different hosts in Europe (Hemiptera, Aphididae

    Directory of Open Access Journals (Sweden)

    Rimantas Rakauskas

    2013-07-01

    Full Text Available Forty three European population samples of mealy aphids from various winter and summer host plants were attributed to respective species of Hyalopterus by means of their partial sequences of mitochondrial COI gene. Used Hyalopterus samples emerged as monophyletic relative to outgroup and formed three major clades representing three host specific mealy aphid species in the Neighbor joining, Maximum parsimony, Maximum likelihood and Bayesian inference trees. H. pruni and H. persikonus emerged as a sister species, whilst H. amygdali was located basally. Samples representing different clades in the molecular trees were used for canonical discrimination analysis based on twenty two morphological characters. Length of the median dorsal head hair enabled a 97.3 % separation of H. amygdali from the remaining two species. No single character enabled satisfactory discrimination between apterous viviparous females of H. pruni and H. persikonus. A modified key for the morphological identification of Hyalopterus species is suggested and their taxonomic status discussed.

  18. Large-scale runoff generation - parsimonious parameterisation using high-resolution topography

    Science.gov (United States)

    Gong, L.; Halldin, S.; Xu, C.-Y.

    2011-08-01

    World water resources have primarily been analysed by global-scale hydrological models in the last decades. Runoff generation in many of these models are based on process formulations developed at catchments scales. The division between slow runoff (baseflow) and fast runoff is primarily governed by slope and spatial distribution of effective water storage capacity, both acting at very small scales. Many hydrological models, e.g. VIC, account for the spatial storage variability in terms of statistical distributions; such models are generally proven to perform well. The statistical approaches, however, use the same runoff-generation parameters everywhere in a basin. The TOPMODEL concept, on the other hand, links the effective maximum storage capacity with real-world topography. Recent availability of global high-quality, high-resolution topographic data makes TOPMODEL attractive as a basis for a physically-based runoff-generation algorithm at large scales, even if its assumptions are not valid in flat terrain or for deep groundwater systems. We present a new runoff-generation algorithm for large-scale hydrology based on TOPMODEL concepts intended to overcome these problems. The TRG (topography-derived runoff generation) algorithm relaxes the TOPMODEL equilibrium assumption so baseflow generation is not tied to topography. TRG only uses the topographic index to distribute average storage to each topographic index class. The maximum storage capacity is proportional to the range of topographic index and is scaled by one parameter. The distribution of storage capacity within large-scale grid cells is obtained numerically through topographic analysis. The new topography-derived distribution function is then inserted into a runoff-generation framework similar VIC's. Different basin parts are parameterised by different storage capacities, and different shapes of the storage-distribution curves depend on their topographic characteristics. The TRG algorithm is driven by the

  19. Large-scale runoff generation – parsimonious parameterisation using high-resolution topography

    Directory of Open Access Journals (Sweden)

    L. Gong

    2011-08-01

    Full Text Available World water resources have primarily been analysed by global-scale hydrological models in the last decades. Runoff generation in many of these models are based on process formulations developed at catchments scales. The division between slow runoff (baseflow and fast runoff is primarily governed by slope and spatial distribution of effective water storage capacity, both acting at very small scales. Many hydrological models, e.g. VIC, account for the spatial storage variability in terms of statistical distributions; such models are generally proven to perform well. The statistical approaches, however, use the same runoff-generation parameters everywhere in a basin. The TOPMODEL concept, on the other hand, links the effective maximum storage capacity with real-world topography. Recent availability of global high-quality, high-resolution topographic data makes TOPMODEL attractive as a basis for a physically-based runoff-generation algorithm at large scales, even if its assumptions are not valid in flat terrain or for deep groundwater systems. We present a new runoff-generation algorithm for large-scale hydrology based on TOPMODEL concepts intended to overcome these problems. The TRG (topography-derived runoff generation algorithm relaxes the TOPMODEL equilibrium assumption so baseflow generation is not tied to topography. TRG only uses the topographic index to distribute average storage to each topographic index class. The maximum storage capacity is proportional to the range of topographic index and is scaled by one parameter. The distribution of storage capacity within large-scale grid cells is obtained numerically through topographic analysis. The new topography-derived distribution function is then inserted into a runoff-generation framework similar VIC's. Different basin parts are parameterised by different storage capacities, and different shapes of the storage-distribution curves depend on their topographic characteristics. The TRG algorithm

  20. Perils of parsimony: properties of reduced-rank estimates of genetic covariance matrices.

    Science.gov (United States)

    Meyer, Karin; Kirkpatrick, Mark

    2008-10-01

    Eigenvalues and eigenvectors of covariance matrices are important statistics for multivariate problems in many applications, including quantitative genetics. Estimates of these quantities are subject to different types of bias. This article reviews and extends the existing theory on these biases, considering a balanced one-way classification and restricted maximum-likelihood estimation. Biases are due to the spread of sample roots and arise from ignoring selected principal components when imposing constraints on the parameter space, to ensure positive semidefinite estimates or to estimate covariance matrices of chosen, reduced rank. In addition, it is shown that reduced-rank estimators that consider only the leading eigenvalues and -vectors of the "between-group" covariance matrix may be biased due to selecting the wrong subset of principal components. In a genetic context, with groups representing families, this bias is inverse proportional to the degree of genetic relationship among family members, but is independent of sample size. Theoretical results are supplemented by a simulation study, demonstrating close agreement between predicted and observed bias for large samples. It is emphasized that the rank of the genetic covariance matrix should be chosen sufficiently large to accommodate all important genetic principal components, even though, paradoxically, this may require including a number of components with negligible eigenvalues. A strategy for rank selection in practical analyses is outlined.

  1. Evapotranspiration estimation using a parameter-parsimonious energy partition model over Amazon basin

    Science.gov (United States)

    Xu, D.; Agee, E.; Wang, J.; Ivanov, V. Y.

    2017-12-01

    The increased frequency and severity of droughts in the Amazon region have emphasized the potential vulnerability of the rainforests to heat and drought-induced stresses, highlighting the need to reduce the uncertainty in estimates of regional evapotranspiration (ET) and quantify resilience of the forest. Ground-based observations for estimating ET are resource intensive, making methods based on remotely sensed observations an attractive alternative. Several methodologies have been developed to estimate ET from satellite data, but challenges remained in model parameterization and satellite limited coverage reducing their utility for monitoring biodiverse regions. In this work, we apply a novel surface energy partition method (Maximum Entropy Production; MEP) based on Bayesian probability theory and nonequilibrium thermodynamics to derive ET time series using satellite data for Amazon basin. For a large, sparsely monitored region such as the Amazon, this approach has the advantage methods of only using single level measurements of net radiation, temperature, and specific humidity data. Furthermore, it is not sensitive to the uncertainty of the input data and model parameters. In this first application of MEP theory for a tropical forest biome, we assess its performance at various spatiotemporal scales against a diverse field data sets. Specifically, the objective of this work is to test this method using eddy flux data for several locations across the Amazonia at sub-daily, monthly, and annual scales and compare the new estimates with those using traditional methods. Analyses of the derived ET time series will contribute to reducing the current knowledge gap surrounding the much debated response of the Amazon Basin region to droughts and offer a template for monitoring the long-term changes in global hydrologic cycle due to anthropogenic and natural causes.

  2. Comparison of Boolean analysis and standard phylogenetic methods using artificially evolved and natural mt-tRNA sequences from great apes.

    Science.gov (United States)

    Ari, Eszter; Ittzés, Péter; Podani, János; Thi, Quynh Chi Le; Jakó, Eena

    2012-04-01

    Boolean analysis (or BOOL-AN; Jakó et al., 2009. BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction. Mol. Phylogenet. Evol. 52, 887-97.), a recently developed method for sequence comparison uses the Iterative Canonical Form of Boolean functions. It considers sequence information in a way entirely different from standard phylogenetic methods (i.e. Maximum Parsimony, Maximum-Likelihood, Neighbor-Joining, and Bayesian analysis). The performance and reliability of Boolean analysis were tested and compared with the standard phylogenetic methods, using artificially evolved - simulated - nucleotide sequences and the 22 mitochondrial tRNA genes of the great apes. At the outset, we assumed that the phylogeny of Hominidae is generally well established, and the guide tree of artificial sequence evolution can also be used as a benchmark. These offer a possibility to compare and test the performance of different phylogenetic methods. Trees were reconstructed by each method from 2500 simulated sequences and 22 mitochondrial tRNA sequences. We also introduced a special re-sampling method for Boolean analysis on permuted sequence sites, the P-BOOL-AN procedure. Considering the reliability values (branch support values of consensus trees and Robinson-Foulds distances) we used for simulated sequence trees produced by different phylogenetic methods, BOOL-AN appeared as the most reliable method. Although the mitochondrial tRNA sequences of great apes are relatively short (59-75 bases long) and the ratio of their constant characters is about 75%, BOOL-AN, P-BOOL-AN and the Bayesian approach produced the same tree-topology as the established phylogeny, while the outcomes of Maximum Parsimony, Maximum-Likelihood and Neighbor-Joining methods were equivocal. We conclude that Boolean analysis is a promising alternative to existing methods of sequence comparison for phylogenetic reconstruction and congruence analysis. Copyright © 2012 Elsevier Inc. All

  3. Méthodes avancées pour la résolution du problème de maximum parcimonie

    OpenAIRE

    Vazquez Ortiz , Karla Esmeralda

    2016-01-01

    Phylogenetic reconstruction is considered a central underpinning of diverse fields like ecology, molecular biology and physiology where genealogical relationships of species or gene sequences represented as trees can provide the most meaningful insights into biology. Maximum Parsimony (MP) is an important approach to solve the phylogenetic reconstruction based on an optimality criterion under which the tree that minimizes the total number of genetic transformations is preferred. In this thesi...

  4. constNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints.

    Science.gov (United States)

    Matsen, Frederick A

    2010-06-01

    This article introduces constNJ (constrained neighbor-joining), an algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune-regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees that must fit into a recombination, hybridization, or similar network. Rather than first finding a set of trees that are optimal according to a phylogenetic criterion (e.g., likelihood or parsimony) and then attempting to fit them into a network, constNJ estimates the trees while enforcing specified rSPR distance constraints. The primary input for constNJ is a collection of distance matrices derived from sequence blocks which are assumed to have evolved in a tree-like manner, such as blocks of an alignment which do not contain any recombination breakpoints. The other input is a set of rSPR constraint inequalities for any set of pairs of trees. constNJ is consistent and a strict generalization of the neighbor-joining algorithm; it uses the new notion of maximum agreement partitions (MAPs) to assure that the resulting trees satisfy the given rSPR distance constraints.

  5. Credal Networks under Maximum Entropy

    OpenAIRE

    Lukasiewicz, Thomas

    2013-01-01

    We apply the principle of maximum entropy to select a unique joint probability distribution from the set of all joint probability distributions specified by a credal network. In detail, we start by showing that the unique joint distribution of a Bayesian tree coincides with the maximum entropy model of its conditional distributions. This result, however, does not hold anymore for general Bayesian networks. We thus present a new kind of maximum entropy models, which are computed sequentially. ...

  6. Where and why hyporheic exchange is important: Inferences from a parsimonious, physically-based river network model

    Science.gov (United States)

    Gomez-Velez, J. D.; Harvey, J. W.

    2014-12-01

    Hyporheic exchange has been hypothesized to have basin-scale consequences; however, predictions throughout river networks are limited by available geomorphic and hydrogeologic data as well as models that can analyze and aggregate hyporheic exchange flows across large spatial scales. We developed a parsimonious but physically-based model of hyporheic flow for application in large river basins: Networks with EXchange and Subsurface Storage (NEXSS). At the core of NEXSS is a characterization of the channel geometry, geomorphic features, and related hydraulic drivers based on scaling equations from the literature and readily accessible information such as river discharge, bankfull width, median grain size, sinuosity, channel slope, and regional groundwater gradients. Multi-scale hyporheic flow is computed based on combining simple but powerful analytical and numerical expressions that have been previously published. We applied NEXSS across a broad range of geomorphic diversity in river reaches and synthetic river networks. NEXSS demonstrates that vertical exchange beneath submerged bedforms dominates hyporheic fluxes and turnover rates along the river corridor. Moreover, the hyporheic zone's potential for biogeochemical transformations is comparable across stream orders, but the abundance of lower-order channels results in a considerably higher cumulative effect for low-order streams. Thus, vertical exchange beneath submerged bedforms has more potential for biogeochemical transformations than lateral exchange beneath banks, although lateral exchange through meanders may be important in large rivers. These results have implications for predicting outcomes of river and basin management practices.

  7. Analysis of the first and second internal transcribed spacer sequences of the ribosomal DNA in Biomphalaria tenagophila complex (Mollusca: Planorbidae

    Directory of Open Access Journals (Sweden)

    Teofânia HDA Vidigal

    2004-03-01

    Full Text Available The first and second internal transcribed spacer regions (ITS1 and ITS2 of the ribosomal DNA of Biomphalaria tenagophila complex (B. tenagophila, B. occidentalis, and B. t. guaibensis were sequenced and compared. The alignment lengths of these regions were about 655 bp and 481 bp, respectively. Phylogenetic relationships among the Biomphalaria species were inferred by Maximum Parsimony and Neighbor-joining methods. The phylogenetic trees produced, in most of the cases, were in accordance with morphological systematics and other molecular data previously obtained by polymerase chain reaction and restriction fragment length polymorphism analysis. The present results provide support for the proposal that B. tenagophila represents a complex comprising B. tenagophila, B. occidentalis and B. t. guaibensis.

  8. Phylogenetic inferences of Nepenthes species in Peninsular Malaysia revealed by chloroplast (trnL intron) and nuclear (ITS) DNA sequences.

    Science.gov (United States)

    Bunawan, Hamidun; Yen, Choong Chee; Yaakop, Salmah; Noor, Normah Mohd

    2017-01-26

    The chloroplastic trnL intron and the nuclear internal transcribed spacer (ITS) region were sequenced for 11 Nepenthes species recorded in Peninsular Malaysia to examine their phylogenetic relationship and to evaluate the usage of trnL intron and ITS sequences for phylogenetic reconstruction of this genus. Phylogeny reconstruction was carried out using neighbor-joining, maximum parsimony and Bayesian analyses. All the trees revealed two major clusters, a lowland group consisting of N. ampullaria, N. mirabilis, N. gracilis and N. rafflesiana, and another containing both intermediately distributed species (N. albomarginata and N. benstonei) and four highland species (N. sanguinea, N. macfarlanei, N. ramispina and N. alba). The trnL intron and ITS sequences proved to provide phylogenetic informative characters for deriving a phylogeny of Nepenthes species in Peninsular Malaysia. To our knowledge, this is the first molecular phylogenetic study of Nepenthes species occurring along an altitudinal gradient in Peninsular Malaysia.

  9. Phylogenetic relationships of Malayan gaur with other species of the genus Bos based on cytochrome b gene DNA sequences.

    Science.gov (United States)

    Rosli, M K A; Zakaria, S S; Syed-Shabthar, S M F; Zainal, Z Z; Shukor, M N; Mahani, M C; Abas-Mazni, O; Md-Zain, B M

    2011-03-22

    The Malayan gaur (Bos gaurus hubbacki) is one of the three subspecies of gaurs that can be found in Malaysia. We examined the phylogenetic relationships of this subspecies with other species of the genus Bos (B. javanicus, B. indicus, B. taurus, and B. grunniens). The sequence of a key gene, cytochrome b, was compared among 20 Bos species and the bongo antelope, used as an outgroup. Phylogenetic reconstruction was employed using neighbor joining and maximum parsimony in PAUP and Bayesian inference in MrBayes 3.1. All tree topologies indicated that the Malayan gaur is in its own monophyletic clade, distinct from other species of the genus Bos. We also found significant branching differences in the tree topologies between wild and domestic cattle.

  10. Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment?

    Directory of Open Access Journals (Sweden)

    Hartmann Stefanie

    2008-03-01

    Full Text Available Abstract Background While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood and studied ways to improve the accuracy of trees obtained from such datasets. Results We found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25% to 40% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences. Conclusion These results demonstrate that partial gene

  11. Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

    Science.gov (United States)

    Hartmann, Stefanie; Vision, Todd J

    2008-03-26

    While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood) and studied ways to improve the accuracy of trees obtained from such datasets. We found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25% to 40% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences. These results demonstrate that partial gene sequences and gappy multiple sequence alignments can pose a

  12. Data driven discrete-time parsimonious identification of a nonlinear state-space model for a weakly nonlinear system with short data record

    Science.gov (United States)

    Relan, Rishi; Tiels, Koen; Marconato, Anna; Dreesen, Philippe; Schoukens, Johan

    2018-05-01

    Many real world systems exhibit a quasi linear or weakly nonlinear behavior during normal operation, and a hard saturation effect for high peaks of the input signal. In this paper, a methodology to identify a parsimonious discrete-time nonlinear state space model (NLSS) for the nonlinear dynamical system with relatively short data record is proposed. The capability of the NLSS model structure is demonstrated by introducing two different initialisation schemes, one of them using multivariate polynomials. In addition, a method using first-order information of the multivariate polynomials and tensor decomposition is employed to obtain the parsimonious decoupled representation of the set of multivariate real polynomials estimated during the identification of NLSS model. Finally, the experimental verification of the model structure is done on the cascaded water-benchmark identification problem.

  13. Parsimonious classification of binary lacunarity data computed from food surface images using kernel principal component analysis and artificial neural networks.

    Science.gov (United States)

    Iqbal, Abdullah; Valous, Nektarios A; Sun, Da-Wen; Allen, Paul

    2011-02-01

    Lacunarity is about quantifying the degree of spatial heterogeneity in the visual texture of imagery through the identification of the relationships between patterns and their spatial configurations in a two-dimensional setting. The computed lacunarity data can designate a mathematical index of spatial heterogeneity, therefore the corresponding feature vectors should possess the necessary inter-class statistical properties that would enable them to be used for pattern recognition purposes. The objectives of this study is to construct a supervised parsimonious classification model of binary lacunarity data-computed by Valous et al. (2009)-from pork ham slice surface images, with the aid of kernel principal component analysis (KPCA) and artificial neural networks (ANNs), using a portion of informative salient features. At first, the dimension of the initial space (510 features) was reduced by 90% in order to avoid any noise effects in the subsequent classification. Then, using KPCA, the first nineteen kernel principal components (99.04% of total variance) were extracted from the reduced feature space, and were used as input in the ANN. An adaptive feedforward multilayer perceptron (MLP) classifier was employed to obtain a suitable mapping from the input dataset. The correct classification percentages for the training, test and validation sets were 86.7%, 86.7%, and 85.0%, respectively. The results confirm that the classification performance was satisfactory. The binary lacunarity spatial metric captured relevant information that provided a good level of differentiation among pork ham slice images. Copyright © 2010 The American Meat Science Association. Published by Elsevier Ltd. All rights reserved.

  14. A Parsimonious Model of the Rabbit Action Potential Elucidates the Minimal Physiological Requirements for Alternans and Spiral Wave Breakup.

    Science.gov (United States)

    Gray, Richard A; Pathmanathan, Pras

    2016-10-01

    Elucidating the underlying mechanisms of fatal cardiac arrhythmias requires a tight integration of electrophysiological experiments, models, and theory. Existing models of transmembrane action potential (AP) are complex (resulting in over parameterization) and varied (leading to dissimilar predictions). Thus, simpler models are needed to elucidate the "minimal physiological requirements" to reproduce significant observable phenomena using as few parameters as possible. Moreover, models have been derived from experimental studies from a variety of species under a range of environmental conditions (for example, all existing rabbit AP models incorporate a formulation of the rapid sodium current, INa, based on 30 year old data from chick embryo cell aggregates). Here we develop a simple "parsimonious" rabbit AP model that is mathematically identifiable (i.e., not over parameterized) by combining a novel Hodgkin-Huxley formulation of INa with a phenomenological model of repolarization similar to the voltage dependent, time-independent rectifying outward potassium current (IK). The model was calibrated using the following experimental data sets measured from the same species (rabbit) under physiological conditions: dynamic current-voltage (I-V) relationships during the AP upstroke; rapid recovery of AP excitability during the relative refractory period; and steady-state INa inactivation via voltage clamp. Simulations reproduced several important "emergent" phenomena including cellular alternans at rates > 250 bpm as observed in rabbit myocytes, reentrant spiral waves as observed on the surface of the rabbit heart, and spiral wave breakup. Model variants were studied which elucidated the minimal requirements for alternans and spiral wave break up, namely the kinetics of INa inactivation and the non-linear rectification of IK.The simplicity of the model, and the fact that its parameters have physiological meaning, make it ideal for engendering generalizable mechanistic

  15. Maximum Entropy in Drug Discovery

    Directory of Open Access Journals (Sweden)

    Chih-Yuan Tseng

    2014-07-01

    Full Text Available Drug discovery applies multidisciplinary approaches either experimentally, computationally or both ways to identify lead compounds to treat various diseases. While conventional approaches have yielded many US Food and Drug Administration (FDA-approved drugs, researchers continue investigating and designing better approaches to increase the success rate in the discovery process. In this article, we provide an overview of the current strategies and point out where and how the method of maximum entropy has been introduced in this area. The maximum entropy principle has its root in thermodynamics, yet since Jaynes’ pioneering work in the 1950s, the maximum entropy principle has not only been used as a physics law, but also as a reasoning tool that allows us to process information in hand with the least bias. Its applicability in various disciplines has been abundantly demonstrated. We give several examples of applications of maximum entropy in different stages of drug discovery. Finally, we discuss a promising new direction in drug discovery that is likely to hinge on the ways of utilizing maximum entropy.

  16. Molecular phylogeny of the neritidae (Gastropoda: Neritimorpha) based on the mitochondrial genes cytochrome oxidase I (COI) and 16S rRNA

    International Nuclear Information System (INIS)

    Quintero Galvis, Julian Fernando; Castro, Lyda Raquel

    2013-01-01

    The family Neritidae has representatives in tropical and subtropical regions that occur in a variety of environments, and its known fossil record dates back to the late Cretaceous. However there have been few studies of molecular phylogeny in this family. We performed a phylogenetic reconstruction of the family Neritidae using the COI (722 bp) and the 16S rRNA (559 bp) regions of the mitochondrial genome. Neighbor-joining, maximum parsimony and Bayesian inference were performed. The best phylogenetic reconstruction was obtained using the COI region, and we consider it an appropriate marker for phylogenetic studies within the group. Consensus analysis (COI +16S rRNA) generally obtained the same tree topologies and confirmed that the genus Nerita is monophyletic. The consensus analysis using parsimony recovered a monophyletic group consisting of the genera Neritina, Septaria, Theodoxus, Puperita, and Clithon, while in the Bayesian analyses Theodoxus is separated from the other genera. The phylogenetic status of the species from the genus Nerita from the Colombian Caribbean generated in this study was consistent with that reported for the genus in previous studies. In the resulting consensus tree obtained using maximum parsimony, we included information on habitat type for each species, to map the evolution by habitat. Species of the family Neritidae possibly have their origin in marine environments, which is consistent with conclusions from previous reports based on anatomical studies.

  17. A practical exact maximum compatibility algorithm for reconstruction of recent evolutionary history.

    Science.gov (United States)

    Cherry, Joshua L

    2017-02-23

    Maximum compatibility is a method of phylogenetic reconstruction that is seldom applied to molecular sequences. It may be ideal for certain applications, such as reconstructing phylogenies of closely-related bacteria on the basis of whole-genome sequencing. Here I present an algorithm that rapidly computes phylogenies according to a compatibility criterion. Although based on solutions to the maximum clique problem, this algorithm deals properly with ambiguities in the data. The algorithm is applied to bacterial data sets containing up to nearly 2000 genomes with several thousand variable nucleotide sites. Run times are several seconds or less. Computational experiments show that maximum compatibility is less sensitive than maximum parsimony to the inclusion of nucleotide data that, though derived from actual sequence reads, has been identified as likely to be misleading. Maximum compatibility is a useful tool for certain phylogenetic problems, such as inferring the relationships among closely-related bacteria from whole-genome sequence data. The algorithm presented here rapidly solves fairly large problems of this type, and provides robustness against misleading characters than can pollute large-scale sequencing data.

  18. Hide and vanish: data sets where the most parsimonious tree is known but hard to find, and their implications for tree search methods.

    Science.gov (United States)

    Goloboff, Pablo A

    2014-10-01

    Three different types of data sets, for which the uniquely most parsimonious tree can be known exactly but is hard to find with heuristic tree search methods, are studied. Tree searches are complicated more by the shape of the tree landscape (i.e. the distribution of homoplasy on different trees) than by the sheer abundance of homoplasy or character conflict. Data sets of Type 1 are those constructed by Radel et al. (2013). Data sets of Type 2 present a very rugged landscape, with narrow peaks and valleys, but relatively low amounts of homoplasy. For such a tree landscape, subjecting the trees to TBR and saving suboptimal trees produces much better results when the sequence of clipping for the tree branches is randomized instead of fixed. An unexpected finding for data sets of Types 1 and 2 is that starting a search from a random tree instead of a random addition sequence Wagner tree may increase the probability that the search finds the most parsimonious tree; a small artificial example where these probabilities can be calculated exactly is presented. Data sets of Type 3, the most difficult data sets studied here, comprise only congruent characters, and a single island with only one most parsimonious tree. Even if there is a single island, missing entries create a very flat landscape which is difficult to traverse with tree search algorithms because the number of equally parsimonious trees that need to be saved and swapped to effectively move around the plateaus is too large. Minor modifications of the parameters of tree drifting, ratchet, and sectorial searches allow travelling around these plateaus much more efficiently than saving and swapping large numbers of equally parsimonious trees with TBR. For these data sets, two new related criteria for selecting taxon addition sequences in Wagner trees (the "selected" and "informative" addition sequences) produce much better results than the standard random or closest addition sequences. These new methods for Wagner

  19. Maximum stellar iron core mass

    Indian Academy of Sciences (India)

    60, No. 3. — journal of. March 2003 physics pp. 415–422. Maximum stellar iron core mass. F W GIACOBBE. Chicago Research Center/American Air Liquide ... iron core compression due to the weight of non-ferrous matter overlying the iron cores within large .... thermal equilibrium velocities will tend to be non-relativistic.

  20. Maximum entropy beam diagnostic tomography

    International Nuclear Information System (INIS)

    Mottershead, C.T.

    1985-01-01

    This paper reviews the formalism of maximum entropy beam diagnostic tomography as applied to the Fusion Materials Irradiation Test (FMIT) prototype accelerator. The same formalism has also been used with streak camera data to produce an ultrahigh speed movie of the beam profile of the Experimental Test Accelerator (ETA) at Livermore. 11 refs., 4 figs

  1. Maximum entropy beam diagnostic tomography

    International Nuclear Information System (INIS)

    Mottershead, C.T.

    1985-01-01

    This paper reviews the formalism of maximum entropy beam diagnostic tomography as applied to the Fusion Materials Irradiation Test (FMIT) prototype accelerator. The same formalism has also been used with streak camera data to produce an ultrahigh speed movie of the beam profile of the Experimental Test Accelerator (ETA) at Livermore

  2. A portable storage maximum thermometer

    International Nuclear Information System (INIS)

    Fayart, Gerard.

    1976-01-01

    A clinical thermometer storing the voltage corresponding to the maximum temperature in an analog memory is described. End of the measurement is shown by a lamp switch out. The measurement time is shortened by means of a low thermal inertia platinum probe. This portable thermometer is fitted with cell test and calibration system [fr

  3. Neutron spectra unfolding with maximum entropy and maximum likelihood

    International Nuclear Information System (INIS)

    Itoh, Shikoh; Tsunoda, Toshiharu

    1989-01-01

    A new unfolding theory has been established on the basis of the maximum entropy principle and the maximum likelihood method. This theory correctly embodies the Poisson statistics of neutron detection, and always brings a positive solution over the whole energy range. Moreover, the theory unifies both problems of overdetermined and of underdetermined. For the latter, the ambiguity in assigning a prior probability, i.e. the initial guess in the Bayesian sense, has become extinct by virtue of the principle. An approximate expression of the covariance matrix for the resultant spectra is also presented. An efficient algorithm to solve the nonlinear system, which appears in the present study, has been established. Results of computer simulation showed the effectiveness of the present theory. (author)

  4. Flood modelling with a distributed event-based parsimonious rainfall-runoff model: case of the karstic Lez river catchment

    Directory of Open Access Journals (Sweden)

    M. Coustau

    2012-04-01

    Full Text Available Rainfall-runoff models are crucial tools for the statistical prediction of flash floods and real-time forecasting. This paper focuses on a karstic basin in the South of France and proposes a distributed parsimonious event-based rainfall-runoff model, coherent with the poor knowledge of both evaporative and underground fluxes. The model combines a SCS runoff model and a Lag and Route routing model for each cell of a regular grid mesh. The efficiency of the model is discussed not only to satisfactorily simulate floods but also to get powerful relationships between the initial condition of the model and various predictors of the initial wetness state of the basin, such as the base flow, the Hu2 index from the Meteo-France SIM model and the piezometric levels of the aquifer. The advantage of using meteorological radar rainfall in flood modelling is also assessed. Model calibration proved to be satisfactory by using an hourly time step with Nash criterion values, ranging between 0.66 and 0.94 for eighteen of the twenty-one selected events. The radar rainfall inputs significantly improved the simulations or the assessment of the initial condition of the model for 5 events at the beginning of autumn, mostly in September–October (mean improvement of Nash is 0.09; correction in the initial condition ranges from −205 to 124 mm, but were less efficient for the events at the end of autumn. In this period, the weak vertical extension of the precipitation system and the low altitude of the 0 °C isotherm could affect the efficiency of radar measurements due to the distance between the basin and the radar (~60 km. The model initial condition S is correlated with the three tested predictors (R2 > 0.6. The interpretation of the model suggests that groundwater does not affect the first peaks of the flood, but can strongly impact subsequent peaks in the case of a multi-storm event. Because this kind of model is based on a limited

  5. On Maximum Entropy and Inference

    Directory of Open Access Journals (Sweden)

    Luigi Gresele

    2017-11-01

    Full Text Available Maximum entropy is a powerful concept that entails a sharp separation between relevant and irrelevant variables. It is typically invoked in inference, once an assumption is made on what the relevant variables are, in order to estimate a model from data, that affords predictions on all other (dependent variables. Conversely, maximum entropy can be invoked to retrieve the relevant variables (sufficient statistics directly from the data, once a model is identified by Bayesian model selection. We explore this approach in the case of spin models with interactions of arbitrary order, and we discuss how relevant interactions can be inferred. In this perspective, the dimensionality of the inference problem is not set by the number of parameters in the model, but by the frequency distribution of the data. We illustrate the method showing its ability to recover the correct model in a few prototype cases and discuss its application on a real dataset.

  6. Maximum Water Hammer Sensitivity Analysis

    OpenAIRE

    Jalil Emadi; Abbas Solemani

    2011-01-01

    Pressure waves and Water Hammer occur in a pumping system when valves are closed or opened suddenly or in the case of sudden failure of pumps. Determination of maximum water hammer is considered one of the most important technical and economical items of which engineers and designers of pumping stations and conveyance pipelines should take care. Hammer Software is a recent application used to simulate water hammer. The present study focuses on determining significance of ...

  7. LCLS Maximum Credible Beam Power

    International Nuclear Information System (INIS)

    Clendenin, J.

    2005-01-01

    The maximum credible beam power is defined as the highest credible average beam power that the accelerator can deliver to the point in question, given the laws of physics, the beam line design, and assuming all protection devices have failed. For a new accelerator project, the official maximum credible beam power is determined by project staff in consultation with the Radiation Physics Department, after examining the arguments and evidence presented by the appropriate accelerator physicist(s) and beam line engineers. The definitive parameter becomes part of the project's safety envelope. This technical note will first review the studies that were done for the Gun Test Facility (GTF) at SSRL, where a photoinjector similar to the one proposed for the LCLS is being tested. In Section 3 the maximum charge out of the gun for a single rf pulse is calculated. In Section 4, PARMELA simulations are used to track the beam from the gun to the end of the photoinjector. Finally in Section 5 the beam through the matching section and injected into Linac-1 is discussed

  8. Generic maximum likely scale selection

    DEFF Research Database (Denmark)

    Pedersen, Kim Steenstrup; Loog, Marco; Markussen, Bo

    2007-01-01

    in this work is on applying this selection principle under a Brownian image model. This image model provides a simple scale invariant prior for natural images and we provide illustrative examples of the behavior of our scale estimation on such images. In these illustrative examples, estimation is based......The fundamental problem of local scale selection is addressed by means of a novel principle, which is based on maximum likelihood estimation. The principle is generally applicable to a broad variety of image models and descriptors, and provides a generic scale estimation methodology. The focus...

  9. Extreme Maximum Land Surface Temperatures.

    Science.gov (United States)

    Garratt, J. R.

    1992-09-01

    There are numerous reports in the literature of observations of land surface temperatures. Some of these, almost all made in situ, reveal maximum values in the 50°-70°C range, with a few, made in desert regions, near 80°C. Consideration of a simplified form of the surface energy balance equation, utilizing likely upper values of absorbed shortwave flux (1000 W m2) and screen air temperature (55°C), that surface temperatures in the vicinity of 90°-100°C may occur for dry, darkish soils of low thermal conductivity (0.1-0.2 W m1 K1). Numerical simulations confirm this and suggest that temperature gradients in the first few centimeters of soil may reach 0.5°-1°C mm1 under these extreme conditions. The study bears upon the intrinsic interest of identifying extreme maximum temperatures and yields interesting information regarding the comfort zone of animals (including man).

  10. System for memorizing maximum values

    Science.gov (United States)

    Bozeman, Richard J., Jr.

    1992-08-01

    The invention discloses a system capable of memorizing maximum sensed values. The system includes conditioning circuitry which receives the analog output signal from a sensor transducer. The conditioning circuitry rectifies and filters the analog signal and provides an input signal to a digital driver, which may be either linear or logarithmic. The driver converts the analog signal to discrete digital values, which in turn triggers an output signal on one of a plurality of driver output lines n. The particular output lines selected is dependent on the converted digital value. A microfuse memory device connects across the driver output lines, with n segments. Each segment is associated with one driver output line, and includes a microfuse that is blown when a signal appears on the associated driver output line.

  11. Remarks on the maximum luminosity

    Science.gov (United States)

    Cardoso, Vitor; Ikeda, Taishi; Moore, Christopher J.; Yoo, Chul-Moon

    2018-04-01

    The quest for fundamental limitations on physical processes is old and venerable. Here, we investigate the maximum possible power, or luminosity, that any event can produce. We show, via full nonlinear simulations of Einstein's equations, that there exist initial conditions which give rise to arbitrarily large luminosities. However, the requirement that there is no past horizon in the spacetime seems to limit the luminosity to below the Planck value, LP=c5/G . Numerical relativity simulations of critical collapse yield the largest luminosities observed to date, ≈ 0.2 LP . We also present an analytic solution to the Einstein equations which seems to give an unboundedly large luminosity; this will guide future numerical efforts to investigate super-Planckian luminosities.

  12. Maximum mutual information regularized classification

    KAUST Repository

    Wang, Jim Jing-Yan

    2014-09-07

    In this paper, a novel pattern classification approach is proposed by regularizing the classifier learning to maximize mutual information between the classification response and the true class label. We argue that, with the learned classifier, the uncertainty of the true class label of a data sample should be reduced by knowing its classification response as much as possible. The reduced uncertainty is measured by the mutual information between the classification response and the true class label. To this end, when learning a linear classifier, we propose to maximize the mutual information between classification responses and true class labels of training samples, besides minimizing the classification error and reducing the classifier complexity. An objective function is constructed by modeling mutual information with entropy estimation, and it is optimized by a gradient descend method in an iterative algorithm. Experiments on two real world pattern classification problems show the significant improvements achieved by maximum mutual information regularization.

  13. Scintillation counter, maximum gamma aspect

    International Nuclear Information System (INIS)

    Thumim, A.D.

    1975-01-01

    A scintillation counter, particularly for counting gamma ray photons, includes a massive lead radiation shield surrounding a sample-receiving zone. The shield is disassembleable into a plurality of segments to allow facile installation and removal of a photomultiplier tube assembly, the segments being so constructed as to prevent straight-line access of external radiation through the shield into radiation-responsive areas. Provisions are made for accurately aligning the photomultiplier tube with respect to one or more sample-transmitting bores extending through the shield to the sample receiving zone. A sample elevator, used in transporting samples into the zone, is designed to provide a maximum gamma-receiving aspect to maximize the gamma detecting efficiency. (U.S.)

  14. Maximum mutual information regularized classification

    KAUST Repository

    Wang, Jim Jing-Yan; Wang, Yi; Zhao, Shiguang; Gao, Xin

    2014-01-01

    In this paper, a novel pattern classification approach is proposed by regularizing the classifier learning to maximize mutual information between the classification response and the true class label. We argue that, with the learned classifier, the uncertainty of the true class label of a data sample should be reduced by knowing its classification response as much as possible. The reduced uncertainty is measured by the mutual information between the classification response and the true class label. To this end, when learning a linear classifier, we propose to maximize the mutual information between classification responses and true class labels of training samples, besides minimizing the classification error and reducing the classifier complexity. An objective function is constructed by modeling mutual information with entropy estimation, and it is optimized by a gradient descend method in an iterative algorithm. Experiments on two real world pattern classification problems show the significant improvements achieved by maximum mutual information regularization.

  15. Comprehensive Phylogenetic Analysis of Bovine Non-aureus Staphylococci Species Based on Whole-Genome Sequencing

    Science.gov (United States)

    Naushad, Sohail; Barkema, Herman W.; Luby, Christopher; Condas, Larissa A. Z.; Nobrega, Diego B.; Carson, Domonique A.; De Buck, Jeroen

    2016-01-01

    Non-aureus staphylococci (NAS), a heterogeneous group of a large number of species and subspecies, are the most frequently isolated pathogens from intramammary infections in dairy cattle. Phylogenetic relationships among bovine NAS species are controversial and have mostly been determined based on single-gene trees. Herein, we analyzed phylogeny of bovine NAS species using whole-genome sequencing (WGS) of 441 distinct isolates. In addition, evolutionary relationships among bovine NAS were estimated from multilocus data of 16S rRNA, hsp60, rpoB, sodA, and tuf genes and sequences from these and numerous other single genes/proteins. All phylogenies were created with FastTree, Maximum-Likelihood, Maximum-Parsimony, and Neighbor-Joining methods. Regardless of methodology, WGS-trees clearly separated bovine NAS species into five monophyletic coherent clades. Furthermore, there were consistent interspecies relationships within clades in all WGS phylogenetic reconstructions. Except for the Maximum-Parsimony tree, multilocus data analysis similarly produced five clades. There were large variations in determining clades and interspecies relationships in single gene/protein trees, under different methods of tree constructions, highlighting limitations of using single genes for determining bovine NAS phylogeny. However, based on WGS data, we established a robust phylogeny of bovine NAS species, unaffected by method or model of evolutionary reconstructions. Therefore, it is now possible to determine associations between phylogeny and many biological traits, such as virulence, antimicrobial resistance, environmental niche, geographical distribution, and host specificity. PMID:28066335

  16. Maximum entropy and Bayesian methods

    International Nuclear Information System (INIS)

    Smith, C.R.; Erickson, G.J.; Neudorfer, P.O.

    1992-01-01

    Bayesian probability theory and Maximum Entropy methods are at the core of a new view of scientific inference. These 'new' ideas, along with the revolution in computational methods afforded by modern computers allow astronomers, electrical engineers, image processors of any type, NMR chemists and physicists, and anyone at all who has to deal with incomplete and noisy data, to take advantage of methods that, in the past, have been applied only in some areas of theoretical physics. The title workshops have been the focus of a group of researchers from many different fields, and this diversity is evident in this book. There are tutorial and theoretical papers, and applications in a very wide variety of fields. Almost any instance of dealing with incomplete and noisy data can be usefully treated by these methods, and many areas of theoretical research are being enhanced by the thoughtful application of Bayes' theorem. Contributions contained in this volume present a state-of-the-art overview that will be influential and useful for many years to come

  17. Maximum entropy principal for transportation

    International Nuclear Information System (INIS)

    Bilich, F.; Da Silva, R.

