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Sample records for maximally parsimonious trees

  1. 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.

  2. 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 .

  3. 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

  4. 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.

  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. 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.

  7. 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.

  8. 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

  9. 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.

  10. Enumerating all maximal frequent subtrees in collections of phylogenetic trees.

    Science.gov (United States)

    Deepak, Akshay; Fernández-Baca, David

    2014-01-01

    A common problem in phylogenetic analysis is to identify frequent patterns in a collection of phylogenetic trees. The goal is, roughly, to find a subset of the species (taxa) on which all or some significant subset of the trees agree. One popular method to do so is through maximum agreement subtrees (MASTs). MASTs are also used, among other things, as a metric for comparing phylogenetic trees, computing congruence indices and to identify horizontal gene transfer events. We give algorithms and experimental results for two approaches to identify common patterns in a collection of phylogenetic trees, one based on agreement subtrees, called maximal agreement subtrees, the other on frequent subtrees, called maximal frequent subtrees. These approaches can return subtrees on larger sets of taxa than MASTs, and can reveal new common phylogenetic relationships not present in either MASTs or the majority rule tree (a popular consensus method). Our current implementation is available on the web at https://code.google.com/p/mfst-miner/. Our computational results confirm that maximal agreement subtrees and all maximal frequent subtrees can reveal a more complete phylogenetic picture of the common patterns in collections of phylogenetic trees than maximum agreement subtrees; they are also often more resolved than the majority rule tree. Further, our experiments show that enumerating maximal frequent subtrees is considerably more practical than enumerating ordinary (not necessarily maximal) frequent subtrees.

  11. Enumerating all maximal frequent subtrees in collections of phylogenetic trees

    Science.gov (United States)

    2014-01-01

    Background A common problem in phylogenetic analysis is to identify frequent patterns in a collection of phylogenetic trees. The goal is, roughly, to find a subset of the species (taxa) on which all or some significant subset of the trees agree. One popular method to do so is through maximum agreement subtrees (MASTs). MASTs are also used, among other things, as a metric for comparing phylogenetic trees, computing congruence indices and to identify horizontal gene transfer events. Results We give algorithms and experimental results for two approaches to identify common patterns in a collection of phylogenetic trees, one based on agreement subtrees, called maximal agreement subtrees, the other on frequent subtrees, called maximal frequent subtrees. These approaches can return subtrees on larger sets of taxa than MASTs, and can reveal new common phylogenetic relationships not present in either MASTs or the majority rule tree (a popular consensus method). Our current implementation is available on the web at https://code.google.com/p/mfst-miner/. Conclusions Our computational results confirm that maximal agreement subtrees and all maximal frequent subtrees can reveal a more complete phylogenetic picture of the common patterns in collections of phylogenetic trees than maximum agreement subtrees; they are also often more resolved than the majority rule tree. Further, our experiments show that enumerating maximal frequent subtrees is considerably more practical than enumerating ordinary (not necessarily maximal) frequent subtrees. PMID:25061474

  12. Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals.

    Science.gov (United States)

    Heydari, Mahdi; Marashi, Sayed-Amir; Tusserkani, Ruzbeh; Sadeghi, Mehdi

    2014-10-01

    One of the fundamental problems in bioinformatics is phylogenetic tree reconstruction, which can be used for classifying living organisms into different taxonomic clades. The classical approach to this problem is based on a marker such as 16S ribosomal RNA. Since evolutionary events like genomic rearrangements are not included in reconstructions of phylogenetic trees based on single genes, much effort has been made to find other characteristics for phylogenetic reconstruction in recent years. With the increasing availability of completely sequenced genomes, gene order can be considered as a new solution for this problem. In the present work, we applied maximal common intervals (MCIs) in two or more genomes to infer their distance and to reconstruct their evolutionary relationship. Additionally, measures based on uncommon segments (UCS's), i.e., those genomic segments which are not detected as part of any of the MCIs, are also used for phylogenetic tree reconstruction. We applied these two types of measures for reconstructing the phylogenetic tree of 63 prokaryotes with known COG (clusters of orthologous groups) families. Similarity between the MCI-based (resp. UCS-based) reconstructed phylogenetic trees and the phylogenetic tree obtained from NCBI taxonomy browser is as high as 93.1% (resp. 94.9%). We show that in the case of this diverse dataset of prokaryotes, tree reconstruction based on MCI and UCS outperforms most of the currently available methods based on gene orders, including breakpoint distance and DCJ. We additionally tested our new measures on a dataset of 13 closely-related bacteria from the genus Prochlorococcus. In this case, distances like rearrangement distance, breakpoint distance and DCJ proved to be useful, while our new measures are still appropriate for phylogenetic reconstruction. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  13. 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

  14. 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.

  15. Intermediate tree cover can maximize groundwater recharge in the seasonally dry tropics

    Science.gov (United States)

    Ilstedt, U.; Bargués Tobella, A.; Bazié, H. R.; Bayala, J.; Verbeeten, E.; Nyberg, G.; Sanou, J.; Benegas, L.; Murdiyarso, D.; Laudon, H.; Sheil, D.; Malmer, A.

    2016-01-01

    Water scarcity contributes to the poverty of around one-third of the world’s people. Despite many benefits, tree planting in dry regions is often discouraged by concerns that trees reduce water availability. Yet relevant studies from the tropics are scarce, and the impacts of intermediate tree cover remain unexplored. We developed and tested an optimum tree cover theory in which groundwater recharge is maximized at an intermediate tree density. Below this optimal tree density the benefits from any additional trees on water percolation exceed their extra water use, leading to increased groundwater recharge, while above the optimum the opposite occurs. Our results, based on groundwater budgets calibrated with measurements of drainage and transpiration in a cultivated woodland in West Africa, demonstrate that groundwater recharge was maximised at intermediate tree densities. In contrast to the prevailing view, we therefore find that moderate tree cover can increase groundwater recharge, and that tree planting and various tree management options can improve groundwater resources. We evaluate the necessary conditions for these results to hold and suggest that they are likely to be common in the seasonally dry tropics, offering potential for widespread tree establishment and increased benefits for hundreds of millions of people. PMID:26908158

  16. 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

  17. Effects of stand and inter-specific stocking on maximizing standing tree carbon stocks in the eastern United States

    Science.gov (United States)

    Christopher W. Woodall; Anthony W. D' Amato; John B. Bradford; Andrew O. Finley

    2011-01-01

    There is expanding interest in management strategies that maximize forest carbon (C) storage to mitigate increased atmospheric carbon dioxide. The tremendous tree species diversity and range of stand stocking found across the eastern United States presents a challenge for determining optimal combinations for the maximization of standing tree C storage. Using a...

  18. Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees

    Directory of Open Access Journals (Sweden)

    Stadler Peter F

    2010-06-01

    Full Text Available Abstract Background The Maximal Pairing Problem (MPP is the prototype of a class of combinatorial optimization problems that are of considerable interest in bioinformatics: Given an arbitrary phylogenetic tree T and weights ωxy for the paths between any two pairs of leaves (x, y, what is the collection of edge-disjoint paths between pairs of leaves that maximizes the total weight? Special cases of the MPP for binary trees and equal weights have been described previously; algorithms to solve the general MPP are still missing, however. Results We describe a relatively simple dynamic programming algorithm for the special case of binary trees. We then show that the general case of multifurcating trees can be treated by interleaving solutions to certain auxiliary Maximum Weighted Matching problems with an extension of this dynamic programming approach, resulting in an overall polynomial-time solution of complexity (n4 log n w.r.t. the number n of leaves. The source code of a C implementation can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/Targeting. For binary trees, we furthermore discuss several constrained variants of the MPP as well as a partition function approach to the probabilistic version of the MPP. Conclusions The algorithms introduced here make it possible to solve the MPP also for large trees with high-degree vertices. This has practical relevance in the field of comparative phylogenetics and, for example, in the context of phylogenetic targeting, i.e., data collection with resource limitations.

  19. 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.

  20. 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 (...

  1. How should leaf area, sapwood area and stomatal conductance vary with tree height to maximize growth?

    Science.gov (United States)

    Buckley, Thomas N; Roberts, David W

    2006-02-01

    Conventional wisdom holds that the ratio of leaf area to sapwood area (L/S) should decline during height (H) growth to maintain hydraulic homeostasis and prevent stomatal conductance (g(s)) from declining. We contend that L/S should increase with H based on a numerical simulation, a mathematical analysis and a conceptual argument: (1) numerical simulation--a tree growth model, DESPOT (Deducing Emergent Structure and Physiology Of Trees), in which carbon (C) allocation is regulated to maximize C gain, predicts L/S should increase during most of H growth; (2) mathematical analysis--the formal criterion for optimal C allocation, applied to a simplified analytical model of whole tree carbon-water balance, predicts L/S should increase with H if leaf-level gas exchange parameters including g(s) are conserved; and (3) conceptual argument--photosynthesis is limited by several substitutable resources (chiefly nitrogen (N), water and light) and H growth increases the C cost of water transport but not necessarily of N and light capture, so if the goal is to maximize C gain or growth, allocation should shift in favor of increasing photosynthetic capacity and irradiance, rather than sustaining g(s). Although many data are consistent with the prediction that L/S should decline with H, many others are not, and we discuss possible reasons for these discrepancies.

  2. 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.

  3. 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...

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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 ...

  16. 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.

  17. 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.

  18. An O(n²) maximal planarization algorithm based on PQ-trees

    NARCIS (Netherlands)

    Kant, G.

    1992-01-01

    In this paper we investigate the problem how to delete a number of edges from a nonplanar graph G such that the resulting graph G’ is maximal planar, i.e., such that we cannot add an edge e E G – G’ to G’ without destroying planarity. Actually, our algorithm is a corrected and more generalized

  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. 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.

  1. 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.

  2. 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...

  3. 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/.

  4. 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/.

  5. Stock market network’s topological stability: Evidence from planar maximally filtered graph and minimal spanning tree

    Science.gov (United States)

    Yan, Xin-Guo; Xie, Chi; Wang, Gang-Jin

    2015-08-01

    We study the topological stability of stock market network by investigating the topological robustness, namely the ability of the network to resist structural or topological changes. The stock market network is extracted by minimal spanning tree (MST) and planar maximally filtered graph (PMFG). We find that the specific delisting thresholds of the listed companies exist in both MST and PMFG networks. In comparison with MST, PMFG provides more information and is better for the aim of exploring stock market network’s robustness. The PMFG before the US sub-prime crisis (i.e., from June 2005 to May 2007) has a stronger robustness against the intentional topological damage than the other two sub-periods (i.e., from June 2007 to May 2009 and from June 2009 to May 2011). We also find that the nonfractal property exists in MSTs of S&P 500, i.e., the highly connected nodes link with each other directly, which indicates that the MSTs are vulnerable to the removal of such important nodes. Moreover, the financial institutions and high technology companies are important in maintaining the stability of S&P 500 network.

  6. 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.

  7. 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....

  8. 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...

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Maximizing the Diversity of Ensemble Random Forests for Tree Genera Classification Using High Density LiDAR Data

    Directory of Open Access Journals (Sweden)

    Connie Ko

    2016-08-01

    Full Text Available Recent research into improving the effectiveness of forest inventory management using airborne LiDAR data has focused on developing advanced theories in data analytics. Furthermore, supervised learning as a predictive model for classifying tree genera (and species, where possible has been gaining popularity in order to minimize this labor-intensive task. However, bottlenecks remain that hinder the immediate adoption of supervised learning methods. With supervised classification, training samples are required for learning the parameters that govern the performance of a classifier, yet the selection of training data is often subjective and the quality of such samples is critically important. For LiDAR scanning in forest environments, the quantification of data quality is somewhat abstract, normally referring to some metric related to the completeness of individual tree crowns; however, this is not an issue that has received much attention in the literature. Intuitively the choice of training samples having varying quality will affect classification accuracy. In this paper a Diversity Index (DI is proposed that characterizes the diversity of data quality (Qi among selected training samples required for constructing a classification model of tree genera. The training sample is diversified in terms of data quality as opposed to the number of samples per class. The diversified training sample allows the classifier to better learn the positive and negative instances and; therefore; has a higher classification accuracy in discriminating the “unknown” class samples from the “known” samples. Our algorithm is implemented within the Random Forests base classifiers with six derived geometric features from LiDAR data. The training sample contains three tree genera (pine; poplar; and maple and the validation samples contains four labels (pine; poplar; maple; and “unknown”. Classification accuracy improved from 72.8%; when training samples were

  14. Non-perturbative renormalization in coordinate space for N{sub f}=2 maximally twisted mass fermions with tree-level Symanzik improved gauge action

    Energy Technology Data Exchange (ETDEWEB)

    Cichy, Krzysztof [DESY, Zeuthen (Germany). NIC; Adam Mickiewicz Univ., Poznan (Poland). Faculty of Physics; Jansen, Karl [DESY, Zeuthen (Germany). NIC; Korcyl, Piotr [DESY, Zeuthen (Germany). NIC; Jagiellonian Univ., Krakow (Poland). M. Smoluchowski Inst. of Physics

    2012-07-15

    We present results of a lattice QCD application of a coordinate space renormalization scheme for the extraction of renormalization constants for flavour non-singlet bilinear quark operators. The method consists in the analysis of the small-distance behaviour of correlation functions in Euclidean space and has several theoretical and practical advantages, in particular: it is gauge invariant, easy to implement and has relatively low computational cost. The values of renormalization constants in the X-space scheme can be converted to the MS scheme via 4-loop continuum perturbative formulae. Our results for N{sub f}=2 maximally twisted mass fermions with tree-level Symanzik improved gauge action are compared to the ones from the RI-MOM scheme and show full agreement with this method. (orig.)