    2008-01-01

    In this work we deal with modeling of the transportation phenomenon for use in the transportation planning process and policy-impact studies. The model developed is based on the dependence concept, i.e., the notion that the probability of a trip starting at origin i is dependent on the probability of a trip ending at destination j given that the factors (such as travel time, cost, etc.) which affect travel between origin i and destination j assume some specific values. The derivation of the solution of the model employs the maximum entropy principle combining a priori multinomial distribution with a trip utility concept. This model is utilized to forecast trip distributions under a variety of policy changes and scenarios. The dependence coefficients are obtained from a regression equation where the functional form is derived based on conditional probability and perception of factors from experimental psychology. The dependence coefficients encode all the information that was previously encoded in the form of constraints. In addition, the dependence coefficients encode information that cannot be expressed in the form of constraints for practical reasons, namely, computational tractability. The equivalence between the standard formulation (i.e., objective function with constraints) and the dependence formulation (i.e., without constraints) is demonstrated. The parameters of the dependence-based trip-distribution model are estimated, and the model is also validated using commercial air travel data in the U.S. In addition, policy impact analyses (such as allowance of supersonic flights inside the U.S. and user surcharge at noise-impacted airports) on air travel are performed.

  18. Last Glacial Maximum Salinity Reconstruction

    Science.gov (United States)

    Homola, K.; Spivack, A. J.

    2016-12-01

    It has been previously demonstrated that salinity can be reconstructed from sediment porewater. The goal of our study is to reconstruct high precision salinity during the Last Glacial Maximum (LGM). Salinity is usually determined at high precision via conductivity, which requires a larger volume of water than can be extracted from a sediment core, or via chloride titration, which yields lower than ideal precision. It has been demonstrated for water column samples that high precision density measurements can be used to determine salinity at the precision of a conductivity measurement using the equation of state of seawater. However, water column seawater has a relatively constant composition, in contrast to porewater, where variations from standard seawater composition occur. These deviations, which affect the equation of state, must be corrected for through precise measurements of each ion's concentration and knowledge of apparent partial molar density in seawater. We have developed a density-based method for determining porewater salinity that requires only 5 mL of sample, achieving density precisions of 10-6 g/mL. We have applied this method to porewater samples extracted from long cores collected along a N-S transect across the western North Atlantic (R/V Knorr cruise KN223). Density was determined to a precision of 2.3x10-6 g/mL, which translates to salinity uncertainty of 0.002 gms/kg if the effect of differences in composition is well constrained. Concentrations of anions (Cl-, and SO4-2) and cations (Na+, Mg+, Ca+2, and K+) were measured. To correct salinities at the precision required to unravel LGM Meridional Overturning Circulation, our ion precisions must be better than 0.1% for SO4-/Cl- and Mg+/Na+, and 0.4% for Ca+/Na+, and K+/Na+. Alkalinity, pH and Dissolved Inorganic Carbon of the porewater were determined to precisions better than 4% when ratioed to Cl-, and used to calculate HCO3-, and CO3-2. Apparent partial molar densities in seawater were

  19. Molecular phylogeny and larval morphological diversity of the lanternfish genus Hygophum (Teleostei: Myctophidae).

    Science.gov (United States)

    Yamaguchi, M; Miya, M; Okiyama, M; Nishida, M

    2000-04-01

    Larvae of the deep-sea lanternfish genus Hygophum (Myctophidae) exhibit a remarkable morphological diversity that is quite unexpected, considering their homogeneous adult morphology. In an attempt to elucidate the evolutionary patterns of such larval morphological diversity, nucleotide sequences of a portion of the mitochondrially encoded 16S ribosomal RNA gene were determined for seven Hygophum species and three outgroup taxa. Secondary structure-based alignment resulted in a character matrix consisting of 1172 bp of unambiguously aligned sequences, which were subjected to phylogenetic analyses using maximum-parsimony, maximum-likelihood, and neighbor-joining methods. The resultant tree topologies from the three methods were congruent, with most nodes, including that of the genus Hygophum, being strongly supported by various tree statistics. The most parsimonious reconstruction of the three previously recognized, distinct larval morphs onto the molecular phylogeny revealed that one of the morphs had originated as the common ancestor of the genus, the other two having diversified separately in two subsequent major clades. The patterns of such diversification are discussed in terms of the unusual larval eye morphology and geographic distribution. Copyright 2000 Academic Press.

  20. Two-dimensional maximum entropy image restoration

    International Nuclear Information System (INIS)

    Brolley, J.E.; Lazarus, R.B.; Suydam, B.R.; Trussell, H.J.

    1977-07-01

    An optical check problem was constructed to test P LOG P maximum entropy restoration of an extremely distorted image. Useful recovery of the original image was obtained. Comparison with maximum a posteriori restoration is made. 7 figures

  1. Receiver function estimated by maximum entropy deconvolution

    Institute of Scientific and Technical Information of China (English)

    吴庆举; 田小波; 张乃铃; 李卫平; 曾融生

    2003-01-01

    Maximum entropy deconvolution is presented to estimate receiver function, with the maximum entropy as the rule to determine auto-correlation and cross-correlation functions. The Toeplitz equation and Levinson algorithm are used to calculate the iterative formula of error-predicting filter, and receiver function is then estimated. During extrapolation, reflective coefficient is always less than 1, which keeps maximum entropy deconvolution stable. The maximum entropy of the data outside window increases the resolution of receiver function. Both synthetic and real seismograms show that maximum entropy deconvolution is an effective method to measure receiver function in time-domain.

  2. Maximum Power from a Solar Panel

    Directory of Open Access Journals (Sweden)

    Michael Miller

    2010-01-01

    Full Text Available Solar energy has become a promising alternative to conventional fossil fuel sources. Solar panels are used to collect solar radiation and convert it into electricity. One of the techniques used to maximize the effectiveness of this energy alternative is to maximize the power output of the solar collector. In this project the maximum power is calculated by determining the voltage and the current of maximum power. These quantities are determined by finding the maximum value for the equation for power using differentiation. After the maximum values are found for each time of day, each individual quantity, voltage of maximum power, current of maximum power, and maximum power is plotted as a function of the time of day.

  3. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

    Directory of Open Access Journals (Sweden)

    Galperin Michael Y

    2003-01-01

    Full Text Available Abstract Background Comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (HGT, at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task. Results We addressed the problem of constructing parsimonious scenarios for individual sets of orthologous genes given a species tree. The orthologous sets were taken from the database of Clusters of Orthologous Groups of proteins (COGs. We show that the phyletic patterns (patterns of presence-absence in completely sequenced genomes of almost 90% of the COGs are inconsistent with the hypothetical species tree. Algorithms were developed to reconcile the phyletic patterns with the species tree by postulating gene loss, COG emergence and HGT (the latter two classes of events were collectively treated as gene gains. We prove that each of these algorithms produces a parsimonious evolutionary scenario, which can be represented as mapping of loss and gain events on the species tree. The distribution of the evolutionary events among the tree nodes substantially depends on the underlying assumptions of the reconciliation algorithm, e.g. whether or not independent gene gains (gain after loss after gain are permitted. Biological considerations suggest that, on average, gene loss might be a more likely event than gene gain. Therefore different gain penalties were used and the resulting series of reconstructed gene sets for the last universal common ancestor (LUCA of the extant life forms were analysed. The number of genes in the reconstructed LUCA gene sets grows as the gain penalty increases. However, qualitative examination of the LUCA versions reconstructed with different gain penalties

  4. Towards a formal genealogical classification of the Lezgian languages (North Caucasus: testing various phylogenetic methods on lexical data.

    Directory of Open Access Journals (Sweden)

    Alexei Kassian

    Full Text Available A lexicostatistical classification is proposed for 20 languages and dialects of the Lezgian group of the North Caucasian family, based on meticulously compiled 110-item wordlists, published as part of the Global Lexicostatistical Database project. The lexical data have been subsequently analyzed with the aid of the principal phylogenetic methods, both distance-based and character-based: Starling neighbor joining (StarlingNJ, Neighbor joining (NJ, Unweighted pair group method with arithmetic mean (UPGMA, Bayesian Markov chain Monte Carlo (MCMC, Unweighted maximum parsimony (UMP. Cognation indexes within the input matrix were marked by two different algorithms: traditional etymological approach and phonetic similarity, i.e., the automatic method of consonant classes (Levenshtein distances. Due to certain reasons (first of all, high lexicographic quality of the wordlists and a consensus about the Lezgian phylogeny among Caucasologists, the Lezgian database is a perfect testing area for appraisal of phylogenetic methods. For the etymology-based input matrix, all the phylogenetic methods, with the possible exception of UMP, have yielded trees that are sufficiently compatible with each other to generate a consensus phylogenetic tree of the Lezgian lects. The obtained consensus tree agrees with the traditional expert classification as well as some of the previously proposed formal classifications of this linguistic group. Contrary to theoretical expectations, the UMP method has suggested the least plausible tree of all. In the case of the phonetic similarity-based input matrix, the distance-based methods (StarlingNJ, NJ, UPGMA have produced the trees that are rather close to the consensus etymology-based tree and the traditional expert classification, whereas the character-based methods (Bayesian MCMC, UMP have yielded less likely topologies.

  5. Towards a formal genealogical classification of the Lezgian languages (North Caucasus): testing various phylogenetic methods on lexical data.

    Science.gov (United States)

    Kassian, Alexei

    2015-01-01

    A lexicostatistical classification is proposed for 20 languages and dialects of the Lezgian group of the North Caucasian family, based on meticulously compiled 110-item wordlists, published as part of the Global Lexicostatistical Database project. The lexical data have been subsequently analyzed with the aid of the principal phylogenetic methods, both distance-based and character-based: Starling neighbor joining (StarlingNJ), Neighbor joining (NJ), Unweighted pair group method with arithmetic mean (UPGMA), Bayesian Markov chain Monte Carlo (MCMC), Unweighted maximum parsimony (UMP). Cognation indexes within the input matrix were marked by two different algorithms: traditional etymological approach and phonetic similarity, i.e., the automatic method of consonant classes (Levenshtein distances). Due to certain reasons (first of all, high lexicographic quality of the wordlists and a consensus about the Lezgian phylogeny among Caucasologists), the Lezgian database is a perfect testing area for appraisal of phylogenetic methods. For the etymology-based input matrix, all the phylogenetic methods, with the possible exception of UMP, have yielded trees that are sufficiently compatible with each other to generate a consensus phylogenetic tree of the Lezgian lects. The obtained consensus tree agrees with the traditional expert classification as well as some of the previously proposed formal classifications of this linguistic group. Contrary to theoretical expectations, the UMP method has suggested the least plausible tree of all. In the case of the phonetic similarity-based input matrix, the distance-based methods (StarlingNJ, NJ, UPGMA) have produced the trees that are rather close to the consensus etymology-based tree and the traditional expert classification, whereas the character-based methods (Bayesian MCMC, UMP) have yielded less likely topologies.

  6. Hyainailourine and teratodontine cranial material from the late Eocene of Egypt and the application of parsimony and Bayesian methods to the phylogeny and biogeography of Hyaenodonta (Placentalia, Mammalia).

    Science.gov (United States)

    Borths, Matthew R; Holroyd, Patricia A; Seiffert, Erik R

    2016-01-01

    recovered from each phylogenetic method, we reconstructed the biogeographic history of Hyaenodonta using parsimony optimization (PO), likelihood optimization (LO), and Bayesian Binary Markov chain Monte Carlo (MCMC) to examine support for the Afro-Arabian origin of Hyaenodonta. Across all analyses, we found that Hyaenodonta most likely originated in Europe, rather than Afro-Arabia. The clade is estimated by tip-dating analysis to have undergone a rapid radiation in the Late Cretaceous and Paleocene; a radiation currently not documented by fossil evidence. During the Paleocene, lineages are reconstructed as dispersing to Asia, Afro-Arabia, and North America. The place of origin of Hyainailouroidea is likely Afro-Arabia according to the Bayesian topologies but it is ambiguous using parsimony. All topologies support the constituent clades-Hyainailourinae, Apterodontinae, and Teratodontinae-as Afro-Arabian and tip-dating estimates that each clade is established in Afro-Arabia by the middle Eocene.

  7. Maximum permissible voltage of YBCO coated conductors

    Energy Technology Data Exchange (ETDEWEB)

    Wen, J.; Lin, B.; Sheng, J.; Xu, J.; Jin, Z. [Department of Electrical Engineering, Shanghai Jiao Tong University, Shanghai (China); Hong, Z., E-mail: zhiyong.hong@sjtu.edu.cn [Department of Electrical Engineering, Shanghai Jiao Tong University, Shanghai (China); Wang, D.; Zhou, H.; Shen, X.; Shen, C. [Qingpu Power Supply Company, State Grid Shanghai Municipal Electric Power Company, Shanghai (China)

    2014-06-15

    Highlights: • We examine three kinds of tapes’ maximum permissible voltage. • We examine the relationship between quenching duration and maximum permissible voltage. • Continuous I{sub c} degradations under repetitive quenching where tapes reaching maximum permissible voltage. • The relationship between maximum permissible voltage and resistance, temperature. - Abstract: Superconducting fault current limiter (SFCL) could reduce short circuit currents in electrical power system. One of the most important thing in developing SFCL is to find out the maximum permissible voltage of each limiting element. The maximum permissible voltage is defined as the maximum voltage per unit length at which the YBCO coated conductors (CC) do not suffer from critical current (I{sub c}) degradation or burnout. In this research, the time of quenching process is changed and voltage is raised until the I{sub c} degradation or burnout happens. YBCO coated conductors test in the experiment are from American superconductor (AMSC) and Shanghai Jiao Tong University (SJTU). Along with the quenching duration increasing, the maximum permissible voltage of CC decreases. When quenching duration is 100 ms, the maximum permissible of SJTU CC, 12 mm AMSC CC and 4 mm AMSC CC are 0.72 V/cm, 0.52 V/cm and 1.2 V/cm respectively. Based on the results of samples, the whole length of CCs used in the design of a SFCL can be determined.

  8. Revealing the Maximum Strength in Nanotwinned Copper

    DEFF Research Database (Denmark)

    Lu, L.; Chen, X.; Huang, Xiaoxu

    2009-01-01

    boundary–related processes. We investigated the maximum strength of nanotwinned copper samples with different twin thicknesses. We found that the strength increases with decreasing twin thickness, reaching a maximum at 15 nanometers, followed by a softening at smaller values that is accompanied by enhanced...

  9. Modelling maximum canopy conductance and transpiration in ...

    African Journals Online (AJOL)

    There is much current interest in predicting the maximum amount of water that can be transpired by Eucalyptus trees. It is possible that industrial waste water may be applied as irrigation water to eucalypts and it is important to predict the maximum transpiration rates of these plantations in an attempt to dispose of this ...

  10. The Use of Parsimonious Questionnaires in Occupational Health Surveillance: Psychometric Properties of the Short Italian Version of the Effort/Reward Imbalance Questionnaire

    Directory of Open Access Journals (Sweden)

    Nicola Magnavita

    2012-01-01

    Full Text Available Purpose. To perform a parsimonious measurement of workplace psychosocial stress in routine occupational health surveillance, this study tests the psychometric properties of a short version of the original Italian effort-reward imbalance (ERI questionnaire. Methods. 1,803 employees (63 percent women from 19 service companies in the Italian region of Latium participated in a cross-sectional survey containing the short version of the ERI questionnaire (16 items and questions related to self-reported health, musculoskeletal complaints and job satisfaction. Exploratory factor analysis, internal consistency of scales and criterion validity were utilized. Results. The internal consistency of scales was satisfactory. Principal component analysis enabled to identify the model’s main factors. Significant associations with health and job satisfaction in the majority of cases support the notion of criterion validity. A high score on the effort-reward ratio was associated with an elevated odds ratio (OR = 2.71; 95% CI 1.86–3.95 of musculoskeletal complaints in the upper arm. Conclusions. The short form of the Italian ERI questionnaire provides a psychometrically useful tool for routine occupational health surveillance, although further validation is recommended.

  11. The transboundary non-renewable Nubian Aquifer System of Chad, Egypt, Libya and Sudan: classical groundwater questions and parsimonious hydrogeologic analysis and modeling

    Science.gov (United States)

    Voss, Clifford I.; Soliman, Safaa M.

    2014-03-01

    Parsimonious groundwater modeling provides insight into hydrogeologic functioning of the Nubian Aquifer System (NAS), the world's largest non-renewable groundwater system (belonging to Chad, Egypt, Libya, and Sudan). Classical groundwater-resource issues exist (magnitude and lateral extent of drawdown near pumping centers) with joint international management questions regarding transboundary drawdown. Much of NAS is thick, containing a large volume of high-quality groundwater, but receives insignificant recharge, so water-resource availability is time-limited. Informative aquifer data are lacking regarding large-scale response, providing only local-scale information near pumps. Proxy data provide primary underpinning for understanding regional response: Holocene water-table decline from the previous pluvial period, after thousands of years, results in current oasis/sabkha locations where the water table still intersects the ground. Depletion is found to be controlled by two regional parameters, hydraulic diffusivity and vertical anisotropy of permeability. Secondary data that provide insight are drawdowns near pumps and isotope-groundwater ages (million-year-old groundwaters in Egypt). The resultant strong simply structured three-dimensional model representation captures the essence of NAS regional groundwater-flow behavior. Model forecasts inform resource management that transboundary drawdown will likely be minimal—a nonissue—whereas drawdown within pumping centers may become excessive, requiring alternative extraction schemes; correspondingly, significant water-table drawdown may occur in pumping centers co-located with oases, causing oasis loss and environmental impacts.

  12. MXLKID: a maximum likelihood parameter identifier

    International Nuclear Information System (INIS)

    Gavel, D.T.

    1980-07-01

    MXLKID (MaXimum LiKelihood IDentifier) is a computer program designed to identify unknown parameters in a nonlinear dynamic system. Using noisy measurement data from the system, the maximum likelihood identifier computes a likelihood function (LF). Identification of system parameters is accomplished by maximizing the LF with respect to the parameters. The main body of this report briefly summarizes the maximum likelihood technique and gives instructions and examples for running the MXLKID program. MXLKID is implemented LRLTRAN on the CDC7600 computer at LLNL. A detailed mathematical description of the algorithm is given in the appendices. 24 figures, 6 tables

  13. Maximum neutron flux in thermal reactors

    International Nuclear Information System (INIS)

    Strugar, P.V.

    1968-12-01

    Direct approach to the problem is to calculate spatial distribution of fuel concentration if the reactor core directly using the condition of maximum neutron flux and comply with thermal limitations. This paper proved that the problem can be solved by applying the variational calculus, i.e. by using the maximum principle of Pontryagin. Mathematical model of reactor core is based on the two-group neutron diffusion theory with some simplifications which make it appropriate from maximum principle point of view. Here applied theory of maximum principle are suitable for application. The solution of optimum distribution of fuel concentration in the reactor core is obtained in explicit analytical form. The reactor critical dimensions are roots of a system of nonlinear equations and verification of optimum conditions can be done only for specific examples

  14. Maximum allowable load on wheeled mobile manipulators

    International Nuclear Information System (INIS)

    Habibnejad Korayem, M.; Ghariblu, H.

    2003-01-01

    This paper develops a computational technique for finding the maximum allowable load of mobile manipulator during a given trajectory. The maximum allowable loads which can be achieved by a mobile manipulator during a given trajectory are limited by the number of factors; probably the dynamic properties of mobile base and mounted manipulator, their actuator limitations and additional constraints applied to resolving the redundancy are the most important factors. To resolve extra D.O.F introduced by the base mobility, additional constraint functions are proposed directly in the task space of mobile manipulator. Finally, in two numerical examples involving a two-link planar manipulator mounted on a differentially driven mobile base, application of the method to determining maximum allowable load is verified. The simulation results demonstrates the maximum allowable load on a desired trajectory has not a unique value and directly depends on the additional constraint functions which applies to resolve the motion redundancy

  15. Maximum phytoplankton concentrations in the sea

    DEFF Research Database (Denmark)

    Jackson, G.A.; Kiørboe, Thomas

    2008-01-01

    A simplification of plankton dynamics using coagulation theory provides predictions of the maximum algal concentration sustainable in aquatic systems. These predictions have previously been tested successfully against results from iron fertilization experiments. We extend the test to data collect...

  16. Maximum-Likelihood Detection Of Noncoherent CPM

    Science.gov (United States)

    Divsalar, Dariush; Simon, Marvin K.

    1993-01-01

    Simplified detectors proposed for use in maximum-likelihood-sequence detection of symbols in alphabet of size M transmitted by uncoded, full-response continuous phase modulation over radio channel with additive white Gaussian noise. Structures of receivers derived from particular interpretation of maximum-likelihood metrics. Receivers include front ends, structures of which depends only on M, analogous to those in receivers of coherent CPM. Parts of receivers following front ends have structures, complexity of which would depend on N.

  17. Are our dynamic water quality models too complex? A comparison of a new parsimonious phosphorus model, SimplyP, and INCA-P

    Science.gov (United States)

    Jackson-Blake, L. A.; Sample, J. E.; Wade, A. J.; Helliwell, R. C.; Skeffington, R. A.

    2017-07-01

    Catchment-scale water quality models are increasingly popular tools for exploring the potential effects of land management, land use change and climate change on water quality. However, the dynamic, catchment-scale nutrient models in common usage are complex, with many uncertain parameters requiring calibration, limiting their usability and robustness. A key question is whether this complexity is justified. To explore this, we developed a parsimonious phosphorus model, SimplyP, incorporating a rainfall-runoff model and a biogeochemical model able to simulate daily streamflow, suspended sediment, and particulate and dissolved phosphorus dynamics. The model's complexity was compared to one popular nutrient model, INCA-P, and the performance of the two models was compared in a small rural catchment in northeast Scotland. For three land use classes, less than six SimplyP parameters must be determined through calibration, the rest may be based on measurements, while INCA-P has around 40 unmeasurable parameters. Despite substantially simpler process-representation, SimplyP performed comparably to INCA-P in both calibration and validation and produced similar long-term projections in response to changes in land management. Results support the hypothesis that INCA-P is overly complex for the study catchment. We hope our findings will help prompt wider model comparison exercises, as well as debate among the water quality modeling community as to whether today's models are fit for purpose. Simpler models such as SimplyP have the potential to be useful management and research tools, building blocks for future model development (prototype code is freely available), or benchmarks against which more complex models could be evaluated.

  18. Origin and spread of the 1278insTATC mutation causing Tay-Sachs disease in Ashkenazi Jews: genetic drift as a robust and parsimonious hypothesis.

    Science.gov (United States)

    Frisch, Amos; Colombo, Roberto; Michaelovsky, Elena; Karpati, Mazal; Goldman, Boleslaw; Peleg, Leah

    2004-03-01

    The 1278insTATC is the most prevalent beta-hexosaminidase A ( HEXA) gene mutation causing Tay-Sachs disease (TSD), one of the four lysosomal storage diseases (LSDs) occurring at elevated frequencies among Ashkenazi Jews (AJs). To investigate the genetic history of this mutation in the AJ population, a conserved haplotype (D15S981:175-D15S131:240-D15S1050:284-D15S197:144-D15S188:418) was identified in 1278insTATC chromosomes from 55 unrelated AJ individuals (15 homozygotes and 40 heterozygotes for the TSD mutation), suggesting the occurrence of a common founder. When two methods were used for analysis of linkage disequilibrium (LD) between flanking polymorphic markers and the disease locus and for the study of the decay of LD over time, the estimated age of the insertion was found to be 40+/-12 generations (95% confidence interval: 30-50 generations), so that the most recent common ancestor of the mutation-bearing chromosomes would date to the 8th-9th century. This corresponds with the demographic expansion of AJs in central Europe, following the founding of the Ashkenaz settlement in the early Middle Ages. The results are consistent with the geographic distribution of the main TSD mutation, 1278insTATC being more common in central Europe, and with the coalescent times of mutations causing two other LSDs, Gaucher disease and mucolipidosis type IV. Evidence for the absence of a determinant positive selection (heterozygote advantage) over the mutation is provided by a comparison between the estimated age of 1278insTATC and the probability of the current AJ frequency of the mutant allele as a function of its age, calculated by use of a branching-process model. Therefore, the founder effect in a rapidly expanding population arising from a bottleneck provides a robust parsimonious hypothesis explaining the spread of 1278insTATC-linked TSD in AJ individuals.

  19. Maximum gravitational redshift of white dwarfs

    International Nuclear Information System (INIS)

    Shapiro, S.L.; Teukolsky, S.A.

    1976-01-01

    The stability of uniformly rotating, cold white dwarfs is examined in the framework of the Parametrized Post-Newtonian (PPN) formalism of Will and Nordtvedt. The maximum central density and gravitational redshift of a white dwarf are determined as functions of five of the nine PPN parameters (γ, β, zeta 2 , zeta 3 , and zeta 4 ), the total angular momentum J, and the composition of the star. General relativity predicts that the maximum redshifts is 571 km s -1 for nonrotating carbon and helium dwarfs, but is lower for stars composed of heavier nuclei. Uniform rotation can increase the maximum redshift to 647 km s -1 for carbon stars (the neutronization limit) and to 893 km s -1 for helium stars (the uniform rotation limit). The redshift distribution of a larger sample of white dwarfs may help determine the composition of their cores

  20. Maximum entropy analysis of EGRET data

    DEFF Research Database (Denmark)

    Pohl, M.; Strong, A.W.

    1997-01-01

    EGRET data are usually analysed on the basis of the Maximum-Likelihood method \\cite{ma96} in a search for point sources in excess to a model for the background radiation (e.g. \\cite{hu97}). This method depends strongly on the quality of the background model, and thus may have high systematic unce...... uncertainties in region of strong and uncertain background like the Galactic Center region. Here we show images of such regions obtained by the quantified Maximum-Entropy method. We also discuss a possible further use of MEM in the analysis of problematic regions of the sky....

  1. The Maximum Resource Bin Packing Problem

    DEFF Research Database (Denmark)

    Boyar, J.; Epstein, L.; Favrholdt, L.M.

    2006-01-01

    Usually, for bin packing problems, we try to minimize the number of bins used or in the case of the dual bin packing problem, maximize the number or total size of accepted items. This paper presents results for the opposite problems, where we would like to maximize the number of bins used...... algorithms, First-Fit-Increasing and First-Fit-Decreasing for the maximum resource variant of classical bin packing. For the on-line variant, we define maximum resource variants of classical and dual bin packing. For dual bin packing, no on-line algorithm is competitive. For classical bin packing, we find...

  2. Shower maximum detector for SDC calorimetry

    International Nuclear Information System (INIS)

    Ernwein, J.

    1994-01-01

    A prototype for the SDC end-cap (EM) calorimeter complete with a pre-shower and a shower maximum detector was tested in beams of electrons and Π's at CERN by an SDC subsystem group. The prototype was manufactured from scintillator tiles and strips read out with 1 mm diameter wave-length shifting fibers. The design and construction of the shower maximum detector is described, and results of laboratory tests on light yield and performance of the scintillator-fiber system are given. Preliminary results on energy and position measurements with the shower max detector in the test beam are shown. (authors). 4 refs., 5 figs

  3. Topics in Bayesian statistics and maximum entropy

    International Nuclear Information System (INIS)

    Mutihac, R.; Cicuttin, A.; Cerdeira, A.; Stanciulescu, C.

    1998-12-01

    Notions of Bayesian decision theory and maximum entropy methods are reviewed with particular emphasis on probabilistic inference and Bayesian modeling. The axiomatic approach is considered as the best justification of Bayesian analysis and maximum entropy principle applied in natural sciences. Particular emphasis is put on solving the inverse problem in digital image restoration and Bayesian modeling of neural networks. Further topics addressed briefly include language modeling, neutron scattering, multiuser detection and channel equalization in digital communications, genetic information, and Bayesian court decision-making. (author)

  4. Density estimation by maximum quantum entropy

    International Nuclear Information System (INIS)

    Silver, R.N.; Wallstrom, T.; Martz, H.F.

    1993-01-01

    A new Bayesian method for non-parametric density estimation is proposed, based on a mathematical analogy to quantum statistical physics. The mathematical procedure is related to maximum entropy methods for inverse problems and image reconstruction. The information divergence enforces global smoothing toward default models, convexity, positivity, extensivity and normalization. The novel feature is the replacement of classical entropy by quantum entropy, so that local smoothing is enforced by constraints on differential operators. The linear response of the estimate is proportional to the covariance. The hyperparameters are estimated by type-II maximum likelihood (evidence). The method is demonstrated on textbook data sets

  5. Nonsymmetric entropy and maximum nonsymmetric entropy principle

    International Nuclear Information System (INIS)

    Liu Chengshi

    2009-01-01

    Under the frame of a statistical model, the concept of nonsymmetric entropy which generalizes the concepts of Boltzmann's entropy and Shannon's entropy, is defined. Maximum nonsymmetric entropy principle is proved. Some important distribution laws such as power law, can be derived from this principle naturally. Especially, nonsymmetric entropy is more convenient than other entropy such as Tsallis's entropy in deriving power laws.

  6. Maximum speed of dewetting on a fiber

    NARCIS (Netherlands)

    Chan, Tak Shing; Gueudre, Thomas; Snoeijer, Jacobus Hendrikus

    2011-01-01

    A solid object can be coated by a nonwetting liquid since a receding contact line cannot exceed a critical speed. We theoretically investigate this forced wetting transition for axisymmetric menisci on fibers of varying radii. First, we use a matched asymptotic expansion and derive the maximum speed

  7. Maximum potential preventive effect of hip protectors

    NARCIS (Netherlands)

    van Schoor, N.M.; Smit, J.H.; Bouter, L.M.; Veenings, B.; Asma, G.B.; Lips, P.T.A.M.

    2007-01-01

    OBJECTIVES: To estimate the maximum potential preventive effect of hip protectors in older persons living in the community or homes for the elderly. DESIGN: Observational cohort study. SETTING: Emergency departments in the Netherlands. PARTICIPANTS: Hip fracture patients aged 70 and older who

  8. Maximum gain of Yagi-Uda arrays

    DEFF Research Database (Denmark)

    Bojsen, J.H.; Schjær-Jacobsen, Hans; Nilsson, E.

    1971-01-01

    Numerical optimisation techniques have been used to find the maximum gain of some specific parasitic arrays. The gain of an array of infinitely thin, equispaced dipoles loaded with arbitrary reactances has been optimised. The results show that standard travelling-wave design methods are not optimum....... Yagi–Uda arrays with equal and unequal spacing have also been optimised with experimental verification....

  9. correlation between maximum dry density and cohesion

    African Journals Online (AJOL)

    HOD

    represents maximum dry density, signifies plastic limit and is liquid limit. Researchers [6, 7] estimate compaction parameters. Aside from the correlation existing between compaction parameters and other physical quantities there are some other correlations that have been investigated by other researchers. The well-known.

  10. Weak scale from the maximum entropy principle

    Science.gov (United States)

    Hamada, Yuta; Kawai, Hikaru; Kawana, Kiyoharu

    2015-03-01

    The theory of the multiverse and wormholes suggests that the parameters of the Standard Model (SM) are fixed in such a way that the radiation of the S3 universe at the final stage S_rad becomes maximum, which we call the maximum entropy principle. Although it is difficult to confirm this principle generally, for a few parameters of the SM, we can check whether S_rad actually becomes maximum at the observed values. In this paper, we regard S_rad at the final stage as a function of the weak scale (the Higgs expectation value) vh, and show that it becomes maximum around vh = {{O}} (300 GeV) when the dimensionless couplings in the SM, i.e., the Higgs self-coupling, the gauge couplings, and the Yukawa couplings are fixed. Roughly speaking, we find that the weak scale is given by vh ˜ T_{BBN}2 / (M_{pl}ye5), where ye is the Yukawa coupling of electron, T_BBN is the temperature at which the Big Bang nucleosynthesis starts, and M_pl is the Planck mass.

  11. The maximum-entropy method in superspace

    Czech Academy of Sciences Publication Activity Database

    van Smaalen, S.; Palatinus, Lukáš; Schneider, M.

    2003-01-01

    Roč. 59, - (2003), s. 459-469 ISSN 0108-7673 Grant - others:DFG(DE) XX Institutional research plan: CEZ:AV0Z1010914 Keywords : maximum-entropy method, * aperiodic crystals * electron density Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.558, year: 2003

  12. Achieving maximum sustainable yield in mixed fisheries

    NARCIS (Netherlands)

    Ulrich, Clara; Vermard, Youen; Dolder, Paul J.; Brunel, Thomas; Jardim, Ernesto; Holmes, Steven J.; Kempf, Alexander; Mortensen, Lars O.; Poos, Jan Jaap; Rindorf, Anna

    2017-01-01

    Achieving single species maximum sustainable yield (MSY) in complex and dynamic fisheries targeting multiple species (mixed fisheries) is challenging because achieving the objective for one species may mean missing the objective for another. The North Sea mixed fisheries are a representative example

  13. 5 CFR 534.203 - Maximum stipends.

    Science.gov (United States)

    2010-01-01

    ... maximum stipend established under this section. (e) A trainee at a non-Federal hospital, clinic, or medical or dental laboratory who is assigned to a Federal hospital, clinic, or medical or dental... Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY UNDER OTHER SYSTEMS Student...

  14. Minimal length, Friedmann equations and maximum density

    Energy Technology Data Exchange (ETDEWEB)

    Awad, Adel [Center for Theoretical Physics, British University of Egypt,Sherouk City 11837, P.O. Box 43 (Egypt); Department of Physics, Faculty of Science, Ain Shams University,Cairo, 11566 (Egypt); Ali, Ahmed Farag [Centre for Fundamental Physics, Zewail City of Science and Technology,Sheikh Zayed, 12588, Giza (Egypt); Department of Physics, Faculty of Science, Benha University,Benha, 13518 (Egypt)

    2014-06-16

    Inspired by Jacobson’s thermodynamic approach, Cai et al. have shown the emergence of Friedmann equations from the first law of thermodynamics. We extend Akbar-Cai derivation http://dx.doi.org/10.1103/PhysRevD.75.084003 of Friedmann equations to accommodate a general entropy-area law. Studying the resulted Friedmann equations using a specific entropy-area law, which is motivated by the generalized uncertainty principle (GUP), reveals the existence of a maximum energy density closed to Planck density. Allowing for a general continuous pressure p(ρ,a) leads to bounded curvature invariants and a general nonsingular evolution. In this case, the maximum energy density is reached in a finite time and there is no cosmological evolution beyond this point which leaves the big bang singularity inaccessible from a spacetime prospective. The existence of maximum energy density and a general nonsingular evolution is independent of the equation of state and the spacial curvature k. As an example we study the evolution of the equation of state p=ωρ through its phase-space diagram to show the existence of a maximum energy which is reachable in a finite time.

  15. Invariant Versus Classical Quartet Inference When Evolution is Heterogeneous Across Sites and Lineages.

    Science.gov (United States)

    Fernández-Sánchez, Jesús; Casanellas, Marta

    2016-03-01

    One reason why classical phylogenetic reconstruction methods fail to correctly infer the underlying topology is because they assume oversimplified models. In this article, we propose a quartet reconstruction method consistent with the most general Markov model of nucleotide substitution, which can also deal with data coming from mixtures on the same topology. Our proposed method uses phylogenetic invariants and provides a system of weights that can be used as input for quartet-based methods. We study its performance on real data and on a wide range of simulated 4-taxon data (both time-homogeneous and nonhomogeneous, with or without among-site rate heterogeneity, and with different branch length settings). We compare it to the classical methods of neighbor-joining (with paralinear distance), maximum likelihood (with different underlying models), and maximum parsimony. Our results show that this method is accurate and robust, has a similar performance to maximum likelihood when data satisfies the assumptions of both methods, and outperform the other methods when these are based on inappropriate substitution models. If alignments are long enough, then it also outperforms other methods when some of its assumptions are violated. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  16. Maximum concentrations at work and maximum biologically tolerable concentration for working materials 1991

    International Nuclear Information System (INIS)

    1991-01-01

    The meaning of the term 'maximum concentration at work' in regard of various pollutants is discussed. Specifically, a number of dusts and smokes are dealt with. The valuation criteria for maximum biologically tolerable concentrations for working materials are indicated. The working materials in question are corcinogeneous substances or substances liable to cause allergies or mutate the genome. (VT) [de

  17. 75 FR 43840 - Inflation Adjustment of the Ordinary Maximum and Aggravated Maximum Civil Monetary Penalties for...

    Science.gov (United States)

    2010-07-27

    ...-17530; Notice No. 2] RIN 2130-ZA03 Inflation Adjustment of the Ordinary Maximum and Aggravated Maximum... remains at $250. These adjustments are required by the Federal Civil Penalties Inflation Adjustment Act [email protected] . SUPPLEMENTARY INFORMATION: The Federal Civil Penalties Inflation Adjustment Act of 1990...

  18. Zipf's law, power laws and maximum entropy

    International Nuclear Information System (INIS)

    Visser, Matt

    2013-01-01

    Zipf's law, and power laws in general, have attracted and continue to attract considerable attention in a wide variety of disciplines—from astronomy to demographics to software structure to economics to linguistics to zoology, and even warfare. A recent model of random group formation (RGF) attempts a general explanation of such phenomena based on Jaynes' notion of maximum entropy applied to a particular choice of cost function. In the present paper I argue that the specific cost function used in the RGF model is in fact unnecessarily complicated, and that power laws can be obtained in a much simpler way by applying maximum entropy ideas directly to the Shannon entropy subject only to a single constraint: that the average of the logarithm of the observable quantity is specified. (paper)

  19. Maximum-entropy description of animal movement.

    Science.gov (United States)

    Fleming, Chris H; Subaşı, Yiğit; Calabrese, Justin M

    2015-03-01

    We introduce a class of maximum-entropy states that naturally includes within it all of the major continuous-time stochastic processes that have been applied to animal movement, including Brownian motion, Ornstein-Uhlenbeck motion, integrated Ornstein-Uhlenbeck motion, a recently discovered hybrid of the previous models, and a new model that describes central-place foraging. We are also able to predict a further hierarchy of new models that will emerge as data quality improves to better resolve the underlying continuity of animal movement. Finally, we also show that Langevin equations must obey a fluctuation-dissipation theorem to generate processes that fall from this class of maximum-entropy distributions when the constraints are purely kinematic.

  20. Pareto versus lognormal: a maximum entropy test.

    Science.gov (United States)

    Bee, Marco; Riccaboni, Massimo; Schiavo, Stefano

    2011-08-01

    It is commonly found that distributions that seem to be lognormal over a broad range change to a power-law (Pareto) distribution for the last few percentiles. The distributions of many physical, natural, and social events (earthquake size, species abundance, income and wealth, as well as file, city, and firm sizes) display this structure. We present a test for the occurrence of power-law tails in statistical distributions based on maximum entropy. This methodology allows one to identify the true data-generating processes even in the case when it is neither lognormal nor Pareto. The maximum entropy approach is then compared with other widely used methods and applied to different levels of aggregation of complex systems. Our results provide support for the theory that distributions with lognormal body and Pareto tail can be generated as mixtures of lognormally distributed units.

  1. Maximum likelihood estimation for integrated diffusion processes

    DEFF Research Database (Denmark)

    Baltazar-Larios, Fernando; Sørensen, Michael

    We propose a method for obtaining maximum likelihood estimates of parameters in diffusion models when the data is a discrete time sample of the integral of the process, while no direct observations of the process itself are available. The data are, moreover, assumed to be contaminated...... EM-algorithm to obtain maximum likelihood estimates of the parameters in the diffusion model. As part of the algorithm, we use a recent simple method for approximate simulation of diffusion bridges. In simulation studies for the Ornstein-Uhlenbeck process and the CIR process the proposed method works...... by measurement errors. Integrated volatility is an example of this type of observations. Another example is ice-core data on oxygen isotopes used to investigate paleo-temperatures. The data can be viewed as incomplete observations of a model with a tractable likelihood function. Therefore we propose a simulated...

  2. A Maximum Radius for Habitable Planets.

    Science.gov (United States)

    Alibert, Yann

    2015-09-01

    We compute the maximum radius a planet can have in order to fulfill two constraints that are likely necessary conditions for habitability: 1- surface temperature and pressure compatible with the existence of liquid water, and 2- no ice layer at the bottom of a putative global ocean, that would prevent the operation of the geologic carbon cycle to operate. We demonstrate that, above a given radius, these two constraints cannot be met: in the Super-Earth mass range (1-12 Mearth), the overall maximum that a planet can have varies between 1.8 and 2.3 Rearth. This radius is reduced when considering planets with higher Fe/Si ratios, and taking into account irradiation effects on the structure of the gas envelope.

  3. Maximum entropy analysis of liquid diffraction data

    International Nuclear Information System (INIS)

    Root, J.H.; Egelstaff, P.A.; Nickel, B.G.

    1986-01-01

    A maximum entropy method for reducing truncation effects in the inverse Fourier transform of structure factor, S(q), to pair correlation function, g(r), is described. The advantages and limitations of the method are explored with the PY hard sphere structure factor as model input data. An example using real data on liquid chlorine, is then presented. It is seen that spurious structure is greatly reduced in comparison to traditional Fourier transform methods. (author)

  4. A Maximum Resonant Set of Polyomino Graphs

    Directory of Open Access Journals (Sweden)

    Zhang Heping

    2016-05-01

    Full Text Available A polyomino graph P is a connected finite subgraph of the infinite plane grid such that each finite face is surrounded by a regular square of side length one and each edge belongs to at least one square. A dimer covering of P corresponds to a perfect matching. Different dimer coverings can interact via an alternating cycle (or square with respect to them. A set of disjoint squares of P is a resonant set if P has a perfect matching M so that each one of those squares is M-alternating. In this paper, we show that if K is a maximum resonant set of P, then P − K has a unique perfect matching. We further prove that the maximum forcing number of a polyomino graph is equal to the cardinality of a maximum resonant set. This confirms a conjecture of Xu et al. [26]. We also show that if K is a maximal alternating set of P, then P − K has a unique perfect matching.

  5. Automatic maximum entropy spectral reconstruction in NMR

    International Nuclear Information System (INIS)

    Mobli, Mehdi; Maciejewski, Mark W.; Gryk, Michael R.; Hoch, Jeffrey C.

    2007-01-01

    Developments in superconducting magnets, cryogenic probes, isotope labeling strategies, and sophisticated pulse sequences together have enabled the application, in principle, of high-resolution NMR spectroscopy to biomolecular systems approaching 1 megadalton. In practice, however, conventional approaches to NMR that utilize the fast Fourier transform, which require data collected at uniform time intervals, result in prohibitively lengthy data collection times in order to achieve the full resolution afforded by high field magnets. A variety of approaches that involve nonuniform sampling have been proposed, each utilizing a non-Fourier method of spectrum analysis. A very general non-Fourier method that is capable of utilizing data collected using any of the proposed nonuniform sampling strategies is maximum entropy reconstruction. A limiting factor in the adoption of maximum entropy reconstruction in NMR has been the need to specify non-intuitive parameters. Here we describe a fully automated system for maximum entropy reconstruction that requires no user-specified parameters. A web-accessible script generator provides the user interface to the system

  6. maximum neutron flux at thermal nuclear reactors

    International Nuclear Information System (INIS)

    Strugar, P.

    1968-10-01

    Since actual research reactors are technically complicated and expensive facilities it is important to achieve savings by appropriate reactor lattice configurations. There is a number of papers, and practical examples of reactors with central reflector, dealing with spatial distribution of fuel elements which would result in higher neutron flux. Common disadvantage of all the solutions is that the choice of best solution is done starting from the anticipated spatial distributions of fuel elements. The weakness of these approaches is lack of defined optimization criteria. Direct approach is defined as follows: determine the spatial distribution of fuel concentration starting from the condition of maximum neutron flux by fulfilling the thermal constraints. Thus the problem of determining the maximum neutron flux is solving a variational problem which is beyond the possibilities of classical variational calculation. This variational problem has been successfully solved by applying the maximum principle of Pontrjagin. Optimum distribution of fuel concentration was obtained in explicit analytical form. Thus, spatial distribution of the neutron flux and critical dimensions of quite complex reactor system are calculated in a relatively simple way. In addition to the fact that the results are innovative this approach is interesting because of the optimization procedure itself [sr

  7. Maximum Entropy Production Modeling of Evapotranspiration Partitioning on Heterogeneous Terrain and Canopy Cover: advantages and limitations.

    Science.gov (United States)

    Gutierrez-Jurado, H. A.; Guan, H.; Wang, J.; Wang, H.; Bras, R. L.; Simmons, C. T.

    2015-12-01

    Quantification of evapotranspiration (ET) and its partition over regions of heterogeneous topography and canopy poses a challenge using traditional approaches. In this study, we report the results of a novel field experiment design guided by the Maximum Entropy Production model of ET (MEP-ET), formulated for estimating evaporation and transpiration from homogeneous soil and canopy. A catchment with complex terrain and patchy vegetation in South Australia was instrumented to measure temperature, humidity and net radiation at soil and canopy surfaces. Performance of the MEP-ET model to quantify transpiration and soil evaporation was evaluated during wet and dry conditions with independently and directly measured transpiration from sapflow and soil evaporation using the Bowen Ratio Energy Balance (BREB). MEP-ET transpiration shows remarkable agreement with that obtained through sapflow measurements during wet conditions, but consistently overestimates the flux during dry periods. However, an additional term introduced to the original MEP-ET model accounting for higher stomatal regulation during dry spells, based on differences between leaf and air vapor pressure deficits and temperatures, significantly improves the model performance. On the other hand, MEP-ET soil evaporation is in good agreement with that from BREB regardless of moisture conditions. The experimental design allows a plot and tree scale quantification of evaporation and transpiration respectively. This study confirms for the first time that the MEP-ET originally developed for homogeneous open bare soil and closed canopy can be used for modeling ET over heterogeneous land surfaces. Furthermore, we show that with the addition of an empirical function simulating the plants ability to regulate transpiration, and based on the same measurements of temperature and humidity, the method can produce reliable estimates of ET during both wet and dry conditions without compromising its parsimony.

  8. Maximum likelihood inference of small trees in the presence of long branches.

    Science.gov (United States)

    Parks, Sarah L; Goldman, Nick

    2014-09-01

    The statistical basis of maximum likelihood (ML), its robustness, and the fact that it appears to suffer less from biases lead to it being one of the most popular methods for tree reconstruction. Despite its popularity, very few analytical solutions for ML exist, so biases suffered by ML are not well understood. One possible bias is long branch attraction (LBA), a regularly cited term generally used to describe a propensity for long branches to be joined together in estimated trees. Although initially mentioned in connection with inconsistency of parsimony, LBA has been claimed to affect all major phylogenetic reconstruction methods, including ML. Despite the widespread use of this term in the literature, exactly what LBA is and what may be causing it is poorly understood, even for simple evolutionary models and small model trees. Studies looking at LBA have focused on the effect of two long branches on tree reconstruction. However, to understand the effect of two long branches it is also important to understand the effect of just one long branch. If ML struggles to reconstruct one long branch, then this may have an impact on LBA. In this study, we look at the effect of one long branch on three-taxon tree reconstruction. We show that, counterintuitively, long branches are preferentially placed at the tips of the tree. This can be understood through the use of analytical solutions to the ML equation and distance matrix methods. We go on to look at the placement of two long branches on four-taxon trees, showing that there is no attraction between long branches, but that for extreme branch lengths long branches are joined together disproportionally often. These results illustrate that even small model trees are still interesting to help understand how ML phylogenetic reconstruction works, and that LBA is a complicated phenomenon that deserves further study. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

  9. Sequence Variation in Toxoplasma gondii rop17 Gene among Strains from Different Hosts and Geographical Locations

    Directory of Open Access Journals (Sweden)

    Nian-Zhang Zhang

    2014-01-01

    Full Text Available Genetic diversity of T. gondii is a concern of many studies, due to the biological and epidemiological diversity of this parasite. The present study examined sequence variation in rhoptry protein 17 (ROP17 gene among T. gondii isolates from different hosts and geographical regions. The rop17 gene was amplified and sequenced from 10 T. gondii strains, and phylogenetic relationship among these T. gondii strains was reconstructed using maximum parsimony (MP, neighbor-joining (NJ, and maximum likelihood (ML analyses. The partial rop17 gene sequences were 1375 bp in length and A+T contents varied from 49.45% to 50.11% among all examined T. gondii strains. Sequence analysis identified 33 variable nucleotide positions (2.1%, 16 of which were identified as transitions. Phylogeny reconstruction based on rop17 gene data revealed two major clusters which could readily distinguish Type I and Type II strains. Analyses of sequence variations in nucleotides and amino acids among these strains revealed high ratio of nonsynonymous to synonymous polymorphisms (>1, indicating that rop17 shows signs of positive selection. This study demonstrated the existence of slightly high sequence variability in the rop17 gene sequences among T. gondii strains from different hosts and geographical regions, suggesting that rop17 gene may represent a new genetic marker for population genetic studies of T. gondii isolates.

  10. Breaking up and getting together: evolution of symbiosis and cloning by fission in sea anemones (Genus Anthopleura).

    Science.gov (United States)

    Geller, J B; Walton, E D

    2001-09-01

    Clonal growth and symbiosis with photosynthetic zooxanthellae typify many genera of marine organisms, suggesting that these traits are usually conserved. However, some, such as Anthopleura, a genus of sea anemones, contain members lacking one or both of these traits. The evolutionary origins of these traits in 13 species of Anthopleura were inferred from a molecular phylogeny derived from 395 bp of the mitochondrial 16S rRNA gene and 410 bp of the mitochondrial cytochrome oxidase subunit III gene. Sequences from these genes were combined and analyzed by maximum-parsimony, maximum-likelihood, and neighbor-joining methods. Best trees from each method indicated a minimum of four changes in growth mode and that symbiosis with zooxanthellae has arisen independently in eastern and western Pacific species. Alternative trees in which species sharing growth modes or the symbiotic condition were constrained to be monophyletic were significantly worse than best trees. Although clade composition was mostly consistent with geographic sympatry, A. artemisia from California was included in the western Pacific clade. Likewise, A. midori from Japan was not placed in a clade containing only other Asian congeners. The history of Anthopleura includes repeated shifts between clonality and solitariness, repeated attainment of symbiosis with zooxanthellae, and intercontinental dispersal.

  11. Phylogenetic position of the giant anuran trypanosomes Trypanosoma chattoni, Trypanosoma fallisi, Trypanosoma mega, Trypanosoma neveulemairei, and Trypanosoma ranarum inferred from 18S rRNA gene sequences.

    Science.gov (United States)

    Martin, Donald S; Wright, André-Denis G; Barta, John R; Desser, Sherwin S

    2002-06-01

    Phylogenetic relationships within the kinetoplastid flagellates were inferred from comparisons of small-subunit ribosomal RNA gene sequences. These included 5 new gene sequences, Trypanosoma fallisi (2,239 bp), Trypanosoma chattoni (2,180 bp), Trypanosoma mega (2,211 bp), Trypanosoma neveulemairei (2,197 bp), and Trypanosoma ranarum (2,203 bp). Trees produced using maximum-parsimony and distance-matrix methods (least-squares, neighbor-joining, and maximum-likelihood), supported by strong bootstrap and quartet-puzzle analyses, indicated that the trypanosomes are a monophyletic group that divides into 2 major lineages, the salivarian trypanosomes and the nonsalivarian trypanosomes. The nonsalivarian trypanosomes further divide into 2 lineages, 1 containing trypanosomes of birds, mammals, and reptiles and the other containing trypanosomes of fish, reptiles, and anurans. Among the giant trypanosomes, T. chattoni is clearly shown to be distantly related to all the other anuran trypanosome species. Trypanosoma mega is closely associated with T. fallisi and T. ranarum, whereas T. neveulemairei and Trypanosoma rotatorium are sister taxa. The branching order of the anuran trypanosomes suggests that some toad trypanosomes may have evolved by host switching from frogs to toads.

  12. Efficiency of nuclear and mitochondrial markers recovering and supporting known amniote groups.

    Science.gov (United States)

    Lambret-Frotté, Julia; Perini, Fernando Araújo; de Moraes Russo, Claudia Augusta

    2012-01-01

    We have analysed the efficiency of all mitochondrial protein coding genes and six nuclear markers (Adora3, Adrb2, Bdnf, Irbp, Rag2 and Vwf) in reconstructing and statistically supporting known amniote groups (murines, rodents, primates, eutherians, metatherians, therians). The efficiencies of maximum likelihood, Bayesian inference, maximum parsimony, neighbor-joining and UPGMA were also evaluated, by assessing the number of correct and incorrect recovered groupings. In addition, we have compared support values using the conservative bootstrap test and the Bayesian posterior probabilities. First, no correlation was observed between gene size and marker efficiency in recovering or supporting correct nodes. As expected, tree-building methods performed similarly, even UPGMA that, in some cases, outperformed other most extensively used methods. Bayesian posterior probabilities tend to show much higher support values than the conservative bootstrap test, for correct and incorrect nodes. Our results also suggest that nuclear markers do not necessarily show a better performance than mitochondrial genes. The so-called dependency among mitochondrial markers was not observed comparing genome performances. Finally, the amniote groups with lowest recovery rates were therians and rodents, despite the morphological support for their monophyletic status. We suggest that, regardless of the tree-building method, a few carefully selected genes are able to unfold a detailed and robust scenario of phylogenetic hypotheses, particularly if taxon sampling is increased.

  13. Partial characterization of Maize rayado fino virus isolates from Ecuador: phylogenetic analysis supports a Central American origin of the virus.

    Science.gov (United States)

    Chicas, Mauricio; Caviedes, Mario; Hammond, Rosemarie; Madriz, Kenneth; Albertazzi, Federico; Villalobos, Heydi; Ramírez, Pilar

    2007-06-01

    Maize rayado fino virus (MRFV) infects maize and appears to be restricted to, yet widespread in, the Americas. MRFV was previously unreported from Ecuador. Maize plants exhibiting symptoms of MRFV infection were collected at the Santa Catalina experiment station in Quito, Ecuador. RT-PCR reactions were performed on total RNA extracted from the symptomatic leaves using primers specific for the capsid protein (CP) gene and 3' non-translated region of MRFV and first strand cDNA as a template. Nucleotide sequence comparisons to previously sequenced MRFV isolates from other geographic regions revealed 88-91% sequence identity. Phylogenetic trees constructed using Maximum Likelihood, UPGMA, Minimal Evolution, Neighbor Joining, and Maximum Parsimony methods separated the MRFV isolates into four groups. These groups may represent geographic isolation generated by the mountainous chains of the American continent. Analysis of the sequences and the genetic distances among the different isolates suggests that MRFV may have originated in Mexico and/or Guatemala and from there it dispersed to the rest of the Americas.

  14. Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees.

    Science.gov (United States)

    Keller, Alexander; Förster, Frank; Müller, Tobias; Dandekar, Thomas; Schultz, Jörg; Wolf, Matthias

    2010-01-15

    In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. For the full reviews, please go to the Reviewers' comments section.

  15. Molecular discrimination of pouched four-eyed opossums from the Mamirauá Reserve in the Brazilian Amazon

    Directory of Open Access Journals (Sweden)

    Cláudia Nunes

    2006-01-01

    Full Text Available Previous cytochrome B (CytB mtDNA studies have suggested four species for the opossum genus Philander (four-eyed opossums, three (P. mcilhennyi, P. andersoni and P. opossum from the Amazon and one (P. frenata from the Brazilian Atlantic forest. During a faunal survey nine specimens of Philander sp. and four of Didelphis marsupialis were collected in the Mamirauá Sustainable Reserve, Amazonas State, Brazil. Preliminary analyses based on morphology and geographical distributions were not conclusive, suggesting that Philander specimens could belong to either P. andersoni or P. opossum. In order to elucidate the relationship of this taxon to the remaining Amazonian taxa, seven Philander and two Didelphis specimens animals were sequenced for the cytB mtDNA gene and compared to other previously studied taxa. The maximum likelihood (ML, neighbor-Joining (NJ and maximum parsimony (MP consensus bootstrap trees depicted six groups: Didelphis., P. frenata, P andersoni, P. mcilhennyi, P.o. opossum and Philander sp. and Philander canus in a common assemblage supported by significant bootstrap values, suggesting that the Philander sp. from Mamiraua in fact belongs to the species Philander canus.

  16. Complete mitochondrial genomes reveal phylogeny relationship and evolutionary history of the family Felidae.

    Science.gov (United States)

    Zhang, W Q; Zhang, M H

    2013-09-03

    Many mitochondrial DNA sequences are used to estimate phylogenetic relationships among animal taxa and perform molecular phylogenetic evolution analysis. With the continuous development of sequencing technology, numerous mitochondrial sequences have been released in public databases, especially complete mitochondrial DNA sequences. Using multiple sequences is better than using single sequences for phylogenetic analysis of animals because multiple sequences have sufficient information for evolutionary process reconstruction. Therefore, we performed phylogenetic analyses of 14 species of Felidae based on complete mitochondrial genome sequences, with Canis familiaris as an outgroup, using neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods. The consensus phylogenetic trees supported the monophyly of Felidae, and the family could be divided into 2 subfamilies, Felinae and Pantherinae. The genus Panthera and species tigris were also studied in detail. Meanwhile, the divergence of this family was estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock, and the results shown were consistent with previous studies. In summary, the evolution of Felidae was reconstructed by phylogenetic analysis based on mitochondrial genome sequences. The described method may be broadly applicable for phylogenetic analyses of anima taxa.

  17. Multiple sequence alignment accuracy and phylogenetic inference.

    Science.gov (United States)

    Ogden, T Heath; Rosenberg, Michael S

    2006-04-01

    Phylogenies are often thought to be more dependent upon the specifics of the sequence alignment rather than on the method of reconstruction. Simulation of sequences containing insertion and deletion events was performed in order to determine the role that alignment accuracy plays during phylogenetic inference. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (ultrametric equal branch length, ultrametric random branch length, nonultrametric random branch length). Comparisons between hypothesized alignments and true alignments enabled determination of two measures of alignment accuracy, that of the total data set and that of individual branches. In general, our results indicate that as alignment error increases, topological accuracy decreases. This trend was much more pronounced for data sets derived from more pectinate topologies. In contrast, for balanced, ultrametric, equal branch length tree shapes, alignment inaccuracy had little average effect on tree reconstruction. These conclusions are based on average trends of many analyses under different conditions, and any one specific analysis, independent of the alignment accuracy, may recover very accurate or inaccurate topologies. Maximum likelihood and Bayesian, in general, outperformed neighbor joining and maximum parsimony in terms of tree reconstruction accuracy. Results also indicated that as the length of the branch and of the neighboring branches increase, alignment accuracy decreases, and the length of the neighboring branches is the major factor in topological accuracy. Thus, multiple-sequence alignment can be an important factor in downstream effects on topological reconstruction.

  18. Maximum entropy decomposition of quadrupole mass spectra

    International Nuclear Information System (INIS)

    Toussaint, U. von; Dose, V.; Golan, A.

    2004-01-01

    We present an information-theoretic method called generalized maximum entropy (GME) for decomposing mass spectra of gas mixtures from noisy measurements. In this GME approach to the noisy, underdetermined inverse problem, the joint entropies of concentration, cracking, and noise probabilities are maximized subject to the measured data. This provides a robust estimation for the unknown cracking patterns and the concentrations of the contributing molecules. The method is applied to mass spectroscopic data of hydrocarbons, and the estimates are compared with those received from a Bayesian approach. We show that the GME method is efficient and is computationally fast

  19. Maximum power operation of interacting molecular motors

    DEFF Research Database (Denmark)

    Golubeva, Natalia; Imparato, Alberto

    2013-01-01

    , as compared to the non-interacting system, in a wide range of biologically compatible scenarios. We furthermore consider the case where the motor-motor interaction directly affects the internal chemical cycle and investigate the effect on the system dynamics and thermodynamics.......We study the mechanical and thermodynamic properties of different traffic models for kinesin which are relevant in biological and experimental contexts. We find that motor-motor interactions play a fundamental role by enhancing the thermodynamic efficiency at maximum power of the motors...

  20. Maximum entropy method in momentum density reconstruction

    International Nuclear Information System (INIS)

    Dobrzynski, L.; Holas, A.

    1997-01-01

    The Maximum Entropy Method (MEM) is applied to the reconstruction of the 3-dimensional electron momentum density distributions observed through the set of Compton profiles measured along various crystallographic directions. It is shown that the reconstruction of electron momentum density may be reliably carried out with the aid of simple iterative algorithm suggested originally by Collins. A number of distributions has been simulated in order to check the performance of MEM. It is shown that MEM can be recommended as a model-free approach. (author). 13 refs, 1 fig

  1. On the maximum drawdown during speculative bubbles

    Science.gov (United States)

    Rotundo, Giulia; Navarra, Mauro

    2007-08-01

    A taxonomy of large financial crashes proposed in the literature locates the burst of speculative bubbles due to endogenous causes in the framework of extreme stock market crashes, defined as falls of market prices that are outlier with respect to the bulk of drawdown price movement distribution. This paper goes on deeper in the analysis providing a further characterization of the rising part of such selected bubbles through the examination of drawdown and maximum drawdown movement of indices prices. The analysis of drawdown duration is also performed and it is the core of the risk measure estimated here.

  2. Multi-Channel Maximum Likelihood Pitch Estimation

    DEFF Research Database (Denmark)

    Christensen, Mads Græsbøll

    2012-01-01

    In this paper, a method for multi-channel pitch estimation is proposed. The method is a maximum likelihood estimator and is based on a parametric model where the signals in the various channels share the same fundamental frequency but can have different amplitudes, phases, and noise characteristics....... This essentially means that the model allows for different conditions in the various channels, like different signal-to-noise ratios, microphone characteristics and reverberation. Moreover, the method does not assume that a certain array structure is used but rather relies on a more general model and is hence...

  3. Conductivity maximum in a charged colloidal suspension

    Energy Technology Data Exchange (ETDEWEB)

    Bastea, S

    2009-01-27

    Molecular dynamics simulations of a charged colloidal suspension in the salt-free regime show that the system exhibits an electrical conductivity maximum as a function of colloid charge. We attribute this behavior to two main competing effects: colloid effective charge saturation due to counterion 'condensation' and diffusion slowdown due to the relaxation effect. In agreement with previous observations, we also find that the effective transported charge is larger than the one determined by the Stern layer and suggest that it corresponds to the boundary fluid layer at the surface of the colloidal particles.

  4. Dynamical maximum entropy approach to flocking.

    Science.gov (United States)

    Cavagna, Andrea; Giardina, Irene; Ginelli, Francesco; Mora, Thierry; Piovani, Duccio; Tavarone, Raffaele; Walczak, Aleksandra M

    2014-04-01

    We derive a new method to infer from data the out-of-equilibrium alignment dynamics of collectively moving animal groups, by considering the maximum entropy model distribution consistent with temporal and spatial correlations of flight direction. When bird neighborhoods evolve rapidly, this dynamical inference correctly learns the parameters of the model, while a static one relying only on the spatial correlations fails. When neighbors change slowly and the detailed balance is satisfied, we recover the static procedure. We demonstrate the validity of the method on simulated data. The approach is applicable to other systems of active matter.

  5. Maximum Temperature Detection System for Integrated Circuits

    Science.gov (United States)

    Frankiewicz, Maciej; Kos, Andrzej

    2015-03-01

    The paper describes structure and measurement results of the system detecting present maximum temperature on the surface of an integrated circuit. The system consists of the set of proportional to absolute temperature sensors, temperature processing path and a digital part designed in VHDL. Analogue parts of the circuit where designed with full-custom technique. The system is a part of temperature-controlled oscillator circuit - a power management system based on dynamic frequency scaling method. The oscillator cooperates with microprocessor dedicated for thermal experiments. The whole system is implemented in UMC CMOS 0.18 μm (1.8 V) technology.

  6. Maximum entropy PDF projection: A review

    Science.gov (United States)

    Baggenstoss, Paul M.

    2017-06-01

    We review maximum entropy (MaxEnt) PDF projection, a method with wide potential applications in statistical inference. The method constructs a sampling distribution for a high-dimensional vector x based on knowing the sampling distribution p(z) of a lower-dimensional feature z = T (x). Under mild conditions, the distribution p(x) having highest possible entropy among all distributions consistent with p(z) may be readily found. Furthermore, the MaxEnt p(x) may be sampled, making the approach useful in Monte Carlo methods. We review the theorem and present a case study in model order selection and classification for handwritten character recognition.

  7. Multiperiod Maximum Loss is time unit invariant.

    Science.gov (United States)

    Kovacevic, Raimund M; Breuer, Thomas

    2016-01-01

    Time unit invariance is introduced as an additional requirement for multiperiod risk measures: for a constant portfolio under an i.i.d. risk factor process, the multiperiod risk should equal the one period risk of the aggregated loss, for an appropriate choice of parameters and independent of the portfolio and its distribution. Multiperiod Maximum Loss over a sequence of Kullback-Leibler balls is time unit invariant. This is also the case for the entropic risk measure. On the other hand, multiperiod Value at Risk and multiperiod Expected Shortfall are not time unit invariant.

  8. Maximum a posteriori decoder for digital communications

    Science.gov (United States)

    Altes, Richard A. (Inventor)

    1997-01-01

    A system and method for decoding by identification of the most likely phase coded signal corresponding to received data. The present invention has particular application to communication with signals that experience spurious random phase perturbations. The generalized estimator-correlator uses a maximum a posteriori (MAP) estimator to generate phase estimates for correlation with incoming data samples and for correlation with mean phases indicative of unique hypothesized signals. The result is a MAP likelihood statistic for each hypothesized transmission, wherein the highest value statistic identifies the transmitted signal.

  9. Objective Bayesianism and the Maximum Entropy Principle

    Directory of Open Access Journals (Sweden)

    Jon Williamson

    2013-09-01

    Full Text Available Objective Bayesian epistemology invokes three norms: the strengths of our beliefs should be probabilities; they should be calibrated to our evidence of physical probabilities; and they should otherwise equivocate sufficiently between the basic propositions that we can express. The three norms are sometimes explicated by appealing to the maximum entropy principle, which says that a belief function should be a probability function, from all those that are calibrated to evidence, that has maximum entropy. However, the three norms of objective Bayesianism are usually justified in different ways. In this paper, we show that the three norms can all be subsumed under a single justification in terms of minimising worst-case expected loss. This, in turn, is equivalent to maximising a generalised notion of entropy. We suggest that requiring language invariance, in addition to minimising worst-case expected loss, motivates maximisation of standard entropy as opposed to maximisation of other instances of generalised entropy. Our argument also provides a qualified justification for updating degrees of belief by Bayesian conditionalisation. However, conditional probabilities play a less central part in the objective Bayesian account than they do under the subjective view of Bayesianism, leading to a reduced role for Bayes’ Theorem.

  10. Efficient heuristics for maximum common substructure search.

    Science.gov (United States)

    Englert, Péter; Kovács, Péter

    2015-05-26

    Maximum common substructure search is a computationally hard optimization problem with diverse applications in the field of cheminformatics, including similarity search, lead optimization, molecule alignment, and clustering. Most of these applications have strict constraints on running time, so heuristic methods are often preferred. However, the development of an algorithm that is both fast enough and accurate enough for most practical purposes is still a challenge. Moreover, in some applications, the quality of a common substructure depends not only on its size but also on various topological features of the one-to-one atom correspondence it defines. Two state-of-the-art heuristic algorithms for finding maximum common substructures have been implemented at ChemAxon Ltd., and effective heuristics have been developed to improve both their efficiency and the relevance of the atom mappings they provide. The implementations have been thoroughly evaluated and compared with existing solutions (KCOMBU and Indigo). The heuristics have been found to greatly improve the performance and applicability of the algorithms. The purpose of this paper is to introduce the applied methods and present the experimental results.

  11. Hydraulic Limits on Maximum Plant Transpiration

    Science.gov (United States)

    Manzoni, S.; Vico, G.; Katul, G. G.; Palmroth, S.; Jackson, R. B.; Porporato, A. M.

    2011-12-01

    Photosynthesis occurs at the expense of water losses through transpiration. As a consequence of this basic carbon-water interaction at the leaf level, plant growth and ecosystem carbon exchanges are tightly coupled to transpiration. In this contribution, the hydraulic constraints that limit transpiration rates under well-watered conditions are examined across plant functional types and climates. The potential water flow through plants is proportional to both xylem hydraulic conductivity (which depends on plant carbon economy) and the difference in water potential between the soil and the atmosphere (the driving force that pulls water from the soil). Differently from previous works, we study how this potential flux changes with the amplitude of the driving force (i.e., we focus on xylem properties and not on stomatal regulation). Xylem hydraulic conductivity decreases as the driving force increases due to cavitation of the tissues. As a result of this negative feedback, more negative leaf (and xylem) water potentials would provide a stronger driving force for water transport, while at the same time limiting xylem hydraulic conductivity due to cavitation. Here, the leaf water potential value that allows an optimum balance between driving force and xylem conductivity is quantified, thus defining the maximum transpiration rate that can be sustained by the soil-to-leaf hydraulic system. To apply the proposed framework at the global scale, a novel database of xylem conductivity and cavitation vulnerability across plant types and biomes is developed. Conductivity and water potential at 50% cavitation are shown to be complementary (in particular between angiosperms and conifers), suggesting a tradeoff between transport efficiency and hydraulic safety. Plants from warmer and drier biomes tend to achieve larger maximum transpiration than plants growing in environments with lower atmospheric water demand. The predicted maximum transpiration and the corresponding leaf water

  12. Analogue of Pontryagin's maximum principle for multiple integrals minimization problems

    OpenAIRE

    Mikhail, Zelikin

    2016-01-01

    The theorem like Pontryagin's maximum principle for multiple integrals is proved. Unlike the usual maximum principle, the maximum should be taken not over all matrices, but only on matrices of rank one. Examples are given.

  13. Lake Basin Fetch and Maximum Length/Width

    Data.gov (United States)

    Minnesota Department of Natural Resources — Linear features representing the Fetch, Maximum Length and Maximum Width of a lake basin. Fetch, maximum length and average width are calcuated from the lake polygon...

  14. Maximum Likelihood Reconstruction for Magnetic Resonance Fingerprinting.

    Science.gov (United States)

    Zhao, Bo; Setsompop, Kawin; Ye, Huihui; Cauley, Stephen F; Wald, Lawrence L

    2016-08-01

    This paper introduces a statistical estimation framework for magnetic resonance (MR) fingerprinting, a recently proposed quantitative imaging paradigm. Within this framework, we present a maximum likelihood (ML) formalism to estimate multiple MR tissue parameter maps directly from highly undersampled, noisy k-space data. A novel algorithm, based on variable splitting, the alternating direction method of multipliers, and the variable projection method, is developed to solve the resulting optimization problem. Representative results from both simulations and in vivo experiments demonstrate that the proposed approach yields significantly improved accuracy in parameter estimation, compared to the conventional MR fingerprinting reconstruction. Moreover, the proposed framework provides new theoretical insights into the conventional approach. We show analytically that the conventional approach is an approximation to the ML reconstruction; more precisely, it is exactly equivalent to the first iteration of the proposed algorithm for the ML reconstruction, provided that a gridding reconstruction is used as an initialization.

  15. Maximum Profit Configurations of Commercial Engines

    Directory of Open Access Journals (Sweden)

    Yiran Chen

    2011-06-01

    Full Text Available An investigation of commercial engines with finite capacity low- and high-price economic subsystems and a generalized commodity transfer law [n ∝ Δ (P m] in commodity flow processes, in which effects of the price elasticities of supply and demand are introduced, is presented in this paper. Optimal cycle configurations of commercial engines for maximum profit are obtained by applying optimal control theory. In some special cases, the eventual state—market equilibrium—is solely determined by the initial conditions and the inherent characteristics of two subsystems; while the different ways of transfer affect the model in respects of the specific forms of the paths of prices and the instantaneous commodity flow, i.e., the optimal configuration.

  16. Modelling maximum likelihood estimation of availability

    International Nuclear Information System (INIS)

    Waller, R.A.; Tietjen, G.L.; Rock, G.W.

    1975-01-01

    Suppose the performance of a nuclear powered electrical generating power plant is continuously monitored to record the sequence of failure and repairs during sustained operation. The purpose of this study is to assess one method of estimating the performance of the power plant when the measure of performance is availability. That is, we determine the probability that the plant is operational at time t. To study the availability of a power plant, we first assume statistical models for the variables, X and Y, which denote the time-to-failure and the time-to-repair variables, respectively. Once those statistical models are specified, the availability, A(t), can be expressed as a function of some or all of their parameters. Usually those parameters are unknown in practice and so A(t) is unknown. This paper discusses the maximum likelihood estimator of A(t) when the time-to-failure model for X is an exponential density with parameter, lambda, and the time-to-repair model for Y is an exponential density with parameter, theta. Under the assumption of exponential models for X and Y, it follows that the instantaneous availability at time t is A(t)=lambda/(lambda+theta)+theta/(lambda+theta)exp[-[(1/lambda)+(1/theta)]t] with t>0. Also, the steady-state availability is A(infinity)=lambda/(lambda+theta). We use the observations from n failure-repair cycles of the power plant, say X 1 , X 2 , ..., Xsub(n), Y 1 , Y 2 , ..., Ysub(n) to present the maximum likelihood estimators of A(t) and A(infinity). The exact sampling distributions for those estimators and some statistical properties are discussed before a simulation model is used to determine 95% simulation intervals for A(t). The methodology is applied to two examples which approximate the operating history of two nuclear power plants. (author)

  17. A maximum power point tracking for photovoltaic-SPE system using a maximum current controller

    Energy Technology Data Exchange (ETDEWEB)

    Muhida, Riza [Osaka Univ., Dept. of Physical Science, Toyonaka, Osaka (Japan); Osaka Univ., Dept. of Electrical Engineering, Suita, Osaka (Japan); Park, Minwon; Dakkak, Mohammed; Matsuura, Kenji [Osaka Univ., Dept. of Electrical Engineering, Suita, Osaka (Japan); Tsuyoshi, Akira; Michira, Masakazu [Kobe City College of Technology, Nishi-ku, Kobe (Japan)

    2003-02-01

    Processes to produce hydrogen from solar photovoltaic (PV)-powered water electrolysis using solid polymer electrolysis (SPE) are reported. An alternative control of maximum power point tracking (MPPT) in the PV-SPE system based on the maximum current searching methods has been designed and implemented. Based on the characteristics of voltage-current and theoretical analysis of SPE, it can be shown that the tracking of the maximum current output of DC-DC converter in SPE side will track the MPPT of photovoltaic panel simultaneously. This method uses a proportional integrator controller to control the duty factor of DC-DC converter with pulse-width modulator (PWM). The MPPT performance and hydrogen production performance of this method have been evaluated and discussed based on the results of the experiment. (Author)

  18. Maximum mass of magnetic white dwarfs

    International Nuclear Information System (INIS)

    Paret, Daryel Manreza; Horvath, Jorge Ernesto; Martínez, Aurora Perez

    2015-01-01

    We revisit the problem of the maximum masses of magnetized white dwarfs (WDs). The impact of a strong magnetic field on the structure equations is addressed. The pressures become anisotropic due to the presence of the magnetic field and split into parallel and perpendicular components. We first construct stable solutions of the Tolman-Oppenheimer-Volkoff equations for parallel pressures and find that physical solutions vanish for the perpendicular pressure when B ≳ 10 13 G. This fact establishes an upper bound for a magnetic field and the stability of the configurations in the (quasi) spherical approximation. Our findings also indicate that it is not possible to obtain stable magnetized WDs with super-Chandrasekhar masses because the values of the magnetic field needed for them are higher than this bound. To proceed into the anisotropic regime, we can apply results for structure equations appropriate for a cylindrical metric with anisotropic pressures that were derived in our previous work. From the solutions of the structure equations in cylindrical symmetry we have confirmed the same bound for B ∼ 10 13 G, since beyond this value no physical solutions are possible. Our tentative conclusion is that massive WDs with masses well beyond the Chandrasekhar limit do not constitute stable solutions and should not exist. (paper)

  19. TRENDS IN ESTIMATED MIXING DEPTH DAILY MAXIMUMS

    Energy Technology Data Exchange (ETDEWEB)

    Buckley, R; Amy DuPont, A; Robert Kurzeja, R; Matt Parker, M

    2007-11-12

    Mixing depth is an important quantity in the determination of air pollution concentrations. Fireweather forecasts depend strongly on estimates of the mixing depth as a means of determining the altitude and dilution (ventilation rates) of smoke plumes. The Savannah River United States Forest Service (USFS) routinely conducts prescribed fires at the Savannah River Site (SRS), a heavily wooded Department of Energy (DOE) facility located in southwest South Carolina. For many years, the Savannah River National Laboratory (SRNL) has provided forecasts of weather conditions in support of the fire program, including an estimated mixing depth using potential temperature and turbulence change with height at a given location. This paper examines trends in the average estimated mixing depth daily maximum at the SRS over an extended period of time (4.75 years) derived from numerical atmospheric simulations using two versions of the Regional Atmospheric Modeling System (RAMS). This allows for differences to be seen between the model versions, as well as trends on a multi-year time frame. In addition, comparisons of predicted mixing depth for individual days in which special balloon soundings were released are also discussed.

  20. Mammographic image restoration using maximum entropy deconvolution

    International Nuclear Information System (INIS)

    Jannetta, A; Jackson, J C; Kotre, C J; Birch, I P; Robson, K J; Padgett, R

    2004-01-01

    An image restoration approach based on a Bayesian maximum entropy method (MEM) has been applied to a radiological image deconvolution problem, that of reduction of geometric blurring in magnification mammography. The aim of the work is to demonstrate an improvement in image spatial resolution in realistic noisy radiological images with no associated penalty in terms of reduction in the signal-to-noise ratio perceived by the observer. Images of the TORMAM mammographic image quality phantom were recorded using the standard magnification settings of 1.8 magnification/fine focus and also at 1.8 magnification/broad focus and 3.0 magnification/fine focus; the latter two arrangements would normally give rise to unacceptable geometric blurring. Measured point-spread functions were used in conjunction with the MEM image processing to de-blur these images. The results are presented as comparative images of phantom test features and as observer scores for the raw and processed images. Visualization of high resolution features and the total image scores for the test phantom were improved by the application of the MEM processing. It is argued that this successful demonstration of image de-blurring in noisy radiological images offers the possibility of weakening the link between focal spot size and geometric blurring in radiology, thus opening up new approaches to system optimization

  1. Maximum Margin Clustering of Hyperspectral Data

    Science.gov (United States)

    Niazmardi, S.; Safari, A.; Homayouni, S.

    2013-09-01

    In recent decades, large margin methods such as Support Vector Machines (SVMs) are supposed to be the state-of-the-art of supervised learning methods for classification of hyperspectral data. However, the results of these algorithms mainly depend on the quality and quantity of available training data. To tackle down the problems associated with the training data, the researcher put effort into extending the capability of large margin algorithms for unsupervised learning. One of the recent proposed algorithms is Maximum Margin Clustering (MMC). The MMC is an unsupervised SVMs algorithm that simultaneously estimates both the labels and the hyperplane parameters. Nevertheless, the optimization of the MMC algorithm is a non-convex problem. Most of the existing MMC methods rely on the reformulating and the relaxing of the non-convex optimization problem as semi-definite programs (SDP), which are computationally very expensive and only can handle small data sets. Moreover, most of these algorithms are two-class classification, which cannot be used for classification of remotely sensed data. In this paper, a new MMC algorithm is used that solve the original non-convex problem using Alternative Optimization method. This algorithm is also extended for multi-class classification and its performance is evaluated. The results of the proposed algorithm show that the algorithm has acceptable results for hyperspectral data clustering.

  2. Paving the road to maximum productivity.

    Science.gov (United States)

    Holland, C

    1998-01-01

    "Job security" is an oxymoron in today's environment of downsizing, mergers, and acquisitions. Workers find themselves living by new rules in the workplace that they may not understand. How do we cope? It is the leader's charge to take advantage of this chaos and create conditions under which his or her people can understand the need for change and come together with a shared purpose to effect that change. The clinical laboratory at Arkansas Children's Hospital has taken advantage of this chaos to down-size and to redesign how the work gets done to pave the road to maximum productivity. After initial hourly cutbacks, the workers accepted the cold, hard fact that they would never get their old world back. They set goals to proactively shape their new world through reorganizing, flexing staff with workload, creating a rapid response laboratory, exploiting information technology, and outsourcing. Today the laboratory is a lean, productive machine that accepts change as a way of life. We have learned to adapt, trust, and support each other as we have journeyed together over the rough roads. We are looking forward to paving a new fork in the road to the future.

  3. Maximum power flux of auroral kilometric radiation

    International Nuclear Information System (INIS)

    Benson, R.F.; Fainberg, J.

    1991-01-01

    The maximum auroral kilometric radiation (AKR) power flux observed by distant satellites has been increased by more than a factor of 10 from previously reported values. This increase has been achieved by a new data selection criterion and a new analysis of antenna spin modulated signals received by the radio astronomy instrument on ISEE 3. The method relies on selecting AKR events containing signals in the highest-frequency channel (1980, kHz), followed by a careful analysis that effectively increased the instrumental dynamic range by more than 20 dB by making use of the spacecraft antenna gain diagram during a spacecraft rotation. This analysis has allowed the separation of real signals from those created in the receiver by overloading. Many signals having the appearance of AKR harmonic signals were shown to be of spurious origin. During one event, however, real second harmonic AKR signals were detected even though the spacecraft was at a great distance (17 R E ) from Earth. During another event, when the spacecraft was at the orbital distance of the Moon and on the morning side of Earth, the power flux of fundamental AKR was greater than 3 x 10 -13 W m -2 Hz -1 at 360 kHz normalized to a radial distance r of 25 R E assuming the power falls off as r -2 . A comparison of these intense signal levels with the most intense source region values (obtained by ISIS 1 and Viking) suggests that multiple sources were observed by ISEE 3

  4. Maximum likelihood window for time delay estimation

    International Nuclear Information System (INIS)

    Lee, Young Sup; Yoon, Dong Jin; Kim, Chi Yup

    2004-01-01

    Time delay estimation for the detection of leak location in underground pipelines is critically important. Because the exact leak location depends upon the precision of the time delay between sensor signals due to leak noise and the speed of elastic waves, the research on the estimation of time delay has been one of the key issues in leak lovating with the time arrival difference method. In this study, an optimal Maximum Likelihood window is considered to obtain a better estimation of the time delay. This method has been proved in experiments, which can provide much clearer and more precise peaks in cross-correlation functions of leak signals. The leak location error has been less than 1 % of the distance between sensors, for example the error was not greater than 3 m for 300 m long underground pipelines. Apart from the experiment, an intensive theoretical analysis in terms of signal processing has been described. The improved leak locating with the suggested method is due to the windowing effect in frequency domain, which offers a weighting in significant frequencies.