  15. Non-perturbative renormalization in coordinate space for Nf=2 maximally twisted mass fermions with tree-level Symanzik improved gauge action

    International Nuclear Information System (INIS)

    Cichy, Krzysztof; Adam Mickiewicz Univ., Poznan; Jansen, Karl; Korcyl, Piotr; Jagiellonian Univ., Krakow

    2012-07-01

    We present results of a lattice QCD application of a coordinate space renormalization scheme for the extraction of renormalization constants for flavour non-singlet bilinear quark operators. The method consists in the analysis of the small-distance behaviour of correlation functions in Euclidean space and has several theoretical and practical advantages, in particular: it is gauge invariant, easy to implement and has relatively low computational cost. The values of renormalization constants in the X-space scheme can be converted to the MS scheme via 4-loop continuum perturbative formulae. Our results for N f =2 maximally twisted mass fermions with tree-level Symanzik improved gauge action are compared to the ones from the RI-MOM scheme and show full agreement with this method. (orig.)

  16. Trees

    Science.gov (United States)

    Al-Khaja, Nawal

    2007-01-01

    This is a thematic lesson plan for young learners about palm trees and the importance of taking care of them. The two part lesson teaches listening, reading and speaking skills. The lesson includes parts of a tree; the modal auxiliary, can; dialogues and a role play activity.

  17. 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

  18. 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.

  19. 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....

  20. 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.

  1. 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.

  2. 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

  3. There's Life in Hazard Trees

    Science.gov (United States)

    Mary Torsello; Toni McLellan

    The goals of hazard tree management programs are to maximize public safety and maintain a healthy sustainable tree resource. Although hazard tree management frequently targets removal of trees or parts of trees that attract wildlife, it can take into account a diversity of tree values. With just a little extra planning, hazard tree management can be highly beneficial...

  4. Finding Maximal Quasiperiodicities in Strings

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Pedersen, Christian N. S.

    2000-01-01

    of length n in time O(n log n) and space O(n). Our algorithm uses the suffix tree as the fundamental data structure combined with efficient methods for merging and performing multiple searches in search trees. Besides finding all maximal quasiperiodic substrings, our algorithm also marks the nodes......Apostolico and Ehrenfeucht defined the notion of a maximal quasiperiodic substring and gave an algorithm that finds all maximal quasiperiodic substrings in a string of length n in time O(n log2 n). In this paper we give an algorithm that finds all maximal quasiperiodic substrings in a string...... in the suffix tree that have a superprimitive path-label....

  5. Entropy maximization

    Indian Academy of Sciences (India)

    Abstract. It is shown that (i) every probability density is the unique maximizer of relative entropy in an appropriate class and (ii) in the class of all pdf f that satisfy. ∫ fhi dμ = λi for i = 1, 2,...,...k the maximizer of entropy is an f0 that is pro- portional to exp(. ∑ ci hi ) for some choice of ci . An extension of this to a continuum of.

  6. Entropy Maximization

    Indian Academy of Sciences (India)

    It is shown that (i) every probability density is the unique maximizer of relative entropy in an appropriate class and (ii) in the class of all pdf that satisfy ∫ f h i d = i for i = 1 , 2 , … , … k the maximizer of entropy is an f 0 that is proportional to exp ⁡ ( ∑ c i h i ) for some choice of c i . An extension of this to a continuum of ...

  7. Seeking parsimony in hydrology and water resources technology

    Science.gov (United States)

    Koutsoyiannis, D.

    2009-04-01

    The principle of parsimony, also known as the principle of simplicity, the principle of economy and Ockham's razor, advises scientists to prefer the simplest theory among those that fit the data equally well. In this, it is an epistemic principle but reflects an ontological characterization that the universe is ultimately parsimonious. Is this principle useful and can it really be reconciled with, and implemented to, our modelling approaches of complex hydrological systems, whose elements and events are extraordinarily numerous, different and unique? The answer underlying the mainstream hydrological research of the last two decades seems to be negative. Hopes were invested to the power of computers that would enable faithful and detailed representation of the diverse system elements and the hydrological processes, based on merely "first principles" and resulting in "physically-based" models that tend to approach in complexity the real world systems. Today the account of such research endeavour seems not positive, as it did not improve model predictive capacity and processes comprehension. A return to parsimonious modelling seems to be again the promising route. The experience from recent research and from comparisons of parsimonious and complicated models indicates that the former can facilitate insight and comprehension, improve accuracy and predictive capacity, and increase efficiency. In addition - and despite aspiration that "physically based" models will have lower data requirements and, even, they ultimately become "data-free" - parsimonious models require fewer data to achieve the same accuracy with more complicated models. Naturally, the concepts that reconcile the simplicity of parsimonious models with the complexity of hydrological systems are probability theory and statistics. Probability theory provides the theoretical basis for moving from a microscopic to a macroscopic view of phenomena, by mapping sets of diverse elements and events of hydrological

  8. Modelling functional trait acclimation for trees of different height in a forest light gradient: emergent patterns driven by carbon gain maximization

    NARCIS (Netherlands)

    Sterck, F.J.; Schieving, F.

    2011-01-01

    Forest trees show large changes in functional traits as they develop from a sapling in the shaded understorey to an adult in the light-exposed canopy. The adaptive function of such changes remains poorly understood. The carbon gain hypothesis suggests that these changes should be adaptive

  9. 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

  10. 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.

  11. Modeling time-to-event (survival) data using classification tree analysis.

    Science.gov (United States)

    Linden, Ariel; Yarnold, Paul R

    2017-12-01

    Time to the occurrence of an event is often studied in health research. Survival analysis differs from other designs in that follow-up times for individuals who do not experience the event by the end of the study (called censored) are accounted for in the analysis. Cox regression is the standard method for analysing censored data, but the assumptions required of these models are easily violated. In this paper, we introduce classification tree analysis (CTA) as a flexible alternative for modelling censored data. Classification tree analysis is a "decision-tree"-like classification model that provides parsimonious, transparent (ie, easy to visually display and interpret) decision rules that maximize predictive accuracy, derives exact P values via permutation tests, and evaluates model cross-generalizability. Using empirical data, we identify all statistically valid, reproducible, longitudinally consistent, and cross-generalizable CTA survival models and then compare their predictive accuracy to estimates derived via Cox regression and an unadjusted naïve model. Model performance is assessed using integrated Brier scores and a comparison between estimated survival curves. The Cox regression model best predicts average incidence of the outcome over time, whereas CTA survival models best predict either relatively high, or low, incidence of the outcome over time. Classification tree analysis survival models offer many advantages over Cox regression, such as explicit maximization of predictive accuracy, parsimony, statistical robustness, and transparency. Therefore, researchers interested in accurate prognoses and clear decision rules should consider developing models using the CTA-survival framework. © 2017 John Wiley & Sons, Ltd.

  12. 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

  13. 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

  14. 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...

  15. 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.

  16. Using tree diversity to compare phylogenetic heuristics.

    Science.gov (United States)

    Sul, Seung-Jin; Matthews, Suzanne; Williams, Tiffani L

    2009-04-29

    Evolutionary trees are family trees that represent the relationships between a group of organisms. Phylogenetic heuristics are used to search stochastically for the best-scoring trees in tree space. Given that better tree scores are believed to be better approximations of the true phylogeny, traditional evaluation techniques have used tree scores to determine the heuristics that find the best scores in the fastest time. We develop new techniques to evaluate phylogenetic heuristics based on both tree scores and topologies to compare Pauprat and Rec-I-DCM3, two popular Maximum Parsimony search algorithms. Our results show that although Pauprat and Rec-I-DCM3 find the trees with the same best scores, topologically these trees are quite different. Furthermore, the Rec-I-DCM3 trees cluster distinctly from the Pauprat trees. In addition to our heatmap visualizations of using parsimony scores and the Robinson-Foulds distance to compare best-scoring trees found by the two heuristics, we also develop entropy-based methods to show the diversity of the trees found. Overall, Pauprat identifies more diverse trees than Rec-I-DCM3. Overall, our work shows that there is value to comparing heuristics beyond the parsimony scores that they find. Pauprat is a slower heuristic than Rec-I-DCM3. However, our work shows that there is tremendous value in using Pauprat to reconstruct trees-especially since it finds identical scoring but topologically distinct trees. Hence, instead of discounting Pauprat, effort should go in improving its implementation. Ultimately, improved performance measures lead to better phylogenetic heuristics and will result in better approximations of the true evolutionary history of the organisms of interest.

  17. 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.

  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. Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance

    Science.gov (United States)

    2013-01-01

    Background Constructing species trees from multi-copy gene trees remains a challenging problem in phylogenetics. One difficulty is that the underlying genes can be incongruent due to evolutionary processes such as gene duplication and loss, deep coalescence, or lateral gene transfer. Gene tree estimation errors may further exacerbate the difficulties of species tree estimation. Results We present a new approach for inferring species trees from incongruent multi-copy gene trees that is based on a generalization of the Robinson-Foulds (RF) distance measure to multi-labeled trees (mul-trees). We prove that it is NP-hard to compute the RF distance between two mul-trees; however, it is easy to calculate this distance between a mul-tree and a singly-labeled species tree. Motivated by this, we formulate the RF problem for mul-trees (MulRF) as follows: Given a collection of multi-copy gene trees, find a singly-labeled species tree that minimizes the total RF distance from the input mul-trees. We develop and implement a fast SPR-based heuristic algorithm for the NP-hard MulRF problem. We compare the performance of the MulRF method (available at http://genome.cs.iastate.edu/CBL/MulRF/) with several gene tree parsimony approaches using gene tree simulations that incorporate gene tree error, gene duplications and losses, and/or lateral transfer. The MulRF method produces more accurate species trees than gene tree parsimony approaches. We also demonstrate that the MulRF method infers in minutes a credible plant species tree from a collection of nearly 2,000 gene trees. Conclusions Our new phylogenetic inference method, based on a generalized RF distance, makes it possible to quickly estimate species trees from large genomic data sets. Since the MulRF method, unlike gene tree parsimony, is based on a generic tree distance measure, it is appealing for analyses of genomic data sets, in which many processes such as deep coalescence, recombination, gene duplication and losses as

  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. Profit maximization mitigates competition

    DEFF Research Database (Denmark)

    Dierker, Egbert; Grodal, Birgit

    1996-01-01

    We consider oligopolistic markets in which the notion of shareholders' utility is well-defined and compare the Bertrand-Nash equilibria in case of utility maximization with those under the usual profit maximization hypothesis. Our main result states that profit maximization leads to less price...... competition than utility maximization. Since profit maximization tends to raise prices, it may be regarded as beneficial for the owners as a whole. Moreover, if profit maximization is a good proxy for utility maximization, then there is no need for a general equilibrium analysis that takes the distribution...... of profits among consumers fully into account and partial equilibrium analysis suffices...

  6. 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

  7. Maximal Entanglement in High Energy Physics

    Directory of Open Access Journals (Sweden)

    Alba Cervera-Lierta, José I. Latorre, Juan Rojo, Luca Rottoli

    2017-11-01

    Full Text Available We analyze how maximal entanglement is generated at the fundamental level in QED by studying correlations between helicity states in tree-level scattering processes at high energy. We demonstrate that two mechanisms for the generation of maximal entanglement are at work: i $s$-channel processes where the virtual photon carries equal overlaps of the helicities of the final state particles, and ii the indistinguishable superposition between $t$- and $u$-channels. We then study whether requiring maximal entanglement constrains the coupling structure of QED and the weak interactions. In the case of photon-electron interactions unconstrained by gauge symmetry, we show how this requirement allows reproducing QED. For $Z$-mediated weak scattering, the maximal entanglement principle leads to non-trivial predictions for the value of the weak mixing angle $\\theta_W$. Our results are a first step towards understanding the connections between maximal entanglement and the fundamental symmetries of high-energy physics.