  5. 49 CFR 230.24 - Maximum allowable stress.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 4 2010-10-01 2010-10-01 false Maximum allowable stress. 230.24 Section 230.24... Allowable Stress § 230.24 Maximum allowable stress. (a) Maximum allowable stress value. The maximum allowable stress value on any component of a steam locomotive boiler shall not exceed 1/4 of the ultimate...

  6. 20 CFR 226.52 - Total annuity subject to maximum.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Total annuity subject to maximum. 226.52... COMPUTING EMPLOYEE, SPOUSE, AND DIVORCED SPOUSE ANNUITIES Railroad Retirement Family Maximum § 226.52 Total annuity subject to maximum. The total annuity amount which is compared to the maximum monthly amount to...

  7. Half-width at half-maximum, full-width at half-maximum analysis

    Indian Academy of Sciences (India)

    addition to the well-defined parameter full-width at half-maximum (FWHM). The distribution of ... optical side-lobes in the diffraction pattern resulting in steep central maxima [6], reduc- tion of effects of ... and broad central peak. The idea of.

  8. Cosmic shear measurement with maximum likelihood and maximum a posteriori inference

    Science.gov (United States)

    Hall, Alex; Taylor, Andy

    2017-06-01

    We investigate the problem of noise bias in maximum likelihood and maximum a posteriori estimators for cosmic shear. We derive the leading and next-to-leading order biases and compute them in the context of galaxy ellipticity measurements, extending previous work on maximum likelihood inference for weak lensing. We show that a large part of the bias on these point estimators can be removed using information already contained in the likelihood when a galaxy model is specified, without the need for external calibration. We test these bias-corrected estimators on simulated galaxy images similar to those expected from planned space-based weak lensing surveys, with promising results. We find that the introduction of an intrinsic shape prior can help with mitigation of noise bias, such that the maximum a posteriori estimate can be made less biased than the maximum likelihood estimate. Second-order terms offer a check on the convergence of the estimators, but are largely subdominant. We show how biases propagate to shear estimates, demonstrating in our simple set-up that shear biases can be reduced by orders of magnitude and potentially to within the requirements of planned space-based surveys at mild signal-to-noise ratio. We find that second-order terms can exhibit significant cancellations at low signal-to-noise ratio when Gaussian noise is assumed, which has implications for inferring the performance of shear-measurement algorithms from simplified simulations. We discuss the viability of our point estimators as tools for lensing inference, arguing that they allow for the robust measurement of ellipticity and shear.

  9. The current status of the New World monkey phylogeny

    Directory of Open Access Journals (Sweden)

    SCHNEIDER HORACIO

    2000-01-01

    Full Text Available Four DNA datasets were combined in tandem (6700 bp and Maximum parsimony and Neighbor-Joining analyses were performed. The results suggest three groups emerging almost at the same time: Atelidae, Pitheciidae and Cebidae. The total analysis strongly supports the monophyly of the Cebidae family, grouping Aotus, Cebus and Saimiri with the small callitrichines. In the callitrichines, the data link Cebuela to Callithrix, place Callimico as a sister group of Callithrix/Cebuella, and show Saguinus to be the earliest offshoot of the callitrichines. In the family Pithecidae, Callicebus is the basal genus. Finally, combined molecular data showed congruent branching in the atelid clade, setting up Alouatta as the basal lineage and Brachyteles-Lagothrix as a sister group and the most derived branch. Two major points remain to be clarified in the platyrrhine phylogeny: (i what is the exact branching pattern of Aotus, Cebus, Saimiri and the small callitrichines, and (ii, which two of these three lineages, pitheciines, atelines or cebids, are more closely related?

  10. Complete Mitochondrial Genome of the Red Fox (Vuples vuples) and Phylogenetic Analysis with Other Canid Species.

    Science.gov (United States)

    Zhong, Hua-Ming; Zhang, Hong-Hai; Sha, Wei-Lai; Zhang, Cheng-De; Chen, Yu-Cai

    2010-04-01

    The whole mitochondrial genome sequence of red fox (Vuples vuples) was determined. It had a total length of 16 723 bp. As in most mammal mitochondrial genome, it contained 13 protein coding genes, two ribosome RNA genes, 22 transfer RNA genes and one control region. The base composition was 31.3% A, 26.1% C, 14.8% G and 27.8% T, respectively. The codon usage of red fox, arctic fox, gray wolf, domestic dog and coyote followed the same pattern except for an unusual ATT start codon, which initiates the NADH dehydrogenase subunit 3 gene in the red fox. A long tandem repeat rich in AC was found between conserved sequence block 1 and 2 in the control region. In order to confirm the phylogenetic relationships of red fox to other canids, phylogenetic trees were reconstructed by neighbor-joining and maximum parsimony methods using 12 concatenated heavy-strand protein-coding genes. The result indicated that arctic fox was the sister group of red fox and they both belong to the red fox-like clade in family Canidae, while gray wolf, domestic dog and coyote belong to wolf-like clade. The result was in accordance with existing phylogenetic results.

  11. Sequence analysis and typing of Saprolegnia strains isolated from freshwater fish from Southern Chinese regions

    Directory of Open Access Journals (Sweden)

    Siya Liu

    2017-09-01

    Full Text Available Saprolegniasis, caused by Saprolegnia infection, is one of the most common diseases in freshwater fish. Our study aimed to determine the epidemiological characteristics of saprolegniasis in Chinese regions of high incidence. Saprolegnia were isolated and identified by morphological and molecular methods targeting the internal transcribed spacer (ITS ribosomal DNA (rDNA and building neighbor-joining (NJ and maximum parsimony (MP phylogenetic trees. The ITS sequences of eight isolated strains were compared with GenBank sequences and all strains fell into three clades: CLADE1 (02, LP, 04 and 14, CLADE2 (S1, and CLADE3 (CP, S2, L5 and the reference ATCC200013. Isolates 02 and LP shared 80% sequence similarity with S. diclina, S. longicaulis, S. ferax, S. mixta, and S. anomalies. Further, isolates 04 and 14 shared 80% similarity with S. bulbosa and S. oliviae. Finally, extremely high ITS sequence similarities were identified between isolates S1 and S. australis (100%; CP and S. hypogyna (96%; and S2, L5, ATCC200013 and S. salmonis (98%. This research provides insights into the identification, prevention and control of saprolegniasis pathogens and the potential development of effective drugs.

  12. Growth hormone and prolactin in Andrias davidianus: cDNA cloning, tissue distribution and phylogenetic analysis.

    Science.gov (United States)

    Yang, Liping; Meng, Zining; Liu, Yun; Zhang, Yong; Liu, Xiaochun; Lu, Danqi; Huang, Junhai; Lin, Haoran

    2010-01-15

    The Chinese giant salamander (Andrias davidianus) is one of the largest and 'living fossil' species of amphibian. To obtain genetic information for this species, the cDNAs encoding growth hormone (adGH) and prolactin (adPRL) were cloned from a pituitary cDNA library. The isolated adGH cDNA consisted of 864 bp and encoded a propeptide of 215 amino acids, while the cDNA of adPRL was 1106 bp in length and encoded a putative peptide of 229 amino acids. Expression of the GH and PRL mRNA was only detected in the pituitary. Phylogenetic analyses were performed based on the isolated pituitary hormone sequences using maximum parsimony and neighbor-joining algorithms. The clustering results are similar to that based on the morphological characteristics or the rRNA genes, which indicate that the two orders (Anura and Caudata) of amphibian were monophyletic, and that A. davidianus was diverged early in the Caudate clade. These results indicated that both the GH and PRL sequence might be useful to study the phylogenies of relatively moderate evolved groups.

  13. Subspecies identification of captive Orang Utan in Melaka based on D-loop mitochondria DNA

    Science.gov (United States)

    Kamaluddin, Siti Norsyuhada; Yaakop, Salmah; Idris, Wan Mohd Razi; Rovie-Ryan, Jeffrine Japning; Md-Zain, Badrul Munir

    2018-04-01

    Mitochondrial DNA of Bornean Orang Utan populations suggests that there are three different subspecies (Pongo pygmaeus pygmaeus; Sarawak & Northwest Kalimantan, P. p. wurmbii; Southern West Kalimantan and Central Kalimantan, P. p. morio; East Kalimantan and Sabah). The subspecies of Orang Utans in captivity are difficult to determine through morphological observation. Thus, misidentification by ranger or zoo staffs leads to unwanted consequences especially towards conservation efforts of Orang Utan. The main objective of this study was to identify the subspecies and the geographic origin of 10 Orang Utans in Zoo Melaka and A' Famosa by using partial mitochondrial D-loop gene sequences. DNA of all individuals was extracted from FTA Card. Data analyses were performed using Maximum Parsimony, MP and Neighbor Joining, NJ. Molecular phylogeny analysis revealed that all the samples likely belong to one species of Sumatran Orang Utan (P. abelii) and three different subspecies of Bornean Orang Utans (P. p. pygmaeus, P. p. morio, and P. p. wurmbii). The results obtained in this study indirectly help the management of zoos in term of conservation and visitor's education.

  14. Molecular Characterization of Leishmania Species Isolated from Cutaneous Leishmaniasis in Yemen

    Science.gov (United States)

    Mahdy, Mohammed A. K.; Al-Mekhlafi, Hesham M.; Al-Mekhlafi, Abdulsalam M.; Lim, Yvonne A. L.; Bin Shuaib, Naemah O. M.; Azazy, Ahmed A.; Mahmud, Rohela

    2010-01-01

    Background Cutaneous leishmaniasis (CL) is a neglected tropical disease endemic in the tropics and subtropics with a global yearly incidence of 1.5 million. Although CL is the most common form of leishmaniasis, which is responsible for 60% of DALYs lost due to tropical-cluster diseases prevalent in Yemen, available information is very limited. Methodology/Principal Findings This study was conducted to determine the molecular characterization of Leishmania species isolated from human cutaneous lesions in Yemen. Dermal scrapes were collected and examined for Leishmania amastigotes using the Giemsa staining technique. Amplification of the ribosomal internal transcribed spacer 1(ITS-1) gene was carried out using nested PCR and subsequent sequencing. The sequences from Leishmania isolates were subjected to phylogenetic analysis using the neighbor-joining and maximum parsimony methods. The trees identified Leishmania tropica from 16 isolates which were represented by two sequence types. Conclusions/Significance The predominance of the anthroponotic species (i.e. L. tropica) indicates the probability of anthroponotic transmission of cutaneous leishmaniasis in Yemen. These findings will help public health authorities to build an effective control strategy taking into consideration person–to-person transmission as the main dynamic of transmission of CL. PMID:20862227

  15. Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

    Science.gov (United States)

    Damkliang, Kasikrit; Tandayya, Pichaya; Sangket, Unitsa; Pasomsub, Ekawat

    2016-11-28

    At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow's execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. All local services have been deployed at our portal http://bioservices.sci.psu.ac.th.

  16. Molecular phylogeny of mitochondrial cytochrome b and 12S rRNA sequences in the Felidae: ocelot and domestic cat lineages.

    Science.gov (United States)

    Masuda, R; Lopez, J V; Slattery, J P; Yuhki, N; O'Brien, S J

    1996-12-01

    Molecular phylogeny of the cat family Felidae is derived using two mitochondrial genes, cytochrome b and 12S rRNA. Phylogenetic methods of weighted maximum parsimony and minimum evolution estimated by neighbor-joining are employed to reconstruct topologies among 20 extant felid species. Sequence analyses of 363 bp of cytochrome b and 376 bp of the 12S rRNA genes yielded average pair-wise similarity values between felids ranging from 94 to 99% and from 85 to 99%, respectively. Phylogenetic reconstruction supports more recent, intralineage associations but fails to completely resolve interlineage relationships. Both genes produce a monophyletic group of Felis species but vary in the placement of the pallas cat. The ocelot lineage represents an early divergence within the Felidae, with strong associations between ocelot and margay, Geoffroy's cat and kodkod, and pampas cat and tigrina. Implications of the relative recency of felid evolution, presence of ancestral polymorphisms, and influence of outgroups in placement of the topological root are discussed.

  17. Phylogenetic reconstruction of South American felids defined by protein electrophoresis.

    Science.gov (United States)

    Slattery, J P; Johnson, W E; Goldman, D; O'Brien, S J

    1994-09-01

    Phylogenetic associations among six closely related South American felid species were defined by changes in protein-encoding gene loci. We analyzed proteins isolated from skin fibroblasts using two-dimensional electrophoresis and allozymes extracted from blood cells. Genotypes were determined for multiple individuals of ocelot, margay, tigrina, Geoffroy's cat, kodkod, and pampas cat at 548 loci resolved by two-dimensional electrophoresis and 44 allozyme loci. Phenograms were constructed using the methods of Fitch-Margoliash and neighbor-joining on a matrix of Nei's unbiased genetic distances for all pairs of species. Results of a relative-rate test indicate changes in two-dimensional electrophoresis data are constant among all South American felids with respect to a hyena outgroup. Allelic frequencies were transformed to discrete character states for maximum parsimony analysis. Phylogenetic reconstruction indicates a major split occurred approximately 5-6 million years ago, leading to three groups within the ocelot lineage. The earliest divergence led to Leopardus tigrina, followed by a split between an ancestor of an unresolved trichotomy of three species (Oncifelis guigna, O. geoffroyi, and Lynchailuris colocolo) and a recent common ancestor of Leopardus pardalis and L. wiedii. The results suggest that modern South American felids are monophyletic and evolved rapidly after the formation of the Panama land bridge between North and South America.

  18. ITS1 locus: a major determinant of genetic diversity of Plantago spp. (plantaginaceae)

    International Nuclear Information System (INIS)

    Altantestseg, K.; Baatartsogt, O.; Enkhchimeg, V.

    2018-01-01

    By this study, ITS (Internal Transcribed Spacer) regions in the nuclear DNA of 10 Plantago samples collected from Mongolia (5 samples) and Vietnam (5 samples) were sequenced and constructed Maximum Parsimony (MP) and Neighbor-Joining (NJ) phylogenetic trees for establishing the genetic relationship. The results showed that 10 samples belonged to 2 species (7 Plantago major and 3 Plantago depressa). The length of sequences ranged from 632 to 644 bp (ITS1 ranged from 210-222 bp, 5.8S was 162 bp, and ITS2 259 - 261 bp). The ITS1 region was highly variable among the sequences whereas ITS2 and 5.8S regions were more conservative. The MP and NJ trees apparently separated P. major and P. depressa into 2 different groups, supported with high bootstrap values. P. depressa was first time reported in Mongolia. The results highlighted that ITS sequences could distinguish P. major and P. depressa, which is certainly important for pharmacist to use crude drugs derived from Plantago. (author)

  19. Genetic relatedness among indigenous rice varieties in the Eastern Himalayan region based on nucleotide sequences of the Waxy gene.

    Science.gov (United States)

    Choudhury, Baharul I; Khan, Mohammed L; Dayanandan, Selvadurai

    2014-12-29

    Indigenous rice varieties in the Eastern Himalayan region of Northeast India are traditionally classified into sali, boro and jum ecotypes based on geographical locality and the season of cultivation. In this study, we used DNA sequence data from the Waxy (Wx) gene to infer the genetic relatedness among indigenous rice varieties in Northeast India and to assess the genetic distinctiveness of ecotypes. The results of all three analyses (Bayesian, Maximum Parsimony and Neighbor Joining) were congruent and revealed two genetically distinct clusters of rice varieties in the region. The large group comprised several varieties of sali and boro ecotypes, and all agronomically improved varieties. The small group consisted of only traditionally cultivated indigenous rice varieties, which included one boro, few sali and all jum varieties. The fixation index analysis revealed a very low level of differentiation between sali and boro (F(ST) = 0.005), moderate differentiation between sali and jum (F(ST) = 0.108) and high differentiation between jum and boro (F(ST) = 0.230) ecotypes. The genetic relatedness analyses revealed that sali, boro and jum ecotypes are genetically heterogeneous, and the current classification based on cultivation type is not congruent with the genetic background of rice varieties. Indigenous rice varieties chosen from genetically distinct clusters could be used in breeding programs to improve genetic gain through heterosis, while maintaining high genetic diversity.

  20. Phylogenetic relationships in Taxodiaceae and Cupressaceae sensu stricto based on matK gene, chlL gene, trnL-trnF IGS region, and trnL intron sequences.

    Science.gov (United States)

    Kusumi, J; Tsumura, Y; Yoshimaru, H; Tachida, H

    2000-10-01

    Nucleotide sequences from four chloroplast genes, the matK, chlL, intergenic spacer (IGS) region between trnL and trnF, and an intron of trnL, were determined from all species of Taxodiaceae and five species of Cupressaceae sensu stricto (s.s.). Phylogenetic trees were constructed using the maximum parsimony and the neighbor-joining methods with Cunninghamia as an outgroup. These analyses provided greater resolution of relationships among genera and higher bootstrap supports for clades compared to previous analyses. Results indicate that Taiwania diverged first, and then Athrotaxis diverged from the remaining genera. Metasequoia, Sequoia, and Sequoiadendron form a clade. Taxodium and Glyptostrobus form a clade, which is the sister to Cryptomeria. Cupressaceae s.s. are derived from within Taxodiaceae, being the most closely related to the Cryptomeria/Taxodium/Glyptostrobus clade. These relationships are consistent with previous morphological groupings and the analyses of molecular data. In addition, we found acceleration of evolutionary rates in Cupressaceae s.s. Possible causes for the acceleration are discussed.

  1. TeachEnG: a Teaching Engine for Genomics.

    Science.gov (United States)

    Kim, Minji; Kim, Yeonsung; Qian, Lei; Song, Jun S

    2017-10-15

    Bioinformatics is a rapidly growing field that has emerged from the synergy of computer science, statistics and biology. Given the interdisciplinary nature of bioinformatics, many students from diverse fields struggle with grasping bioinformatic concepts only from classroom lectures. Interactive tools for helping students reinforce their learning would be thus desirable. Here, we present an interactive online educational tool called TeachEnG (acronym for Teaching Engine for Genomics) for reinforcing key concepts in sequence alignment and phylogenetic tree reconstruction. Our instructional games allow students to align sequences by hand, fill out the dynamic programming matrix in the Needleman-Wunsch global sequence alignment algorithm, and reconstruct phylogenetic trees via the maximum parsimony, Unweighted Pair Group Method with Arithmetic mean (UPGMA) and Neighbor-Joining algorithms. With an easily accessible interface and instant visual feedback, TeachEnG will help promote active learning in bioinformatics. TeachEnG is freely available at http://teacheng.illinois.edu. The source code is available from https://github.com/KnowEnG/TeachEnG under the Artistic License 2.0. It is written in JavaScript and compatible with Firefox, Safari, Chrome and Microsoft Edge. songj@illinois.edu. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  2. Population explosion in the yellow-spined bamboo locust Ceracris kiangsu and inferences for the impact of human activity.

    Directory of Open Access Journals (Sweden)

    Zhou Fan

    Full Text Available Geographic distance and geographical barriers likely play a considerable role in structuring genetic variation in species, although some migratory species may have less phylogeographic structure on a smaller spatial scale. Here, genetic diversity and the phylogenetic structure among geographical populations of the yellow-spined bamboo locust, Ceracris kiangsu, were examined with 16S rDNA and amplified fragment length polymorphisms (AFLPs. In this study, no conspicuous phylogeographical structure was discovered from either Maximum parsimony (MP and Neighbor-joining (NJ phylogenetic analyses. The effect of geographical isolation was not conspicuous on a large spatial scale.At smaller spatial scales local diversity of some populations within mountainous areas were detected using Nei's genetic distance and AMOVA. There is a high level of genetic diversity and a low genetic differentiation among populations in the C. kiangsu of South and Southeast China. Our analyses indicate that C. kiangsu is a monophyletic group. Our results also support the hypothesis that the C. kiangsu population is in a primary differentiation stage. Given the mismatch distribution, it is likely that a population expansion in C. kiangsu occurred about 0.242 Ma during the Quaternary interglaciation. Based on historical reports, we conjecture that human activities had significant impacts on the C. kiangsu gene flow.

  3. Phylogenetic relationships of the Orang Asli and Iban of Malaysia based on maternal markers.

    Science.gov (United States)

    Ang, K C; Leow, J W H; Yeap, W K; Hood, S; Mahani, M C; Md-Zain, B M

    2011-04-12

    Malaysia remains as a crossroad of different cultures and peoples, and it has long been recognized that studying its population history can provide crucial insight into the prehistory of Southeast Asia as a whole. The earliest inhabitants were the Orang Asli in Peninsular Malaysia and the indigenous groups in Sabah and Sarawak. Although they were the earliest migrants in this region, these tribes are divided geographically by the South China Sea. We analyzed DNA sequences of 18 Orang Asli using mitochondrial DNA extracted from blood samples, each representing one sub-tribe, and from five Sarawakian Iban. Mitochondrial DNA was extracted from hair samples in order to examine relationships with the main ethnic groups in Malaysia. The D-loop region and cytochrome b genes were used as the candidate loci. Phylogenetic relationships were investigated using maximum parsimony and neighbor joining algorithms, and each tree was subjected to bootstrap analysis with 1000 replicates. Analyses of the HVS I region showed that the Iban are not a distinct group from the Orang Asli; they form a sub-clade within the Orang Asli. Based on the cytochrome b gene, the Iban clustered with the Orang Asli in the same clade. We found evidence for considerable gene flow between Orang Asli and Iban. We concluded that the Orang Asli, Iban and the main ethnic groups of Malaysia are probably derived from a common ancestor. This is in agreement with a single-route migration theory, but it does not dismiss a two-route migration theory.

  4. An Antarctic hypotrichous ciliate, Parasterkiella thompsoni (Foissner) nov. gen., nov. comb., recorded in Argentinean peat-bogs: morphology, morphogenesis, and molecular phylogeny.

    Science.gov (United States)

    Küppers, Gabriela Cristina; Paiva, Thiago da Silva; Borges, Bárbara do Nascimento; Harada, Maria Lúcia; Garraza, Gabriela González; Mataloni, Gabriela

    2011-05-01

    The ciliate Parasterkiella thompsoni (Foissner, 1996) nov. gen., nov. comb. was originally described from Antarctica. In the present study, we report the morphology, morphogenesis during cell division, and molecular phylogeny inferred from the 18S-rDNA sequence of a population isolated from the Rancho Hambre peat bog, Tierra del Fuego Province (Argentina). The study is based on live and protargol-impregnated specimens. Molecular phylogeny was inferred from trees constructed by means of the maximum parsimony, neighbor joining, and Bayesian analyses. The interphase morphology matches the original description of the species. During the cell division, stomatogenesis begins with the de novo proliferation of two fields of basal bodies, each one left of the postoral ventral cirri and of transverse cirri, which later unify. Primordia IV-VI of the proter develop from disaggregation of cirrus IV/3, while primordium IV of the opisthe develops from cirrus IV/2 and primordia V and VI from cirrus V/4. Dorsal morphogenesis occurs in the Urosomoida pattern-that is, the fragmentation of kinety 3 is lacking. Three macronuclear nodules are generated before cytokinesis. Phylogenetic analyses consistently placed P. thompsoni within the stylonychines. New data on the morphogenesis of the dorsal ciliature justifies the transference of Sterkiella thompsoni to a new genus Parasterkiella. Copyright © 2011 Elsevier GmbH. All rights reserved.

  5. Taxonomic relationships among Phenacomys voles as inferred by cytochrome b

    Science.gov (United States)

    Bellinger, M.R.; Haig, S.M.; Forsman, E.D.; Mullins, T.D.

    2005-01-01

    Taxonomic relationships among red tree voles (Phenacomys longicaudus longicaudus, P. l. silvicola), the Sonoma tree vole (P. pomo), the white-footed vole (P. albipes), and the heather vole (P. intermedius) were examined using 664 base pairs of the mitochondrial cytochrome b gene. Results indicate specific differences among red tree voles, Sonoma tree voles, white-footed voles, and heather voles, but no clear difference between the 2 Oregon subspecies of red tree voles (P. l. longicaudus and P. l. silvicola). Our data further indicated a close relationship between tree voles and albipes, validating inclusion of albipes in the subgenus Arborimus. These 3 congeners shared a closer relationship to P. intermedius than to other arvicolids. A moderate association between porno and albipes was indicated by maximum parsimony and neighbor-joining phylogenetic analyses. Molecular clock estimates suggest a Pleistocene radiation of the Arborimus clade, which is concordant with pulses of diversification observed in other murid rodents. The generic rank of Arborimus is subject to interpretation of data.

  6. A maximum likelihood framework for protein design

    Directory of Open Access Journals (Sweden)

    Philippe Hervé

    2006-06-01

    Full Text Available Abstract Background The aim of protein design is to predict amino-acid sequences compatible with a given target structure. Traditionally envisioned as a purely thermodynamic question, this problem can also be understood in a wider context, where additional constraints are captured by learning the sequence patterns displayed by natural proteins of known conformation. In this latter perspective, however, we still need a theoretical formalization of the question, leading to general and efficient learning methods, and allowing for the selection of fast and accurate objective functions quantifying sequence/structure compatibility. Results We propose a formulation of the protein design problem in terms of model-based statistical inference. Our framework uses the maximum likelihood principle to optimize the unknown parameters of a statistical potential, which we call an inverse potential to contrast with classical potentials used for structure prediction. We propose an implementation based on Markov chain Monte Carlo, in which the likelihood is maximized by gradient descent and is numerically estimated by thermodynamic integration. The fit of the models is evaluated by cross-validation. We apply this to a simple pairwise contact potential, supplemented with a solvent-accessibility term, and show that the resulting models have a better predictive power than currently available pairwise potentials. Furthermore, the model comparison method presented here allows one to measure the relative contribution of each component of the potential, and to choose the optimal number of accessibility classes, which turns out to be much higher than classically considered. Conclusion Altogether, this reformulation makes it possible to test a wide diversity of models, using different forms of potentials, or accounting for other factors than just the constraint of thermodynamic stability. Ultimately, such model-based statistical analyses may help to understand the forces

  7. Molecular phylogenetic and scanning electron microscopical analyses places the Choanephoraceae and the Gilbertellaceae in a monophyletic group within the Mucorales (Zygomycetes, Fungi).

    Science.gov (United States)

    Voigt, Kerstin; Olsson, L

    2008-09-01

    A multi-gene genealogy based on maximum parsimony and distance analyses of the exonic genes for actin (act) and translation elongation factor 1 alpha (tef), the nuclear genes for the small (18S) and large (28S) subunit ribosomal RNA (comprising 807, 1092, 1863, 389 characters, respectively) of all 50 genera of the Mucorales (Zygomycetes) suggests that the Choanephoraceae is a monophyletic group. The monotypic Gilbertellaceae appears in close phylogenetic relatedness to the Choanephoraceae. The monophyly of the Choanephoraceae has moderate to strong support (bootstrap proportions 67% and 96% in distance and maximum parsimony analyses, respectively), whereas the monophyly of the Choanephoraceae-Gilbertellaceae clade is supported by high bootstrap values (100% and 98%). This suggests that the two families can be joined into one family, which leads to the elimination of the Gilbertellaceae as a separate family. In order to test this hypothesis single-locus neighbor-joining analyses were performed on nuclear genes of the 18S, 5.8S, 28S and internal transcribed spacer (ITS) 1 ribosomal RNA and the translation elongation factor 1 alpha (tef) and beta tubulin (betatub) nucleotide sequences. The common monophyletic origin of the Choanephoraceae-Gilbertellaceae clade could be confirmed in all gene trees and by investigation of their ultrastructure. Sporangia with persistent, sutured walls splitting in half at maturity and ellipsoidal sporangiospores with striated ornamentations and polar ciliate appendages arising from spores in persistent sporangia and dehiscent sporangiola represent synapomorphic characters of this group. We discuss our data in the context of the historical development of their taxonomy and physiology and propose a reduction of the two families to one family, the Choanephoraceae sensu lato comprising species which are facultative plant pathogens and parasites, especially in subtropical to tropical regions.

  8. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

    Science.gov (United States)

    Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent; Anisimova, Maria; Hordijk, Wim; Gascuel, Olivier

    2010-05-01

    PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.

  9. Maximum entropy production rate in quantum thermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Beretta, Gian Paolo, E-mail: beretta@ing.unibs.i [Universita di Brescia, via Branze 38, 25123 Brescia (Italy)

    2010-06-01

    In the framework of the recent quest for well-behaved nonlinear extensions of the traditional Schroedinger-von Neumann unitary dynamics that could provide fundamental explanations of recent experimental evidence of loss of quantum coherence at the microscopic level, a recent paper [Gheorghiu-Svirschevski 2001 Phys. Rev. A 63 054102] reproposes the nonlinear equation of motion proposed by the present author [see Beretta G P 1987 Found. Phys. 17 365 and references therein] for quantum (thermo)dynamics of a single isolated indivisible constituent system, such as a single particle, qubit, qudit, spin or atomic system, or a Bose-Einstein or Fermi-Dirac field. As already proved, such nonlinear dynamics entails a fundamental unifying microscopic proof and extension of Onsager's reciprocity and Callen's fluctuation-dissipation relations to all nonequilibrium states, close and far from thermodynamic equilibrium. In this paper we propose a brief but self-contained review of the main results already proved, including the explicit geometrical construction of the equation of motion from the steepest-entropy-ascent ansatz and its exact mathematical and conceptual equivalence with the maximal-entropy-generation variational-principle formulation presented in Gheorghiu-Svirschevski S 2001 Phys. Rev. A 63 022105. Moreover, we show how it can be extended to the case of a composite system to obtain the general form of the equation of motion, consistent with the demanding requirements of strong separability and of compatibility with general thermodynamics principles. The irreversible term in the equation of motion describes the spontaneous attraction of the state operator in the direction of steepest entropy ascent, thus implementing the maximum entropy production principle in quantum theory. The time rate at which the path of steepest entropy ascent is followed has so far been left unspecified. As a step towards the identification of such rate, here we propose a possible

  10. Determination of the maximum-depth to potential field sources by a maximum structural index method

    Science.gov (United States)

    Fedi, M.; Florio, G.

    2013-01-01

    A simple and fast determination of the limiting depth to the sources may represent a significant help to the data interpretation. To this end we explore the possibility of determining those source parameters shared by all the classes of models fitting the data. One approach is to determine the maximum depth-to-source compatible with the measured data, by using for example the well-known Bott-Smith rules. These rules involve only the knowledge of the field and its horizontal gradient maxima, and are independent from the density contrast. Thanks to the direct relationship between structural index and depth to sources we work out a simple and fast strategy to obtain the maximum depth by using the semi-automated methods, such as Euler deconvolution or depth-from-extreme-points method (DEXP). The proposed method consists in estimating the maximum depth as the one obtained for the highest allowable value of the structural index (Nmax). Nmax may be easily determined, since it depends only on the dimensionality of the problem (2D/3D) and on the nature of the analyzed field (e.g., gravity field or magnetic field). We tested our approach on synthetic models against the results obtained by the classical Bott-Smith formulas and the results are in fact very similar, confirming the validity of this method. However, while Bott-Smith formulas are restricted to the gravity field only, our method is applicable also to the magnetic field and to any derivative of the gravity and magnetic field. Our method yields a useful criterion to assess the source model based on the (∂f/∂x)max/fmax ratio. The usefulness of the method in real cases is demonstrated for a salt wall in the Mississippi basin, where the estimation of the maximum depth agrees with the seismic information.

  11. Weighted Maximum-Clique Transversal Sets of Graphs

    OpenAIRE

    Chuan-Min Lee

    2011-01-01

    A maximum-clique transversal set of a graph G is a subset of vertices intersecting all maximum cliques of G. The maximum-clique transversal set problem is to find a maximum-clique transversal set of G of minimum cardinality. Motivated by the placement of transmitters for cellular telephones, Chang, Kloks, and Lee introduced the concept of maximum-clique transversal sets on graphs in 2001. In this paper, we study the weighted version of the maximum-clique transversal set problem for split grap...

  12. Pattern formation, logistics, and maximum path probability

    Science.gov (United States)

    Kirkaldy, J. S.

    1985-05-01

    The concept of pattern formation, which to current researchers is a synonym for self-organization, carries the connotation of deductive logic together with the process of spontaneous inference. Defining a pattern as an equivalence relation on a set of thermodynamic objects, we establish that a large class of irreversible pattern-forming systems, evolving along idealized quasisteady paths, approaches the stable steady state as a mapping upon the formal deductive imperatives of a propositional function calculus. In the preamble the classical reversible thermodynamics of composite systems is analyzed as an externally manipulated system of space partitioning and classification based on ideal enclosures and diaphragms. The diaphragms have discrete classification capabilities which are designated in relation to conserved quantities by descriptors such as impervious, diathermal, and adiabatic. Differentiability in the continuum thermodynamic calculus is invoked as equivalent to analyticity and consistency in the underlying class or sentential calculus. The seat of inference, however, rests with the thermodynamicist. In the transition to an irreversible pattern-forming system the defined nature of the composite reservoirs remains, but a given diaphragm is replaced by a pattern-forming system which by its nature is a spontaneously evolving volume partitioner and classifier of invariants. The seat of volition or inference for the classification system is thus transferred from the experimenter or theoretician to the diaphragm, and with it the full deductive facility. The equivalence relations or partitions associated with the emerging patterns may thus be associated with theorems of the natural pattern-forming calculus. The entropy function, together with its derivatives, is the vehicle which relates the logistics of reservoirs and diaphragms to the analog logistics of the continuum. Maximum path probability or second-order differentiability of the entropy in isolation are

  13. Phylogenetic relationships among the species of the genus testudo (Testudines : Testudinidae) inferred from mitochondrial 12S rRNA gene sequences

    NARCIS (Netherlands)

    van der Kuyl, Antoinette C.; Ph Ballasina, Donato L.; Dekker, John T.; Maas, Jolanda; Willemsen, Ronald E.; Goudsmit, Jaap

    2002-01-01

    To test phylogenetic relationships within the genus Testudo (Testudines: Testudinidae), we have sequenced a fragment of the mitochondrial (mt) 12S rRNA gene of 98 tortoise specimens belonging to the genera Testudo, Indotestudo, and Geochelone. Maximum likelihood and neighbor-joining methods identify

  14. Accurate modeling and maximum power point detection of ...

    African Journals Online (AJOL)

    Accurate modeling and maximum power point detection of photovoltaic ... Determination of MPP enables the PV system to deliver maximum available power. ..... adaptive artificial neural network: Proposition for a new sizing procedure.

  15. Maximum power per VA control of vector controlled interior ...

    Indian Academy of Sciences (India)

    Thakur Sumeet Singh

    2018-04-11

    Apr 11, 2018 ... Department of Electrical Engineering, Indian Institute of Technology Delhi, New ... The MPVA operation allows maximum-utilization of the drive-system. ... Permanent magnet motor; unity power factor; maximum VA utilization; ...

  16. Electron density distribution in Si and Ge using multipole, maximum ...

    Indian Academy of Sciences (India)

    Si and Ge has been studied using multipole, maximum entropy method (MEM) and ... and electron density distribution using the currently available versatile ..... data should be subjected to maximum possible utility for the characterization of.

  17. 40 CFR 141.13 - Maximum contaminant levels for turbidity.

    Science.gov (United States)

    2010-07-01

    ... turbidity. 141.13 Section 141.13 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER... Maximum contaminant levels for turbidity. The maximum contaminant levels for turbidity are applicable to... part. The maximum contaminant levels for turbidity in drinking water, measured at a representative...

  18. Maximum Power Training and Plyometrics for Cross-Country Running.

    Science.gov (United States)

    Ebben, William P.

    2001-01-01

    Provides a rationale for maximum power training and plyometrics as conditioning strategies for cross-country runners, examining: an evaluation of training methods (strength training and maximum power training and plyometrics); biomechanic and velocity specificity (role in preventing injury); and practical application of maximum power training and…

  19. 13 CFR 107.840 - Maximum term of Financing.

    Science.gov (United States)

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Maximum term of Financing. 107.840... COMPANIES Financing of Small Businesses by Licensees Structuring Licensee's Financing of An Eligible Small Business: Terms and Conditions of Financing § 107.840 Maximum term of Financing. The maximum term of any...

  20. 7 CFR 3565.210 - Maximum interest rate.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 15 2010-01-01 2010-01-01 false Maximum interest rate. 3565.210 Section 3565.210... AGRICULTURE GUARANTEED RURAL RENTAL HOUSING PROGRAM Loan Requirements § 3565.210 Maximum interest rate. The interest rate for a guaranteed loan must not exceed the maximum allowable rate specified by the Agency in...

  1. Characterizing graphs of maximum matching width at most 2

    DEFF Research Database (Denmark)

    Jeong, Jisu; Ok, Seongmin; Suh, Geewon

    2017-01-01

    The maximum matching width is a width-parameter that is de ned on a branch-decomposition over the vertex set of a graph. The size of a maximum matching in the bipartite graph is used as a cut-function. In this paper, we characterize the graphs of maximum matching width at most 2 using the minor o...

  2. Phylogenetic analysis of subgenus vigna species using nuclear ribosomal RNA ITS: evidence of hybridization among Vigna unguiculata subspecies.

    Science.gov (United States)

    Vijaykumar, Archana; Saini, Ajay; Jawali, Narendra

    2010-01-01

    Molecular phylogeny among species belonging to subgenus Vigna (genus Vigna) was inferred based on internal transcribed spacer (ITS) sequences of 18S-5.8S-26S ribosomal RNA gene unit. Analysis showed a total of 356 polymorphic sites of which approximately 80% were parsimony informative. Phylogenetic reconstruction by neighbor joining and maximum parsimony methods placed the 57 Vigna accessions (belonging to 15 species) into 5 major clades. Five species viz. Vigna heterophylla, Vigna pubigera, Vigna parkeri, Vigna laurentii, and Vigna gracilis whose position in the subgenus was previously not known were placed in the section Vigna. A single accession (Vigna unguiculata ssp. tenuis, NI 1637) harbored 2 intragenomic ITS variants, indicative of 2 different types of ribosomal DNA (rDNA) repeat units. ITS variant type-I was close to ITS from V. unguiculata ssp. pubescens, whereas type-II was close to V. unguiculata ssp. tenuis. Transcript analysis clearly demonstrates that in accession NI 1637, rDNA repeat units with only type-II ITS variants are transcriptionally active. Evidence from sequence analysis (of 5.8S, ITS1, and ITS2) and secondary structure analysis (of ITS1 and ITS2) indicates that the type-I ITS variant probably does not belong to the pseudogenic rDNA repeat units. The results from phylogenetic and transcript analysis suggest that the rDNA units with the type-I ITS may have introgressed as a result of hybridization (between ssp. tenuis and ssp. pubescens); however, it has been epigenetically silenced. The results also demonstrate differential evolution of ITS sequence among wild and cultivated forms of V. unguiculata.

  3. 40 CFR 1042.140 - Maximum engine power, displacement, power density, and maximum in-use engine speed.

    Science.gov (United States)

    2010-07-01

    ... cylinders having an internal diameter of 13.0 cm and a 15.5 cm stroke length, the rounded displacement would... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Maximum engine power, displacement... Maximum engine power, displacement, power density, and maximum in-use engine speed. This section describes...

  4. The maximum entropy production and maximum Shannon information entropy in enzyme kinetics

    Science.gov (United States)

    Dobovišek, Andrej; Markovič, Rene; Brumen, Milan; Fajmut, Aleš

    2018-04-01

    We demonstrate that the maximum entropy production principle (MEPP) serves as a physical selection principle for the description of the most probable non-equilibrium steady states in simple enzymatic reactions. A theoretical approach is developed, which enables maximization of the density of entropy production with respect to the enzyme rate constants for the enzyme reaction in a steady state. Mass and Gibbs free energy conservations are considered as optimization constraints. In such a way computed optimal enzyme rate constants in a steady state yield also the most uniform probability distribution of the enzyme states. This accounts for the maximal Shannon information entropy. By means of the stability analysis it is also demonstrated that maximal density of entropy production in that enzyme reaction requires flexible enzyme structure, which enables rapid transitions between different enzyme states. These results are supported by an example, in which density of entropy production and Shannon information entropy are numerically maximized for the enzyme Glucose Isomerase.

  5. Solar Maximum Mission Experiment - Ultraviolet Spectroscopy and Polarimetry on the Solar Maximum Mission

    Science.gov (United States)

    Tandberg-Hanssen, E.; Cheng, C. C.; Woodgate, B. E.; Brandt, J. C.; Chapman, R. D.; Athay, R. G.; Beckers, J. M.; Bruner, E. C.; Gurman, J. B.; Hyder, C. L.

    1981-01-01

    The Ultraviolet Spectrometer and Polarimeter on the Solar Maximum Mission spacecraft is described. It is pointed out that the instrument, which operates in the wavelength range 1150-3600 A, has a spatial resolution of 2-3 arcsec and a spectral resolution of 0.02 A FWHM in second order. A Gregorian telescope, with a focal length of 1.8 m, feeds a 1 m Ebert-Fastie spectrometer. A polarimeter comprising rotating Mg F2 waveplates can be inserted behind the spectrometer entrance slit; it permits all four Stokes parameters to be determined. Among the observing modes are rasters, spectral scans, velocity measurements, and polarimetry. Examples of initial observations made since launch are presented.

  6. Binary versus non-binary information in real time series: empirical results and maximum-entropy matrix models

    Science.gov (United States)

    Almog, Assaf; Garlaschelli, Diego

    2014-09-01

    The dynamics of complex systems, from financial markets to the brain, can be monitored in terms of multiple time series of activity of the constituent units, such as stocks or neurons, respectively. While the main focus of time series analysis is on the magnitude of temporal increments, a significant piece of information is encoded into the binary projection (i.e. the sign) of such increments. In this paper we provide further evidence of this by showing strong nonlinear relations between binary and non-binary properties of financial time series. These relations are a novel quantification of the fact that extreme price increments occur more often when most stocks move in the same direction. We then introduce an information-theoretic approach to the analysis of the binary signature of single and multiple time series. Through the definition of maximum-entropy ensembles of binary matrices and their mapping to spin models in statistical physics, we quantify the information encoded into the simplest binary properties of real time series and identify the most informative property given a set of measurements. Our formalism is able to accurately replicate, and mathematically characterize, the observed binary/non-binary relations. We also obtain a phase diagram allowing us to identify, based only on the instantaneous aggregate return of a set of multiple time series, a regime where the so-called ‘market mode’ has an optimal interpretation in terms of collective (endogenous) effects, a regime where it is parsimoniously explained by pure noise, and a regime where it can be regarded as a combination of endogenous and exogenous factors. Our approach allows us to connect spin models, simple stochastic processes, and ensembles of time series inferred from partial information.

  7. Binary versus non-binary information in real time series: empirical results and maximum-entropy matrix models

    International Nuclear Information System (INIS)

    Almog, Assaf; Garlaschelli, Diego

    2014-01-01

    The dynamics of complex systems, from financial markets to the brain, can be monitored in terms of multiple time series of activity of the constituent units, such as stocks or neurons, respectively. While the main focus of time series analysis is on the magnitude of temporal increments, a significant piece of information is encoded into the binary projection (i.e. the sign) of such increments. In this paper we provide further evidence of this by showing strong nonlinear relations between binary and non-binary properties of financial time series. These relations are a novel quantification of the fact that extreme price increments occur more often when most stocks move in the same direction. We then introduce an information-theoretic approach to the analysis of the binary signature of single and multiple time series. Through the definition of maximum-entropy ensembles of binary matrices and their mapping to spin models in statistical physics, we quantify the information encoded into the simplest binary properties of real time series and identify the most informative property given a set of measurements. Our formalism is able to accurately replicate, and mathematically characterize, the observed binary/non-binary relations. We also obtain a phase diagram allowing us to identify, based only on the instantaneous aggregate return of a set of multiple time series, a regime where the so-called ‘market mode’ has an optimal interpretation in terms of collective (endogenous) effects, a regime where it is parsimoniously explained by pure noise, and a regime where it can be regarded as a combination of endogenous and exogenous factors. Our approach allows us to connect spin models, simple stochastic processes, and ensembles of time series inferred from partial information. (paper)

  8. Benefits of the maximum tolerated dose (MTD) and maximum tolerated concentration (MTC) concept in aquatic toxicology

    International Nuclear Information System (INIS)

    Hutchinson, Thomas H.; Boegi, Christian; Winter, Matthew J.; Owens, J. Willie

    2009-01-01

    There is increasing recognition of the need to identify specific sublethal effects of chemicals, such as reproductive toxicity, and specific modes of actions of the chemicals, such as interference with the endocrine system. To achieve these aims requires criteria which provide a basis to interpret study findings so as to separate these specific toxicities and modes of action from not only acute lethality per se but also from severe inanition and malaise that non-specifically compromise reproductive capacity and the response of endocrine endpoints. Mammalian toxicologists have recognized that very high dose levels are sometimes required to elicit both specific adverse effects and present the potential of non-specific 'systemic toxicity'. Mammalian toxicologists have developed the concept of a maximum tolerated dose (MTD) beyond which a specific toxicity or action cannot be attributed to a test substance due to the compromised state of the organism. Ecotoxicologists are now confronted by a similar challenge and must develop an analogous concept of a MTD and the respective criteria. As examples of this conundrum, we note recent developments in efforts to validate protocols for fish reproductive toxicity and endocrine screens (e.g. some chemicals originally selected as 'negatives' elicited decreases in fecundity or changes in endpoints intended to be biomarkers for endocrine modes of action). Unless analogous criteria can be developed, the potentially confounding effects of systemic toxicity may then undermine the reliable assessment of specific reproductive effects or biomarkers such as vitellogenin or spiggin. The same issue confronts other areas of aquatic toxicology (e.g., genotoxicity) and the use of aquatic animals for preclinical assessments of drugs (e.g., use of zebrafish for drug safety assessment). We propose that there are benefits to adopting the concept of an MTD for toxicology and pharmacology studies using fish and other aquatic organisms and the

  9. Microprocessor Controlled Maximum Power Point Tracker for Photovoltaic Application

    International Nuclear Information System (INIS)

    Jiya, J. D.; Tahirou, G.

    2002-01-01

    This paper presents a microprocessor controlled maximum power point tracker for photovoltaic module. Input current and voltage are measured and multiplied within the microprocessor, which contains an algorithm to seek the maximum power point. The duly cycle of the DC-DC converter, at which the maximum power occurs is obtained, noted and adjusted. The microprocessor constantly seeks for improvement of obtained power by varying the duty cycle

  10. 49 CFR 195.406 - Maximum operating pressure.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 3 2010-10-01 2010-10-01 false Maximum operating pressure. 195.406 Section 195.406 Transportation Other Regulations Relating to Transportation (Continued) PIPELINE AND HAZARDOUS... HAZARDOUS LIQUIDS BY PIPELINE Operation and Maintenance § 195.406 Maximum operating pressure. (a) Except for...

  11. 78 FR 49370 - Inflation Adjustment of Maximum Forfeiture Penalties

    Science.gov (United States)

    2013-08-14

    ... ``civil monetary penalties provided by law'' at least once every four years. DATES: Effective September 13... increases the maximum civil monetary forfeiture penalties available to the Commission under its rules... maximum civil penalties established in that section to account for inflation since the last adjustment to...

  12. 22 CFR 201.67 - Maximum freight charges.

    Science.gov (United States)

    2010-04-01

    ..., commodity rate classification, quantity, vessel flag category (U.S.-or foreign-flag), choice of ports, and... the United States. (2) Maximum charter rates. (i) USAID will not finance ocean freight under any... owner(s). (4) Maximum liner rates. USAID will not finance ocean freight for a cargo liner shipment at a...

  13. Maximum penetration level of distributed generation without violating voltage limits

    NARCIS (Netherlands)

    Morren, J.; Haan, de S.W.H.

    2009-01-01

    Connection of Distributed Generation (DG) units to a distribution network will result in a local voltage increase. As there will be a maximum on the allowable voltage increase, this will limit the maximum allowable penetration level of DG. By reactive power compensation (by the DG unit itself) a

  14. Particle Swarm Optimization Based of the Maximum Photovoltaic ...

    African Journals Online (AJOL)

    Photovoltaic electricity is seen as an important source of renewable energy. The photovoltaic array is an unstable source of power since the peak power point depends on the temperature and the irradiation level. A maximum peak power point tracking is then necessary for maximum efficiency. In this work, a Particle Swarm ...

  15. Maximum-entropy clustering algorithm and its global convergence analysis

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Constructing a batch of differentiable entropy functions touniformly approximate an objective function by means of the maximum-entropy principle, a new clustering algorithm, called maximum-entropy clustering algorithm, is proposed based on optimization theory. This algorithm is a soft generalization of the hard C-means algorithm and possesses global convergence. Its relations with other clustering algorithms are discussed.

  16. Application of maximum entropy to neutron tunneling spectroscopy

    International Nuclear Information System (INIS)

    Mukhopadhyay, R.; Silver, R.N.

    1990-01-01

    We demonstrate the maximum entropy method for the deconvolution of high resolution tunneling data acquired with a quasielastic spectrometer. Given a precise characterization of the instrument resolution function, a maximum entropy analysis of lutidine data obtained with the IRIS spectrometer at ISIS results in an effective factor of three improvement in resolution. 7 refs., 4 figs

  17. The regulation of starch accumulation in Panicum maximum Jacq ...

    African Journals Online (AJOL)

    ... decrease the starch level. These observations are discussed in relation to the photosynthetic characteristics of P. maximum. Keywords: accumulation; botany; carbon assimilation; co2 fixation; growth conditions; mesophyll; metabolites; nitrogen; nitrogen levels; nitrogen supply; panicum maximum; plant physiology; starch; ...

  18. 32 CFR 842.35 - Depreciation and maximum allowances.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Depreciation and maximum allowances. 842.35... LITIGATION ADMINISTRATIVE CLAIMS Personnel Claims (31 U.S.C. 3701, 3721) § 842.35 Depreciation and maximum allowances. The military services have jointly established the “Allowance List-Depreciation Guide” to...

  19. The maximum significant wave height in the Southern North Sea

    NARCIS (Netherlands)

    Bouws, E.; Tolman, H.L.; Holthuijsen, L.H.; Eldeberky, Y.; Booij, N.; Ferier, P.

    1995-01-01

    The maximum possible wave conditions along the Dutch coast, which seem to be dominated by the limited water depth, have been estimated in the present study with numerical simulations. Discussions with meteorologists suggest that the maximum possible sustained wind speed in North Sea conditions is

  20. 5 CFR 838.711 - Maximum former spouse survivor annuity.

    Science.gov (United States)

    2010-01-01

    ... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Maximum former spouse survivor annuity... Orders Awarding Former Spouse Survivor Annuities Limitations on Survivor Annuities § 838.711 Maximum former spouse survivor annuity. (a) Under CSRS, payments under a court order may not exceed the amount...

  1. Maximum physical capacity testing in cancer patients undergoing chemotherapy

    DEFF Research Database (Denmark)

    Knutsen, L.; Quist, M; Midtgaard, J

    2006-01-01

    BACKGROUND: Over the past few years there has been a growing interest in the field of physical exercise in rehabilitation of cancer patients, leading to requirements for objective maximum physical capacity measurement (maximum oxygen uptake (VO(2max)) and one-repetition maximum (1RM)) to determin...... early in the treatment process. However, the patients were self-referred and thus highly motivated and as such are not necessarily representative of the whole population of cancer patients treated with chemotherapy....... in performing maximum physical capacity tests as these motivated them through self-perceived competitiveness and set a standard that served to encourage peak performance. CONCLUSION: The positive attitudes in this sample towards maximum physical capacity open the possibility of introducing physical testing...

  2. Maximum Principles for Discrete and Semidiscrete Reaction-Diffusion Equation

    Directory of Open Access Journals (Sweden)

    Petr Stehlík

    2015-01-01

    Full Text Available We study reaction-diffusion equations with a general reaction function f on one-dimensional lattices with continuous or discrete time ux′  (or  Δtux=k(ux-1-2ux+ux+1+f(ux, x∈Z. We prove weak and strong maximum and minimum principles for corresponding initial-boundary value problems. Whereas the maximum principles in the semidiscrete case (continuous time exhibit similar features to those of fully continuous reaction-diffusion model, in the discrete case the weak maximum principle holds for a smaller class of functions and the strong maximum principle is valid in a weaker sense. We describe in detail how the validity of maximum principles depends on the nonlinearity and the time step. We illustrate our results on the Nagumo equation with the bistable nonlinearity.

  3. 78 FR 9845 - Minimum and Ordinary Maximum and Aggravated Maximum Civil Monetary Penalties for a Violation of...

    Science.gov (United States)

    2013-02-12

    ... maximum penalty amount of $75,000 for each violation, except that if the violation results in death... the maximum civil penalty for a violation is $175,000 if the violation results in death, serious... Penalties for a Violation of the Hazardous Materials Transportation Laws or Regulations, Orders, Special...

  4. The power and robustness of maximum LOD score statistics.

    Science.gov (United States)

    Yoo, Y J; Mendell, N R

    2008-07-01

    The maximum LOD score statistic is extremely powerful for gene mapping when calculated using the correct genetic parameter value. When the mode of genetic transmission is unknown, the maximum of the LOD scores obtained using several genetic parameter values is reported. This latter statistic requires higher critical value than the maximum LOD score statistic calculated from a single genetic parameter value. In this paper, we compare the power of maximum LOD scores based on three fixed sets of genetic parameter values with the power of the LOD score obtained after maximizing over the entire range of genetic parameter values. We simulate family data under nine generating models. For generating models with non-zero phenocopy rates, LOD scores maximized over the entire range of genetic parameters yielded greater power than maximum LOD scores for fixed sets of parameter values with zero phenocopy rates. No maximum LOD score was consistently more powerful than the others for generating models with a zero phenocopy rate. The power loss of the LOD score maximized over the entire range of genetic parameters, relative to the maximum LOD score calculated using the correct genetic parameter value, appeared to be robust to the generating models.

  5. Parameters determining maximum wind velocity in a tropical cyclone

    International Nuclear Information System (INIS)

    Choudhury, A.M.

    1984-09-01

    The spiral structure of a tropical cyclone was earlier explained by a tangential velocity distribution which varies inversely as the distance from the cyclone centre outside the circle of maximum wind speed. The case has been extended in the present paper by adding a radial velocity. It has been found that a suitable combination of radial and tangential velocities can account for the spiral structure of a cyclone. This enables parametrization of the cyclone. Finally a formula has been derived relating maximum velocity in a tropical cyclone with angular momentum, radius of maximum wind speed and the spiral angle. The shapes of the spirals have been computed for various spiral angles. (author)

  6. Incoming editorial: bigger, purple, pragmatic, and parsimony.

    Science.gov (United States)

    Hilsenroth, Mark J

    2011-03-01

    It is with great excitement and enthusiasm that I write to you regarding several updates, new initiatives and changes with our journal. As you may have already noticed, this includes the change to a larger format, and a return to the color purple that helped define this journal from the early 1980s through the turn of the century, as well as to the original title "Psychotherapy." The change in format will allow us to benefit from the standard American Psychological Association (APA) journal design and layout, leading to more efficient processing and arrangement within their electronic journal system. I have found this first year as the Incoming Editor of Psychotherapy to be as challenging, rewarding, and intellectually stimulating as I imagined it would be, and I remain quite excited and enthusiastic about the work ahead. (PsycINFO Database Record (c) 2011 APA, all rights reserved).

  7. Parsimony in personality: predicting sexual prejudice.

    Science.gov (United States)

    Miller, Audrey K; Wagner, Maverick M; Hunt, Amy N

    2012-01-01

    Extant research has established numerous demographic, personal-history, attitudinal, and ideological correlates of sexual prejudice, also known as homophobia. The present study investigated whether Five-Factor Model (FFM) personality domains, particularly Openness, and FFM facets, particularly Openness to Values, contribute independent and incremental variance to the prediction of sexual prejudice beyond these established correlates. Participants were 117 college students who completed a comprehensive FFM measure, measures of sexual prejudice, and a demographics, personal-history, and attitudes-and-ideologies questionnaire. Results of stepwise multiple regression analyses demonstrated that, whereas Openness domain score predicted only marginal incremental variance in sexual prejudice, Openness facet scores (particularly Openness to Values) predicted independent and substantial incremental variance beyond numerous other zero-order correlates of sexual prejudice. The importance of integrating FFM personality variables, especially facet-level variables, into conceptualizations of sexual prejudice is highlighted. Study strengths and weaknesses are discussed as are potential implications for prejudice-reduction interventions.

  8. Environmental Monitoring, Water Quality - Total Maximum Daily Load (TMDL)

    Data.gov (United States)

    NSGIC Education | GIS Inventory — The Clean Water Act Section 303(d) establishes the Total Maximum Daily Load (TMDL) program. The purpose of the TMDL program is to identify sources of pollution and...

  9. Probabilistic maximum-value wind prediction for offshore environments

    DEFF Research Database (Denmark)

    Staid, Andrea; Pinson, Pierre; Guikema, Seth D.

    2015-01-01

    statistical models to predict the full distribution of the maximum-value wind speeds in a 3 h interval. We take a detailed look at the performance of linear models, generalized additive models and multivariate adaptive regression splines models using meteorological covariates such as gust speed, wind speed......, convective available potential energy, Charnock, mean sea-level pressure and temperature, as given by the European Center for Medium-Range Weather Forecasts forecasts. The models are trained to predict the mean value of maximum wind speed, and the residuals from training the models are used to develop...... the full probabilistic distribution of maximum wind speed. Knowledge of the maximum wind speed for an offshore location within a given period can inform decision-making regarding turbine operations, planned maintenance operations and power grid scheduling in order to improve safety and reliability...

  10. Combining Experiments and Simulations Using the Maximum Entropy Principle

    DEFF Research Database (Denmark)

    Boomsma, Wouter; Ferkinghoff-Borg, Jesper; Lindorff-Larsen, Kresten

    2014-01-01

    are not in quantitative agreement with experimental data. The principle of maximum entropy is a general procedure for constructing probability distributions in the light of new data, making it a natural tool in cases when an initial model provides results that are at odds with experiments. The number of maximum entropy...... in the context of a simple example, after which we proceed with a real-world application in the field of molecular simulations, where the maximum entropy procedure has recently provided new insight. Given the limited accuracy of force fields, macromolecular simulations sometimes produce results....... Three very recent papers have explored this problem using the maximum entropy approach, providing both new theoretical and practical insights to the problem. We highlight each of these contributions in turn and conclude with a discussion on remaining challenges....

  11. Parametric optimization of thermoelectric elements footprint for maximum power generation

    DEFF Research Database (Denmark)

    Rezania, A.; Rosendahl, Lasse; Yin, Hao

    2014-01-01

    The development studies in thermoelectric generator (TEG) systems are mostly disconnected to parametric optimization of the module components. In this study, optimum footprint ratio of n- and p-type thermoelectric (TE) elements is explored to achieve maximum power generation, maximum cost......-performance, and variation of efficiency in the uni-couple over a wide range of the heat transfer coefficient on the cold junction. The three-dimensional (3D) governing equations of the thermoelectricity and the heat transfer are solved using the finite element method (FEM) for temperature dependent properties of TE...... materials. The results, which are in good agreement with the previous computational studies, show that the maximum power generation and the maximum cost-performance in the module occur at An/Ap

  12. Ethylene Production Maximum Achievable Control Technology (MACT) Compliance Manual

    Science.gov (United States)

    This July 2006 document is intended to help owners and operators of ethylene processes understand and comply with EPA's maximum achievable control technology standards promulgated on July 12, 2002, as amended on April 13, 2005 and April 20, 2006.

  13. ORIGINAL ARTICLES Surgical practice in a maximum security prison

    African Journals Online (AJOL)

    Prison Clinic, Mangaung Maximum Security Prison, Bloemfontein. F Kleinhans, BA (Cur) .... HIV positivity rate and the use of the rectum to store foreign objects. ... fruit in sunlight. Other positive health-promoting factors may also play a role,.

  14. A technique for estimating maximum harvesting effort in a stochastic ...

    Indian Academy of Sciences (India)

    Unknown

    Estimation of maximum harvesting effort has a great impact on the ... fluctuating environment has been developed in a two-species competitive system, which shows that under realistic .... The existence and local stability properties of the equi-.

  15. Water Quality Assessment and Total Maximum Daily Loads Information (ATTAINS)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Water Quality Assessment TMDL Tracking And Implementation System (ATTAINS) stores and tracks state water quality assessment decisions, Total Maximum Daily Loads...

  16. Post optimization paradigm in maximum 3-satisfiability logic programming

    Science.gov (United States)

    Mansor, Mohd. Asyraf; Sathasivam, Saratha; Kasihmuddin, Mohd Shareduwan Mohd

    2017-08-01

    Maximum 3-Satisfiability (MAX-3SAT) is a counterpart of the Boolean satisfiability problem that can be treated as a constraint optimization problem. It deals with a conundrum of searching the maximum number of satisfied clauses in a particular 3-SAT formula. This paper presents the implementation of enhanced Hopfield network in hastening the Maximum 3-Satisfiability (MAX-3SAT) logic programming. Four post optimization techniques are investigated, including the Elliot symmetric activation function, Gaussian activation function, Wavelet activation function and Hyperbolic tangent activation function. The performances of these post optimization techniques in accelerating MAX-3SAT logic programming will be discussed in terms of the ratio of maximum satisfied clauses, Hamming distance and the computation time. Dev-C++ was used as the platform for training, testing and validating our proposed techniques. The results depict the Hyperbolic tangent activation function and Elliot symmetric activation function can be used in doing MAX-3SAT logic programming.

  17. Maximum likelihood estimation of finite mixture model for economic data

    Science.gov (United States)

    Phoong, Seuk-Yen; Ismail, Mohd Tahir

    2014-06-01

    Finite mixture model is a mixture model with finite-dimension. This models are provides a natural representation of heterogeneity in a finite number of latent classes. In addition, finite mixture models also known as latent class models or unsupervised learning models. Recently, maximum likelihood estimation fitted finite mixture models has greatly drawn statistician's attention. The main reason is because maximum likelihood estimation is a powerful statistical method which provides consistent findings as the sample sizes increases to infinity. Thus, the application of maximum likelihood estimation is used to fit finite mixture model in the present paper in order to explore the relationship between nonlinear economic data. In this paper, a two-component normal mixture model is fitted by maximum likelihood estimation in order to investigate the relationship among stock market price and rubber price for sampled countries. Results described that there is a negative effect among rubber price and stock market price for Malaysia, Thailand, Philippines and Indonesia.

  18. Encoding Strategy for Maximum Noise Tolerance Bidirectional Associative Memory

    National Research Council Canada - National Science Library

    Shen, Dan

    2003-01-01

    In this paper, the Basic Bidirectional Associative Memory (BAM) is extended by choosing weights in the correlation matrix, for a given set of training pairs, which result in a maximum noise tolerance set for BAM...

  19. Narrow band interference cancelation in OFDM: Astructured maximum likelihood approach

    KAUST Repository

    Sohail, Muhammad Sadiq; Al-Naffouri, Tareq Y.; Al-Ghadhban, Samir N.

    2012-01-01

    This paper presents a maximum likelihood (ML) approach to mitigate the effect of narrow band interference (NBI) in a zero padded orthogonal frequency division multiplexing (ZP-OFDM) system. The NBI is assumed to be time variant and asynchronous

  20. Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory.

    Science.gov (United States)

    Reeb, Valérie; Lutzoni, François; Roux, Claude

    2004-09-01

    Despite the recent progress in molecular phylogenetics, many of the deepest relationships among the main lineages of the largest fungal phylum, Ascomycota, remain unresolved. To increase both resolution and support on a large-scale phylogeny of lichenized and non-lichenized ascomycetes, we combined the protein coding-gene RPB2 with the traditionally used nuclear ribosomal genes SSU and LSU. Our analyses resulted in the naming of the new subclasses Acarosporomycetidae and Ostropomycetidae, and the new class Lichinomycetes, as well as the establishment of the phylogenetic placement and novel circumscription of the lichen-forming fungi family Acarosporaceae. The delimitation of this family has been problematic over the past century, because its main diagnostic feature, true polyspory (numerous spores issued from multiple post-meiosis mitoses) with over 100 spores per ascus, is probably not restricted to the Acarosporaceae. This observation was confirmed by our reconstruction of the origin and evolution of this form of true polyspory using maximum likelihood as the optimality criterion. The various phylogenetic analyses carried out on our data sets allowed us to conclude that: (1) the inclusion of phylogenetic signal from ambiguously aligned regions into the maximum parsimony analyses proved advantageous in reconstructing phylogeny; however, when more data become available, Bayesian analysis using different models of evolution is likely to be more efficient; (2) neighbor-joining bootstrap proportions seem to be more appropriate in detecting topological conflict between data partitions of large-scale phylogenies than posterior probabilities; and (3) Bayesian bootstrap proportion provides a compromise between posterior probability outcomes (i.e., higher accuracy, but with a higher number of significantly supported wrong internodes) vs. maximum likelihood bootstrap proportion outcomes (i.e., lower accuracy, with a lower number of significantly supported wrong internodes).

  1. Maximum entropy deconvolution of low count nuclear medicine images

    International Nuclear Information System (INIS)

    McGrath, D.M.

    1998-12-01

    Maximum entropy is applied to the problem of deconvolving nuclear medicine images, with special consideration for very low count data. The physics of the formation of scintigraphic images is described, illustrating the phenomena which degrade planar estimates of the tracer distribution. Various techniques which are used to restore these images are reviewed, outlining the relative merits of each. The development and theoretical justification of maximum entropy as an image processing technique is discussed. Maximum entropy is then applied to the problem of planar deconvolution, highlighting the question of the choice of error parameters for low count data. A novel iterative version of the algorithm is suggested which allows the errors to be estimated from the predicted Poisson mean values. This method is shown to produce the exact results predicted by combining Poisson statistics and a Bayesian interpretation of the maximum entropy approach. A facility for total count preservation has also been incorporated, leading to improved quantification. In order to evaluate this iterative maximum entropy technique, two comparable methods, Wiener filtering and a novel Bayesian maximum likelihood expectation maximisation technique, were implemented. The comparison of results obtained indicated that this maximum entropy approach may produce equivalent or better measures of image quality than the compared methods, depending upon the accuracy of the system model used. The novel Bayesian maximum likelihood expectation maximisation technique was shown to be preferable over many existing maximum a posteriori methods due to its simplicity of implementation. A single parameter is required to define the Bayesian prior, which suppresses noise in the solution and may reduce the processing time substantially. Finally, maximum entropy deconvolution was applied as a pre-processing step in single photon emission computed tomography reconstruction of low count data. Higher contrast results were

  2. What controls the maximum magnitude of injection-induced earthquakes?

    Science.gov (United States)

    Eaton, D. W. S.

    2017-12-01

    Three different approaches for estimation of maximum magnitude are considered here, along with their implications for managing risk. The first approach is based on a deterministic limit for seismic moment proposed by McGarr (1976), which was originally designed for application to mining-induced seismicity. This approach has since been reformulated for earthquakes induced by fluid injection (McGarr, 2014). In essence, this method assumes that the upper limit for seismic moment release is constrained by the pressure-induced stress change. A deterministic limit is given by the product of shear modulus and the net injected fluid volume. This method is based on the assumptions that the medium is fully saturated and in a state of incipient failure. An alternative geometrical approach was proposed by Shapiro et al. (2011), who postulated that the rupture area for an induced earthquake falls entirely within the stimulated volume. This assumption reduces the maximum-magnitude problem to one of estimating the largest potential slip surface area within a given stimulated volume. Finally, van der Elst et al. (2016) proposed that the maximum observed magnitude, statistically speaking, is the expected maximum value for a finite sample drawn from an unbounded Gutenberg-Richter distribution. These three models imply different approaches for risk management. The deterministic method proposed by McGarr (2014) implies that a ceiling on the maximum magnitude can be imposed by limiting the net injected volume, whereas the approach developed by Shapiro et al. (2011) implies that the time-dependent maximum magnitude is governed by the spatial size of the microseismic event cloud. Finally, the sample-size hypothesis of Van der Elst et al. (2016) implies that the best available estimate of the maximum magnitude is based upon observed seismicity rate. The latter two approaches suggest that real-time monitoring is essential for effective management of risk. A reliable estimate of maximum

  3. Maximum organic carbon limits at different melter feed rates (U)

    International Nuclear Information System (INIS)

    Choi, A.S.

    1995-01-01

    This report documents the results of a study to assess the impact of varying melter feed rates on the maximum total organic carbon (TOC) limits allowable in the DWPF melter feed. Topics discussed include: carbon content; feed rate; feed composition; melter vapor space temperature; combustion and dilution air; off-gas surges; earlier work on maximum TOC; overview of models; and the results of the work completed

  4. A tropospheric ozone maximum over the equatorial Southern Indian Ocean

    Directory of Open Access Journals (Sweden)

    L. Zhang

    2012-05-01

    Full Text Available We examine the distribution of tropical tropospheric ozone (O3 from the Microwave Limb Sounder (MLS and the Tropospheric Emission Spectrometer (TES by using a global three-dimensional model of tropospheric chemistry (GEOS-Chem. MLS and TES observations of tropospheric O3 during 2005 to 2009 reveal a distinct, persistent O3 maximum, both in mixing ratio and tropospheric column, in May over the Equatorial Southern Indian Ocean (ESIO. The maximum is most pronounced in 2006 and 2008 and less evident in the other three years. This feature is also consistent with the total column O3 observations from the Ozone Mapping Instrument (OMI and the Atmospheric Infrared Sounder (AIRS. Model results reproduce the observed May O3 maximum and the associated interannual variability. The origin of the maximum reflects a complex interplay of chemical and dynamic factors. The O3 maximum is dominated by the O3 production driven by lightning nitrogen oxides (NOx emissions, which accounts for 62% of the tropospheric column O3 in May 2006. We find the contribution from biomass burning, soil, anthropogenic and biogenic sources to the O3 maximum are rather small. The O3 productions in the lightning outflow from Central Africa and South America both peak in May and are directly responsible for the O3 maximum over the western ESIO. The lightning outflow from Equatorial Asia dominates over the eastern ESIO. The interannual variability of the O3 maximum is driven largely by the anomalous anti-cyclones over the southern Indian Ocean in May 2006 and 2008. The lightning outflow from Central Africa and South America is effectively entrained by the anti-cyclones followed by northward transport to the ESIO.

  5. Dinosaur Metabolism and the Allometry of Maximum Growth Rate

    OpenAIRE

    Myhrvold, Nathan P.

    2016-01-01

    The allometry of maximum somatic growth rate has been used in prior studies to classify the metabolic state of both extant vertebrates and dinosaurs. The most recent such studies are reviewed, and their data is reanalyzed. The results of allometric regressions on growth rate are shown to depend on the choice of independent variable; the typical choice used in prior studies introduces a geometric shear transformation that exaggerates the statistical power of the regressions. The maximum growth...

  6. MAXIMUM PRINCIPLE FOR SUBSONIC FLOW WITH VARIABLE ENTROPY

    Directory of Open Access Journals (Sweden)

    B. Sizykh Grigory

    2017-01-01

    Full Text Available Maximum principle for subsonic flow is fair for stationary irrotational subsonic gas flows. According to this prin- ciple, if the value of the velocity is not constant everywhere, then its maximum is achieved on the boundary and only on the boundary of the considered domain. This property is used when designing form of an aircraft with a maximum critical val- ue of the Mach number: it is believed that if the local Mach number is less than unit in the incoming flow and on the body surface, then the Mach number is less then unit in all points of flow. The known proof of maximum principle for subsonic flow is based on the assumption that in the whole considered area of the flow the pressure is a function of density. For the ideal and perfect gas (the role of diffusion is negligible, and the Mendeleev-Clapeyron law is fulfilled, the pressure is a function of density if entropy is constant in the entire considered area of the flow. Shows an example of a stationary sub- sonic irrotational flow, in which the entropy has different values on different stream lines, and the pressure is not a function of density. The application of the maximum principle for subsonic flow with respect to such a flow would be unreasonable. This example shows the relevance of the question about the place of the points of maximum value of the velocity, if the entropy is not a constant. To clarify the regularities of the location of these points, was performed the analysis of the com- plete Euler equations (without any simplifying assumptions in 3-D case. The new proof of the maximum principle for sub- sonic flow was proposed. This proof does not rely on the assumption that the pressure is a function of density. Thus, it is shown that the maximum principle for subsonic flow is true for stationary subsonic irrotational flows of ideal perfect gas with variable entropy.

  7. On semidefinite programming relaxations of maximum k-section

    NARCIS (Netherlands)

    de Klerk, E.; Pasechnik, D.V.; Sotirov, R.; Dobre, C.

    2012-01-01

    We derive a new semidefinite programming bound for the maximum k -section problem. For k=2 (i.e. for maximum bisection), the new bound is at least as strong as a well-known bound by Poljak and Rendl (SIAM J Optim 5(3):467–487, 1995). For k ≥ 3the new bound dominates a bound of Karisch and Rendl

  8. Maximum power point tracker based on fuzzy logic

    International Nuclear Information System (INIS)

    Daoud, A.; Midoun, A.

    2006-01-01

    The solar energy is used as power source in photovoltaic power systems and the need for an intelligent power management system is important to obtain the maximum power from the limited solar panels. With the changing of the sun illumination due to variation of angle of incidence of sun radiation and of the temperature of the panels, Maximum Power Point Tracker (MPPT) enables optimization of solar power generation. The MPPT is a sub-system designed to extract the maximum power from a power source. In the case of solar panels power source. the maximum power point varies as a result of changes in its electrical characteristics which in turn are functions of radiation dose, temperature, ageing and other effects. The MPPT maximum the power output from panels for a given set of conditions by detecting the best working point of the power characteristic and then controls the current through the panels or the voltage across them. Many MPPT methods have been reported in literature. These techniques of MPPT can be classified into three main categories that include: lookup table methods, hill climbing methods and computational methods. The techniques vary according to the degree of sophistication, processing time and memory requirements. The perturbation and observation algorithm (hill climbing technique) is commonly used due to its ease of implementation, and relative tracking efficiency. However, it has been shown that when the insolation changes rapidly, the perturbation and observation method is slow to track the maximum power point. In recent years, the fuzzy controllers are used for maximum power point tracking. This method only requires the linguistic control rules for maximum power point, the mathematical model is not required and therefore the implementation of this control method is easy to real control system. In this paper, we we present a simple robust MPPT using fuzzy set theory where the hardware consists of the microchip's microcontroller unit control card and

  9. Maximum spectral demands in the near-fault region

    Science.gov (United States)

    Huang, Yin-Nan; Whittaker, Andrew S.; Luco, Nicolas

    2008-01-01

    The Next Generation Attenuation (NGA) relationships for shallow crustal earthquakes in the western United States predict a rotated geometric mean of horizontal spectral demand, termed GMRotI50, and not maximum spectral demand. Differences between strike-normal, strike-parallel, geometric-mean, and maximum spectral demands in the near-fault region are investigated using 147 pairs of records selected from the NGA strong motion database. The selected records are for earthquakes with moment magnitude greater than 6.5 and for closest site-to-fault distance less than 15 km. Ratios of maximum spectral demand to NGA-predicted GMRotI50 for each pair of ground motions are presented. The ratio shows a clear dependence on period and the Somerville directivity parameters. Maximum demands can substantially exceed NGA-predicted GMRotI50 demands in the near-fault region, which has significant implications for seismic design, seismic performance assessment, and the next-generation seismic design maps. Strike-normal spectral demands are a significantly unconservative surrogate for maximum spectral demands for closest distance greater than 3 to 5 km. Scale factors that transform NGA-predicted GMRotI50 to a maximum spectral demand in the near-fault region are proposed.

  10. Maximum vehicle cabin temperatures under different meteorological conditions

    Science.gov (United States)

    Grundstein, Andrew; Meentemeyer, Vernon; Dowd, John

    2009-05-01

    A variety of studies have documented the dangerously high temperatures that may occur within the passenger compartment (cabin) of cars under clear sky conditions, even at relatively low ambient air temperatures. Our study, however, is the first to examine cabin temperatures under variable weather conditions. It uses a unique maximum vehicle cabin temperature dataset in conjunction with directly comparable ambient air temperature, solar radiation, and cloud cover data collected from April through August 2007 in Athens, GA. Maximum cabin temperatures, ranging from 41-76°C, varied considerably depending on the weather conditions and the time of year. Clear days had the highest cabin temperatures, with average values of 68°C in the summer and 61°C in the spring. Cloudy days in both the spring and summer were on average approximately 10°C cooler. Our findings indicate that even on cloudy days with lower ambient air temperatures, vehicle cabin temperatures may reach deadly levels. Additionally, two predictive models of maximum daily vehicle cabin temperatures were developed using commonly available meteorological data. One model uses maximum ambient air temperature and average daily solar radiation while the other uses cloud cover percentage as a surrogate for solar radiation. From these models, two maximum vehicle cabin temperature indices were developed to assess the level of danger. The models and indices may be useful for forecasting hazardous conditions, promoting public awareness, and to estimate past cabin temperatures for use in forensic analyses.

  11. Fractal Dimension and Maximum Sunspot Number in Solar Cycle

    Directory of Open Access Journals (Sweden)

    R.-S. Kim

    2006-09-01

    Full Text Available The fractal dimension is a quantitative parameter describing the characteristics of irregular time series. In this study, we use this parameter to analyze the irregular aspects of solar activity and to predict the maximum sunspot number in the following solar cycle by examining time series of the sunspot number. For this, we considered the daily sunspot number since 1850 from SIDC (Solar Influences Data analysis Center and then estimated cycle variation of the fractal dimension by using Higuchi's method. We examined the relationship between this fractal dimension and the maximum monthly sunspot number in each solar cycle. As a result, we found that there is a strong inverse relationship between the fractal dimension and the maximum monthly sunspot number. By using this relation we predicted the maximum sunspot number in the solar cycle from the fractal dimension of the sunspot numbers during the solar activity increasing phase. The successful prediction is proven by a good correlation (r=0.89 between the observed and predicted maximum sunspot numbers in the solar cycles.

  12. Size dependence of efficiency at maximum power of heat engine

    KAUST Repository

    Izumida, Y.; Ito, N.

    2013-01-01

    We perform a molecular dynamics computer simulation of a heat engine model to study how the engine size difference affects its performance. Upon tactically increasing the size of the model anisotropically, we determine that there exists an optimum size at which the model attains the maximum power for the shortest working period. This optimum size locates between the ballistic heat transport region and the diffusive heat transport one. We also study the size dependence of the efficiency at the maximum power. Interestingly, we find that the efficiency at the maximum power around the optimum size attains a value that has been proposed as a universal upper bound, and it even begins to exceed the bound as the size further increases. We explain this behavior of the efficiency at maximum power by using a linear response theory for the heat engine operating under a finite working period, which naturally extends the low-dissipation Carnot cycle model [M. Esposito, R. Kawai, K. Lindenberg, C. Van den Broeck, Phys. Rev. Lett. 105, 150603 (2010)]. The theory also shows that the efficiency at the maximum power under an extreme condition may reach the Carnot efficiency in principle.© EDP Sciences Società Italiana di Fisica Springer-Verlag 2013.

  13. Size dependence of efficiency at maximum power of heat engine

    KAUST Repository

    Izumida, Y.

    2013-10-01

    We perform a molecular dynamics computer simulation of a heat engine model to study how the engine size difference affects its performance. Upon tactically increasing the size of the model anisotropically, we determine that there exists an optimum size at which the model attains the maximum power for the shortest working period. This optimum size locates between the ballistic heat transport region and the diffusive heat transport one. We also study the size dependence of the efficiency at the maximum power. Interestingly, we find that the efficiency at the maximum power around the optimum size attains a value that has been proposed as a universal upper bound, and it even begins to exceed the bound as the size further increases. We explain this behavior of the efficiency at maximum power by using a linear response theory for the heat engine operating under a finite working period, which naturally extends the low-dissipation Carnot cycle model [M. Esposito, R. Kawai, K. Lindenberg, C. Van den Broeck, Phys. Rev. Lett. 105, 150603 (2010)]. The theory also shows that the efficiency at the maximum power under an extreme condition may reach the Carnot efficiency in principle.© EDP Sciences Società Italiana di Fisica Springer-Verlag 2013.