  8. 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

  9. Maximally incompatible quantum observables

    Energy Technology Data Exchange (ETDEWEB)

    Heinosaari, Teiko, E-mail: teiko.heinosaari@utu.fi [Turku Centre for Quantum Physics, Department of Physics and Astronomy, University of Turku, FI-20014 Turku (Finland); Schultz, Jussi, E-mail: jussi.schultz@gmail.com [Dipartimento di Matematica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano (Italy); Toigo, Alessandro, E-mail: alessandro.toigo@polimi.it [Dipartimento di Matematica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Milano, Via Celoria 16, I-20133 Milano (Italy); Ziman, Mario, E-mail: ziman@savba.sk [RCQI, Institute of Physics, Slovak Academy of Sciences, Dúbravská cesta 9, 84511 Bratislava (Slovakia); Faculty of Informatics, Masaryk University, Botanická 68a, 60200 Brno (Czech Republic)

    2014-05-01

    The existence of maximally incompatible quantum observables in the sense of a minimal joint measurability region is investigated. Employing the universal quantum cloning device it is argued that only infinite dimensional quantum systems can accommodate maximal incompatibility. It is then shown that two of the most common pairs of complementary observables (position and momentum; number and phase) are maximally incompatible.

  10. Maximally incompatible quantum observables

    International Nuclear Information System (INIS)

    Heinosaari, Teiko; Schultz, Jussi; Toigo, Alessandro; Ziman, Mario

    2014-01-01

    The existence of maximally incompatible quantum observables in the sense of a minimal joint measurability region is investigated. Employing the universal quantum cloning device it is argued that only infinite dimensional quantum systems can accommodate maximal incompatibility. It is then shown that two of the most common pairs of complementary observables (position and momentum; number and phase) are maximally incompatible.

  11. Maximizers versus satisficers

    OpenAIRE

    Andrew M. Parker; Wandi Bruine de Bruin; Baruch Fischhoff

    2007-01-01

    Our previous research suggests that people reporting a stronger desire to maximize obtain worse life outcomes (Bruine de Bruin et al., 2007). Here, we examine whether this finding may be explained by the decision-making styles of self-reported maximizers. Expanding on Schwartz et al. (2002), we find that self-reported maximizers are more likely to show problematic decision-making styles, as evidenced by self-reports of less behavioral coping, greater dependence on others when making decisions...

  12. Maximal combustion temperature estimation

    International Nuclear Information System (INIS)

    Golodova, E; Shchepakina, E

    2006-01-01

    This work is concerned with the phenomenon of delayed loss of stability and the estimation of the maximal temperature of safe combustion. Using the qualitative theory of singular perturbations and canard techniques we determine the maximal temperature on the trajectories located in the transition region between the slow combustion regime and the explosive one. This approach is used to estimate the maximal temperature of safe combustion in multi-phase combustion models

  13. On defining a unique phylogenetic tree with homoplastic characters.

    Science.gov (United States)

    Goloboff, Pablo A; Wilkinson, Mark

    2018-05-01

    This paper discusses the problem of whether creating a matrix with all the character state combinations that have a fixed number of steps (or extra steps) on a given tree T, produces the same tree T when analyzed with maximum parsimony or maximum likelihood. Exhaustive enumeration of cases up to 20 taxa for binary characters, and up to 12 taxa for 4-state characters, shows that the same tree is recovered (as unique most likely or most parsimonious tree) as long as the number of extra steps is within 1/4 of the number of taxa. This dependence, 1/4 of the number of taxa, is discussed with a general argumentation, in terms of the spread of the character changes on the tree used to select character state distributions. The present finding allows creating matrices which have as much homoplasy as possible for the most parsimonious or likely tree to be predictable, and examination of these matrices with hill-climbing search algorithms provides additional evidence on the (lack of a) necessary relationship between homoplasy and the ability of search methods to find optimal trees. Copyright © 2018 Elsevier Inc. All rights reserved.

  14. 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

  15. Maximally multipartite entangled states

    Science.gov (United States)

    Facchi, Paolo; Florio, Giuseppe; Parisi, Giorgio; Pascazio, Saverio

    2008-06-01

    We introduce the notion of maximally multipartite entangled states of n qubits as a generalization of the bipartite case. These pure states have a bipartite entanglement that does not depend on the bipartition and is maximal for all possible bipartitions. They are solutions of a minimization problem. Examples for small n are investigated, both analytically and numerically.

  16. Maximizers versus satisficers

    Directory of Open Access Journals (Sweden)

    Andrew M. Parker

    2007-12-01

    Full Text Available Our previous research suggests that people reporting a stronger desire to maximize obtain worse life outcomes (Bruine de Bruin et al., 2007. Here, we examine whether this finding may be explained by the decision-making styles of self-reported maximizers. Expanding on Schwartz et al. (2002, we find that self-reported maximizers are more likely to show problematic decision-making styles, as evidenced by self-reports of less behavioral coping, greater dependence on others when making decisions, more avoidance of decision making, and greater tendency to experience regret. Contrary to predictions, self-reported maximizers were more likely to report spontaneous decision making. However, the relationship between self-reported maximizing and worse life outcomes is largely unaffected by controls for measures of other decision-making styles, decision-making competence, and demographic variables.

  17. Coalescent methods for estimating phylogenetic trees.

    Science.gov (United States)

    Liu, Liang; Yu, Lili; Kubatko, Laura; Pearl, Dennis K; Edwards, Scott V

    2009-10-01

    We review recent models to estimate phylogenetic trees under the multispecies coalescent. Although the distinction between gene trees and species trees has come to the fore of phylogenetics, only recently have methods been developed that explicitly estimate species trees. Of the several factors that can cause gene tree heterogeneity and discordance with the species tree, deep coalescence due to random genetic drift in branches of the species tree has been modeled most thoroughly. Bayesian approaches to estimating species trees utilizes two likelihood functions, one of which has been widely used in traditional phylogenetics and involves the model of nucleotide substitution, and the second of which is less familiar to phylogeneticists and involves the probability distribution of gene trees given a species tree. Other recent parametric and nonparametric methods for estimating species trees involve parsimony criteria, summary statistics, supertree and consensus methods. Species tree approaches are an appropriate goal for systematics, appear to work well in some cases where concatenation can be misleading, and suggest that sampling many independent loci will be paramount. Such methods can also be challenging to implement because of the complexity of the models and computational time. In addition, further elaboration of the simplest of coalescent models will be required to incorporate commonly known issues such as deviation from the molecular clock, gene flow and other genetic forces.

  18. Calculating the probability of multitaxon evolutionary trees: bootstrappers Gambit.

    OpenAIRE

    Lake, J A

    1995-01-01

    The reconstruction of multitaxon trees from molecular sequences is confounded by the variety of algorithms and criteria used to evaluate trees, making it difficult to compare the results of different analyses. A global method of multitaxon phylogenetic reconstruction described here, Bootstrappers Gambit, can be used with any four-taxon algorithm, including distance, maximum likelihood, and parsimony methods. It incorporates a Bayesian-Jeffreys'-bootstrap analysis to provide a uniform probabil...

  19. 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.

  20. 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,…

  1. 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…

  2. 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.

  3. 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...

  4. 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

  5. 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

  6. Is CP violation maximal

    International Nuclear Information System (INIS)

    Gronau, M.

    1984-01-01

    Two ambiguities are noted in the definition of the concept of maximal CP violation. The phase convention ambiguity is overcome by introducing a CP violating phase in the quark mixing matrix U which is invariant under rephasing transformations. The second ambiguity, related to the parametrization of U, is resolved by finding a single empirically viable definition of maximal CP violation when assuming that U does not single out one generation. Considerable improvement in the calculation of nonleptonic weak amplitudes is required to test the conjecture of maximal CP violation. 21 references

  7. A bicriterion Steiner tree problem on graph

    Directory of Open Access Journals (Sweden)

    Vujošević Mirko B.

    2003-01-01

    Full Text Available This paper presents a formulation of bicriterion Steiner tree problem which is stated as a task of finding a Steiner tree with maximal capacity and minimal length. It is considered as a lexicographic multicriteria problem. This means that the bottleneck Steiner tree problem is solved first. After that, the next optimization problem is stated as a classical minimums Steiner tree problem under the constraint on capacity of the tree. The paper also presents some computational experiments with the multicriteria problem.

  8. 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.

  9. 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...

  10. 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...

  11. 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 ...

  12. 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...

  13. 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.

  14. 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.

  15. 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.

  16. Guinea pig maximization test

    DEFF Research Database (Denmark)

    Andersen, Klaus Ejner

    1985-01-01

    Guinea pig maximization tests (GPMT) with chlorocresol were performed to ascertain whether the sensitization rate was affected by minor changes in the Freund's complete adjuvant (FCA) emulsion used. Three types of emulsion were evaluated: the oil phase was mixed with propylene glycol, saline...

  17. Submodular unsplittable flow on trees

    DEFF Research Database (Denmark)

    Adamaszek, Anna Maria; Chalermsook, Parinya; Ene, Alina

    2016-01-01

    We study the Unsplittable Flow problem (UFP) on trees with a submodular objective function. The input to this problem is a tree with edge capacities and a collection of tasks, each characterized by a source node, a sink node, and a demand. A subset of the tasks is feasible if the tasks can...... simultaneously send their demands from the source to the sink without violating the edge capacities. The goal is to select a feasible subset of the tasks that maximizes a submodular objective function. Our main result is an O(k log n)-approximation algorithm for Submodular UFP on trees where k denotes...... the pathwidth of the given tree. Since every tree has pathwidth O(log n), we obtain an O(log2 n) approximation for arbitrary trees. This is the first non-trivial approximation guarantee for the problem and it matches the best approximation known for UFP on trees with a linear objective function. Our main...

  18. Tri-maximal vs. bi-maximal neutrino mixing

    International Nuclear Information System (INIS)

    Scott, W.G

    2000-01-01

    It is argued that data from atmospheric and solar neutrino experiments point strongly to tri-maximal or bi-maximal lepton mixing. While ('optimised') bi-maximal mixing gives an excellent a posteriori fit to the data, tri-maximal mixing is an a priori hypothesis, which is not excluded, taking account of terrestrial matter effects

  19. 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.

  20. MAXIM: The Blackhole Imager

    Science.gov (United States)

    Gendreau, Keith; Cash, Webster; Gorenstein, Paul; Windt, David; Kaaret, Phil; Reynolds, Chris

    2004-01-01

    The Beyond Einstein Program in NASA's Office of Space Science Structure and Evolution of the Universe theme spells out the top level scientific requirements for a Black Hole Imager in its strategic plan. The MAXIM mission will provide better than one tenth of a microarcsecond imaging in the X-ray band in order to satisfy these requirements. We will overview the driving requirements to achieve these goals and ultimately resolve the event horizon of a supermassive black hole. We will present the current status of this effort that includes a study of a baseline design as well as two alternative approaches.

  1. Social group utility maximization

    CERN Document Server

    Gong, Xiaowen; Yang, Lei; Zhang, Junshan

    2014-01-01

    This SpringerBrief explains how to leverage mobile users' social relationships to improve the interactions of mobile devices in mobile networks. It develops a social group utility maximization (SGUM) framework that captures diverse social ties of mobile users and diverse physical coupling of mobile devices. Key topics include random access control, power control, spectrum access, and location privacy.This brief also investigates SGUM-based power control game and random access control game, for which it establishes the socially-aware Nash equilibrium (SNE). It then examines the critical SGUM-b

  2. 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.

  3. 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.

  4. Reconciliation with non-binary species trees.

    Science.gov (United States)

    Vernot, Benjamin; Stolzer, Maureen; Goldman, Aiton; Durand, Dannie

    2008-10-01

    Reconciliation extracts information from the topological incongruence between gene and species trees to infer duplications and losses in the history of a gene family. The inferred duplication-loss histories provide valuable information for a broad range of biological applications, including ortholog identification, estimating gene duplication times, and rooting and correcting gene trees. While reconciliation for binary trees is a tractable and well studied problem, there are no algorithms for reconciliation with non-binary species trees. Yet a striking proportion of species trees are non-binary. For example, 64% of branch points in the NCBI taxonomy have three or more children. When applied to non-binary species trees, current algorithms overestimate the number of duplications because they cannot distinguish between duplication and incomplete lineage sorting. We present the first algorithms for reconciling binary gene trees with non-binary species trees under a duplication-loss parsimony model. Our algorithms utilize an efficient mapping from gene to species trees to infer the minimum number of duplications in O(|V(G) | x (k(S) + h(S))) time, where |V(G)| is the number of nodes in the gene tree, h(S) is the height of the species tree and k(S) is the size of its largest polytomy. We present a dynamic programming algorithm which also minimizes the total number of losses. Although this algorithm is exponential in the size of the largest polytomy, it performs well in practice for polytomies with outdegree of 12 or less. We also present a heuristic which estimates the minimal number of losses in polynomial time. In empirical tests, this algorithm finds an optimal loss history 99% of the time. Our algorithms have been implemented in NOTUNG, a robust, production quality, tree-fitting program, which provides a graphical user interface for exploratory analysis and also supports automated, high-throughput analysis of large data sets.

  5. 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.

  6. 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.