  14. How long do centenarians survive? Life expectancy and maximum lifespan.

    Science.gov (United States)

    Modig, K; Andersson, T; Vaupel, J; Rau, R; Ahlbom, A

    2017-08-01

    The purpose of this study was to explore the pattern of mortality above the age of 100 years. In particular, we aimed to examine whether Scandinavian data support the theory that mortality reaches a plateau at particularly old ages. Whether the maximum length of life increases with time was also investigated. The analyses were based on individual level data on all Swedish and Danish centenarians born from 1870 to 1901; in total 3006 men and 10 963 women were included. Birth cohort-specific probabilities of dying were calculated. Exact ages were used for calculations of maximum length of life. Whether maximum age changed over time was analysed taking into account increases in cohort size. The results confirm that there has not been any improvement in mortality amongst centenarians in the past 30 years and that the current rise in life expectancy is driven by reductions in mortality below the age of 100 years. The death risks seem to reach a plateau of around 50% at the age 103 years for men and 107 years for women. Despite the rising life expectancy, the maximum age does not appear to increase, in particular after accounting for the increasing number of individuals of advanced age. Mortality amongst centenarians is not changing despite improvements at younger ages. An extension of the maximum lifespan and a sizeable extension of life expectancy both require reductions in mortality above the age of 100 years. © 2017 The Association for the Publication of the Journal of Internal Medicine.

  15. Modeling multisite streamflow dependence with maximum entropy copula

    Science.gov (United States)

    Hao, Z.; Singh, V. P.

    2013-10-01

    Synthetic streamflows at different sites in a river basin are needed for planning, operation, and management of water resources projects. Modeling the temporal and spatial dependence structure of monthly streamflow at different sites is generally required. In this study, the maximum entropy copula method is proposed for multisite monthly streamflow simulation, in which the temporal and spatial dependence structure is imposed as constraints to derive the maximum entropy copula. The monthly streamflows at different sites are then generated by sampling from the conditional distribution. A case study for the generation of monthly streamflow at three sites in the Colorado River basin illustrates the application of the proposed method. Simulated streamflow from the maximum entropy copula is in satisfactory agreement with observed streamflow.

  16. Quality, precision and accuracy of the maximum No. 40 anemometer

    Energy Technology Data Exchange (ETDEWEB)

    Obermeir, J. [Otech Engineering, Davis, CA (United States); Blittersdorf, D. [NRG Systems Inc., Hinesburg, VT (United States)

    1996-12-31

    This paper synthesizes available calibration data for the Maximum No. 40 anemometer. Despite its long history in the wind industry, controversy surrounds the choice of transfer function for this anemometer. Many users are unaware that recent changes in default transfer functions in data loggers are producing output wind speed differences as large as 7.6%. Comparison of two calibration methods used for large samples of Maximum No. 40 anemometers shows a consistent difference of 4.6% in output speeds. This difference is significantly larger than estimated uncertainty levels. Testing, initially performed to investigate related issues, reveals that Gill and Maximum cup anemometers change their calibration transfer functions significantly when calibrated in the open atmosphere compared with calibration in a laminar wind tunnel. This indicates that atmospheric turbulence changes the calibration transfer function of cup anemometers. These results call into question the suitability of standard wind tunnel calibration testing for cup anemometers. 6 refs., 10 figs., 4 tabs.

  17. Beat the Deviations in Estimating Maximum Power of Thermoelectric Modules

    DEFF Research Database (Denmark)

    Gao, Junling; Chen, Min

    2013-01-01

    Under a certain temperature difference, the maximum power of a thermoelectric module can be estimated by the open-circuit voltage and the short-circuit current. In practical measurement, there exist two switch modes, either from open to short or from short to open, but the two modes can give...... different estimations on the maximum power. Using TEG-127-2.8-3.5-250 and TEG-127-1.4-1.6-250 as two examples, the difference is about 10%, leading to some deviations with the temperature change. This paper analyzes such differences by means of a nonlinear numerical model of thermoelectricity, and finds out...... that the main cause is the influence of various currents on the produced electromotive potential. A simple and effective calibration method is proposed to minimize the deviations in specifying the maximum power. Experimental results validate the method with improved estimation accuracy....

  18. Mass mortality of the vermetid gastropod Ceraesignum maximum

    Science.gov (United States)

    Brown, A. L.; Frazer, T. K.; Shima, J. S.; Osenberg, C. W.

    2016-09-01

    Ceraesignum maximum (G.B. Sowerby I, 1825), formerly Dendropoma maximum, was subject to a sudden, massive die-off in the Society Islands, French Polynesia, in 2015. On Mo'orea, where we have detailed documentation of the die-off, these gastropods were previously found in densities up to 165 m-2. In July 2015, we surveyed shallow back reefs of Mo'orea before, during and after the die-off, documenting their swift decline. All censused populations incurred 100% mortality. Additional surveys and observations from Mo'orea, Tahiti, Bora Bora, and Huahine (but not Taha'a) suggested a similar, and approximately simultaneous, die-off. The cause(s) of this cataclysmic mass mortality are currently unknown. Given the previously documented negative effects of C. maximum on corals, we expect the die-off will have cascading effects on the reef community.

  19. Stationary neutrino radiation transport by maximum entropy closure

    International Nuclear Information System (INIS)

    Bludman, S.A.

    1994-11-01

    The authors obtain the angular distributions that maximize the entropy functional for Maxwell-Boltzmann (classical), Bose-Einstein, and Fermi-Dirac radiation. In the low and high occupancy limits, the maximum entropy closure is bounded by previously known variable Eddington factors that depend only on the flux. For intermediate occupancy, the maximum entropy closure depends on both the occupation density and the flux. The Fermi-Dirac maximum entropy variable Eddington factor shows a scale invariance, which leads to a simple, exact analytic closure for fermions. This two-dimensional variable Eddington factor gives results that agree well with exact (Monte Carlo) neutrino transport calculations out of a collapse residue during early phases of hydrostatic neutron star formation

  20. Spatio-temporal observations of the tertiary ozone maximum

    Directory of Open Access Journals (Sweden)

    V. F. Sofieva

    2009-07-01

    Full Text Available We present spatio-temporal distributions of the tertiary ozone maximum (TOM, based on GOMOS (Global Ozone Monitoring by Occultation of Stars ozone measurements in 2002–2006. The tertiary ozone maximum is typically observed in the high-latitude winter mesosphere at an altitude of ~72 km. Although the explanation for this phenomenon has been found recently – low concentrations of odd-hydrogen cause the subsequent decrease in odd-oxygen losses – models have had significant deviations from existing observations until recently. Good coverage of polar night regions by GOMOS data has allowed for the first time to obtain spatial and temporal observational distributions of night-time ozone mixing ratio in the mesosphere.

    The distributions obtained from GOMOS data have specific features, which are variable from year to year. In particular, due to a long lifetime of ozone in polar night conditions, the downward transport of polar air by the meridional circulation is clearly observed in the tertiary ozone maximum time series. Although the maximum tertiary ozone mixing ratio is achieved close to the polar night terminator (as predicted by the theory, TOM can be observed also at very high latitudes, not only in the beginning and at the end, but also in the middle of winter. We have compared the observational spatio-temporal distributions of the tertiary ozone maximum with that obtained using WACCM (Whole Atmosphere Community Climate Model and found that the specific features are reproduced satisfactorily by the model.

    Since ozone in the mesosphere is very sensitive to HOx concentrations, energetic particle precipitation can significantly modify the shape of the ozone profiles. In particular, GOMOS observations have shown that the tertiary ozone maximum was temporarily destroyed during the January 2005 and December 2006 solar proton events as a result of the HOx enhancement from the increased ionization.

  1. Estimating the maximum potential revenue for grid connected electricity storage :

    Energy Technology Data Exchange (ETDEWEB)

    Byrne, Raymond Harry; Silva Monroy, Cesar Augusto.

    2012-12-01

    The valuation of an electricity storage device is based on the expected future cash flow generated by the device. Two potential sources of income for an electricity storage system are energy arbitrage and participation in the frequency regulation market. Energy arbitrage refers to purchasing (stor- ing) energy when electricity prices are low, and selling (discharging) energy when electricity prices are high. Frequency regulation is an ancillary service geared towards maintaining system frequency, and is typically procured by the independent system operator in some type of market. This paper outlines the calculations required to estimate the maximum potential revenue from participating in these two activities. First, a mathematical model is presented for the state of charge as a function of the storage device parameters and the quantities of electricity purchased/sold as well as the quantities o ered into the regulation market. Using this mathematical model, we present a linear programming optimization approach to calculating the maximum potential revenue from an elec- tricity storage device. The calculation of the maximum potential revenue is critical in developing an upper bound on the value of storage, as a benchmark for evaluating potential trading strate- gies, and a tool for capital nance risk assessment. Then, we use historical California Independent System Operator (CAISO) data from 2010-2011 to evaluate the maximum potential revenue from the Tehachapi wind energy storage project, an American Recovery and Reinvestment Act of 2009 (ARRA) energy storage demonstration project. We investigate the maximum potential revenue from two di erent scenarios: arbitrage only and arbitrage combined with the regulation market. Our analysis shows that participation in the regulation market produces four times the revenue compared to arbitrage in the CAISO market using 2010 and 2011 data. Then we evaluate several trading strategies to illustrate how they compare to the

  2. Discontinuity of maximum entropy inference and quantum phase transitions

    International Nuclear Information System (INIS)

    Chen, Jianxin; Ji, Zhengfeng; Yu, Nengkun; Zeng, Bei; Li, Chi-Kwong; Poon, Yiu-Tung; Shen, Yi; Zhou, Duanlu

    2015-01-01

    In this paper, we discuss the connection between two genuinely quantum phenomena—the discontinuity of quantum maximum entropy inference and quantum phase transitions at zero temperature. It is shown that the discontinuity of the maximum entropy inference of local observable measurements signals the non-local type of transitions, where local density matrices of the ground state change smoothly at the transition point. We then propose to use the quantum conditional mutual information of the ground state as an indicator to detect the discontinuity and the non-local type of quantum phase transitions in the thermodynamic limit. (paper)

  3. On an Objective Basis for the Maximum Entropy Principle

    Directory of Open Access Journals (Sweden)

    David J. Miller

    2015-01-01

    Full Text Available In this letter, we elaborate on some of the issues raised by a recent paper by Neapolitan and Jiang concerning the maximum entropy (ME principle and alternative principles for estimating probabilities consistent with known, measured constraint information. We argue that the ME solution for the “problematic” example introduced by Neapolitan and Jiang has stronger objective basis, rooted in results from information theory, than their alternative proposed solution. We also raise some technical concerns about the Bayesian analysis in their work, which was used to independently support their alternative to the ME solution. The letter concludes by noting some open problems involving maximum entropy statistical inference.

  4. The maximum economic depth of groundwater abstraction for irrigation

    Science.gov (United States)

    Bierkens, M. F.; Van Beek, L. P.; de Graaf, I. E. M.; Gleeson, T. P.

    2017-12-01

    Over recent decades, groundwater has become increasingly important for agriculture. Irrigation accounts for 40% of the global food production and its importance is expected to grow further in the near future. Already, about 70% of the globally abstracted water is used for irrigation, and nearly half of that is pumped groundwater. In many irrigated areas where groundwater is the primary source of irrigation water, groundwater abstraction is larger than recharge and we see massive groundwater head decline in these areas. An important question then is: to what maximum depth can groundwater be pumped for it to be still economically recoverable? The objective of this study is therefore to create a global map of the maximum depth of economically recoverable groundwater when used for irrigation. The maximum economic depth is the maximum depth at which revenues are still larger than pumping costs or the maximum depth at which initial investments become too large compared to yearly revenues. To this end we set up a simple economic model where costs of well drilling and the energy costs of pumping, which are a function of well depth and static head depth respectively, are compared with the revenues obtained for the irrigated crops. Parameters for the cost sub-model are obtained from several US-based studies and applied to other countries based on GDP/capita as an index of labour costs. The revenue sub-model is based on gross irrigation water demand calculated with a global hydrological and water resources model, areal coverage of crop types from MIRCA2000 and FAO-based statistics on crop yield and market price. We applied our method to irrigated areas in the world overlying productive aquifers. Estimated maximum economic depths range between 50 and 500 m. Most important factors explaining the maximum economic depth are the dominant crop type in the area and whether or not initial investments in well infrastructure are limiting. In subsequent research, our estimates of

  5. Efficiency of autonomous soft nanomachines at maximum power.

    Science.gov (United States)

    Seifert, Udo

    2011-01-14

    We consider nanosized artificial or biological machines working in steady state enforced by imposing nonequilibrium concentrations of solutes or by applying external forces, torques, or electric fields. For unicyclic and strongly coupled multicyclic machines, efficiency at maximum power is not bounded by the linear response value 1/2. For strong driving, it can even approach the thermodynamic limit 1. Quite generally, such machines fall into three different classes characterized, respectively, as "strong and efficient," "strong and inefficient," and "balanced." For weakly coupled multicyclic machines, efficiency at maximum power has lost any universality even in the linear response regime.

  6. A comparison of methods of predicting maximum oxygen uptake.

    OpenAIRE

    Grant, S; Corbett, K; Amjad, A M; Wilson, J; Aitchison, T

    1995-01-01

    The aim of this study was to compare the results from a Cooper walk run test, a multistage shuttle run test, and a submaximal cycle test with the direct measurement of maximum oxygen uptake on a treadmill. Three predictive tests of maximum oxygen uptake--linear extrapolation of heart rate of VO2 collected from a submaximal cycle ergometer test (predicted L/E), the Cooper 12 min walk, run test, and a multi-stage progressive shuttle run test (MST)--were performed by 22 young healthy males (mean...

  7. Maximum length scale in density based topology optimization

    DEFF Research Database (Denmark)

    Lazarov, Boyan Stefanov; Wang, Fengwen

    2017-01-01

    The focus of this work is on two new techniques for imposing maximum length scale in topology optimization. Restrictions on the maximum length scale provide designers with full control over the optimized structure and open possibilities to tailor the optimized design for broader range...... of manufacturing processes by fulfilling the associated technological constraints. One of the proposed methods is based on combination of several filters and builds on top of the classical density filtering which can be viewed as a low pass filter applied to the design parametrization. The main idea...

  8. A Maximum Entropy Method for a Robust Portfolio Problem

    Directory of Open Access Journals (Sweden)

    Yingying Xu

    2014-06-01

    Full Text Available We propose a continuous maximum entropy method to investigate the robustoptimal portfolio selection problem for the market with transaction costs and dividends.This robust model aims to maximize the worst-case portfolio return in the case that allof asset returns lie within some prescribed intervals. A numerical optimal solution tothe problem is obtained by using a continuous maximum entropy method. Furthermore,some numerical experiments indicate that the robust model in this paper can result in betterportfolio performance than a classical mean-variance model.

  9. Different phylogenomic approaches to resolve the evolutionary relationships among model fish species.

    Science.gov (United States)

    Negrisolo, Enrico; Kuhl, Heiner; Forcato, Claudio; Vitulo, Nicola; Reinhardt, Richard; Patarnello, Tomaso; Bargelloni, Luca

    2010-12-01

    Comparative genomics holds the promise to magnify the information obtained from individual genome sequencing projects, revealing common features conserved across genomes and identifying lineage-specific characteristics. To implement such a comparative approach, a robust phylogenetic framework is required to accurately reconstruct evolution at the genome level. Among vertebrate taxa, teleosts represent the second best characterized group, with high-quality draft genome sequences for five model species (Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes, and Tetraodon nigroviridis), and several others are in the finishing lane. However, the relationships among the acanthomorph teleost model fishes remain an unresolved taxonomic issue. Here, a genomic region spanning over 1.2 million base pairs was sequenced in the teleost fish Dicentrarchus labrax. Together with genomic data available for the above fish models, the new sequence was used to identify unique orthologous genomic regions shared across all target taxa. Different strategies were applied to produce robust multiple gene and genomic alignments spanning from 11,802 to 186,474 amino acid/nucleotide positions. Ten data sets were analyzed according to Bayesian inference, maximum likelihood, maximum parsimony, and neighbor joining methods. Extensive analyses were performed to explore the influence of several factors (e.g., alignment methodology, substitution model, data set partitions, and long-branch attraction) on the tree topology. Although a general consensus was observed for a closer relationship between G. aculeatus (Gasterosteidae) and Di. labrax (Moronidae) with the atherinomorph O. latipes (Beloniformes) sister taxon of this clade, with the tetraodontiform group Ta. rubripes and Te. nigroviridis (Tetraodontiformes) representing a more distantly related taxon among acanthomorph model fish species, conflicting results were obtained between data sets and methods, especially with respect

  10. Identifying the Basal Angiosperm Node in Chloroplast GenomePhylogenies: Sampling One's Way Out of the Felsenstein Zone

    Energy Technology Data Exchange (ETDEWEB)

    Leebens-Mack, Jim; Raubeson, Linda A.; Cui, Liying; Kuehl,Jennifer V.; Fourcade, Matthew H.; Chumley, Timothy W.; Boore, JeffreyL.; Jansen, Robert K.; dePamphilis, Claude W.

    2005-05-27

    While there has been strong support for Amborella and Nymphaeales (water lilies) as branching from basal-most nodes in the angiosperm phylogeny, this hypothesis has recently been challenged by phylogenetic analyses of 61 protein-coding genes extracted from the chloroplast genome sequences of Amborella, Nymphaea and 12 other available land plant chloroplast genomes. These character-rich analyses placed the monocots, represented by three grasses (Poaceae), as sister to all other extant angiosperm lineages. We have extracted protein-coding regions from draft sequences for six additional chloroplast genomes to test whether this surprising result could be an artifact of long-branch attraction due to limited taxon sampling. The added taxa include three monocots (Acorus, Yucca and Typha), a water lily (Nuphar), a ranunculid(Ranunculus), and a gymnosperm (Ginkgo). Phylogenetic analyses of the expanded DNA and protein datasets together with microstructural characters (indels) provided unambiguous support for Amborella and the Nymphaeales as branching from the basal-most nodes in the angiospermphylogeny. However, their relative positions proved to be dependent on method of analysis, with parsimony favoring Amborella as sister to all other angiosperms, and maximum likelihood and neighbor-joining methods favoring an Amborella + Nympheales clade as sister. The maximum likelihood phylogeny supported the later hypothesis, but the likelihood for the former hypothesis was not significantly different. Parametric bootstrap analysis, single gene phylogenies, estimated divergence dates and conflicting in del characters all help to illuminate the nature of the conflict in resolution of the most basal nodes in the angiospermphylogeny. Molecular dating analyses provided median age estimates of 161 mya for the most recent common ancestor of all extant angiosperms and 145 mya for the most recent common ancestor of monocots, magnoliids andeudicots. Whereas long sequences reduce variance in

  11. Lineage diversification and hybridization in the Cayratia japonica-Cayratia tenuifolia species complex.

    Science.gov (United States)

    Ishikawa, Naoko; Ikeda, Hajime; Yi, Ting-shuang; Takabe-Ito, Eriko; Okada, Hiroshi; Tsukaya, Hirokazu

    2014-06-01

    The Cayratia japonica-Cayratia tenuifolia species complex (Vitaceae) is distributed from temperate to tropical East Asia, Southeast Asia, India, and Australia. The spatiotemporal diversification history of this complex was assessed through phylogenetic and biogeographic analyses. Maximum parsimony, neighbor-joining, and maximum likelihood methods were used to analyze sequences of one nuclear (AS1) and two plastid regions (trnL-F and trnC-petN). Bayesian dating analysis was conducted to estimate the divergence times of clades. The likelihood method LAGRANGE was used to infer ancestral areas. The Asian C. japonica and C. tenuifolia should be treated as an unresolved complex, and Australian C. japonica is distinct from the Asian C. japonica-C. tenuifolia species complex and should be treated as separate taxa. The Asian C. japonica-C. tenuifolia species complex was estimated to have diverged from its closest relatives during the Late Eocene (35.1 million years ago [Ma], 95% highest posterior densities [HPD]=23.3-47.3Ma) and most likely first diverged in mid-continental Asia. This complex was first divided into a northern clade and a southern clade during the middle Oligocene (27.3Ma; 95% HPD=17.4-38.1Ma), which is consistent with a large southeastward extrusion of the Indochina region relative to South China along the Red River. Each of the northern and southern clades then further diverged into multiple subclades through a series of dispersal and divergence events following significant geological and climatic changes in East and Southeast Asia during the Miocene. Multiple inter-lineage hybridizations among four lineages were inferred to have occurred following this diversification process, which caused some Asian lineages to be morphologically cryptic. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia).

    Science.gov (United States)

    Pyron, R Alexander; Hendry, Catriona R; Chou, Vincent M; Lemmon, Emily M; Lemmon, Alan R; Burbrink, Frank T

    2014-12-01

    Next-generation genomic sequencing promises to quickly and cheaply resolve remaining contentious nodes in the Tree of Life, and facilitates species-tree estimation while taking into account stochastic genealogical discordance among loci. Recent methods for estimating species trees bypass full likelihood-based estimates of the multi-species coalescent, and approximate the true species-tree using simpler summary metrics. These methods converge on the true species-tree with sufficient genomic sampling, even in the anomaly zone. However, no studies have yet evaluated their efficacy on a large-scale phylogenomic dataset, and compared them to previous concatenation strategies. Here, we generate such a dataset for Caenophidian snakes, a group with >2500 species that contains several rapid radiations that were poorly resolved with fewer loci. We generate sequence data for 333 single-copy nuclear loci with ∼100% coverage (∼0% missing data) for 31 major lineages. We estimate phylogenies using neighbor joining, maximum parsimony, maximum likelihood, and three summary species-tree approaches (NJst, STAR, and MP-EST). All methods yield similar resolution and support for most nodes. However, not all methods support monophyly of Caenophidia, with Acrochordidae placed as the sister taxon to Pythonidae in some analyses. Thus, phylogenomic species-tree estimation may occasionally disagree with well-supported relationships from concatenated analyses of small numbers of nuclear or mitochondrial genes, a consideration for future studies. In contrast for at least two diverse, rapid radiations (Lamprophiidae and Colubridae), phylogenomic data and species-tree inference do little to improve resolution and support. Thus, certain nodes may lack strong signal, and larger datasets and more sophisticated analyses may still fail to resolve them. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Molecular phylogeny of the genus Saguinus (Platyrrhini, Primates based on the ND1 mitochondrial gene and implications for conservation

    Directory of Open Access Journals (Sweden)

    Claudia Helena Tagliaro

    2005-03-01

    Full Text Available The systematics of the subfamily Callitrichinae (Platyrrhini, Primates, a group of small monkeys from South America and Panama, remains an area of considerable discussion despite many investigations, there being continuing controversy over subgeneric taxonomic classifications based on morphological characters. The purpose of our research was to help elucidate the phylogenetic relationships within the monkey genus Saguinus (Callitrichinae using a molecular approach to discover whether or not the two different sections containing hairy-faced and bare-faced species are monophyletic, whether Saguinus midas midas and Saguinus bicolor are more closely related than are S. midas midas and Saguinus midas niger, and if Saguinus fuscicollis melanoleucus and Saguinus fuscicollis weddelli really are different species. We sequenced the 957 bp ND1 mitochondrial gene of 21 Saguinus monkeys (belonging to six species and nine morphotypes and one Cebus monkey (the outgroup and constructed phylogenetic trees using maximum parsimony, neighbor joining, and maximum likelihood methods. The phylogenetic trees obtained divided the genus Saguinus into two groups, one containing the small-bodied species S. fuscicollis and the other, the large-bodied species S. mystax, S. leucopus, S. oedipus, S. midas, S. bicolor. The most derived taxa, S. midas and S. bicolor, grouped together, while S. fuscicollis melanoleucus and S. f. weddelli showed divergence values that did not support the division of these morphotypes into subspecies. On the other hand, S. midas individuals showed divergence compatible with the existence of three subspecies, two of them with the same morphotype as the subspecies S. midas niger. The results of our study suggest that there is at least one Saguinus subspecies that has not yet been described and that the conservation status of Saguinus species and subspecies should be carefully revised using modern molecular approaches.

  14. Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees

    Directory of Open Access Journals (Sweden)

    Dandekar Thomas

    2010-01-01

    Full Text Available Abstract Background In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. Results This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Conclusions Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. Reviewers This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber and Eugene V. Koonin. Open peer review Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber and Eugene V. Koonin. For the full reviews, please go to the Reviewers' comments section.

  15. On the phylogenetic position of Pseudophilomedinae within Sarsielloidea (Ostracoda, Myodocopida), with a description of one new Harbansus from Ningaloo Reef and redescription of H. paucichelatus from Yucatan

    Science.gov (United States)

    Karanovic, Ivana; Orduña-Martínez, Lorena; Ardisson, Pedro-Luis

    2015-03-01

    Previous studies have suggested incongruence between current systematics and molecular phylogenies of Sarsielloidea, with a possible polyphyly of the family Philomedidae. Here, we provide molecular phylogenetic analyses based on 18S rDNA and 28S rDNA. The former includes five new sequences and 12 from the GenBank, and the latter two new and six sequences from the GenBank. We use three methods, maximum likelihood, maximum parsimony, and neighbor joining, and all reconstructed phylogenies support previously suggested polyphyly, indicating a closer relationship of the subfamily Pseudophilomedinae with one subfamily of Sarsiellidae than with the nominotypical subfamily of Philomedidae. Morphological characters that may be key indicators of the phylogenetic relationships between three Sarsielloidea families are discussed. We also describe the 21st representative of the Pseudophilomedinae genus, Harbansus Kornicker, (Smith Contrib Zool 260:75, 1978), Harbansus ningalooi n. sp., from the Ningaloo Reef, Western Australia. This is the first Harbansus reported from the Australian west coast and the second from the Australian coral reef systems. It differs from all other congeners by peculiar claw-like processes on the posterior infold. Most Harbansus species have relatively restricted distributions, except Harbansus paucichelatus (Kornicker, in Inst Mar Sci 5:195-300, 1958), which has also been postulated to represent a species complex. We present a detailed morphological redescription of this species, based on the freshly collected material from the Yucatan Peninsula, as well as four mitochondrial COI sequences. These become the first COI sequences of the entire superfamily Sarsielloidea available on the GenBank. To facilitate future identification, we include a key to species of Harbansus.

  16. MAXIMUM RUNOFF OF THE FLOOD ON WADIS OF NORTHERN ...

    African Journals Online (AJOL)

    lanez

    The technique of account the maximal runoff of flood for the rivers of northern part of Algeria based on the theory of ... north to south: 1) coastal Tel – fertile, high cultivated and sown zone; 2) territory of Atlas. Mountains ... In the first case the empiric dependence between maximum intensity of precipitation for some calculation ...

  17. Scientific substantination of maximum allowable concentration of fluopicolide in water

    Directory of Open Access Journals (Sweden)

    Pelo I.М.

    2014-03-01

    Full Text Available In order to substantiate fluopicolide maximum allowable concentration in the water of water reservoirs the research was carried out. Methods of study: laboratory hygienic experiment using organoleptic and sanitary-chemical, sanitary-toxicological, sanitary-microbiological and mathematical methods. The results of fluopicolide influence on organoleptic properties of water, sanitary regimen of reservoirs for household purposes were given and its subthreshold concentration in water by sanitary and toxicological hazard index was calculated. The threshold concentration of the substance by the main hazard criteria was established, the maximum allowable concentration in water was substantiated. The studies led to the following conclusions: fluopicolide threshold concentration in water by organoleptic hazard index (limiting criterion – the smell – 0.15 mg/dm3, general sanitary hazard index (limiting criteria – impact on the number of saprophytic microflora, biochemical oxygen demand and nitrification – 0.015 mg/dm3, the maximum noneffective concentration – 0.14 mg/dm3, the maximum allowable concentration - 0.015 mg/dm3.

  18. Image coding based on maximum entropy partitioning for identifying ...

    Indian Academy of Sciences (India)

    A new coding scheme based on maximum entropy partitioning is proposed in our work, particularly to identify the improbable intensities related to different emotions. The improbable intensities when used as a mask decode the facial expression correctly, providing an effectiveplatform for future emotion categorization ...

  19. Computing the maximum volume inscribed ellipsoid of a polytopic projection

    NARCIS (Netherlands)

    Zhen, Jianzhe; den Hertog, Dick

    We introduce a novel scheme based on a blending of Fourier-Motzkin elimination (FME) and adjustable robust optimization techniques to compute the maximum volume inscribed ellipsoid (MVE) in a polytopic projection. It is well-known that deriving an explicit description of a projected polytope is

  20. Computing the Maximum Volume Inscribed Ellipsoid of a Polytopic Projection

    NARCIS (Netherlands)

    Zhen, J.; den Hertog, D.

    2015-01-01

    We introduce a novel scheme based on a blending of Fourier-Motzkin elimination (FME) and adjustable robust optimization techniques to compute the maximum volume inscribed ellipsoid (MVE) in a polytopic projection. It is well-known that deriving an explicit description of a projected polytope is

  1. Maximum super angle optimization method for array antenna pattern synthesis

    DEFF Research Database (Denmark)

    Wu, Ji; Roederer, A. G

    1991-01-01

    Different optimization criteria related to antenna pattern synthesis are discussed. Based on the maximum criteria and vector space representation, a simple and efficient optimization method is presented for array and array fed reflector power pattern synthesis. A sector pattern synthesized by a 2...

  2. correlation between maximum dry density and cohesion of ...

    African Journals Online (AJOL)

    HOD

    investigation on sandy soils to determine the correlation between relative density and compaction test parameter. Using twenty soil samples, they were able to develop correlations between relative density, coefficient of uniformity and maximum dry density. Khafaji [5] using standard proctor compaction method carried out an ...

  3. Molecular markers linked to apomixis in Panicum maximum Jacq ...

    African Journals Online (AJOL)

    Panicum maximum Jacq. is an important forage grass of African origin largely used in the tropics. The genetic breeding of this species is based on the hybridization of sexual and apomictic genotypes and selection of apomictic F1 hybrids. The objective of this work was to identify molecular markers linked to apomixis in P.

  4. Maximum likelihood estimation of the attenuated ultrasound pulse

    DEFF Research Database (Denmark)

    Rasmussen, Klaus Bolding

    1994-01-01

    The attenuated ultrasound pulse is divided into two parts: a stationary basic pulse and a nonstationary attenuation pulse. A standard ARMA model is used for the basic pulse, and a nonstandard ARMA model is derived for the attenuation pulse. The maximum likelihood estimator of the attenuated...

  5. On a Weak Discrete Maximum Principle for hp-FEM

    Czech Academy of Sciences Publication Activity Database

    Šolín, Pavel; Vejchodský, Tomáš

    -, č. 209 (2007), s. 54-65 ISSN 0377-0427 R&D Projects: GA ČR(CZ) GA102/05/0629 Institutional research plan: CEZ:AV0Z20570509; CEZ:AV0Z10190503 Keywords : discrete maximum principle * hp-FEM Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 0.943, year: 2007

  6. Gamma-ray spectra deconvolution by maximum-entropy methods

    International Nuclear Information System (INIS)

    Los Arcos, J.M.

    1996-01-01

    A maximum-entropy method which includes the response of detectors and the statistical fluctuations of spectra is described and applied to the deconvolution of γ-ray spectra. Resolution enhancement of 25% can be reached for experimental peaks and up to 50% for simulated ones, while the intensities are conserved within 1-2%. (orig.)

  7. Modeling maximum daily temperature using a varying coefficient regression model

    Science.gov (United States)

    Han Li; Xinwei Deng; Dong-Yum Kim; Eric P. Smith

    2014-01-01

    Relationships between stream water and air temperatures are often modeled using linear or nonlinear regression methods. Despite a strong relationship between water and air temperatures and a variety of models that are effective for data summarized on a weekly basis, such models did not yield consistently good predictions for summaries such as daily maximum temperature...

  8. Maximum Interconnectedness and Availability for Directional Airborne Range Extension Networks

    Science.gov (United States)

    2016-08-29

    IEEE TRANSACTIONS ON WIRELESS COMMUNICATIONS 1 Maximum Interconnectedness and Availability for Directional Airborne Range Extension Networks Thomas...2 IEEE TRANSACTIONS ON WIRELESS COMMUNICATIONS I. INTRODUCTION Tactical military networks both on land and at sea often have restricted transmission...a standard definition in graph theoretic and networking literature that is related to, but different from, the metric we consider. August 29, 2016

  9. Maximum of difference assessment of typical semitrailers: a global study

    CSIR Research Space (South Africa)

    Kienhofer, F

    2016-11-01

    Full Text Available the maximum allowable width and frontal overhang as stipulated by legislation from Australia, the European Union, Canada, the United States and South Africa. The majority of the Australian, EU and Canadian semitrailer combinations and all of the South African...

  10. The constraint rule of the maximum entropy principle

    NARCIS (Netherlands)

    Uffink, J.

    1995-01-01

    The principle of maximum entropy is a method for assigning values to probability distributions on the basis of partial information. In usual formulations of this and related methods of inference one assumes that this partial information takes the form of a constraint on allowed probability

  11. 24 CFR 232.565 - Maximum loan amount.

    Science.gov (United States)

    2010-04-01

    ... URBAN DEVELOPMENT MORTGAGE AND LOAN INSURANCE PROGRAMS UNDER NATIONAL HOUSING ACT AND OTHER AUTHORITIES MORTGAGE INSURANCE FOR NURSING HOMES, INTERMEDIATE CARE FACILITIES, BOARD AND CARE HOMES, AND ASSISTED... Fire Safety Equipment Eligible Security Instruments § 232.565 Maximum loan amount. The principal amount...

  12. 5 CFR 531.221 - Maximum payable rate rule.

    Science.gov (United States)

    2010-01-01

    ... before the reassignment. (ii) If the rate resulting from the geographic conversion under paragraph (c)(2... previous rate (i.e., the former special rate after the geographic conversion) with the rates on the current... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Maximum payable rate rule. 531.221...

  13. Effects of bruxism on the maximum bite force

    Directory of Open Access Journals (Sweden)

    Todić Jelena T.

    2017-01-01

    Full Text Available Background/Aim. Bruxism is a parafunctional activity of the masticatory system, which is characterized by clenching or grinding of teeth. The purpose of this study was to determine whether the presence of bruxism has impact on maximum bite force, with particular reference to the potential impact of gender on bite force values. Methods. This study included two groups of subjects: without and with bruxism. The presence of bruxism in the subjects was registered using a specific clinical questionnaire on bruxism and physical examination. The subjects from both groups were submitted to the procedure of measuring the maximum bite pressure and occlusal contact area using a single-sheet pressure-sensitive films (Fuji Prescale MS and HS Film. Maximal bite force was obtained by multiplying maximal bite pressure and occlusal contact area values. Results. The average values of maximal bite force were significantly higher in the subjects with bruxism compared to those without bruxism (p 0.01. Maximal bite force was significantly higher in the males compared to the females in all segments of the research. Conclusion. The presence of bruxism influences the increase in the maximum bite force as shown in this study. Gender is a significant determinant of bite force. Registration of maximum bite force can be used in diagnosing and analysing pathophysiological events during bruxism.

  14. MAXIMUM-LIKELIHOOD-ESTIMATION OF THE ENTROPY OF AN ATTRACTOR

    NARCIS (Netherlands)

    SCHOUTEN, JC; TAKENS, F; VANDENBLEEK, CM

    In this paper, a maximum-likelihood estimate of the (Kolmogorov) entropy of an attractor is proposed that can be obtained directly from a time series. Also, the relative standard deviation of the entropy estimate is derived; it is dependent on the entropy and on the number of samples used in the

  15. Adaptive Unscented Kalman Filter using Maximum Likelihood Estimation

    DEFF Research Database (Denmark)

    Mahmoudi, Zeinab; Poulsen, Niels Kjølstad; Madsen, Henrik

    2017-01-01

    The purpose of this study is to develop an adaptive unscented Kalman filter (UKF) by tuning the measurement noise covariance. We use the maximum likelihood estimation (MLE) and the covariance matching (CM) method to estimate the noise covariance. The multi-step prediction errors generated...

  16. Handelman's hierarchy for the maximum stable set problem

    NARCIS (Netherlands)

    Laurent, M.; Sun, Z.

    2014-01-01

    The maximum stable set problem is a well-known NP-hard problem in combinatorial optimization, which can be formulated as the maximization of a quadratic square-free polynomial over the (Boolean) hypercube. We investigate a hierarchy of linear programming relaxations for this problem, based on a

  17. New shower maximum trigger for electrons and photons at CDF

    International Nuclear Information System (INIS)

    Amidei, D.; Burkett, K.; Gerdes, D.; Miao, C.; Wolinski, D.

    1994-01-01

    For the 1994 Tevatron collider run, CDF has upgraded the electron and photo trigger hardware to make use of shower position and size information from the central shower maximum detector. For electrons, the upgrade has resulted in a 50% reduction in backgrounds while retaining approximately 90% of the signal. The new trigger also eliminates the background to photon triggers from single-phototube spikes

  18. New shower maximum trigger for electrons and photons at CDF

    International Nuclear Information System (INIS)

    Gerdes, D.

    1994-08-01

    For the 1994 Tevatron collider run, CDF has upgraded the electron and photon trigger hardware to make use of shower position and size information from the central shower maximum detector. For electrons, the upgrade has resulted in a 50% reduction in backgrounds while retaining approximately 90% of the signal. The new trigger also eliminates the background to photon triggers from single-phototube discharge

  19. Maximum drawdown and the allocation to real estate

    NARCIS (Netherlands)

    Hamelink, F.; Hoesli, M.

    2004-01-01

    The role of real estate in a mixed-asset portfolio is investigated when the maximum drawdown (hereafter MaxDD), rather than the standard deviation, is used as the measure of risk. In particular, it is analysed whether the discrepancy between the optimal allocation to real estate and the actual

  20. A Family of Maximum SNR Filters for Noise Reduction

    DEFF Research Database (Denmark)

    Huang, Gongping; Benesty, Jacob; Long, Tao

    2014-01-01

    significantly increase the SNR but at the expense of tremendous speech distortion. As a consequence, the speech quality improvement, measured by the perceptual evaluation of speech quality (PESQ) algorithm, is marginal if any, regardless of the number of microphones used. In the STFT domain, the maximum SNR...

  1. 5 CFR 581.402 - Maximum garnishment limitations.

    Science.gov (United States)

    2010-01-01

    ... PROCESSING GARNISHMENT ORDERS FOR CHILD SUPPORT AND/OR ALIMONY Consumer Credit Protection Act Restrictions..., pursuant to section 1673(b)(2) (A) and (B) of title 15 of the United States Code (the Consumer Credit... local law, the maximum part of the aggregate disposable earnings subject to garnishment to enforce any...

  2. Distribution of phytoplankton groups within the deep chlorophyll maximum

    KAUST Repository

    Latasa, Mikel; Cabello, Ana Marí a; Moran, Xose Anxelu G.; Massana, Ramon; Scharek, Renate

    2016-01-01

    and optical and FISH microscopy. All groups presented minimum abundances at the surface and a maximum in the DCM layer. The cell distribution was not vertically symmetrical around the DCM peak and cells tended to accumulate in the upper part of the DCM layer

  3. 44 CFR 208.12 - Maximum Pay Rate Table.

    Science.gov (United States)

    2010-10-01

    ...) Physicians. DHS uses the latest Special Salary Rate Table Number 0290 for Medical Officers (Clinical... Personnel, in which case the Maximum Pay Rate Table would not apply. (3) Compensation for Sponsoring Agency... organizations, e.g., HMOs or medical or engineering professional associations, under the revised definition of...

  4. Anti-nutrient components of guinea grass ( Panicum maximum ...

    African Journals Online (AJOL)

    Yomi

    2012-01-31

    Jan 31, 2012 ... A true measure of forage quality is animal ... The anti-nutritional contents of a pasture could be ... nutrient factors in P. maximum; (2) assess the effect of nitrogen ..... 3. http://www.clemson.edu/Fairfield/local/news/quality.

  5. SIMULATION OF NEW SIMPLE FUZZY LOGIC MAXIMUM POWER ...

    African Journals Online (AJOL)

    2010-06-30

    Jun 30, 2010 ... Basic structure photovoltaic system Solar array mathematic ... The equivalent circuit model of a solar cell consists of a current generator and a diode .... control of boost converter (tracker) such that maximum power is achieved at the output of the solar panel. Fig.11. The membership function of input. Fig.12.

  6. Sur les estimateurs du maximum de vraisemblance dans les mod& ...

    African Journals Online (AJOL)

    Abstract. We are interested in the existence and uniqueness of maximum likelihood estimators of parameters in the two multiplicative regression models, with Poisson or negative binomial probability distributions. Following its work on the multiplicative Poisson model with two factors without repeated measures, Haberman ...

  7. Gravitational Waves and the Maximum Spin Frequency of Neutron Stars

    NARCIS (Netherlands)

    Patruno, A.; Haskell, B.; D'Angelo, C.