  7. 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

  8. Rooting gene trees without outgroups: EP rooting.

    Science.gov (United States)

    Sinsheimer, Janet S; Little, Roderick J A; Lake, James A

    2012-01-01

    Gene sequences are routinely used to determine the topologies of unrooted phylogenetic trees, but many of the most important questions in evolution require knowing both the topologies and the roots of trees. However, general algorithms for calculating rooted trees from gene and genomic sequences in the absence of gene paralogs are few. Using the principles of evolutionary parsimony (EP) (Lake JA. 1987a. A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol Biol Evol. 4:167-181) and its extensions (Cavender, J. 1989. Mechanized derivation of linear invariants. Mol Biol Evol. 6:301-316; Nguyen T, Speed TP. 1992. A derivation of all linear invariants for a nonbalanced transversion model. J Mol Evol. 35:60-76), we explicitly enumerate all linear invariants that solely contain rooting information and derive algorithms for rooting gene trees directly from gene and genomic sequences. These new EP linear rooting invariants allow one to determine rooted trees, even in the complete absence of outgroups and gene paralogs. EP rooting invariants are explicitly derived for three taxon trees, and rules for their extension to four or more taxa are provided. The method is demonstrated using 18S ribosomal DNA to illustrate how the new animal phylogeny (Aguinaldo AMA et al. 1997. Evidence for a clade of nematodes, arthropods, and other moulting animals. Nature 387:489-493; Lake JA. 1990. Origin of the metazoa. Proc Natl Acad Sci USA 87:763-766) may be rooted directly from sequences, even when they are short and paralogs are unavailable. These results are consistent with the current root (Philippe H et al. 2011. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470:255-260).

  9. 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.

  10. Flowering Trees

    Indian Academy of Sciences (India)

    Flowering Trees. Boswellia serrata Roxb. ex Colebr. (Indian Frankincense tree) of Burseraceae is a large-sized deciduous tree that is native to India. Bark is thin, greenish-ash-coloured that exfoliates into smooth papery flakes. Stem exudes pinkish resin ... Fruit is a three-valved capsule. A green gum-resin exudes from the ...

  11. Flowering Trees

    Indian Academy of Sciences (India)

    IAS Admin

    Flowering Trees. Ailanthus excelsa Roxb. (INDIAN TREE OF. HEAVEN) of Simaroubaceae is a lofty tree with large pinnately compound alternate leaves, which are ... inflorescences, unisexual and greenish-yellow. Fruits are winged, wings many-nerved. Wood is used in making match sticks. 1. Male flower; 2. Female flower.

  12. Flowering Trees

    Indian Academy of Sciences (India)

    Flowering Trees. Gyrocarpus americanus Jacq. (Helicopter Tree) of Hernandiaceae is a moderate size deciduous tree that grows to about 12 m in height with a smooth, shining, greenish-white bark. The leaves are ovate, rarely irregularly ... flowers which are unpleasant smelling. Fruit is a woody nut with two long thin wings.

  13. Flowering Trees

    Indian Academy of Sciences (India)

    More Details Fulltext PDF. Volume 8 Issue 8 August 2003 pp 112-112 Flowering Trees. Zizyphus jujuba Lam. of Rhamnaceae · More Details Fulltext PDF. Volume 8 Issue 9 September 2003 pp 97-97 Flowering Trees. Moringa oleifera · More Details Fulltext PDF. Volume 8 Issue 10 October 2003 pp 100-100 Flowering Trees.

  14. Phylogenetic tree reconstruction accuracy and model fit when proportions of variable sites change across the tree.

    Science.gov (United States)

    Shavit Grievink, Liat; Penny, David; Hendy, Michael D; Holland, Barbara R

    2010-05-01

    Commonly used phylogenetic models assume a homogeneous process through time in all parts of the tree. However, it is known that these models can be too simplistic as they do not account for nonhomogeneous lineage-specific properties. In particular, it is now widely recognized that as constraints on sequences evolve, the proportion and positions of variable sites can vary between lineages causing heterotachy. The extent to which this model misspecification affects tree reconstruction is still unknown. Here, we evaluate the effect of changes in the proportions and positions of variable sites on model fit and tree estimation. We consider 5 current models of nucleotide sequence evolution in a Bayesian Markov chain Monte Carlo framework as well as maximum parsimony (MP). We show that for a tree with 4 lineages where 2 nonsister taxa undergo a change in the proportion of variable sites tree reconstruction under the best-fitting model, which is chosen using a relative test, often results in the wrong tree. In this case, we found that an absolute test of model fit is a better predictor of tree estimation accuracy. We also found further evidence that MP is not immune to heterotachy. In addition, we show that increased sampling of taxa that have undergone a change in proportion and positions of variable sites is critical for accurate tree reconstruction.

  15. 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.

  16. 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.

  17. 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.

  18. Maximal Bell's inequality violation for non-maximal entanglement

    International Nuclear Information System (INIS)

    Kobayashi, M.; Khanna, F.; Mann, A.; Revzen, M.; Santana, A.

    2004-01-01

    Bell's inequality violation (BIQV) for correlations of polarization is studied for a product state of two two-mode squeezed vacuum (TMSV) states. The violation allowed is shown to attain its maximal limit for all values of the squeezing parameter, ζ. We show via an explicit example that a state whose entanglement is not maximal allow maximal BIQV. The Wigner function of the state is non-negative and the average value of either polarization is nil

  19. Tree compression with top trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Landau, Gad M.

    2013-01-01

    We introduce a new compression scheme for labeled trees based on top trees [3]. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast...

  20. Tree compression with top trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Landau, Gad M.

    2015-01-01

    We introduce a new compression scheme for labeled trees based on top trees. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast...

  1. Maximally Symmetric Composite Higgs Models.

    Science.gov (United States)

    Csáki, Csaba; Ma, Teng; Shu, Jing

    2017-09-29

    Maximal symmetry is a novel tool for composite pseudo Goldstone boson Higgs models: it is a remnant of an enhanced global symmetry of the composite fermion sector involving a twisting with the Higgs field. Maximal symmetry has far-reaching consequences: it ensures that the Higgs potential is finite and fully calculable, and also minimizes the tuning. We present a detailed analysis of the maximally symmetric SO(5)/SO(4) model and comment on its observational consequences.

  2. Principles of maximally classical and maximally realistic quantum ...

    Indian Academy of Sciences (India)

    Principles of maximally classical and maximally realistic quantum mechanics. S M ROY. Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India. Abstract. Recently Auberson, Mahoux, Roy and Singh have proved a long standing conjecture of Roy and Singh: In 2N-dimensional phase space, ...

  3. 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.

  4. 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...

  5. Longest common extensions in trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gawrychowski, Pawel; Gørtz, Inge Li

    2016-01-01

    to trees and suggest a few applications of LCE in trees to tries and XML databases. Given a labeled and rooted tree T of size n, the goal is to preprocess T into a compact data structure that support the following LCE queries between subpaths and subtrees in T. Let v1, v2, w1, and w2 be nodes of T...... such that w1 and w2 are descendants of v1 and v2 respectively. - LCEPP(v1, w1, v2, w2): (path-path LCE) return the longest common prefix of the paths v1 ~→ w1 and v2 ~→ w2. - LCEPT(v1, w1, v2): (path-tree LCE) return maximal path-path LCE of the path v1 ~→ w1 and any path from v2 to a descendant leaf. - LCETT......(v1, v2): (tree-tree LCE) return a maximal path-path LCE of any pair of paths from v1 and v2 to descendant leaves. We present the first non-trivial bounds for supporting these queries. For LCEPP queries, we present a linear-space solution with O(log* n) query time. For LCEPT queries, we present...

  6. Longest Common Extensions in Trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gawrychowski, Pawel; Gørtz, Inge Li

    2015-01-01

    to trees and suggest a few applications of LCE in trees to tries and XML databases. Given a labeled and rooted tree T of size n, the goal is to preprocess T into a compact data structure that support the following LCE queries between subpaths and subtrees in T. Let v1, v2, w1, and w2 be nodes of T...... such that w1 and w2 are descendants of v1 and v2 respectively. - LCEPP(v1, w1, v2, w2): (path-path LCE) return the longest common prefix of the paths v1 ~→ w1 and v2 ~→ w2. - LCEPT(v1, w1, v2): (path-tree LCE) return maximal path-path LCE of the path v1 ~→ w1 and any path from v2 to a descendant leaf. - LCETT......(v1, v2): (tree-tree LCE) return a maximal path-path LCE of any pair of paths from v1 and v2 to descendant leaves. We present the first non-trivial bounds for supporting these queries. For LCEPP queries, we present a linear-space solution with O(log* n) query time. For LCEPT queries, we present...

  7. The key kinematic determinants of undulatory underwater swimming at maximal velocity.

    Science.gov (United States)

    Connaboy, Chris; Naemi, Roozbeh; Brown, Susan; Psycharakis, Stelios; McCabe, Carla; Coleman, Simon; Sanders, Ross

    2016-01-01

    The optimisation of undulatory underwater swimming is highly important in competitive swimming performance. Nineteen kinematic variables were identified from previous research undertaken to assess undulatory underwater swimming performance. The purpose of the present study was to determine which kinematic variables were key to the production of maximal undulatory underwater swimming velocity. Kinematic data at maximal undulatory underwater swimming velocity were collected from 17 skilled swimmers. A series of separate backward-elimination analysis of covariance models was produced with cycle frequency and cycle length as dependent variables (DVs) and participant as a fixed factor, as including cycle frequency and cycle length would explain 100% of the maximal swimming velocity variance. The covariates identified in the cycle-frequency and cycle-length models were used to form the saturated model for maximal swimming velocity. The final parsimonious model identified three covariates (maximal knee joint angular velocity, maximal ankle angular velocity and knee range of movement) as determinants of the variance in maximal swimming velocity (adjusted-r2 = 0.929). However, when participant was removed as a fixed factor there was a large reduction in explained variance (adjusted r2 = 0.397) and only maximal knee joint angular velocity continued to contribute significantly, highlighting its importance to the production of maximal swimming velocity. The reduction in explained variance suggests an emphasis on inter-individual differences in undulatory underwater swimming technique and/or anthropometry. Future research should examine the efficacy of other anthropometric, kinematic and coordination variables to better understand the production of maximal swimming velocity and consider the importance of individual undulatory underwater swimming techniques when interpreting the data.

  8. Tree Nut Allergies

    Science.gov (United States)

    ... Blog Vision Awards Common Allergens Tree Nut Allergy Tree Nut Allergy Learn about tree nut allergy, how ... a Tree Nut Label card . Allergic Reactions to Tree Nuts Tree nuts can cause a severe and ...

  9. Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference.

    Science.gov (United States)

    Chernomor, Olga; Minh, Bui Quang; von Haeseler, Arndt

    2015-12-01

    In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference.

  10. Maximizing and customer loyalty: Are maximizers less loyal?

    Directory of Open Access Journals (Sweden)

    Linda Lai

    2011-06-01

    Full Text Available Despite their efforts to choose the best of all available solutions, maximizers seem to be more inclined than satisficers to regret their choices and to experience post-decisional dissonance. Maximizers may therefore be expected to change their decisions more frequently and hence exhibit lower customer loyalty to providers of products and services compared to satisficers. Findings from the study reported here (N = 1978 support this prediction. Maximizers reported significantly higher intentions to switch to another service provider (television provider than satisficers. Maximizers' intentions to switch appear to be intensified and mediated by higher proneness to regret, increased desire to discuss relevant choices with others, higher levels of perceived knowledge of alternatives, and higher ego involvement in the end product, compared to satisficers. Opportunities for future research are suggested.

  11. Implications of maximal Jarlskog invariant and maximal CP violation

    International Nuclear Information System (INIS)

    Rodriguez-Jauregui, E.; Universidad Nacional Autonoma de Mexico

    2001-04-01

    We argue here why CP violating phase Φ in the quark mixing matrix is maximal, that is, Φ=90 . In the Standard Model CP violation is related to the Jarlskog invariant J, which can be obtained from non commuting Hermitian mass matrices. In this article we derive the conditions to have Hermitian mass matrices which give maximal Jarlskog invariant J and maximal CP violating phase Φ. We find that all squared moduli of the quark mixing elements have a singular point when the CP violation phase Φ takes the value Φ=90 . This special feature of the Jarlskog invariant J and the quark mixing matrix is a clear and precise indication that CP violating Phase Φ is maximal in order to let nature treat democratically all of the quark mixing matrix moduli. (orig.)

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Phenomenology of maximal and near-maximal lepton mixing

    International Nuclear Information System (INIS)

    Gonzalez-Garcia, M. C.; Pena-Garay, Carlos; Nir, Yosef; Smirnov, Alexei Yu.

    2001-01-01

    The possible existence of maximal or near-maximal lepton mixing constitutes an intriguing challenge for fundamental theories of flavor. We study the phenomenological consequences of maximal and near-maximal mixing of the electron neutrino with other (x=tau and/or muon) neutrinos. We describe the deviations from maximal mixing in terms of a parameter ε(equivalent to)1-2sin 2 θ ex and quantify the present experimental status for |ε| e mixing comes from solar neutrino experiments. We find that the global analysis of solar neutrino data allows maximal mixing with confidence level better than 99% for 10 -8 eV 2 ∼ 2 ∼ -7 eV 2 . In the mass ranges Δm 2 ∼>1.5x10 -5 eV 2 and 4x10 -10 eV 2 ∼ 2 ∼ -7 eV 2 the full interval |ε| e mixing in atmospheric neutrinos, supernova neutrinos, and neutrinoless double beta decay

  20. Flowering Trees

    Indian Academy of Sciences (India)

    medium-sized handsome tree with a straight bole that branches at the top. Leaves are once pinnate, with two to three pairs of leaflets. Young parts of the tree are velvety. Inflorescence is a branched raceme borne at the branch ends. Flowers are large, white, attractive, and fragrant. Corolla is funnel-shaped. Fruit is an ...

  1. Flowering Trees

    Indian Academy of Sciences (India)

    Cassia siamia Lamk. (Siamese tree senna) of Caesalpiniaceae is a small or medium size handsome tree. Leaves are alternate, pinnately compound and glandular, upto 18 cm long with 8–12 pairs of leaflets. Inflorescence is axillary or terminal and branched. Flowering lasts for a long period from March to February. Fruit is ...

  2. Flowering Trees

    Indian Academy of Sciences (India)

    Flowering Trees. Cerbera manghasL. (SEA MANGO) of Apocynaceae is a medium-sized evergreen coastal tree with milky latex. The bark is grey-brown, thick and ... Fruit is large. (5–10 cm long), oval containing two flattened seeds and resembles a mango, hence the name Mangas or. Manghas. Leaves and fruits contain ...

  3. Flowering Trees

    Indian Academy of Sciences (India)

    user

    Flowering Trees. Gliricidia sepium(Jacq.) Kunta ex Walp. (Quickstick) of Fabaceae is a small deciduous tree with. Pinnately compound leaves. Flower are prroduced in large number in early summer on terminal racemes. They are attractive, pinkish-white and typically like bean flowers. Fruit is a few-seeded flat pod.

  4. Flowering Trees

    Indian Academy of Sciences (India)

    Flowering Trees. Acrocarpus fraxinifolius Wight & Arn. (PINK CEDAR, AUSTRALIAN ASH) of. Caesalpiniaceae is a lofty unarmed deciduous native tree that attains a height of 30–60m with buttresses. Bark is thin and light grey. Leaves are compound and bright red when young. Flowers in dense, erect, axillary racemes.

  5. Talking Trees

    Science.gov (United States)

    Tolman, Marvin

    2005-01-01

    Students love outdoor activities and will love them even more when they build confidence in their tree identification and measurement skills. Through these activities, students will learn to identify the major characteristics of trees and discover how the pace--a nonstandard measuring unit--can be used to estimate not only distances but also the…

  6. Drawing Trees

    DEFF Research Database (Denmark)

    Halkjær From, Andreas; Schlichtkrull, Anders; Villadsen, Jørgen

    2018-01-01

    We formally prove in Isabelle/HOL two properties of an algorithm for laying out trees visually. The first property states that removing layout annotations recovers the original tree. The second property states that nodes are placed at least a unit of distance apart. We have yet to formalize three...

  7. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    Grevillea robusta A. Cunn. ex R. Br. (Sil- ver Oak) of Proteaceae is a daintily lacy ornamental tree while young and growing into a mighty tree (45 m). Young shoots are silvery grey and the leaves are fern- like. Flowers are golden-yellow in one- sided racemes (10 cm). Fruit is a boat- shaped, woody follicle.

  8. Maximal quantum Fisher information matrix

    International Nuclear Information System (INIS)

    Chen, Yu; Yuan, Haidong

    2017-01-01

    We study the existence of the maximal quantum Fisher information matrix in the multi-parameter quantum estimation, which bounds the ultimate precision limit. We show that when the maximal quantum Fisher information matrix exists, it can be directly obtained from the underlying dynamics. Examples are then provided to demonstrate the usefulness of the maximal quantum Fisher information matrix by deriving various trade-off relations in multi-parameter quantum estimation and obtaining the bounds for the scalings of the precision limit. (paper)

  9. Maximize x(a - x)

    Science.gov (United States)

    Lange, L. H.

    1974-01-01

    Five different methods for determining the maximizing condition for x(a - x) are presented. Included is the ancient Greek version and a method attributed to Fermat. None of the proofs use calculus. (LS)

  10. On the maximal diphoton width

    CERN Document Server

    Salvio, Alberto; Strumia, Alessandro; Urbano, Alfredo

    2016-01-01

    Motivated by the 750 GeV diphoton excess found at LHC, we compute the maximal width into $\\gamma\\gamma$ that a neutral scalar can acquire through a loop of charged fermions or scalars as function of the maximal scale at which the theory holds, taking into account vacuum (meta)stability bounds. We show how an extra gauge symmetry can qualitatively weaken such bounds, and explore collider probes and connections with Dark Matter.

  11. New approaches to phylogenetic tree search and their application to large numbers of protein alignments.

    Science.gov (United States)

    Whelan, Simon

    2007-10-01

    Phylogenetic tree estimation plays a critical role in a wide variety of molecular studies, including molecular systematics, phylogenetics, and comparative genomics. Finding the optimal tree relating a set of sequences using score-based (optimality criterion) methods, such as maximum likelihood and maximum parsimony, may require all possible trees to be considered, which is not feasible even for modest numbers of sequences. In practice, trees are estimated using heuristics that represent a trade-off between topological accuracy and speed. I present a series of novel algorithms suitable for score-based phylogenetic tree reconstruction that demonstrably improve the accuracy of tree estimates while maintaining high computational speeds. The heuristics function by allowing the efficient exploration of large numbers of trees through novel hill-climbing and resampling strategies. These heuristics, and other computational approximations, are implemented for maximum likelihood estimation of trees in the program Leaphy, and its performance is compared to other popular phylogenetic programs. Trees are estimated from 4059 different protein alignments using a selection of phylogenetic programs and the likelihoods of the tree estimates are compared. Trees estimated using Leaphy are found to have equal to or better likelihoods than trees estimated using other phylogenetic programs in 4004 (98.6%) families and provide a unique best tree that no other program found in 1102 (27.1%) families. The improvement is particularly marked for larger families (80 to 100 sequences), where Leaphy finds a unique best tree in 81.7% of families.

  12. Which trees should be removed in thinning?

    Directory of Open Access Journals (Sweden)

    Timo Pukkala

    2015-12-01

    Full Text Available Background: In economically optimal management, trees that are removed in a thinning treatment should be selected on the basis of their value, relative value increment and the effect of removal on the growth of remaining trees. Large valuable trees with decreased value increment should be removed, especially when they overtop smaller trees. Methods: This study optimized the tree selection rule in the thinning treatments of continuous cover management when the aim is to maximize the profitability of forest management. The weights of three criteria (stem value, relative value increment and effect of removal on the competition of remaining trees were optimized together with thinning intervals. Results and conclusions: The results confirmed the hypothesis that optimal thinning involves removing predominantly large trees. Increasing stumpage value, decreasing relative value increment, and increasing competitive influence increased the likelihood that removal is optimal decision. However, if the spatial distribution of trees is irregular, it is optimal to leave large trees in sparse places and remove somewhat smaller trees from dense places. However, the benefit of optimal thinning, as compared to diameter limit cutting is not usually large in pure one-species stands. On the contrary, removing the smallest trees from the stand may lead to significant (30–40 % reductions in the net present value of harvest incomes. Keywords: Continuous cover forestry, Tree selection, High thinning, Optimal management, Spatial distribution, Spatial growth model

  13. Phylogenetic trees

    OpenAIRE

    Baños, Hector; Bushek, Nathaniel; Davidson, Ruth; Gross, Elizabeth; Harris, Pamela E.; Krone, Robert; Long, Colby; Stewart, Allen; Walker, Robert

    2016-01-01

    We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees can be used to calculate a generating set for a phylogenetic ideal as well as a lower bound for its dimension. Finally, we show how methods within the package can be used to compute a generating set for the join of any two ideals.

  14. 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.

  15. 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.

  16. 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

  17. Electron Tree

    DEFF Research Database (Denmark)

    Appelt, Ane L; Rønde, Heidi S

    2013-01-01

    The photo shows a close-up of a Lichtenberg figure – popularly called an “electron tree” – produced in a cylinder of polymethyl methacrylate (PMMA). Electron trees are created by irradiating a suitable insulating material, in this case PMMA, with an intense high energy electron beam. Upon discharge......, during dielectric breakdown in the material, the electrons generate branching chains of fractures on leaving the PMMA, producing the tree pattern seen. To be able to create electron trees with a clinical linear accelerator, one needs to access the primary electron beam used for photon treatments. We...... appropriated a linac that was being decommissioned in our department and dismantled the head to circumvent the target and ion chambers. This is one of 24 electron trees produced before we had to stop the fun and allow the rest of the accelerator to be disassembled....

  18. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    shaped corolla. Fruit is large, ellipsoidal, green with a hard and smooth shell containing numerous flattened seeds, which are embedded in fleshy pulp. Calabash tree is commonly grown in the tropical gardens of the world as a botanical oddity.

  19. Maximization

    Directory of Open Access Journals (Sweden)

    A. Garmroodi Asil

    2017-09-01

    To further reduce the sulfur dioxide emission of the entire refining process, two scenarios of acid gas or air preheats are investigated when either of them is used simultaneously with the third enrichment scheme. The maximum overall sulfur recovery efficiency and highest combustion chamber temperature is slightly higher for acid gas preheats but air preheat is more favorable because it is more benign. To the best of our knowledge, optimization of the entire GTU + enrichment section and SRU processes has not been addressed previously.

  20. A fast method for calculating reliable event supports in tree reconciliations via Pareto optimality.

    Science.gov (United States)

    To, Thu-Hien; Jacox, Edwin; Ranwez, Vincent; Scornavacca, Celine

    2015-11-14

    Given a gene and a species tree, reconciliation methods attempt to retrieve the macro-evolutionary events that best explain the discrepancies between the two tree topologies. The DTL parsimonious approach searches for a most parsimonious reconciliation between a gene tree and a (dated) species tree, considering four possible macro-evolutionary events (speciation, duplication, transfer, and loss) with specific costs. Unfortunately, many events are erroneously predicted due to errors in the input trees, inappropriate input cost values or because of the existence of several equally parsimonious scenarios. It is thus crucial to provide a measure of the reliability for predicted events. It has been recently proposed that the reliability of an event can be estimated via its frequency in the set of most parsimonious reconciliations obtained using a variety of reasonable input cost vectors. To compute such a support, a straightforward but time-consuming approach is to generate the costs slightly departing from the original ones, independently compute the set of all most parsimonious reconciliations for each vector, and combine these sets a posteriori. Another proposed approach uses Pareto-optimality to partition cost values into regions which induce reconciliations with the same number of DTL events. The support of an event is then defined as its frequency in the set of regions. However, often, the number of regions is not large enough to provide reliable supports. We present here a method to compute efficiently event supports via a polynomial-sized graph, which can represent all reconciliations for several different costs. Moreover, two methods are proposed to take into account alternative input costs: either explicitly providing an input cost range or allowing a tolerance for the over cost of a reconciliation. Our methods are faster than the region based method, substantially faster than the sampling-costs approach, and have a higher event-prediction accuracy on

  1. Maximizing Entropy over Markov Processes

    DEFF Research Database (Denmark)

    Biondi, Fabrizio; Legay, Axel; Nielsen, Bo Friis

    2013-01-01

    The channel capacity of a deterministic system with confidential data is an upper bound on the amount of bits of data an attacker can learn from the system. We encode all possible attacks to a system using a probabilistic specification, an Interval Markov Chain. Then the channel capacity...... as a reward function, a polynomial algorithm to verify the existence of an system maximizing entropy among those respecting a specification, a procedure for the maximization of reward functions over Interval Markov Chains and its application to synthesize an implementation maximizing entropy. We show how...... to use Interval Markov Chains to model abstractions of deterministic systems with confidential data, and use the above results to compute their channel capacity. These results are a foundation for ongoing work on computing channel capacity for abstractions of programs derived from code....

  2. Maximizing entropy over Markov processes

    DEFF Research Database (Denmark)

    Biondi, Fabrizio; Legay, Axel; Nielsen, Bo Friis

    2014-01-01

    The channel capacity of a deterministic system with confidential data is an upper bound on the amount of bits of data an attacker can learn from the system. We encode all possible attacks to a system using a probabilistic specification, an Interval Markov Chain. Then the channel capacity...... as a reward function, a polynomial algorithm to verify the existence of a system maximizing entropy among those respecting a specification, a procedure for the maximization of reward functions over Interval Markov Chains and its application to synthesize an implementation maximizing entropy. We show how...... to use Interval Markov Chains to model abstractions of deterministic systems with confidential data, and use the above results to compute their channel capacity. These results are a foundation for ongoing work on computing channel capacity for abstractions of programs derived from code. © 2014 Elsevier...