    2012-01-01

    In this paper, we re-examine the idea that gravitational waves are required as a braking mechanism to explain the observed maximum spin frequency of neutron stars. We show that for millisecond X-ray pulsars, the existence of spin equilibrium as set by the disk/magnetosphere interaction is sufficient

  8. Applications of the Maximum Entropy Method in superspace

    Czech Academy of Sciences Publication Activity Database

    van Smaalen, S.; Palatinus, Lukáš

    2004-01-01

    Roč. 305, - (2004), s. 57-62 ISSN 0015-0193 Grant - others:DFG and FCI(DE) XX Institutional research plan: CEZ:AV0Z1010914 Keywords : Maximum Entropy Method * modulated structures * charge density Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.517, year: 2004

  9. Phytophthora stricta isolated from Rhododendron maximum in Pennsylvania

    Science.gov (United States)

    During a survey in October 2013, in the Michaux State Forest in Pennsylvania , necrotic Rhododendron maximum leaves were noticed on mature plants alongside a stream. Symptoms were nondescript necrotic lesions at the tips of mature leaves. Colonies resembling a Phytophthora sp. were observed from c...

  10. Transversals and independence in linear hypergraphs with maximum degree two

    DEFF Research Database (Denmark)

    Henning, Michael A.; Yeo, Anders

    2017-01-01

    , k-uniform hypergraphs with maximum degree 2. It is known [European J. Combin. 36 (2014), 231–236] that if H ∈ Hk, then (k + 1)τ (H) 6 ≤ n + m, and there are only two hypergraphs that achieve equality in the bound. In this paper, we prove a much more powerful result, and establish tight upper bounds...

  11. A conrparison of optirnunl and maximum reproduction using the rat ...

    African Journals Online (AJOL)

    of pigs to increase reproduction rate of sows (te Brake,. 1978; Walker et at., 1979; Kemm et at., 1980). However, no experimental evidence exists that this strategy would in fact improve biological efficiency. In this pilot experiment, an attempt was made to compare systems of optimum or maximum reproduction using the rat.

  12. Revision of regional maximum flood (RMF) estimation in Namibia ...

    African Journals Online (AJOL)

    Extreme flood hydrology in Namibia for the past 30 years has largely been based on the South African Department of Water Affairs Technical Report 137 (TR 137) of 1988. This report proposes an empirically established upper limit of flood peaks for regions called the regional maximum flood (RMF), which could be ...

  13. Maximum entropy estimation via Gauss-LP quadratures

    NARCIS (Netherlands)

    Thély, Maxime; Sutter, Tobias; Mohajerin Esfahani, P.; Lygeros, John; Dochain, Denis; Henrion, Didier; Peaucelle, Dimitri

    2017-01-01

    We present an approximation method to a class of parametric integration problems that naturally appear when solving the dual of the maximum entropy estimation problem. Our method builds up on a recent generalization of Gauss quadratures via an infinite-dimensional linear program, and utilizes a

  14. On the maximum entropy distributions of inherently positive nuclear data

    Energy Technology Data Exchange (ETDEWEB)

    Taavitsainen, A., E-mail: aapo.taavitsainen@gmail.com; Vanhanen, R.

    2017-05-11

    The multivariate log-normal distribution is used by many authors and statistical uncertainty propagation programs for inherently positive quantities. Sometimes it is claimed that the log-normal distribution results from the maximum entropy principle, if only means, covariances and inherent positiveness of quantities are known or assumed to be known. In this article we show that this is not true. Assuming a constant prior distribution, the maximum entropy distribution is in fact a truncated multivariate normal distribution – whenever it exists. However, its practical application to multidimensional cases is hindered by lack of a method to compute its location and scale parameters from means and covariances. Therefore, regardless of its theoretical disadvantage, use of other distributions seems to be a practical necessity. - Highlights: • Statistical uncertainty propagation requires a sampling distribution. • The objective distribution of inherently positive quantities is determined. • The objectivity is based on the maximum entropy principle. • The maximum entropy distribution is the truncated normal distribution. • Applicability of log-normal or normal distribution approximation is limited.

  15. Current opinion about maximum entropy methods in Moessbauer spectroscopy

    International Nuclear Information System (INIS)

    Szymanski, K

    2009-01-01

    Current opinion about Maximum Entropy Methods in Moessbauer Spectroscopy is presented. The most important advantage offered by the method is the correct data processing under circumstances of incomplete information. Disadvantage is the sophisticated algorithm and its application to the specific problems.

  16. The maximum number of minimal codewords in long codes

    DEFF Research Database (Denmark)

    Alahmadi, A.; Aldred, R.E.L.; dela Cruz, R.

    2013-01-01

    Upper bounds on the maximum number of minimal codewords in a binary code follow from the theory of matroids. Random coding provides lower bounds. In this paper, we compare these bounds with analogous bounds for the cycle code of graphs. This problem (in the graphic case) was considered in 1981 by...

  17. Inverse feasibility problems of the inverse maximum flow problems

    Indian Academy of Sciences (India)

    199–209. c Indian Academy of Sciences. Inverse feasibility problems of the inverse maximum flow problems. ADRIAN DEACONU. ∗ and ELEONOR CIUREA. Department of Mathematics and Computer Science, Faculty of Mathematics and Informatics, Transilvania University of Brasov, Brasov, Iuliu Maniu st. 50,. Romania.

  18. Maximum Permissible Concentrations and Negligible Concentrations for pesticides

    NARCIS (Netherlands)

    Crommentuijn T; Kalf DF; Polder MD; Posthumus R; Plassche EJ van de; CSR

    1997-01-01

    Maximum Permissible Concentrations (MPCs) and Negligible Concentrations (NCs) derived for a series of pesticides are presented in this report. These MPCs and NCs are used by the Ministry of Housing, Spatial Planning and the Environment (VROM) to set Environmental Quality Objectives. For some of the

  19. Maximum Safety Regenerative Power Tracking for DC Traction Power Systems

    Directory of Open Access Journals (Sweden)

    Guifu Du

    2017-02-01

    Full Text Available Direct current (DC traction power systems are widely used in metro transport systems, with running rails usually being used as return conductors. When traction current flows through the running rails, a potential voltage known as “rail potential” is generated between the rails and ground. Currently, abnormal rises of rail potential exist in many railway lines during the operation of railway systems. Excessively high rail potentials pose a threat to human life and to devices connected to the rails. In this paper, the effect of regenerative power distribution on rail potential is analyzed. Maximum safety regenerative power tracking is proposed for the control of maximum absolute rail potential and energy consumption during the operation of DC traction power systems. The dwell time of multiple trains at each station and the trigger voltage of the regenerative energy absorbing device (READ are optimized based on an improved particle swarm optimization (PSO algorithm to manage the distribution of regenerative power. In this way, the maximum absolute rail potential and energy consumption of DC traction power systems can be reduced. The operation data of Guangzhou Metro Line 2 are used in the simulations, and the results show that the scheme can reduce the maximum absolute rail potential and energy consumption effectively and guarantee the safety in energy saving of DC traction power systems.

  20. Maximum Mass of Hybrid Stars in the Quark Bag Model

    Science.gov (United States)

    Alaverdyan, G. B.; Vartanyan, Yu. L.

    2017-12-01

    The effect of model parameters in the equation of state for quark matter on the magnitude of the maximum mass of hybrid stars is examined. Quark matter is described in terms of the extended MIT bag model including corrections for one-gluon exchange. For nucleon matter in the range of densities corresponding to the phase transition, a relativistic equation of state is used that is calculated with two-particle correlations taken into account based on using the Bonn meson-exchange potential. The Maxwell construction is used to calculate the characteristics of the first order phase transition and it is shown that for a fixed value of the strong interaction constant αs, the baryon concentrations of the coexisting phases grow monotonically as the bag constant B increases. It is shown that for a fixed value of the strong interaction constant αs, the maximum mass of a hybrid star increases as the bag constant B decreases. For a given value of the bag parameter B, the maximum mass rises as the strong interaction constant αs increases. It is shown that the configurations of hybrid stars with maximum masses equal to or exceeding the mass of the currently known most massive pulsar are possible for values of the strong interaction constant αs > 0.6 and sufficiently low values of the bag constant.

  1. Maximum-Entropy Inference with a Programmable Annealer

    Science.gov (United States)

    Chancellor, Nicholas; Szoke, Szilard; Vinci, Walter; Aeppli, Gabriel; Warburton, Paul A.

    2016-03-01

    Optimisation problems typically involve finding the ground state (i.e. the minimum energy configuration) of a cost function with respect to many variables. If the variables are corrupted by noise then this maximises the likelihood that the solution is correct. The maximum entropy solution on the other hand takes the form of a Boltzmann distribution over the ground and excited states of the cost function to correct for noise. Here we use a programmable annealer for the information decoding problem which we simulate as a random Ising model in a field. We show experimentally that finite temperature maximum entropy decoding can give slightly better bit-error-rates than the maximum likelihood approach, confirming that useful information can be extracted from the excited states of the annealer. Furthermore we introduce a bit-by-bit analytical method which is agnostic to the specific application and use it to show that the annealer samples from a highly Boltzmann-like distribution. Machines of this kind are therefore candidates for use in a variety of machine learning applications which exploit maximum entropy inference, including language processing and image recognition.

  2. Multilevel maximum likelihood estimation with application to covariance matrices

    Czech Academy of Sciences Publication Activity Database

    Turčičová, Marie; Mandel, J.; Eben, Kryštof

    Published online: 23 January ( 2018 ) ISSN 0361-0926 R&D Projects: GA ČR GA13-34856S Institutional support: RVO:67985807 Keywords : Fisher information * High dimension * Hierarchical maximum likelihood * Nested parameter spaces * Spectral diagonal covariance model * Sparse inverse covariance model Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 0.311, year: 2016

  3. Heat Convection at the Density Maximum Point of Water

    Science.gov (United States)

    Balta, Nuri; Korganci, Nuri

    2018-01-01

    Water exhibits a maximum in density at normal pressure at around 4° degree temperature. This paper demonstrates that during cooling, at around 4 °C, the temperature remains constant for a while because of heat exchange associated with convective currents inside the water. Superficial approach implies it as a new anomaly of water, but actually it…

  4. Combining Experiments and Simulations Using the Maximum Entropy Principle

    DEFF Research Database (Denmark)

    Boomsma, Wouter; Ferkinghoff-Borg, Jesper; Lindorff-Larsen, Kresten

    2014-01-01

    in the context of a simple example, after which we proceed with a real-world application in the field of molecular simulations, where the maximum entropy procedure has recently provided new insight. Given the limited accuracy of force fields, macromolecular simulations sometimes produce results...

  5. Optimal item discrimination and maximum information for logistic IRT models

    NARCIS (Netherlands)

    Veerkamp, W.J.J.; Veerkamp, Wim J.J.; Berger, Martijn P.F.; Berger, Martijn

    1999-01-01

    Items with the highest discrimination parameter values in a logistic item response theory model do not necessarily give maximum information. This paper derives discrimination parameter values, as functions of the guessing parameter and distances between person parameters and item difficulty, that

  6. Effect of Training Frequency on Maximum Expiratory Pressure

    Science.gov (United States)

    Anand, Supraja; El-Bashiti, Nour; Sapienza, Christine

    2012-01-01

    Purpose: To determine the effects of expiratory muscle strength training (EMST) frequency on maximum expiratory pressure (MEP). Method: We assigned 12 healthy participants to 2 groups of training frequency (3 days per week and 5 days per week). They completed a 4-week training program on an EMST trainer (Aspire Products, LLC). MEP was the primary…

  7. Assessment of the phytoremediation potential of Panicum maximum ...

    African Journals Online (AJOL)

    Obvious signs of phyto-toxicity however appeared in plants exposed to 120 ppm Pb2+ and Cd2+ at day twenty-three, suggesting that P. maximum may be a moderate metal accumulator. Keywords: phytoremediation, heavy metals, uptake, tissues, accumulator. African Journal of Biotechnology, Vol 13(19), 1979-1984 ...

  8. Atlantic Meridional Overturning Circulation During the Last Glacial Maximum.

    NARCIS (Netherlands)

    Lynch-Stieglitz, J.; Adkins, J.F.; Curry, W.B.; Dokken, T.; Hall, I.R.; Herguera, J.C.; Hirschi, J.J.-M.; Ivanova, E.V.; Kissel, C.; Marchal, O.; Marchitto, T.M.; McCave, I.N.; McManus, J.F.; Mulitza, S.; Ninnemann, U.; Peeters, F.J.C.; Yu, E.-F.; Zahn, R.

    2007-01-01

    The circulation of the deep Atlantic Ocean during the height of the last ice age appears to have been quite different from today. We review observations implying that Atlantic meridional overturning circulation during the Last Glacial Maximum was neither extremely sluggish nor an enhanced version of

  9. Modelling information flow along the human connectome using maximum flow.

    Science.gov (United States)

    Lyoo, Youngwook; Kim, Jieun E; Yoon, Sujung

    2018-01-01

    The human connectome is a complex network that transmits information between interlinked brain regions. Using graph theory, previously well-known network measures of integration between brain regions have been constructed under the key assumption that information flows strictly along the shortest paths possible between two nodes. However, it is now apparent that information does flow through non-shortest paths in many real-world networks such as cellular networks, social networks, and the internet. In the current hypothesis, we present a novel framework using the maximum flow to quantify information flow along all possible paths within the brain, so as to implement an analogy to network traffic. We hypothesize that the connection strengths of brain networks represent a limit on the amount of information that can flow through the connections per unit of time. This allows us to compute the maximum amount of information flow between two brain regions along all possible paths. Using this novel framework of maximum flow, previous network topological measures are expanded to account for information flow through non-shortest paths. The most important advantage of the current approach using maximum flow is that it can integrate the weighted connectivity data in a way that better reflects the real information flow of the brain network. The current framework and its concept regarding maximum flow provides insight on how network structure shapes information flow in contrast to graph theory, and suggests future applications such as investigating structural and functional connectomes at a neuronal level. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Novel TPPO Based Maximum Power Point Method for Photovoltaic System

    Directory of Open Access Journals (Sweden)

    ABBASI, M. A.

    2017-08-01

    Full Text Available Photovoltaic (PV system has a great potential and it is installed more when compared with other renewable energy sources nowadays. However, the PV system cannot perform optimally due to its solid reliance on climate conditions. Due to this dependency, PV system does not operate at its maximum power point (MPP. Many MPP tracking methods have been proposed for this purpose. One of these is the Perturb and Observe Method (P&O which is the most famous due to its simplicity, less cost and fast track. But it deviates from MPP in continuously changing weather conditions, especially in rapidly changing irradiance conditions. A new Maximum Power Point Tracking (MPPT method, Tetra Point Perturb and Observe (TPPO, has been proposed to improve PV system performance in changing irradiance conditions and the effects on characteristic curves of PV array module due to varying irradiance are delineated. The Proposed MPPT method has shown better results in increasing the efficiency of a PV system.

  11. Maximum power point tracker for photovoltaic power plants

    Science.gov (United States)

    Arcidiacono, V.; Corsi, S.; Lambri, L.

    The paper describes two different closed-loop control criteria for the maximum power point tracking of the voltage-current characteristic of a photovoltaic generator. The two criteria are discussed and compared, inter alia, with regard to the setting-up problems that they pose. Although a detailed analysis is not embarked upon, the paper also provides some quantitative information on the energy advantages obtained by using electronic maximum power point tracking systems, as compared with the situation in which the point of operation of the photovoltaic generator is not controlled at all. Lastly, the paper presents two high-efficiency MPPT converters for experimental photovoltaic plants of the stand-alone and the grid-interconnected type.

  12. On the maximum of wave surface of sea waves

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, B

    1980-01-01

    This article considers wave surface as a normal stationary random process to solve the estimation of the maximum of wave surface in a given time interval by means of the theoretical results of probability theory. The results are represented by formulas (13) to (19) in this article. It was proved in this article that when time interval approaches infinite, the formulas (3), (6) of E )eta max) that were derived from the references (Cartwright, Longuet-Higgins) can also be derived by asymptotic distribution of the maximum of wave surface provided by the article. The advantage of the results obtained from this point of view as compared with the results obtained from the references was discussed.

  13. Einstein-Dirac theory in spin maximum I

    International Nuclear Information System (INIS)

    Crumeyrolle, A.

    1975-01-01

    An unitary Einstein-Dirac theory, first in spin maximum 1, is constructed. An original feature of this article is that it is written without any tetrapod technics; basic notions and existence conditions for spinor structures on pseudo-Riemannian fibre bundles are only used. A coupling gravitation-electromagnetic field is pointed out, in the geometric setting of the tangent bundle over space-time. Generalized Maxwell equations for inductive media in presence of gravitational field are obtained. Enlarged Einstein-Schroedinger theory, gives a particular case of this E.D. theory. E. S. theory is a truncated E.D. theory in spin maximum 1. A close relation between torsion-vector and Schroedinger's potential exists and nullity of torsion-vector has a spinor meaning. Finally the Petiau-Duffin-Kemmer theory is incorporated in this geometric setting [fr

  14. GENERALIZATION OF RAYLEIGH MAXIMUM LIKELIHOOD DESPECKLING FILTER USING QUADRILATERAL KERNELS

    Directory of Open Access Journals (Sweden)

    S. Sridevi

    2013-02-01

    Full Text Available Speckle noise is the most prevalent noise in clinical ultrasound images. It visibly looks like light and dark spots and deduce the pixel intensity as murkiest. Gazing at fetal ultrasound images, the impact of edge and local fine details are more palpable for obstetricians and gynecologists to carry out prenatal diagnosis of congenital heart disease. A robust despeckling filter has to be contrived to proficiently suppress speckle noise and simultaneously preserve the features. The proposed filter is the generalization of Rayleigh maximum likelihood filter by the exploitation of statistical tools as tuning parameters and use different shapes of quadrilateral kernels to estimate the noise free pixel from neighborhood. The performance of various filters namely Median, Kuwahura, Frost, Homogenous mask filter and Rayleigh maximum likelihood filter are compared with the proposed filter in terms PSNR and image profile. Comparatively the proposed filters surpass the conventional filters.

  15. Thermoelectric cooler concepts and the limit for maximum cooling

    International Nuclear Information System (INIS)

    Seifert, W; Hinsche, N F; Pluschke, V

    2014-01-01

    The conventional analysis of a Peltier cooler approximates the material properties as independent of temperature using a constant properties model (CPM). Alternative concepts have been published by Bian and Shakouri (2006 Appl. Phys. Lett. 89 212101), Bian (et al 2007 Phys. Rev. B 75 245208) and Snyder et al (2012 Phys. Rev. B 86 045202). While Snyder's Thomson cooler concept results from a consideration of compatibility, the method of Bian et al focuses on the redistribution of heat. Thus, both approaches are based on different principles. In this paper we compare the new concepts to CPM and we reconsider the limit for maximum cooling. The results provide a new perspective on maximum cooling. (paper)

  16. Peyronie's Reconstruction for Maximum Length and Girth Gain: Geometrical Principles

    Directory of Open Access Journals (Sweden)

    Paulo H. Egydio

    2008-01-01

    Full Text Available Peyronie's disease has been associated with penile shortening and some degree of erectile dysfunction. Surgical reconstruction should be based on giving a functional penis, that is, rectifying the penis with rigidity enough to make the sexual intercourse. The procedure should be discussed preoperatively in terms of length and girth reconstruction in order to improve patient satisfaction. The tunical reconstruction for maximum penile length and girth restoration should be based on the maximum length of the dissected neurovascular bundle possible and the application of geometrical principles to define the precise site and size of tunical incision and grafting procedure. As penile rectification and rigidity are required to achieve complete functional restoration of the penis and 20 to 54% of patients experience associated erectile dysfunction, penile straightening alone may not be enough to provide complete functional restoration. Therefore, phosphodiesterase inhibitors, self-injection, or penile prosthesis may need to be added in some cases.

  17. On the maximum Q in feedback controlled subignited plasmas

    International Nuclear Information System (INIS)

    Anderson, D.; Hamnen, H.; Lisak, M.

    1990-01-01

    High Q operation in feedback controlled subignited fusion plasma requires the operating temperature to be close to the ignition temperature. In the present work we discuss technological and physical effects which may restrict this temperature difference. The investigation is based on a simplified, but still accurate, 0=D analytical analysis of the maximum Q of a subignited system. Particular emphasis is given to sawtooth ocsillations which complicate the interpretation of diagnostic neutron emission data into plasma temperatures and may imply an inherent lower bound on the temperature deviation from the ignition point. The estimated maximum Q is found to be marginal (Q = 10-20) from the point of view of a fusion reactor. (authors)

  18. Maximum Likelihood Compton Polarimetry with the Compton Spectrometer and Imager

    Energy Technology Data Exchange (ETDEWEB)

    Lowell, A. W.; Boggs, S. E; Chiu, C. L.; Kierans, C. A.; Sleator, C.; Tomsick, J. A.; Zoglauer, A. C. [Space Sciences Laboratory, University of California, Berkeley (United States); Chang, H.-K.; Tseng, C.-H.; Yang, C.-Y. [Institute of Astronomy, National Tsing Hua University, Taiwan (China); Jean, P.; Ballmoos, P. von [IRAP Toulouse (France); Lin, C.-H. [Institute of Physics, Academia Sinica, Taiwan (China); Amman, M. [Lawrence Berkeley National Laboratory (United States)

    2017-10-20

    Astrophysical polarization measurements in the soft gamma-ray band are becoming more feasible as detectors with high position and energy resolution are deployed. Previous work has shown that the minimum detectable polarization (MDP) of an ideal Compton polarimeter can be improved by ∼21% when an unbinned, maximum likelihood method (MLM) is used instead of the standard approach of fitting a sinusoid to a histogram of azimuthal scattering angles. Here we outline a procedure for implementing this maximum likelihood approach for real, nonideal polarimeters. As an example, we use the recent observation of GRB 160530A with the Compton Spectrometer and Imager. We find that the MDP for this observation is reduced by 20% when the MLM is used instead of the standard method.

  19. Optimal Portfolio Strategy under Rolling Economic Maximum Drawdown Constraints

    Directory of Open Access Journals (Sweden)

    Xiaojian Yu

    2014-01-01

    Full Text Available This paper deals with the problem of optimal portfolio strategy under the constraints of rolling economic maximum drawdown. A more practical strategy is developed by using rolling Sharpe ratio in computing the allocation proportion in contrast to existing models. Besides, another novel strategy named “REDP strategy” is further proposed, which replaces the rolling economic drawdown of the portfolio with the rolling economic drawdown of the risky asset. The simulation tests prove that REDP strategy can ensure the portfolio to satisfy the drawdown constraint and outperforms other strategies significantly. An empirical comparison research on the performances of different strategies is carried out by using the 23-year monthly data of SPTR, DJUBS, and 3-month T-bill. The investment cases of single risky asset and two risky assets are both studied in this paper. Empirical results indicate that the REDP strategy successfully controls the maximum drawdown within the given limit and performs best in both return and risk.

  20. Optimum detection for extracting maximum information from symmetric qubit sets

    International Nuclear Information System (INIS)

    Mizuno, Jun; Fujiwara, Mikio; Sasaki, Masahide; Akiba, Makoto; Kawanishi, Tetsuya; Barnett, Stephen M.

    2002-01-01

    We demonstrate a class of optimum detection strategies for extracting the maximum information from sets of equiprobable real symmetric qubit states of a single photon. These optimum strategies have been predicted by Sasaki et al. [Phys. Rev. A 59, 3325 (1999)]. The peculiar aspect is that the detections with at least three outputs suffice for optimum extraction of information regardless of the number of signal elements. The cases of ternary (or trine), quinary, and septenary polarization signals are studied where a standard von Neumann detection (a projection onto a binary orthogonal basis) fails to access the maximum information. Our experiments demonstrate that it is possible with present technologies to attain about 96% of the theoretical limit

  1. Effect of current on the maximum possible reward.

    Science.gov (United States)

    Gallistel, C R; Leon, M; Waraczynski, M; Hanau, M S

    1991-12-01

    Using a 2-lever choice paradigm with concurrent variable interval schedules of reward, it was found that when pulse frequency is increased, the preference-determining rewarding effect of 0.5-s trains of brief cathodal pulses delivered to the medial forebrain bundle of the rat saturates (stops increasing) at values ranging from 200 to 631 pulses/s (pps). Raising the current lowered the saturation frequency, which confirms earlier, more extensive findings showing that the rewarding effect of short trains saturates at pulse frequencies that vary from less than 100 pps to more than 800 pps, depending on the current. It was also found that the maximum possible reward--the magnitude of the reward at or beyond the saturation pulse frequency--increases with increasing current. Thus, increasing the current reduces the saturation frequency but increases the subjective magnitude of the maximum possible reward.

  2. Jarzynski equality in the context of maximum path entropy

    Science.gov (United States)

    González, Diego; Davis, Sergio

    2017-06-01

    In the global framework of finding an axiomatic derivation of nonequilibrium Statistical Mechanics from fundamental principles, such as the maximum path entropy - also known as Maximum Caliber principle -, this work proposes an alternative derivation of the well-known Jarzynski equality, a nonequilibrium identity of great importance today due to its applications to irreversible processes: biological systems (protein folding), mechanical systems, among others. This equality relates the free energy differences between two equilibrium thermodynamic states with the work performed when going between those states, through an average over a path ensemble. In this work the analysis of Jarzynski's equality will be performed using the formalism of inference over path space. This derivation highlights the wide generality of Jarzynski's original result, which could even be used in non-thermodynamical settings such as social systems, financial and ecological systems.

  3. Maximum mass-particle velocities in Kantor's information mechanics

    International Nuclear Information System (INIS)

    Sverdlik, D.I.

    1989-01-01

    Kantor's information mechanics links phenomena previously regarded as not treatable by a single theory. It is used here to calculate the maximum velocities υ m of single particles. For the electron, υ m /c ∼ 1 - 1.253814 x 10 -77 . The maximum υ m corresponds to υ m /c ∼ 1 -1.097864 x 10 -122 for a single mass particle with a rest mass of 3.078496 x 10 -5 g. This is the fastest that matter can move. Either information mechanics or classical mechanics can be used to show that υ m is less for heavier particles. That υ m is less for lighter particles can be deduced from an information mechanics argument alone

  4. Maximum field capability of energy saver superconducting magnets

    International Nuclear Information System (INIS)

    Turkot, F.; Cooper, W.E.; Hanft, R.; McInturff, A.

    1983-01-01

    At an energy of 1 TeV the superconducting cable in the Energy Saver dipole magnets will be operating at ca. 96% of its nominal short sample limit; the corresponding number in the quadrupole magnets will be 81%. All magnets for the Saver are individually tested for maximum current capability under two modes of operation; some 900 dipoles and 275 quadrupoles have now been measured. The dipole winding is composed of four individually wound coils which in general come from four different reels of cable. As part of the magnet fabrication quality control a short piece of cable from both ends of each reel has its critical current measured at 5T and 4.3K. In this paper the authors describe and present the statistical results of the maximum field tests (including quench and cycle) on Saver dipole and quadrupole magnets and explore the correlation of these tests with cable critical current

  5. Algorithms of maximum likelihood data clustering with applications

    Science.gov (United States)

    Giada, Lorenzo; Marsili, Matteo

    2002-12-01

    We address the problem of data clustering by introducing an unsupervised, parameter-free approach based on maximum likelihood principle. Starting from the observation that data sets belonging to the same cluster share a common information, we construct an expression for the likelihood of any possible cluster structure. The likelihood in turn depends only on the Pearson's coefficient of the data. We discuss clustering algorithms that provide a fast and reliable approximation to maximum likelihood configurations. Compared to standard clustering methods, our approach has the advantages that (i) it is parameter free, (ii) the number of clusters need not be fixed in advance and (iii) the interpretation of the results is transparent. In order to test our approach and compare it with standard clustering algorithms, we analyze two very different data sets: time series of financial market returns and gene expression data. We find that different maximization algorithms produce similar cluster structures whereas the outcome of standard algorithms has a much wider variability.

  6. Optimal Control of Polymer Flooding Based on Maximum Principle

    Directory of Open Access Journals (Sweden)

    Yang Lei

    2012-01-01

    Full Text Available Polymer flooding is one of the most important technologies for enhanced oil recovery (EOR. In this paper, an optimal control model of distributed parameter systems (DPSs for polymer injection strategies is established, which involves the performance index as maximum of the profit, the governing equations as the fluid flow equations of polymer flooding, and the inequality constraint as the polymer concentration limitation. To cope with the optimal control problem (OCP of this DPS, the necessary conditions for optimality are obtained through application of the calculus of variations and Pontryagin’s weak maximum principle. A gradient method is proposed for the computation of optimal injection strategies. The numerical results of an example illustrate the effectiveness of the proposed method.

  7. Maximum heat flux in boiling in a large volume

    International Nuclear Information System (INIS)

    Bergmans, Dzh.

    1976-01-01

    Relationships are derived for the maximum heat flux qsub(max) without basing on the assumptions of both the critical vapor velocity corresponding to the zero growth rate, and planar interface. The Helmholz nonstability analysis of vapor column has been made to this end. The results of this examination have been used to find maximum heat flux for spherical, cylindric and flat plate heaters. The conventional hydrodynamic theory was found to be incapable of producing a satisfactory explanation of qsub(max) for small heaters. The occurrence of qsub(max) in the present case can be explained by inadequate removal of vapor output from the heater (the force of gravity for cylindrical heaters and surface tension for the spherical ones). In case of flat plate heater the qsub(max) value can be explained with the help of the hydrodynamic theory

  8. A Maximum Principle for SDEs of Mean-Field Type

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, Daniel, E-mail: danieand@math.kth.se; Djehiche, Boualem, E-mail: boualem@math.kth.se [Royal Institute of Technology, Department of Mathematics (Sweden)

    2011-06-15

    We study the optimal control of a stochastic differential equation (SDE) of mean-field type, where the coefficients are allowed to depend on some functional of the law as well as the state of the process. Moreover the cost functional is also of mean-field type, which makes the control problem time inconsistent in the sense that the Bellman optimality principle does not hold. Under the assumption of a convex action space a maximum principle of local form is derived, specifying the necessary conditions for optimality. These are also shown to be sufficient under additional assumptions. This maximum principle differs from the classical one, where the adjoint equation is a linear backward SDE, since here the adjoint equation turns out to be a linear mean-field backward SDE. As an illustration, we apply the result to the mean-variance portfolio selection problem.

  9. A Maximum Principle for SDEs of Mean-Field Type

    International Nuclear Information System (INIS)

    Andersson, Daniel; Djehiche, Boualem

    2011-01-01

    We study the optimal control of a stochastic differential equation (SDE) of mean-field type, where the coefficients are allowed to depend on some functional of the law as well as the state of the process. Moreover the cost functional is also of mean-field type, which makes the control problem time inconsistent in the sense that the Bellman optimality principle does not hold. Under the assumption of a convex action space a maximum principle of local form is derived, specifying the necessary conditions for optimality. These are also shown to be sufficient under additional assumptions. This maximum principle differs from the classical one, where the adjoint equation is a linear backward SDE, since here the adjoint equation turns out to be a linear mean-field backward SDE. As an illustration, we apply the result to the mean-variance portfolio selection problem.

  10. Rumor Identification with Maximum Entropy in MicroNet

    Directory of Open Access Journals (Sweden)

    Suisheng Yu

    2017-01-01

    Full Text Available The widely used applications of Microblog, WeChat, and other social networking platforms (that we call MicroNet shorten the period of information dissemination and expand the range of information dissemination, which allows rumors to cause greater harm and have more influence. A hot topic in the information dissemination field is how to identify and block rumors. Based on the maximum entropy model, this paper constructs the recognition mechanism of rumor information in the micronetwork environment. First, based on the information entropy theory, we obtained the characteristics of rumor information using the maximum entropy model. Next, we optimized the original classifier training set and the feature function to divide the information into rumors and nonrumors. Finally, the experimental simulation results show that the rumor identification results using this method are better than the original classifier and other related classification methods.

  11. Maximum Power Point Tracking Based on Sliding Mode Control

    Directory of Open Access Journals (Sweden)

    Nimrod Vázquez

    2015-01-01

    Full Text Available Solar panels, which have become a good choice, are used to generate and supply electricity in commercial and residential applications. This generated power starts with the solar cells, which have a complex relationship between solar irradiation, temperature, and output power. For this reason a tracking of the maximum power point is required. Traditionally, this has been made by considering just current and voltage conditions at the photovoltaic panel; however, temperature also influences the process. In this paper the voltage, current, and temperature in the PV system are considered to be a part of a sliding surface for the proposed maximum power point tracking; this means a sliding mode controller is applied. Obtained results gave a good dynamic response, as a difference from traditional schemes, which are only based on computational algorithms. A traditional algorithm based on MPPT was added in order to assure a low steady state error.

  12. Design and Implementation of Photovoltaic Maximum Power Point Tracking Controller

    Directory of Open Access Journals (Sweden)

    Fawaz S. Abdullah

    2018-03-01

    Full Text Available  The power supplied by any solar array depends upon the environmental conditions as weather conditions (temperature and radiation intensity and the incident angle of the radiant source. The work aims to study the maximum power tracking schemes that used to compare the system performance without and with different types of controllers. The maximum power points of the solar panel under test studied and compared with two controller's types.  The first controller is the proportional- integral - derivative controller type and the second is the perturbation and observation algorithm controller. The associated converter system is a microcontroller based type, whereas the results studied and compared of greatest power point of the Photovoltaic panels under the different two controllers. The experimental tests results compared with simulation results to verify accurate performance.

  13. Maximum credible accident analysis for TR-2 reactor conceptual design

    International Nuclear Information System (INIS)

    Manopulo, E.

    1981-01-01

    A new reactor, TR-2, of 5 MW, designed in cooperation with CEN/GRENOBLE is under construction in the open pool of TR-1 reactor of 1 MW set up by AMF atomics at the Cekmece Nuclear Research and Training Center. In this report the fission product inventory and doses released after the maximum credible accident have been studied. The diffusion of the gaseous fission products to the environment and the potential radiation risks to the population have been evaluated

  14. Maximum Entropy Estimation of Transition Probabilities of Reversible Markov Chains

    Directory of Open Access Journals (Sweden)

    Erik Van der Straeten

    2009-11-01

    Full Text Available In this paper, we develop a general theory for the estimation of the transition probabilities of reversible Markov chains using the maximum entropy principle. A broad range of physical models can be studied within this approach. We use one-dimensional classical spin systems to illustrate the theoretical ideas. The examples studied in this paper are: the Ising model, the Potts model and the Blume-Emery-Griffiths model.

  15. Precise charge density studies by maximum entropy method

    CERN Document Server

    Takata, M

    2003-01-01

    For the production research and development of nanomaterials, their structural information is indispensable. Recently, a sophisticated analytical method, which is based on information theory, the Maximum Entropy Method (MEM) using synchrotron radiation powder data, has been successfully applied to determine precise charge densities of metallofullerenes and nanochannel microporous compounds. The results revealed various endohedral natures of metallofullerenes and one-dimensional array formation of adsorbed gas molecules in nanochannel microporous compounds. The concept of MEM analysis was also described briefly. (author)

  16. PNNL: A Supervised Maximum Entropy Approach to Word Sense Disambiguation

    Energy Technology Data Exchange (ETDEWEB)

    Tratz, Stephen C.; Sanfilippo, Antonio P.; Gregory, Michelle L.; Chappell, Alan R.; Posse, Christian; Whitney, Paul D.

    2007-06-23

    In this paper, we described the PNNL Word Sense Disambiguation system as applied to the English All-Word task in Se-mEval 2007. We use a supervised learning approach, employing a large number of features and using Information Gain for dimension reduction. Our Maximum Entropy approach combined with a rich set of features produced results that are significantly better than baseline and are the highest F-score for the fined-grained English All-Words subtask.

  17. The maximum entropy method of moments and Bayesian probability theory

    Science.gov (United States)

    Bretthorst, G. Larry

    2013-08-01

    The problem of density estimation occurs in many disciplines. For example, in MRI it is often necessary to classify the types of tissues in an image. To perform this classification one must first identify the characteristics of the tissues to be classified. These characteristics might be the intensity of a T1 weighted image and in MRI many other types of characteristic weightings (classifiers) may be generated. In a given tissue type there is no single intensity that characterizes the tissue, rather there is a distribution of intensities. Often this distributions can be characterized by a Gaussian, but just as often it is much more complicated. Either way, estimating the distribution of intensities is an inference problem. In the case of a Gaussian distribution, one must estimate the mean and standard deviation. However, in the Non-Gaussian case the shape of the density function itself must be inferred. Three common techniques for estimating density functions are binned histograms [1, 2], kernel density estimation [3, 4], and the maximum entropy method of moments [5, 6]. In the introduction, the maximum entropy method of moments will be reviewed. Some of its problems and conditions under which it fails will be discussed. Then in later sections, the functional form of the maximum entropy method of moments probability distribution will be incorporated into Bayesian probability theory. It will be shown that Bayesian probability theory solves all of the problems with the maximum entropy method of moments. One gets posterior probabilities for the Lagrange multipliers, and, finally, one can put error bars on the resulting estimated density function.

  18. Bayesian interpretation of Generalized empirical likelihood by maximum entropy

    OpenAIRE

    Rochet , Paul

    2011-01-01

    We study a parametric estimation problem related to moment condition models. As an alternative to the generalized empirical likelihood (GEL) and the generalized method of moments (GMM), a Bayesian approach to the problem can be adopted, extending the MEM procedure to parametric moment conditions. We show in particular that a large number of GEL estimators can be interpreted as a maximum entropy solution. Moreover, we provide a more general field of applications by proving the method to be rob...

  19. The calculation of maximum permissible exposure levels for laser radiation

    International Nuclear Information System (INIS)

    Tozer, B.A.

    1979-01-01

    The maximum permissible exposure data of the revised standard BS 4803 are presented as a set of decision charts which ensure that the user automatically takes into account such details as pulse length and pulse pattern, limiting angular subtense, combinations of multiple wavelength and/or multiple pulse lengths, etc. The two decision charts given are for the calculation of radiation hazards to skin and eye respectively. (author)

  20. The discrete maximum principle for Galerkin solutions of elliptic problems

    Czech Academy of Sciences Publication Activity Database

    Vejchodský, Tomáš

    2012-01-01

    Roč. 10, č. 1 (2012), s. 25-43 ISSN 1895-1074 R&D Projects: GA AV ČR IAA100760702 Institutional research plan: CEZ:AV0Z10190503 Keywords : discrete maximum principle * monotone methods * Galerkin solution Subject RIV: BA - General Mathematics Impact factor: 0.405, year: 2012 http://www.springerlink.com/content/x73624wm23x4wj26

  1. ON A GENERALIZATION OF THE MAXIMUM ENTROPY THEOREM OF BURG

    Directory of Open Access Journals (Sweden)

    JOSÉ MARCANO

    2017-01-01

    Full Text Available In this article we introduce some matrix manipulations that allow us to obtain a version of the original Christoffel-Darboux formula, which is of interest in many applications of linear algebra. Using these developments matrix and Jensen’s inequality, we obtain the main result of this proposal, which is the generalization of the maximum entropy theorem of Burg for multivariate processes.

  2. Determing and monitoring of maximum permissible power for HWRR-3

    International Nuclear Information System (INIS)

    Jia Zhanli; Xiao Shigang; Jin Huajin; Lu Changshen

    1987-01-01

    The operating power of a reactor is an important parameter to be monitored. This report briefly describes the determining and monitoring of maximum permissiable power for HWRR-3. The calculating method is described, and the result of calculation and analysis of error are also given. On-line calculation and real time monitoring have been realized at the heavy water reactor. It provides the reactor with a real time and reliable supervision. This makes operation convenient and increases reliability

  3. Maximum Likelihood, Consistency and Data Envelopment Analysis: A Statistical Foundation

    OpenAIRE

    Rajiv D. Banker

    1993-01-01

    This paper provides a formal statistical basis for the efficiency evaluation techniques of data envelopment analysis (DEA). DEA estimators of the best practice monotone increasing and concave production function are shown to be also maximum likelihood estimators if the deviation of actual output from the efficient output is regarded as a stochastic variable with a monotone decreasing probability density function. While the best practice frontier estimator is biased below the theoretical front...

  4. A maximum modulus theorem for the Oseen problem

    Czech Academy of Sciences Publication Activity Database

    Kračmar, S.; Medková, Dagmar; Nečasová, Šárka; Varnhorn, W.