  3. 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

  4. TESTING TREE-CLASSIFIER VARIANTS AND ALTERNATE MODELING METHODOLOGIES IN THE EAST GREAT BASIN MAPPING UNIT OF THE SOUTHWEST REGIONAL GAP ANALYSIS PROJECT (SW REGAP)

    Science.gov (United States)

    We tested two methods for dataset generation and model construction, and three tree-classifier variants to identify the most parsimonious and thematically accurate mapping methodology for the SW ReGAP project. Competing methodologies were tested in the East Great Basin mapping un...

  5. Treelink: data integration, clustering and visualization of phylogenetic trees.

    Science.gov (United States)

    Allende, Christian; Sohn, Erik; Little, Cedric

    2015-12-29

    Phylogenetic trees are central to a wide range of biological studies. In many of these studies, tree nodes need to be associated with a variety of attributes. For example, in studies concerned with viral relationships, tree nodes are associated with epidemiological information, such as location, age and subtype. Gene trees used in comparative genomics are usually linked with taxonomic information, such as functional annotations and events. A wide variety of tree visualization and annotation tools have been developed in the past, however none of them are intended for an integrative and comparative analysis. Treelink is a platform-independent software for linking datasets and sequence files to phylogenetic trees. The application allows an automated integration of datasets to trees for operations such as classifying a tree based on a field or showing the distribution of selected data attributes in branches and leafs. Genomic and proteonomic sequences can also be linked to the tree and extracted from internal and external nodes. A novel clustering algorithm to simplify trees and display the most divergent clades was also developed, where validation can be achieved using the data integration and classification function. Integrated geographical information allows ancestral character reconstruction for phylogeographic plotting based on parsimony and likelihood algorithms. Our software can successfully integrate phylogenetic trees with different data sources, and perform operations to differentiate and visualize those differences within a tree. File support includes the most popular formats such as newick and csv. Exporting visualizations as images, cluster outputs and genomic sequences is supported. Treelink is available as a web and desktop application at http://www.treelinkapp.com .

  6. Chamaebatiaria millefolium (Torr.) Maxim.: fernbush

    Science.gov (United States)

    Nancy L. Shaw; Emerenciana G. Hurd

    2008-01-01

    Fernbush - Chamaebatiaria millefolium (Torr.) Maxim. - the only species in its genus, is endemic to the Great Basin, Colorado Plateau, and adjacent areas of the western United States. It is an upright, generally multistemmed, sweetly aromatic shrub 0.3 to 2 m tall. Bark of young branches is brown and becomes smooth and gray with age. Leaves are leathery, alternate,...

  7. Flowering Trees

    Indian Academy of Sciences (India)

    deciduous tree with irregularly-shaped trunk, greyish-white scaly bark and milky latex. Leaves in opposite pairs are simple, oblong and whitish beneath. Flowers that occur in branched inflorescence are white, 2–. 3cm across and fragrant. Calyx is glandular inside. Petals bear numerous linear white scales, the corollary.

  8. Flowering Trees

    Indian Academy of Sciences (India)

    Berrya cordifolia (Willd.) Burret (Syn. B. ammonilla Roxb.) – Trincomali Wood of Tiliaceae is a tall evergreen tree with straight trunk, smooth brownish-grey bark and simple broad leaves. Inflorescence is much branched with white flowers. Stamens are many with golden yellow anthers. Fruit is a capsule with six spreading ...

  9. Flowering Trees

    Indian Academy of Sciences (India)

    Canthium parviflorum Lam. of Rubiaceae is a large shrub that often grows into a small tree with conspicuous spines. Leaves are simple, in pairs at each node and are shiny. Inflorescence is an axillary few-flowered cymose fascicle. Flowers are small (less than 1 cm across), 4-merous and greenish-white. Fruit is ellipsoid ...

  10. Flowering Trees

    Indian Academy of Sciences (India)

    sriranga

    Hook.f. ex Brandis (Yellow. Cadamba) of Rubiaceae is a large and handsome deciduous tree. Leaves are simple, large, orbicular, and drawn abruptly at the apex. Flowers are small, yellowish and aggregate into small spherical heads. The corolla is funnel-shaped with five stamens inserted at its mouth. Fruit is a capsule.

  11. Flowering Trees

    Indian Academy of Sciences (India)

    Celtis tetrandra Roxb. of Ulmaceae is a moderately large handsome deciduous tree with green branchlets and grayish-brown bark. Leaves are simple with three to four secondary veins running parallel to the mid vein. Flowers are solitary, male, female and bisexual and inconspicuous. Fruit is berry-like, small and globose ...

  12. Flowering Trees

    Indian Academy of Sciences (India)

    IAS Admin

    Aglaia elaeagnoidea (A.Juss.) Benth. of Meliaceae is a small-sized evergreen tree of both moist and dry deciduous forests. The leaves are alternate and pinnately compound, terminating in a single leaflet. Leaflets are more or less elliptic with entire margin. Flowers are small on branched inflorescence. Fruit is a globose ...

  13. Flowering Trees

    Indian Academy of Sciences (India)

    user

    Flowers are borne on stiff bunches terminally on short shoots. They are 2-3 cm across, white, sweet-scented with light-brown hairy sepals and many stamens. Loquat fruits are round or pear-shaped, 3-5 cm long and are edible. A native of China, Loquat tree is grown in parks as an ornamental and also for its fruits.

  14. Flowering Trees

    Indian Academy of Sciences (India)

    mid-sized slow-growing evergreen tree with spreading branches that form a dense crown. The bark is smooth, thick, dark and flakes off in large shreds. Leaves are thick, oblong, leathery and bright red when young. The female flowers are drooping and are larger than male flowers. Fruit is large, red in color and velvety.

  15. Flowering Trees

    Indian Academy of Sciences (India)

    Andira inermis (wright) DC. , Dog Almond of Fabaceae is a handsome lofty evergreen tree. Leaves are alternate and pinnately compound with 4–7 pairs of leaflets. Flowers are fragrant and are borne on compact branched inflorescences. Fruit is ellipsoidal one-seeded drupe that is peculiar to members of this family.

  16. Flowering Trees

    Indian Academy of Sciences (India)

    narrow towards base. Flowers are large and attrac- tive, but emit unpleasant foetid smell. They appear in small numbers on erect terminal clusters and open at night. Stamens are numerous, pink or white. Style is slender and long, terminating in a small stigma. Fruit is green, ovoid and indistinctly lobed. Flowering Trees.

  17. Flowering Trees

    Indian Academy of Sciences (India)

    Muntingia calabura L. (Singapore cherry) of. Elaeocarpaceae is a medium size handsome ever- green tree. Leaves are simple and alternate with sticky hairs. Flowers are bisexual, bear numerous stamens, white in colour and arise in the leaf axils. Fruit is a berry, edible with several small seeds embedded in a fleshy pulp ...

  18. ~{owering 'Trees

    Indian Academy of Sciences (India)

    . Stamens are fused into a purple staminal tube that is toothed. Fruit is about 0.5 in. across, nearly globose, generally 5-seeded, green but yellow when ripe, quite smooth at first but wrinkled in drying, remaining long on the tree ajier ripening.

  19. Tree Mortality

    Science.gov (United States)

    Mark J. Ambrose

    2012-01-01

    Tree mortality is a natural process in all forest ecosystems. However, extremely high mortality also can be an indicator of forest health issues. On a regional scale, high mortality levels may indicate widespread insect or disease problems. High mortality may also occur if a large proportion of the forest in a particular region is made up of older, senescent stands....

  20. Flowering Trees

    Indian Academy of Sciences (India)

    Guaiacum officinale L. (LIGNUM-VITAE) of Zygophyllaceae is a dense-crowned, squat, knobbly, rough and twisted medium-sized ev- ergreen tree with mottled bark. The wood is very hard and resinous. Leaves are compound. The leaflets are smooth, leathery, ovate-ellipti- cal and appear in two pairs. Flowers (about 1.5.

  1. IMNN: Information Maximizing Neural Networks

    Science.gov (United States)

    Charnock, Tom; Lavaux, Guilhem; Wandelt, Benjamin D.

    2018-04-01

    This software trains artificial neural networks to find non-linear functionals of data that maximize Fisher information: information maximizing neural networks (IMNNs). As compressing large data sets vastly simplifies both frequentist and Bayesian inference, important information may be inadvertently missed. Likelihood-free inference based on automatically derived IMNN summaries produces summaries that are good approximations to sufficient statistics. IMNNs are robustly capable of automatically finding optimal, non-linear summaries of the data even in cases where linear compression fails: inferring the variance of Gaussian signal in the presence of noise, inferring cosmological parameters from mock simulations of the Lyman-α forest in quasar spectra, and inferring frequency-domain parameters from LISA-like detections of gravitational waveforms. In this final case, the IMNN summary outperforms linear data compression by avoiding the introduction of spurious likelihood maxima.

  2. Is the β phase maximal?

    International Nuclear Information System (INIS)

    Ferrandis, Javier

    2005-01-01

    The current experimental determination of the absolute values of the CKM elements indicates that 2 vertical bar V ub /V cb V us vertical bar =(1-z), with z given by z=0.19+/-0.14. This fact implies that irrespective of the form of the quark Yukawa matrices, the measured value of the SM CP phase β is approximately the maximum allowed by the measured absolute values of the CKM elements. This is β=(π/6-z/3) for γ=(π/3+z/3), which implies α=π/2. Alternatively, assuming that β is exactly maximal and using the experimental measurement sin(2β)=0.726+/-0.037, the phase γ is predicted to be γ=(π/2-β)=66.3 o +/-1.7 o . The maximality of β, if confirmed by near-future experiments, may give us some clues as to the origin of CP violation

  3. Strategy to maximize maintenance operation

    OpenAIRE

    Espinoza, Michael

    2005-01-01

    This project presents a strategic analysis to maximize maintenance operations in Alcan Kitimat Works in British Columbia. The project studies the role of maintenance in improving its overall maintenance performance. It provides strategic alternatives and specific recommendations addressing Kitimat Works key strategic issues and problems. A comprehensive industry and competitive analysis identifies the industry structure and its competitive forces. In the mature aluminium industry, the bargain...

  4. Scalable Nonlinear AUC Maximization Methods

    OpenAIRE

    Khalid, Majdi; Ray, Indrakshi; Chitsaz, Hamidreza

    2017-01-01

    The area under the ROC curve (AUC) is a measure of interest in various machine learning and data mining applications. It has been widely used to evaluate classification performance on heavily imbalanced data. The kernelized AUC maximization machines have established a superior generalization ability compared to linear AUC machines because of their capability in modeling the complex nonlinear structure underlying most real world-data. However, the high training complexity renders the kernelize...

  5. Least Squares Methods for Equidistant Tree Reconstruction

    OpenAIRE

    Fahey, Conor; Hosten, Serkan; Krieger, Nathan; Timpe, Leslie

    2008-01-01

    UPGMA is a heuristic method identifying the least squares equidistant phylogenetic tree given empirical distance data among $n$ taxa. We study this classic algorithm using the geometry of the space of all equidistant trees with $n$ leaves, also known as the Bergman complex of the graphical matroid for the complete graph $K_n$. We show that UPGMA performs an orthogonal projection of the data onto a maximal cell of the Bergman complex. We also show that the equidistant tree with the least (Eucl...

  6. FLOUTING MAXIMS IN INDONESIA LAWAK KLUB CONVERSATION

    Directory of Open Access Journals (Sweden)

    Rahmawati Sukmaningrum

    2017-04-01

    Full Text Available This study aims to identify the types of maxims flouted in the conversation in famous comedy show, Indonesia Lawak Club. Likewise, it also tries to reveal the speakers‘ intention of flouting the maxim in the conversation during the show. The writers use descriptive qualitative method in conducting this research. The data is taken from the dialogue of Indonesia Lawak club and then analyzed based on Grice‘s cooperative principles. The researchers read the dialogue‘s transcripts, identify the maxims, and interpret the data to find the speakers‘ intention for flouting the maxims in the communication. The results show that there are four types of maxims flouted in the dialogue. Those are maxim of quality (23%, maxim of quantity (11%, maxim of manner (31%, and maxim of relevance (35. Flouting the maxims in the conversations is intended to make the speakers feel uncomfortable with the conversation, show arrogances, show disagreement or agreement, and ridicule other speakers.

  7. 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.

  8. Rooting the archaebacterial tree: the pivotal role of Thermococcus celer in archaebacterial evolution

    Science.gov (United States)

    Achenbach-Richter, L.; Gupta, R.; Zillig, W.; Woese, C. R.