    2013-01-01

    Roč. 192, č. 6 (2013), s. 1059-1076 ISSN 0373-3114 R&D Projects: GA ČR(CZ) GAP201/11/1304; GA MŠk LC06052 Institutional research plan: CEZ:AV0Z10190503 Keywords : Oseen problem * maximum modulus theorem * Oseen potentials Subject RIV: BA - General Mathematics Impact factor: 0.909, year: 2013 http://link.springer.com/article/10.1007%2Fs10231-012-0258-x

  5. Seeking the epoch of maximum luminosity for dusty quasars

    International Nuclear Information System (INIS)

    Vardanyan, Valeri; Weedman, Daniel; Sargsyan, Lusine

    2014-01-01

    Infrared luminosities νL ν (7.8 μm) arising from dust reradiation are determined for Sloan Digital Sky Survey (SDSS) quasars with 1.4 maximum at any redshift z < 5, reaching a plateau for z ≳ 3 with maximum luminosity νL ν (7.8 μm) ≳ 10 47 erg s –1 ; luminosity functions show one quasar Gpc –3 having νL ν (7.8 μm) > 10 46.6 erg s –1 for all 2 maximum luminosity has not yet been identified at any redshift below 5. The most ultraviolet luminous quasars, defined by rest frame νL ν (0.25 μm), have the largest values of the ratio νL ν (0.25 μm)/νL ν (7.8 μm) with a maximum ratio at z = 2.9. From these results, we conclude that the quasars most luminous in the ultraviolet have the smallest dust content and appear luminous primarily because of lessened extinction. Observed ultraviolet/infrared luminosity ratios are used to define 'obscured' quasars as those having >5 mag of ultraviolet extinction. We present a new summary of obscured quasars discovered with the Spitzer Infrared Spectrograph and determine the infrared luminosity function of these obscured quasars at z ∼ 2.1. This is compared with infrared luminosity functions of optically discovered, unobscured quasars in the SDSS and in the AGN and Galaxy Evolution Survey. The comparison indicates comparable numbers of obscured and unobscured quasars at z ∼ 2.1 with a possible excess of obscured quasars at fainter luminosities.

  6. Industry guidelines for the calibration of maximum anemometers

    Energy Technology Data Exchange (ETDEWEB)

    Bailey, B.H. [AWS Scientific, Inc., Albany, NY (United States)

    1996-12-31

    The purpose of this paper is to report on a framework of guidelines for the calibration of the Maximum Type 40 anemometer. This anemometer model is the wind speed sensor of choice in the majority of wind resource assessment programs in the U.S. These guidelines were established by the Utility Wind Resource Assessment Program. In addition to providing guidelines for anemometers, the appropriate use of non-calibrated anemometers is also discussed. 14 refs., 1 tab.

  7. Max '91: Flare research at the next solar maximum

    Science.gov (United States)

    Dennis, Brian; Canfield, Richard; Bruner, Marilyn; Emslie, Gordon; Hildner, Ernest; Hudson, Hugh; Hurford, Gordon; Lin, Robert; Novick, Robert; Tarbell, Ted

    1988-01-01

    To address the central scientific questions surrounding solar flares, coordinated observations of electromagnetic radiation and energetic particles must be made from spacecraft, balloons, rockets, and ground-based observatories. A program to enhance capabilities in these areas in preparation for the next solar maximum in 1991 is recommended. The major scientific issues are described, and required observations and coordination of observations and analyses are detailed. A program plan and conceptual budgets are provided.

  8. Max '91: flare research at the next solar maximum

    International Nuclear Information System (INIS)

    Dennis, B.; Canfield, R.; Bruner, M.

    1988-01-01

    To address the central scientific questions surrounding solar flares, coordinated observations of electromagnetic radiation and energetic particles must be made from spacecraft, balloons, rockets, and ground-based observatories. A program to enhance capabilities in these areas in preparation for the next solar maximum in 1991 is recommended. The major scientific issues are described, and required observations and coordination of observations and analyses are detailed. A program plan and conceptual budgets are provided

  9. Maximum likelihood convolutional decoding (MCD) performance due to system losses

    Science.gov (United States)

    Webster, L.

    1976-01-01

    A model for predicting the computational performance of a maximum likelihood convolutional decoder (MCD) operating in a noisy carrier reference environment is described. This model is used to develop a subroutine that will be utilized by the Telemetry Analysis Program to compute the MCD bit error rate. When this computational model is averaged over noisy reference phase errors using a high-rate interpolation scheme, the results are found to agree quite favorably with experimental measurements.

  10. Maximum total organic carbon limit for DWPF melter feed

    International Nuclear Information System (INIS)

    Choi, A.S.

    1995-01-01

    DWPF recently decided to control the potential flammability of melter off-gas by limiting the total carbon content in the melter feed and maintaining adequate conditions for combustion in the melter plenum. With this new strategy, all the LFL analyzers and associated interlocks and alarms were removed from both the primary and backup melter off-gas systems. Subsequently, D. Iverson of DWPF- T ampersand E requested that SRTC determine the maximum allowable total organic carbon (TOC) content in the melter feed which can be implemented as part of the Process Requirements for melter feed preparation (PR-S04). The maximum TOC limit thus determined in this study was about 24,000 ppm on an aqueous slurry basis. At the TOC levels below this, the peak concentration of combustible components in the quenched off-gas will not exceed 60 percent of the LFL during off-gas surges of magnitudes up to three times nominal, provided that the melter plenum temperature and the air purge rate to the BUFC are monitored and controlled above 650 degrees C and 220 lb/hr, respectively. Appropriate interlocks should discontinue the feeding when one or both of these conditions are not met. Both the magnitude and duration of an off-gas surge have a major impact on the maximum TOC limit, since they directly affect the melter plenum temperature and combustion. Although the data obtained during recent DWPF melter startup tests showed that the peak magnitude of a surge can be greater than three times nominal, the observed duration was considerably shorter, on the order of several seconds. The long surge duration assumed in this study has a greater impact on the plenum temperature than the peak magnitude, thus making the maximum TOC estimate conservative. Two models were used to make the necessary calculations to determine the TOC limit

  11. The Maximum Entropy Principle and the Modern Portfolio Theory

    Directory of Open Access Journals (Sweden)

    Ailton Cassetari

    2003-12-01

    Full Text Available In this work, a capital allocation methodology base don the Principle of Maximum Entropy was developed. The Shannons entropy is used as a measure, concerning the Modern Portfolio Theory, are also discuted. Particularly, the methodology is tested making a systematic comparison to: 1 the mean-variance (Markovitz approach and 2 the mean VaR approach (capital allocations based on the Value at Risk concept. In principle, such confrontations show the plausibility and effectiveness of the developed method.

  12. Occurrence and Impact of Insects in Maximum Growth Plantations

    Energy Technology Data Exchange (ETDEWEB)

    Nowak, J.T.; Berisford, C.W.

    2001-01-01

    Investigation of the relationships between intensive management practices and insect infestation using maximum growth potential studies of loblolly pine constructed over five years using a hierarchy of cultural treatments-monitoring differences in growth and insect infestation levels related to the increasing management intensities. This study shows that tree fertilization can increase coneworm infestation and demonstrated that tip moth management tree growth, at least initially.

  13. Statistical Bias in Maximum Likelihood Estimators of Item Parameters.

    Science.gov (United States)

    1982-04-01

    34 a> E r’r~e r ,C Ie I# ne,..,.rVi rnd Id.,flfv b1 - bindk numb.r) I; ,t-i i-cd I ’ tiie bias in the maximum likelihood ,st i- i;, ’ t iIeiIrs in...NTC, IL 60088 Psychometric Laboratory University of North Carolina I ERIC Facility-Acquisitions Davie Hall 013A 4833 Rugby Avenue Chapel Hill, NC

  14. Investigation on maximum transition temperature of phonon mediated superconductivity

    Energy Technology Data Exchange (ETDEWEB)

    Fusui, L; Yi, S; Yinlong, S [Physics Department, Beijing University (CN)

    1989-05-01

    Three model effective phonon spectra are proposed to get plots of {ital T}{sub {ital c}}-{omega} adn {lambda}-{omega}. It can be concluded that there is no maximum limit of {ital T}{sub {ital c}} in phonon mediated superconductivity for reasonable values of {lambda}. The importance of high frequency LO phonon is also emphasized. Some discussions on high {ital T}{sub {ital c}} are given.

  15. Study of forecasting maximum demand of electric power

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, B.C.; Hwang, Y.J. [Korea Energy Economics Institute, Euiwang (Korea, Republic of)

    1997-08-01

    As far as the past performances of power supply and demand in Korea is concerned, one of the striking phenomena is that there have been repeated periodic surpluses and shortages of power generation facilities. Precise assumption and prediction of power demands is the basic work in establishing a supply plan and carrying out the right policy since facilities investment of the power generation industry requires a tremendous amount of capital and a long construction period. The purpose of this study is to study a model for the inference and prediction of a more precise maximum demand under these backgrounds. The non-parametric model considered in this study, paying attention to meteorological factors such as temperature and humidity, does not have a simple proportionate relationship with the maximum power demand, but affects it through mutual complicated nonlinear interaction. I used the non-parametric inference technique by introducing meteorological effects without importing any literal assumption on the interaction of temperature and humidity preliminarily. According to the analysis result, it is found that the non-parametric model that introduces the number of tropical nights which shows the continuity of the meteorological effect has better prediction power than the linear model. The non- parametric model that considers both the number of tropical nights and the number of cooling days at the same time is a model for predicting maximum demand. 7 refs., 6 figs., 9 tabs.

  16. Maximum Work of Free-Piston Stirling Engine Generators

    Science.gov (United States)

    Kojima, Shinji

    2017-04-01

    Using the method of adjoint equations described in Ref. [1], we have calculated the maximum thermal efficiencies that are theoretically attainable by free-piston Stirling and Carnot engine generators by considering the work loss due to friction and Joule heat. The net work done by the Carnot cycle is negative even when the duration of heat addition is optimized to give the maximum amount of heat addition, which is the same situation for the Brayton cycle described in our previous paper. For the Stirling cycle, the net work done is positive, and the thermal efficiency is greater than that of the Otto cycle described in our previous paper by a factor of about 2.7-1.4 for compression ratios of 5-30. The Stirling cycle is much better than the Otto, Brayton, and Carnot cycles. We have found that the optimized piston trajectories of the isothermal, isobaric, and adiabatic processes are the same when the compression ratio and the maximum volume of the same working fluid of the three processes are the same, which has facilitated the present analysis because the optimized piston trajectories of the Carnot and Stirling cycles are the same as those of the Brayton and Otto cycles, respectively.

  17. Erich Regener and the ionisation maximum of the atmosphere

    Science.gov (United States)

    Carlson, P.; Watson, A. A.

    2014-12-01

    In the 1930s the German physicist Erich Regener (1881-1955) did important work on the measurement of the rate of production of ionisation deep under water and in the atmosphere. Along with one of his students, Georg Pfotzer, he discovered the altitude at which the production of ionisation in the atmosphere reaches a maximum, often, but misleadingly, called the Pfotzer maximum. Regener was one of the first to estimate the energy density of cosmic rays, an estimate that was used by Baade and Zwicky to bolster their postulate that supernovae might be their source. Yet Regener's name is less recognised by present-day cosmic ray physicists than it should be, largely because in 1937 he was forced to take early retirement by the National Socialists as his wife had Jewish ancestors. In this paper we briefly review his work on cosmic rays and recommend an alternative naming of the ionisation maximum. The influence that Regener had on the field through his son, his son-in-law, his grandsons and his students, and through his links with Rutherford's group in Cambridge, is discussed in an appendix. Regener was nominated for the Nobel Prize in Physics by Schrödinger in 1938. He died in 1955 at the age of 73.

  18. Mid-depth temperature maximum in an estuarine lake

    Science.gov (United States)

    Stepanenko, V. M.; Repina, I. A.; Artamonov, A. Yu; Gorin, S. L.; Lykossov, V. N.; Kulyamin, D. V.

    2018-03-01

    The mid-depth temperature maximum (TeM) was measured in an estuarine Bol’shoi Vilyui Lake (Kamchatka peninsula, Russia) in summer 2015. We applied 1D k-ɛ model LAKE to the case, and found it successfully simulating the phenomenon. We argue that the main prerequisite for mid-depth TeM development is a salinity increase below the freshwater mixed layer, sharp enough in order to increase the temperature with depth not to cause convective mixing and double diffusion there. Given that this condition is satisfied, the TeM magnitude is controlled by physical factors which we identified as: radiation absorption below the mixed layer, mixed-layer temperature dynamics, vertical heat conduction and water-sediments heat exchange. In addition to these, we formulate the mechanism of temperature maximum ‘pumping’, resulting from the phase shift between diurnal cycles of mixed-layer depth and temperature maximum magnitude. Based on the LAKE model results we quantify the contribution of the above listed mechanisms and find their individual significance highly sensitive to water turbidity. Relying on physical mechanisms identified we define environmental conditions favouring the summertime TeM development in salinity-stratified lakes as: small-mixed layer depth (roughly, ~wind and cloudless weather. We exemplify the effect of mixed-layer depth on TeM by a set of selected lakes.

  19. An Efficient Algorithm for the Maximum Distance Problem

    Directory of Open Access Journals (Sweden)

    Gabrielle Assunta Grün

    2001-12-01

    Full Text Available Efficient algorithms for temporal reasoning are essential in knowledge-based systems. This is central in many areas of Artificial Intelligence including scheduling, planning, plan recognition, and natural language understanding. As such, scalability is a crucial consideration in temporal reasoning. While reasoning in the interval algebra is NP-complete, reasoning in the less expressive point algebra is tractable. In this paper, we explore an extension to the work of Gerevini and Schubert which is based on the point algebra. In their seminal framework, temporal relations are expressed as a directed acyclic graph partitioned into chains and supported by a metagraph data structure, where time points or events are represented by vertices, and directed edges are labelled with < or ≤. They are interested in fast algorithms for determining the strongest relation between two events. They begin by developing fast algorithms for the case where all points lie on a chain. In this paper, we are interested in a generalization of this, namely we consider the problem of finding the maximum ``distance'' between two vertices in a chain ; this problem arises in real world applications such as in process control and crew scheduling. We describe an O(n time preprocessing algorithm for the maximum distance problem on chains. It allows queries for the maximum number of < edges between two vertices to be answered in O(1 time. This matches the performance of the algorithm of Gerevini and Schubert for determining the strongest relation holding between two vertices in a chain.

  20. Maximum Aerobic Capacity of Underground Coal Miners in India

    Directory of Open Access Journals (Sweden)

    Ratnadeep Saha

    2011-01-01

    Full Text Available Miners fitness test was assessed in terms of determination of maximum aerobic capacity by an indirect method following a standard step test protocol before going down to mine by taking into consideration of heart rates (Telemetric recording and oxygen consumption of the subjects (Oxylog-II during exercise at different working rates. Maximal heart rate was derived as 220−age. Coal miners reported a maximum aerobic capacity within a range of 35–38.3 mL/kg/min. It also revealed that oldest miners (50–59 yrs had a lowest maximal oxygen uptake (34.2±3.38 mL/kg/min compared to (42.4±2.03 mL/kg/min compared to (42.4±2.03 mL/kg/min the youngest group (20–29 yrs. It was found to be negatively correlated with age (r=−0.55 and −0.33 for younger and older groups respectively and directly associated with the body weight of the subjects (r=0.57 – 0.68, P≤0.001. Carriers showed maximum cardio respiratory capacity compared to other miners. Indian miners VO2max was found to be lower both compared to their abroad mining counterparts and various other non-mining occupational working groups in India.

  1. Exact parallel maximum clique algorithm for general and protein graphs.

    Science.gov (United States)

    Depolli, Matjaž; Konc, Janez; Rozman, Kati; Trobec, Roman; Janežič, Dušanka

    2013-09-23

    A new exact parallel maximum clique algorithm MaxCliquePara, which finds the maximum clique (the fully connected subgraph) in undirected general and protein graphs, is presented. First, a new branch and bound algorithm for finding a maximum clique on a single computer core, which builds on ideas presented in two published state of the art sequential algorithms is implemented. The new sequential MaxCliqueSeq algorithm is faster than the reference algorithms on both DIMACS benchmark graphs as well as on protein-derived product graphs used for protein structural comparisons. Next, the MaxCliqueSeq algorithm is parallelized by splitting the branch-and-bound search tree to multiple cores, resulting in MaxCliquePara algorithm. The ability to exploit all cores efficiently makes the new parallel MaxCliquePara algorithm markedly superior to other tested algorithms. On a 12-core computer, the parallelization provides up to 2 orders of magnitude faster execution on the large DIMACS benchmark graphs and up to an order of magnitude faster execution on protein product graphs. The algorithms are freely accessible on http://commsys.ijs.si/~matjaz/maxclique.

  2. Maximum likelihood as a common computational framework in tomotherapy

    International Nuclear Information System (INIS)

    Olivera, G.H.; Shepard, D.M.; Reckwerdt, P.J.; Ruchala, K.; Zachman, J.; Fitchard, E.E.; Mackie, T.R.

    1998-01-01

    Tomotherapy is a dose delivery technique using helical or axial intensity modulated beams. One of the strengths of the tomotherapy concept is that it can incorporate a number of processes into a single piece of equipment. These processes include treatment optimization planning, dose reconstruction and kilovoltage/megavoltage image reconstruction. A common computational technique that could be used for all of these processes would be very appealing. The maximum likelihood estimator, originally developed for emission tomography, can serve as a useful tool in imaging and radiotherapy. We believe that this approach can play an important role in the processes of optimization planning, dose reconstruction and kilovoltage and/or megavoltage image reconstruction. These processes involve computations that require comparable physical methods. They are also based on equivalent assumptions, and they have similar mathematical solutions. As a result, the maximum likelihood approach is able to provide a common framework for all three of these computational problems. We will demonstrate how maximum likelihood methods can be applied to optimization planning, dose reconstruction and megavoltage image reconstruction in tomotherapy. Results for planning optimization, dose reconstruction and megavoltage image reconstruction will be presented. Strengths and weaknesses of the methodology are analysed. Future directions for this work are also suggested. (author)

  3. Maximum-confidence discrimination among symmetric qudit states

    International Nuclear Information System (INIS)

    Jimenez, O.; Solis-Prosser, M. A.; Delgado, A.; Neves, L.

    2011-01-01

    We study the maximum-confidence (MC) measurement strategy for discriminating among nonorthogonal symmetric qudit states. Restricting to linearly dependent and equally likely pure states, we find the optimal positive operator valued measure (POVM) that maximizes our confidence in identifying each state in the set and minimizes the probability of obtaining inconclusive results. The physical realization of this POVM is completely determined and it is shown that after an inconclusive outcome, the input states may be mapped into a new set of equiprobable symmetric states, restricted, however, to a subspace of the original qudit Hilbert space. By applying the MC measurement again onto this new set, we can still gain some information about the input states, although with less confidence than before. This leads us to introduce the concept of sequential maximum-confidence (SMC) measurements, where the optimized MC strategy is iterated in as many stages as allowed by the input set, until no further information can be extracted from an inconclusive result. Within each stage of this measurement our confidence in identifying the input states is the highest possible, although it decreases from one stage to the next. In addition, the more stages we accomplish within the maximum allowed, the higher will be the probability of correct identification. We will discuss an explicit example of the optimal SMC measurement applied in the discrimination among four symmetric qutrit states and propose an optical network to implement it.

  4. Maximum nondiffracting propagation distance of aperture-truncated Airy beams

    Science.gov (United States)

    Chu, Xingchun; Zhao, Shanghong; Fang, Yingwu

    2018-05-01

    Airy beams have called attention of many researchers due to their non-diffracting, self-healing and transverse accelerating properties. A key issue in research of Airy beams and its applications is how to evaluate their nondiffracting propagation distance. In this paper, the critical transverse extent of physically realizable Airy beams is analyzed under the local spatial frequency methodology. The maximum nondiffracting propagation distance of aperture-truncated Airy beams is formulated and analyzed based on their local spatial frequency. The validity of the formula is verified by comparing the maximum nondiffracting propagation distance of an aperture-truncated ideal Airy beam, aperture-truncated exponentially decaying Airy beam and exponentially decaying Airy beam. Results show that the formula can be used to evaluate accurately the maximum nondiffracting propagation distance of an aperture-truncated ideal Airy beam. Therefore, it can guide us to select appropriate parameters to generate Airy beams with long nondiffracting propagation distance that have potential application in the fields of laser weapons or optical communications.

  5. Extending the maximum operation time of the MNSR reactor.

    Science.gov (United States)

    Dawahra, S; Khattab, K; Saba, G

    2016-09-01

    An effective modification to extend the maximum operation time of the Miniature Neutron Source Reactor (MNSR) to enhance the utilization of the reactor has been tested using the MCNP4C code. This modification consisted of inserting manually in each of the reactor inner irradiation tube a chain of three polyethylene-connected containers filled of water. The total height of the chain was 11.5cm. The replacement of the actual cadmium absorber with B(10) absorber was needed as well. The rest of the core structure materials and dimensions remained unchanged. A 3-D neutronic model with the new modifications was developed to compare the neutronic parameters of the old and modified cores. The results of the old and modified core excess reactivities (ρex) were: 3.954, 6.241 mk respectively. The maximum reactor operation times were: 428, 1025min and the safety reactivity factors were: 1.654 and 1.595 respectively. Therefore, a 139% increase in the maximum reactor operation time was noticed for the modified core. This increase enhanced the utilization of the MNSR reactor to conduct a long time irradiation of the unknown samples using the NAA technique and increase the amount of radioisotope production in the reactor. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. MAXIMUM POWEWR POINT TRACKING SYSTEM FOR PHOTOVOLTAIC STATION: A REVIEW

    Directory of Open Access Journals (Sweden)

    I. Elzein

    2015-01-01

    Full Text Available In recent years there has been a growing attention towards the use of renewable energy sources. Among them solar energy is one of the most promising green energy resources due to its environment sustainability and inexhaustibility. However photovoltaic systems (PhV suffer from big cost of equipment and low efficiency. Moreover, the solar cell V-I characteristic is nonlinear and varies with irradiation and temperature. In general, there is a unique point of PhV operation, called the Maximum Power Point (MPP, in which the PV system operates with maximum efficiency and produces its maximum output power. The location of the MPP is not known in advance, but can be located, either through calculation models or by search algorithms. Therefore MPPT techniques are important to maintain the PV array’s high efficiency. Many different techniques for MPPT are discussed. This review paper hopefully will serve as a convenient tool for future work in PhV power conversion.

  7. Maximum Entropy and Theory Construction: A Reply to Favretti

    Directory of Open Access Journals (Sweden)

    John Harte

    2018-04-01

    Full Text Available In the maximum entropy theory of ecology (METE, the form of a function describing the distribution of abundances over species and metabolic rates over individuals in an ecosystem is inferred using the maximum entropy inference procedure. Favretti shows that an alternative maximum entropy model exists that assumes the same prior knowledge and makes predictions that differ from METE’s. He shows that both cannot be correct and asserts that his is the correct one because it can be derived from a classic microstate-counting calculation. I clarify here exactly what the core entities and definitions are for METE, and discuss the relevance of two critical issues raised by Favretti: the existence of a counting procedure for microstates and the choices of definition of the core elements of a theory. I emphasize that a theorist controls how the core entities of his or her theory are defined, and that nature is the final arbiter of the validity of a theory.

  8. Maximum entropy reconstructions for crystallographic imaging; Cristallographie et reconstruction d`images par maximum d`entropie

    Energy Technology Data Exchange (ETDEWEB)

    Papoular, R

    1997-07-01

    The Fourier Transform is of central importance to Crystallography since it allows the visualization in real space of tridimensional scattering densities pertaining to physical systems from diffraction data (powder or single-crystal diffraction, using x-rays, neutrons, electrons or else). In turn, this visualization makes it possible to model and parametrize these systems, the crystal structures of which are eventually refined by Least-Squares techniques (e.g., the Rietveld method in the case of Powder Diffraction). The Maximum Entropy Method (sometimes called MEM or MaxEnt) is a general imaging technique, related to solving ill-conditioned inverse problems. It is ideally suited for tackling undetermined systems of linear questions (for which the number of variables is much larger than the number of equations). It is already being applied successfully in Astronomy, Radioastronomy and Medical Imaging. The advantages of using MAXIMUM Entropy over conventional Fourier and `difference Fourier` syntheses stem from the following facts: MaxEnt takes the experimental error bars into account; MaxEnt incorporate Prior Knowledge (e.g., the positivity of the scattering density in some instances); MaxEnt allows density reconstructions from incompletely phased data, as well as from overlapping Bragg reflections; MaxEnt substantially reduces truncation errors to which conventional experimental Fourier reconstructions are usually prone. The principles of Maximum Entropy imaging as applied to Crystallography are first presented. The method is then illustrated by a detailed example specific to Neutron Diffraction: the search for proton in solids. (author). 17 refs.

  9. RAPD and Internal Transcribed Spacer Sequence Analyses Reveal Zea nicaraguensis as a Section Luxuriantes Species Close to Zea luxurians

    Science.gov (United States)

    Wang, Pei; Lu, Yanli; Zheng, Mingmin; Rong, Tingzhao; Tang, Qilin

    2011-01-01

    Genetic relationship of a newly discovered teosinte from Nicaragua, Zea nicaraguensis with waterlogging tolerance, was determined based on randomly amplified polymorphic DNA (RAPD) markers and the internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA using 14 accessions from Zea species. RAPD analysis showed that a total of 5,303 fragments were produced by 136 random decamer primers, of which 84.86% bands were polymorphic. RAPD-based UPGMA analysis demonstrated that the genus Zea can be divided into section Luxuriantes including Zea diploperennis, Zea luxurians, Zea perennis and Zea nicaraguensis, and section Zea including Zea mays ssp. mexicana, Zea mays ssp. parviglumis, Zea mays ssp. huehuetenangensis and Zea mays ssp. mays. ITS sequence analysis showed the lengths of the entire ITS region of the 14 taxa in Zea varied from 597 to 605 bp. The average GC content was 67.8%. In addition to the insertion/deletions, 78 variable sites were recorded in the total ITS region with 47 in ITS1, 5 in 5.8S, and 26 in ITS2. Sequences of these taxa were analyzed with neighbor-joining (NJ) and maximum parsimony (MP) methods to construct the phylogenetic trees, selecting Tripsacum dactyloides L. as the outgroup. The phylogenetic relationships of Zea species inferred from the ITS sequences are highly concordant with the RAPD evidence that resolved two major subgenus clades. Both RAPD and ITS sequence analyses indicate that Zea nicaraguensis is more closely related to Zea luxurians than the other teosintes and cultivated maize, which should be regarded as a section Luxuriantes species. PMID:21525982

  10. Identifikasi Penyakit Aeromonad pada Budi Daya Ikan Air Tawar di Bali (IDENTIFICATION OF AEROMONAD DISEASE IN FRESH WATER AQUACULTURE IN DENPASAR, BALI

    Directory of Open Access Journals (Sweden)

    Surya Amanu

    2015-05-01

    Full Text Available Fresh water and marine fish horticulture in Bali is often harmed by the outbreak of diseases such asthose caused by Aeromonas sp (aeromonad disease.Aims ofstudy were 1 to find out the primary agent ofthe aeomonad disease in the fresh water aquaculture in Bali based on conventional and molecularidentification, 2 to find out the genetic variability of Aeromonas species, 3 to determine the effectiveantibiotic against the agent. Samples of fishes were collected from 5 different locations of fresh wateraquaculture that had high number of morbidity and mortality. Many different fishes which showed clinicalsign such as skin lesion and exophthalmus were collected.Aeromonas hydrophila and A. salmonicida wereisolated and identified from fishes, they were then identified molecularly with DNA extraction, DNAamplification in 16S rRNA gene, purification and sequencing. Sequences of both Aeromonas species fromdifferent location were analysed to create the phylogenetic tree with Maximum Parsimony and NeighborJoining method. Sensitivity of 5 antibiotics to both species of Aeromonas were done to determine the bestantibiotic against the disease. Aeromonad disease were found only in 3 regions in Bali. As many as 10isolates of A.salmonicida and 11 isolates of A.hydrophila were examined. The histopathological examinationshowed dermatitis, epicarditis, retinitis, liver and kidney congestion in fish.There were two clusters ofA.salmonicida, subspecies smithiaand subspecies achromogenes.Aeromomas hydrophyla had a close relationwith A. veronii.Aeromonas salmonicida subspecies salmonicida has not been found in Bali. Enrofloxacineand gentamycin was the best antibiotic for treating the Aeromonad disease which were more effective ascompared to3 other antibiot ics (Ampicillin, Doxycycline, and Eritromycin.

  11. Divergence of the phytochrome gene family predates angiosperm evolution and suggests that Selaginella and Equisetum arose prior to Psilotum.

    Science.gov (United States)

    Kolukisaoglu, H U; Marx, S; Wiegmann, C; Hanelt, S; Schneider-Poetsch, H A

    1995-09-01

    Thirty-two partial phytochrome sequences from algae, mosses, ferns, gymnosperms, and angiosperms (11 of them newly released ones from our laboratory) were analyzed by distance and character-state approaches (PHYLIP, TREECON, PAUP). In addition, 12 full-length sequences were analyzed. Despite low bootstrap values at individual internal nodes, the inferred trees (neighbor-joining, Fitch, maximum parsimony) generally showed similar branching orders consistent with other molecular data. Lower plants formed two distinct groups. One basal group consisted of Selaginella, Equisetum, and mosses; the other consisted of a monophyletic cluster of frond-bearing pteridophytes. Psilotum was a member of the latter group and hence perhaps was not, as sometimes suggested, a close relative of the first vascular plants. The results further suggest that phytochrome gene duplication giving rise to a- and b- and later to c-types may have taken place within seedfern genomes. Distance matrices dated the separation of mono- and dicotyledons back to about 260 million years before the present (Myr B.P.) and the separation of Metasequoia and Picea to a fossil record-compatible value of 230 Myr B.P. The Ephedra sequence clustered with the c- or a-type and Metasequoia and Picea sequences clustered with the b-type lineage. The "paleoherb" Nymphaea branched off from the c-type lineage prior to the divergence of mono- and dicotyledons on the a- and b-type branches. Sequences of Piper (another "paleoherb") created problems in that they branched off from different phytochrome lineages at nodes contradicting distance from the inferred trees' origin.

  12. Whole genome sequencing and evolutionary analysis of human respiratory syncytial virus A and B from Milwaukee, WI 1998-2010.

    Directory of Open Access Journals (Sweden)

    Cecilia Rebuffo-Scheer

    Full Text Available BACKGROUND: Respiratory Syncytial Virus (RSV is the leading cause of lower respiratory-tract infections in infants and young children worldwide. Despite this, only six complete genome sequences of original strains have been previously published, the most recent of which dates back 35 and 26 years for RSV group A and group B respectively. METHODOLOGY/PRINCIPAL FINDINGS: We present a semi-automated sequencing method allowing for the sequencing of four RSV whole genomes simultaneously. We were able to sequence the complete coding sequences of 13 RSV A and 4 RSV B strains from Milwaukee collected from 1998-2010. Another 12 RSV A and 5 RSV B strains sequenced in this study cover the majority of the genome. All RSV A and RSV B sequences were analyzed by neighbor-joining, maximum parsimony and Bayesian phylogeny methods. Genetic diversity was high among RSV A viruses in Milwaukee including the circulation of multiple genotypes (GA1, GA2, GA5, GA7 with GA2 persisting throughout the 13 years of the study. However, RSV B genomes showed little variation with all belonging to the BA genotype. For RSV A, the same evolutionary patterns and clades were seen consistently across the whole genome including all intergenic, coding, and non-coding regions sequences. CONCLUSIONS/SIGNIFICANCE: The sequencing strategy presented in this work allows for RSV A and B genomes to be sequenced simultaneously in two working days and with a low cost. We have significantly increased the amount of genomic data that is available for both RSV A and B, providing the basic molecular characteristics of RSV strains circulating in Milwaukee over the last 13 years. This information can be used for comparative analysis with strains circulating in other communities around the world which should also help with the development of new strategies for control of RSV, specifically vaccine development and improvement of RSV diagnostics.

  13. Maximum entropy reconstruction of spin densities involving non uniform prior

    International Nuclear Information System (INIS)

    Schweizer, J.; Ressouche, E.; Papoular, R.J.; Zheludev, A.I.

    1997-01-01

    Diffraction experiments give microscopic information on structures in crystals. A method which uses the concept of maximum of entropy (MaxEnt), appears to be a formidable improvement in the treatment of diffraction data. This method is based on a bayesian approach: among all the maps compatible with the experimental data, it selects that one which has the highest prior (intrinsic) probability. Considering that all the points of the map are equally probable, this probability (flat prior) is expressed via the Boltzman entropy of the distribution. This method has been used for the reconstruction of charge densities from X-ray data, for maps of nuclear densities from unpolarized neutron data as well as for distributions of spin density. The density maps obtained by this method, as compared to those resulting from the usual inverse Fourier transformation, are tremendously improved. In particular, any substantial deviation from the background is really contained in the data, as it costs entropy compared to a map that would ignore such features. However, in most of the cases, before the measurements are performed, some knowledge exists about the distribution which is investigated. It can range from the simple information of the type of scattering electrons to an elaborate theoretical model. In these cases, the uniform prior which considers all the different pixels as equally likely, is too weak a requirement and has to be replaced. In a rigorous bayesian analysis, Skilling has shown that prior knowledge can be encoded into the Maximum Entropy formalism through a model m(rvec r), via a new definition for the entropy given in this paper. In the absence of any data, the maximum of the entropy functional is reached for ρ(rvec r) = m(rvec r). Any substantial departure from the model, observed in the final map, is really contained in the data as, with the new definition, it costs entropy. This paper presents illustrations of model testing

  14. Maximum margin semi-supervised learning with irrelevant data.

    Science.gov (United States)

    Yang, Haiqin; Huang, Kaizhu; King, Irwin; Lyu, Michael R

    2015-10-01

    Semi-supervised learning (SSL) is a typical learning paradigms training a model from both labeled and unlabeled data. The traditional SSL models usually assume unlabeled data are relevant to the labeled data, i.e., following the same distributions of the targeted labeled data. In this paper, we address a different, yet formidable scenario in semi-supervised classification, where the unlabeled data may contain irrelevant data to the labeled data. To tackle this problem, we develop a maximum margin model, named tri-class support vector machine (3C-SVM), to utilize the available training data, while seeking a hyperplane for separating the targeted data well. Our 3C-SVM exhibits several characteristics and advantages. First, it does not need any prior knowledge and explicit assumption on the data relatedness. On the contrary, it can relieve the effect of irrelevant unlabeled data based on the logistic principle and maximum entropy principle. That is, 3C-SVM approaches an ideal classifier. This classifier relies heavily on labeled data and is confident on the relevant data lying far away from the decision hyperplane, while maximally ignoring the irrelevant data, which are hardly distinguished. Second, theoretical analysis is provided to prove that in what condition, the irrelevant data can help to seek the hyperplane. Third, 3C-SVM is a generalized model that unifies several popular maximum margin models, including standard SVMs, Semi-supervised SVMs (S(3)VMs), and SVMs learned from the universum (U-SVMs) as its special cases. More importantly, we deploy a concave-convex produce to solve the proposed 3C-SVM, transforming the original mixed integer programming, to a semi-definite programming relaxation, and finally to a sequence of quadratic programming subproblems, which yields the same worst case time complexity as that of S(3)VMs. Finally, we demonstrate the effectiveness and efficiency of our proposed 3C-SVM through systematical experimental comparisons. Copyright

  15. Catastrophic Disruption Threshold and Maximum Deflection from Kinetic Impact

    Science.gov (United States)

    Cheng, A. F.

    2017-12-01

    The use of a kinetic impactor to deflect an asteroid on a collision course with Earth was described in the NASA Near-Earth Object Survey and Deflection Analysis of Alternatives (2007) as the most mature approach for asteroid deflection and mitigation. The NASA DART mission will demonstrate asteroid deflection by kinetic impact at the Potentially Hazardous Asteroid 65803 Didymos in October, 2022. The kinetic impactor approach is considered to be applicable with warning times of 10 years or more and with hazardous asteroid diameters of 400 m or less. In principle, a larger kinetic impactor bringing greater kinetic energy could cause a larger deflection, but input of excessive kinetic energy will cause catastrophic disruption of the target, leaving possibly large fragments still on collision course with Earth. Thus the catastrophic disruption threshold limits the maximum deflection from a kinetic impactor. An often-cited rule of thumb states that the maximum deflection is 0.1 times the escape velocity before the target will be disrupted. It turns out this rule of thumb does not work well. A comparison to numerical simulation results shows that a similar rule applies in the gravity limit, for large targets more than 300 m, where the maximum deflection is roughly the escape velocity at momentum enhancement factor β=2. In the gravity limit, the rule of thumb corresponds to pure momentum coupling (μ=1/3), but simulations find a slightly different scaling μ=0.43. In the smaller target size range that kinetic impactors would apply to, the catastrophic disruption limit is strength-controlled. A DART-like impactor won't disrupt any target asteroid down to significantly smaller size than the 50 m below which a hazardous object would not penetrate the atmosphere in any case unless it is unusually strong.

  16. Maximum-likelihood method for numerical inversion of Mellin transform

    International Nuclear Information System (INIS)

    Iqbal, M.

    1997-01-01

    A method is described for inverting the Mellin transform which uses an expansion in Laguerre polynomials and converts the Mellin transform to Laplace transform, then the maximum-likelihood regularization method is used to recover the original function of the Mellin transform. The performance of the method is illustrated by the inversion of the test functions available in the literature (J. Inst. Math. Appl., 20 (1977) 73; Math. Comput., 53 (1989) 589). Effectiveness of the method is shown by results obtained through demonstration by means of tables and diagrams

  17. Observations of Halley's Comet by the Solar Maximum Mission (SMM)

    Science.gov (United States)

    Niedner, M. B.

    1986-01-01

    Solar Maximum Mission coronagraph/polarimeter observations of large scale phenomena in Halley's Comet are discussed. Observations of the hydrogen coma with the UV spectrometer are considered. It is concluded that coronograph/polarimeter observations of the disconnection event, in which the entire plasma tail uproots itself from the head of the comet, is convected away in the solar wind at speeds in the 50 to 100 km/sec range (relative to the head), and is replaced by a plasma tail constructed from folding ion-tail rays, are the most interesting.

  18. Maximum entropy principle and hydrodynamic models in statistical mechanics

    International Nuclear Information System (INIS)

    Trovato, M.; Reggiani, L.

    2012-01-01

    This review presents the state of the art of the maximum entropy principle (MEP) in its classical and quantum (QMEP) formulation. Within the classical MEP we overview a general theory able to provide, in a dynamical context, the macroscopic relevant variables for carrier transport in the presence of electric fields of arbitrary strength. For the macroscopic variables the linearized maximum entropy approach is developed including full-band effects within a total energy scheme. Under spatially homogeneous conditions, we construct a closed set of hydrodynamic equations for the small-signal (dynamic) response of the macroscopic variables. The coupling between the driving field and the energy dissipation is analyzed quantitatively by using an arbitrary number of moments of the distribution function. Analogously, the theoretical approach is applied to many one-dimensional n + nn + submicron Si structures by using different band structure models, different doping profiles, different applied biases and is validated by comparing numerical calculations with ensemble Monte Carlo simulations and with available experimental data. Within the quantum MEP we introduce a quantum entropy functional of the reduced density matrix, the principle of quantum maximum entropy is then asserted as fundamental principle of quantum statistical mechanics. Accordingly, we have developed a comprehensive theoretical formalism to construct rigorously a closed quantum hydrodynamic transport within a Wigner function approach. The theory is formulated both in thermodynamic equilibrium and nonequilibrium conditions, and the quantum contributions are obtained by only assuming that the Lagrange multipliers can be expanded in powers of ħ 2 , being ħ the reduced Planck constant. In particular, by using an arbitrary number of moments, we prove that: i) on a macroscopic scale all nonlocal effects, compatible with the uncertainty principle, are imputable to high-order spatial derivatives both of the

  19. Twenty-five years of maximum-entropy principle

    Science.gov (United States)

    Kapur, J. N.

    1983-04-01

    The strengths and weaknesses of the maximum entropy principle (MEP) are examined and some challenging problems that remain outstanding at the end of the first quarter century of the principle are discussed. The original formalism of the MEP is presented and its relationship to statistical mechanics is set forth. The use of MEP for characterizing statistical distributions, in statistical inference, nonlinear spectral analysis, transportation models, population density models, models for brand-switching in marketing and vote-switching in elections is discussed. Its application to finance, insurance, image reconstruction, pattern recognition, operations research and engineering, biology and medicine, and nonparametric density estimation is considered.

  20. Gentile statistics with a large maximum occupation number

    International Nuclear Information System (INIS)

    Dai Wusheng; Xie Mi

    2004-01-01

    In Gentile statistics the maximum occupation number can take on unrestricted integers: 1 1 the Bose-Einstein case is not recovered from Gentile statistics as n goes to N. Attention is also concentrated on the contribution of the ground state which was ignored in related literature. The thermodynamic behavior of a ν-dimensional Gentile ideal gas of particle of dispersion E=p s /2m, where ν and s are arbitrary, is analyzed in detail. Moreover, we provide an alternative derivation of the partition function for Gentile statistics