    1988-01-01

    The sequence of the 16S ribosomal RNA gene from the archaebacterium Thermococcus celer shows the organism to be related to the methanogenic archaebacteria rather than to its phenotypic counterparts, the extremely thermophilic archaebacteria. This conclusion turns on the position of the root of the archaebacterial phylogenetic tree, however. The problems encountered in rooting this tree are analyzed in detail. Under conditions that suppress evolutionary noise both the parsimony and evolutionary distance methods yield a root location (using a number of eubacterial or eukaryotic outgroup sequences) that is consistent with that determined by an "internal rooting" method, based upon an (approximate) determination of relative evolutionary rates.

  9. Maximal Abelian sets of roots

    CERN Document Server

    Lawther, R

    2018-01-01

    In this work the author lets \\Phi be an irreducible root system, with Coxeter group W. He considers subsets of \\Phi which are abelian, meaning that no two roots in the set have sum in \\Phi \\cup \\{ 0 \\}. He classifies all maximal abelian sets (i.e., abelian sets properly contained in no other) up to the action of W: for each W-orbit of maximal abelian sets we provide an explicit representative X, identify the (setwise) stabilizer W_X of X in W, and decompose X into W_X-orbits. Abelian sets of roots are closely related to abelian unipotent subgroups of simple algebraic groups, and thus to abelian p-subgroups of finite groups of Lie type over fields of characteristic p. Parts of the work presented here have been used to confirm the p-rank of E_8(p^n), and (somewhat unexpectedly) to obtain for the first time the 2-ranks of the Monster and Baby Monster sporadic groups, together with the double cover of the latter. Root systems of classical type are dealt with quickly here; the vast majority of the present work con...

  10. Surface tree languages and parallel derivation trees

    NARCIS (Netherlands)

    Engelfriet, Joost

    1976-01-01

    The surface tree languages obtained by top-down finite state transformation of monadic trees are exactly the frontier-preserving homomorphic images of sets of derivation trees of ETOL systems. The corresponding class of tree transformation languages is therefore equal to the class of ETOL languages.

  11. Maximal independent set graph partitions for representations of body-centered cubic lattices

    DEFF Research Database (Denmark)

    Erleben, Kenny

    2009-01-01

    corresponding to the leaves of a quad-tree thus has a smaller memory foot-print. The adjacency information in the graph relieves one from going up and down the quad-tree when searching for neighbors. This results in constant time complexities for refinement and coarsening operations.......A maximal independent set graph data structure for a body-centered cubic lattice is presented. Refinement and coarsening operations are defined in terms of set-operations resulting in robust and easy implementation compared to a quad-tree-based implementation. The graph only stores information...

  12. 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

  13. Survival associated pathway identification with group Lp penalized global AUC maximization

    Directory of Open Access Journals (Sweden)

    Liu Zhenqiu

    2010-08-01

    Full Text Available Abstract It has been demonstrated that genes in a cell do not act independently. They interact with one another to complete certain biological processes or to implement certain molecular functions. How to incorporate biological pathways or functional groups into the model and identify survival associated gene pathways is still a challenging problem. In this paper, we propose a novel iterative gradient based method for survival analysis with group Lp penalized global AUC summary maximization. Unlike LASSO, Lp (p 1. We first extend Lp for individual gene identification to group Lp penalty for pathway selection, and then develop a novel iterative gradient algorithm for penalized global AUC summary maximization (IGGAUCS. This method incorporates the genetic pathways into global AUC summary maximization and identifies survival associated pathways instead of individual genes. The tuning parameters are determined using 10-fold cross validation with training data only. The prediction performance is evaluated using test data. We apply the proposed method to survival outcome analysis with gene expression profile and identify multiple pathways simultaneously. Experimental results with simulation and gene expression data demonstrate that the proposed procedures can be used for identifying important biological pathways that are related to survival phenotype and for building a parsimonious model for predicting the survival times.

  14. Trees are good, but…

    Science.gov (United States)

    E.G. McPherson; F. Ferrini

    2010-01-01

    We know that “trees are good,” and most people believe this to be true. But if this is so, why are so many trees neglected, and so many tree wells empty? An individual’s attitude toward trees may result from their firsthand encounters with specific trees. Understanding how attitudes about trees are shaped, particularly aversion to trees, is critical to the business of...

  15. Maximizing benefits from resource development

    International Nuclear Information System (INIS)

    Skjelbred, B.

    2002-01-01

    The main objectives of Norwegian petroleum policy are to maximize the value creation for the country, develop a national oil and gas industry, and to be at the environmental forefront of long term resource management and coexistence with other industries. The paper presents a graph depicting production and net export of crude oil for countries around the world for 2002. Norway produced 3.41 mill b/d and exported 3.22 mill b/d. Norwegian petroleum policy measures include effective regulation and government ownership, research and technology development, and internationalisation. Research and development has been in five priority areas, including enhanced recovery, environmental protection, deep water recovery, small fields, and the gas value chain. The benefits of internationalisation includes capitalizing on Norwegian competency, exploiting emerging markets and the assurance of long-term value creation and employment. 5 figs

  16. Maximizing synchronizability of duplex networks

    Science.gov (United States)

    Wei, Xiang; Emenheiser, Jeffrey; Wu, Xiaoqun; Lu, Jun-an; D'Souza, Raissa M.

    2018-01-01

    We study the synchronizability of duplex networks formed by two randomly generated network layers with different patterns of interlayer node connections. According to the master stability function, we use the smallest nonzero eigenvalue and the eigenratio between the largest and the second smallest eigenvalues of supra-Laplacian matrices to characterize synchronizability on various duplexes. We find that the interlayer linking weight and linking fraction have a profound impact on synchronizability of duplex networks. The increasingly large inter-layer coupling weight is found to cause either decreasing or constant synchronizability for different classes of network dynamics. In addition, negative node degree correlation across interlayer links outperforms positive degree correlation when most interlayer links are present. The reverse is true when a few interlayer links are present. The numerical results and understanding based on these representative duplex networks are illustrative and instructive for building insights into maximizing synchronizability of more realistic multiplex networks.

  17. 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.

  18. VIOLATION OF CONVERSATION MAXIM ON TV ADVERTISEMENTS

    Directory of Open Access Journals (Sweden)

    Desak Putu Eka Pratiwi

    2015-07-01

    Full Text Available Maxim is a principle that must be obeyed by all participants textually and interpersonally in order to have a smooth communication process. Conversation maxim is divided into four namely maxim of quality, maxim of quantity, maxim of relevance, and maxim of manner of speaking. Violation of the maxim may occur in a conversation in which the information the speaker has is not delivered well to his speaking partner. Violation of the maxim in a conversation will result in an awkward impression. The example of violation is the given information that is redundant, untrue, irrelevant, or convoluted. Advertisers often deliberately violate the maxim to create unique and controversial advertisements. This study aims to examine the violation of maxims in conversations of TV ads. The source of data in this research is food advertisements aired on TV media. Documentation and observation methods are applied to obtain qualitative data. The theory used in this study is a maxim theory proposed by Grice (1975. The results of the data analysis are presented with informal method. The results of this study show an interesting fact that the violation of maxim in a conversation found in the advertisement exactly makes the advertisements very attractive and have a high value.

  19. 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.

  20. Efficient FPT Algorithms for (Strict) Compatibility of Unrooted Phylogenetic Trees.

    Science.gov (United States)

    Baste, Julien; Paul, Christophe; Sau, Ignasi; Scornavacca, Celine

    2017-04-01

    In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species X; these relationships are often depicted via a phylogenetic tree-a tree having its leaves labeled bijectively by elements of X and without degree-2 nodes-called the "species tree." One common approach for reconstructing a species tree consists in first constructing several phylogenetic trees from primary data (e.g., DNA sequences originating from some species in X), and then constructing a single phylogenetic tree maximizing the "concordance" with the input trees. The obtained tree is our estimation of the species tree and, when the input trees are defined on overlapping-but not identical-sets of labels, is called "supertree." In this paper, we focus on two problems that are central when combining phylogenetic trees into a supertree: the compatibility and the strict compatibility problems for unrooted phylogenetic trees. These problems are strongly related, respectively, to the notions of "containing as a minor" and "containing as a topological minor" in the graph community. Both problems are known to be fixed parameter tractable in the number of input trees k, by using their expressibility in monadic second-order logic and a reduction to graphs of bounded treewidth. Motivated by the fact that the dependency on k of these algorithms is prohibitively large, we give the first explicit dynamic programming algorithms for solving these problems, both running in time [Formula: see text], where n is the total size of the input.

  1. Modular tree automata

    DEFF Research Database (Denmark)

    Bahr, Patrick

    2012-01-01

    Tree automata are traditionally used to study properties of tree languages and tree transformations. In this paper, we consider tree automata as the basis for modular and extensible recursion schemes. We show, using well-known techniques, how to derive from standard tree automata highly modular...

  2. Simple street tree sampling

    Science.gov (United States)

    David J. Nowak; Jeffrey T. Walton; James Baldwin; Jerry. Bond

    2015-01-01

    Information on street trees is critical for management of this important resource. Sampling of street tree populations provides an efficient means to obtain street tree population information. Long-term repeat measures of street tree samples supply additional information on street tree changes and can be used to report damages from catastrophic events. Analyses of...

  3. Hydrologic behaviour of the Lake of Monate (Italy): a parsimonious modelling strategy

    Science.gov (United States)

    Tomesani, Giulia; Soligno, Irene; Castellarin, Attilio; Baratti, Emanuele; Cervi, Federico; Montanari, Alberto

    2016-04-01

    the second year as validation data and we compared two calibration strategies which maximize two different objective functions: (1) Nash-Sutcliffe efficiency of simulated daily water-level fluctuations, NSE, and (2) linear correlation coefficient between daily series of simulated groundwater inflow and observed water table elevation multiplied by NSE. The validation exercise seems to point out the value of incorporating groundwater measurements for improving the reliability and robustness of the conceptual model.

  4. Molecular phylogenetic trees - On the validity of the Goodman-Moore augmentation algorithm

    Science.gov (United States)

    Holmquist, R.

    1979-01-01

    A response is made to the reply of Nei and Tateno (1979) to the letter of Holmquist (1978) supporting the validity of the augmentation algorithm of Moore (1977) in reconstructions of nucleotide substitutions by means of the maximum parsimony principle. It is argued that the overestimation of the augmented numbers of nucleotide substitutions (augmented distances) found by Tateno and Nei (1978) is due to an unrepresentative data sample and that it is only necessary that evolution be stochastically uniform in different regions of the phylogenetic network for the augmentation method to be useful. The importance of the average value of the true distance over all links is explained, and the relative variances of the true and augmented distances are calculated to be almost identical. The effects of topological changes in the phylogenetic tree on the augmented distance and the question of the correctness of ancestral sequences inferred by the method of parsimony are also clarified.

  5. Maximizing ROI (return on information)

    Energy Technology Data Exchange (ETDEWEB)

    McDonald, B.

    2000-05-01

    The role and importance of managing information are discussed, underscoring the importance by quoting from the report of the International Data Corporation, according to which Fortune 500 companies lost $ 12 billion in 1999 due to inefficiencies resulting from intellectual re-work, substandard performance , and inability to find knowledge resources. The report predicts that this figure will rise to $ 31.5 billion by 2003. Key impediments to implementing knowledge management systems are identified as : the cost and human resources requirement of deployment; inflexibility of historical systems to adapt to change; and the difficulty of achieving corporate acceptance of inflexible software products that require changes in 'normal' ways of doing business. The author recommends the use of model, document and rule-independent systems with a document centered interface (DCI), employing rapid application development (RAD) and object technologies and visual model development, which eliminate these problems, making it possible for companies to maximize their return on information (ROI), and achieve substantial savings in implementation costs.

  6. Maximizing the optical network capacity.

    Science.gov (United States)

    Bayvel, Polina; Maher, Robert; Xu, Tianhua; Liga, Gabriele; Shevchenko, Nikita A; Lavery, Domaniç; Alvarado, Alex; Killey, Robert I

    2016-03-06

    Most of the digital data transmitted are carried by optical fibres, forming the great part of the national and international communication infrastructure. The information-carrying capacity of these networks has increased vastly over the past decades through the introduction of wavelength division multiplexing, advanced modulation formats, digital signal processing and improved optical fibre and amplifier technology. These developments sparked the communication revolution and the growth of the Internet, and have created an illusion of infinite capacity being available. But as the volume of data continues to increase, is there a limit to the capacity of an optical fibre communication channel? The optical fibre channel is nonlinear, and the intensity-dependent Kerr nonlinearity limit has been suggested as a fundamental limit to optical fibre capacity. Current research is focused on whether this is the case, and on linear and nonlinear techniques, both optical and electronic, to understand, unlock and maximize the capacity of optical communications in the nonlinear regime. This paper describes some of them and discusses future prospects for success in the quest for capacity. © 2016 The Authors.

  7. City of Pittsburgh Trees

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — Trees cared for and managed by the City of Pittsburgh Department of Public Works Forestry Division. Tree Benefits are calculated using the National Tree Benefit...

  8. Does mental exertion alter maximal muscle activation?

    Directory of Open Access Journals (Sweden)

    Vianney eRozand

    2014-09-01

    Full Text Available Mental exertion is known to impair endurance performance, but its effects on neuromuscular function remain unclear. The purpose of this study was to test the hypothesis that mental exertion reduces torque and muscle activation during intermittent maximal voluntary contractions of the knee extensors. Ten subjects performed in a randomized order three separate mental exertion conditions lasting 27 minutes each: i high mental exertion (incongruent Stroop task, ii moderate mental exertion (congruent Stroop task, iii low mental exertion (watching a movie. In each condition, mental exertion was combined with ten intermittent maximal voluntary contractions of the knee extensor muscles (one maximal voluntary contraction every 3 minutes. Neuromuscular function was assessed using electrical nerve stimulation. Maximal voluntary torque, maximal muscle activation and other neuromuscular parameters were similar across mental exertion conditions and did not change over time. These findings suggest that mental exertion does not affect neuromuscular function during intermittent maximal voluntary contractions of the knee extensors.

  9. AUC-Maximizing Ensembles through Metalearning.

    Science.gov (United States)

    LeDell, Erin; van der Laan, Mark J; Petersen, Maya

    2016-05-01

    Area Under the ROC Curve (AUC) is often used to measure the performance of an estimator in binary classification problems. An AUC-maximizing classifier can have significant advantages in cases where ranking correctness is valued or if the outcome is rare. In a Super Learner ensemble, maximization of the AUC can be achieved by the use of an AUC-maximining metalearning algorithm. We discuss an implementation of an AUC-maximization technique that is formulated as a nonlinear optimization problem. We also evaluate the effectiveness of a large number of different nonlinear optimization algorithms to maximize the cross-validated AUC of the ensemble fit. The results provide evidence that AUC-maximizing metalearners can, and often do, out-perform non-AUC-maximizing metalearning methods, with respect to ensemble AUC. The results also demonstrate that as the level of imbalance in the training data increases, the Super Learner ensemble outperforms the top base algorithm by a larger degree.

  10. On maximal massive 3D supergravity

    OpenAIRE

    Bergshoeff , Eric A; Hohm , Olaf; Rosseel , Jan; Townsend , Paul K

    2010-01-01

    ABSTRACT We construct, at the linearized level, the three-dimensional (3D) N = 4 supersymmetric " general massive supergravity " and the maximally supersymmetric N = 8 " new massive supergravity ". We also construct the maximally supersymmetric linearized N = 7 topologically massive supergravity, although we expect N = 6 to be maximal at the non-linear level. (Bergshoeff, Eric A) (Hohm, Olaf) (Rosseel, Jan) P.K.Townsend@da...

  11. Inclusive Fitness Maximization:An Axiomatic Approach

    OpenAIRE

    Okasha, Samir; Weymark, John; Bossert, Walter

    2014-01-01

    Kin selection theorists argue that evolution in social contexts will lead organisms to behave as if maximizing their inclusive, as opposed to personal, fitness. The inclusive fitness concept allows biologists to treat organisms as akin to rational agents seeking to maximize a utility function. Here we develop this idea and place it on a firm footing by employing a standard decision-theoretic methodology. We show how the principle of inclusive fitness maximization and a related principle of qu...

  12. Activity versus outcome maximization in time management.

    Science.gov (United States)

    Malkoc, Selin A; Tonietto, Gabriela N

    2018-04-30

    Feeling time-pressed has become ubiquitous. Time management strategies have emerged to help individuals fit in more of their desired and necessary activities. We provide a review of these strategies. In doing so, we distinguish between two, often competing, motives people have in managing their time: activity maximization and outcome maximization. The emerging literature points to an important dilemma: a given strategy that maximizes the number of activities might be detrimental to outcome maximization. We discuss such factors that might hinder performance in work tasks and enjoyment in leisure tasks. Finally, we provide theoretically grounded recommendations that can help balance these two important goals in time management. Published by Elsevier Ltd.

  13. On the maximal superalgebras of supersymmetric backgrounds

    International Nuclear Information System (INIS)

    Figueroa-O'Farrill, Jose; Hackett-Jones, Emily; Moutsopoulos, George; Simon, Joan

    2009-01-01

    In this paper we give a precise definition of the notion of a maximal superalgebra of certain types of supersymmetric supergravity backgrounds, including the Freund-Rubin backgrounds, and propose a geometric construction extending the well-known construction of its Killing superalgebra. We determine the structure of maximal Lie superalgebras and show that there is a finite number of isomorphism classes, all related via contractions from an orthosymplectic Lie superalgebra. We use the structure theory to show that maximally supersymmetric waves do not possess such a maximal superalgebra, but that the maximally supersymmetric Freund-Rubin backgrounds do. We perform the explicit geometric construction of the maximal superalgebra of AdS 4 X S 7 and find that it is isomorphic to osp(1|32). We propose an algebraic construction of the maximal superalgebra of any background asymptotic to AdS 4 X S 7 and we test this proposal by computing the maximal superalgebra of the M2-brane in its two maximally supersymmetric limits, finding agreement.

  14. Task-oriented maximally entangled states

    International Nuclear Information System (INIS)

    Agrawal, Pankaj; Pradhan, B

    2010-01-01

    We introduce the notion of a task-oriented maximally entangled state (TMES). This notion depends on the task for which a quantum state is used as the resource. TMESs are the states that can be used to carry out the task maximally. This concept may be more useful than that of a general maximally entangled state in the case of a multipartite system. We illustrate this idea by giving an operational definition of maximally entangled states on the basis of communication tasks of teleportation and superdense coding. We also give examples and a procedure to obtain such TMESs for n-qubit systems.

  15. Categorizing ideas about trees: a tree of trees.

    Science.gov (United States)

    Fisler, Marie; Lecointre, Guillaume

    2013-01-01

    The aim of this study is to explore whether matrices and MP trees used to produce systematic categories of organisms could be useful to produce categories of ideas in history of science. We study the history of the use of trees in systematics to represent the diversity of life from 1766 to 1991. We apply to those ideas a method inspired from coding homologous parts of organisms. We discretize conceptual parts of ideas, writings and drawings about trees contained in 41 main writings; we detect shared parts among authors and code them into a 91-characters matrix and use a tree representation to show who shares what with whom. In other words, we propose a hierarchical representation of the shared ideas about trees among authors: this produces a "tree of trees." Then, we categorize schools of tree-representations. Classical schools like "cladists" and "pheneticists" are recovered but others are not: "gradists" are separated into two blocks, one of them being called here "grade theoreticians." We propose new interesting categories like the "buffonian school," the "metaphoricians," and those using "strictly genealogical classifications." We consider that networks are not useful to represent shared ideas at the present step of the study. A cladogram is made for showing who is sharing what with whom, but also heterobathmy and homoplasy of characters. The present cladogram is not modelling processes of transmission of ideas about trees, and here it is mostly used to test for proximity of ideas of the same age and for categorization.

  16. Resummed tree heptagon

    Science.gov (United States)

    Belitsky, A. V.

    2018-04-01

    The form factor program for the regularized space-time S-matrix in planar maximally supersymmetric gauge theory, known as the pentagon operator product expansion, is formulated in terms of flux-tube excitations propagating on a dual two-dimensional world-sheet, whose dynamics is known exactly as a function of 't Hooft coupling. Both MHV and non-MHV amplitudes are described in a uniform, systematic fashion within this framework, with the difference between the two encoded in coupling-dependent helicity form factors expressed via Zhukowski variables. The nontrivial SU(4) tensor structure of flux-tube transitions is coupling independent and is known for any number of charged excitations from solutions of a system of Watson and Mirror equations. This description allows one to resum the infinite series of form factors and recover the space-time S-matrix exactly in kinematical variables at a given order of perturbation series. Recently, this was done for the hexagon. Presently, we successfully perform resummation for the seven-leg tree NMHV amplitude. To this end, we construct the flux-tube integrands of the fifteen independent Grassmann component of the heptagon with an infinite number of small fermion-antifermion pairs accounted for in NMHV two-channel conformal blocks.

  17. Random ancestor trees

    International Nuclear Information System (INIS)

    Ben-Naim, E; Krapivsky, P L

    2010-01-01

    We investigate a network growth model in which the genealogy controls the evolution. In this model, a new node selects a random target node and links either to this target node, or to its parent, or to its grandparent, etc; all nodes from the target node to its most ancient ancestor are equiprobable destinations. The emerging random ancestor tree is very shallow: the fraction g n of nodes at distance n from the root decreases super-exponentially with n, g n = e −1 /(n − 1)!. We find that a macroscopic hub at the root coexists with highly connected nodes at higher generations. The maximal degree of a node at the nth generation grows algebraically as N 1/β n , where N is the system size. We obtain the series of nontrivial exponents which are roots of transcendental equations: β 1 ≅1.351 746, β 2 ≅1.682 201, etc. As a consequence, the fraction p k of nodes with degree k has an algebraic tail, p k ∼ k −γ , with γ = β 1 + 1 = 2.351 746

  18. Urban tree growth modeling

    Science.gov (United States)

    E. Gregory McPherson; Paula J. Peper

    2012-01-01

    This paper describes three long-term tree growth studies conducted to evaluate tree performance because repeated measurements of the same trees produce critical data for growth model calibration and validation. Several empirical and process-based approaches to modeling tree growth are reviewed. Modeling is more advanced in the fields of forestry and...

  19. Keeping trees as assets

    Science.gov (United States)

    Kevin T. Smith

    2009-01-01

    Landscape trees have real value and contribute to making livable communities. Making the most of that value requires providing trees with the proper care and attention. As potentially large and long-lived organisms, trees benefit from commitment to regular care that respects the natural tree system. This system captures, transforms, and uses energy to survive, grow,...

  20. 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.

  1. Maximally Entangled Multipartite States: A Brief Survey

    International Nuclear Information System (INIS)

    Enríquez, M; Wintrowicz, I; Życzkowski, K

    2016-01-01

    The problem of identifying maximally entangled quantum states of a composite quantum systems is analyzed. We review some states of multipartite systems distinguished with respect to certain measures of quantum entanglement. Numerical results obtained for 4-qubit pure states illustrate the fact that the notion of maximally entangled state depends on the measure used. (paper)

  2. Utility maximization and mode of payment

    NARCIS (Netherlands)

    Koning, R.H.; Ridder, G.; Heijmans, R.D.H.; Pollock, D.S.G.; Satorra, A.

    2000-01-01

    The implications of stochastic utility maximization in a model of choice of payment are examined. Three types of compatibility with utility maximization are distinguished: global compatibility, local compatibility on an interval, and local compatibility on a finite set of points. Keywords:

  3. Corporate Social Responsibility and Profit Maximizing Behaviour

    OpenAIRE

    Becchetti, Leonardo; Giallonardo, Luisa; Tessitore, Maria Elisabetta

    2005-01-01

    We examine the behavior of a profit maximizing monopolist in a horizontal differentiation model in which consumers differ in their degree of social responsibility (SR) and consumers SR is dynamically influenced by habit persistence. The model outlines parametric conditions under which (consumer driven) corporate social responsibility is an optimal choice compatible with profit maximizing behavior.

  4. Classification and regression trees

    CERN Document Server

    Breiman, Leo; Olshen, Richard A; Stone, Charles J

    1984-01-01

    The methodology used to construct tree structured rules is the focus of this monograph. Unlike many other statistical procedures, which moved from pencil and paper to calculators, this text's use of trees was unthinkable before computers. Both the practical and theoretical sides have been developed in the authors' study of tree methods. Classification and Regression Trees reflects these two sides, covering the use of trees as a data analysis method, and in a more mathematical framework, proving some of their fundamental properties.

  5. Inclusive fitness maximization: An axiomatic approach.

    Science.gov (United States)

    Okasha, Samir; Weymark, John A; Bossert, Walter

    2014-06-07

    Kin selection theorists argue that evolution in social contexts will lead organisms to behave as if maximizing their inclusive, as opposed to personal, fitness. The inclusive fitness concept allows biologists to treat organisms as akin to rational agents seeking to maximize a utility function. Here we develop this idea and place it on a firm footing by employing a standard decision-theoretic methodology. We show how the principle of inclusive fitness maximization and a related principle of quasi-inclusive fitness maximization can be derived from axioms on an individual׳s 'as if preferences' (binary choices) for the case in which phenotypic effects are additive. Our results help integrate evolutionary theory and rational choice theory, help draw out the behavioural implications of inclusive fitness maximization, and point to a possible way in which evolution could lead organisms to implement it. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

    Science.gov (United States)

    De Oliveira Martins, Leonardo; Mallo, Diego; Posada, David

    2016-01-01

    Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models. PMID:25281847

  7. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction.

    Science.gov (United States)

    De Oliveira Martins, Leonardo; Mallo, Diego; Posada, David

    2016-05-01

    Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

  8. Fault tree handbook

    International Nuclear Information System (INIS)

    Haasl, D.F.; Roberts, N.H.; Vesely, W.E.; Goldberg, F.F.

    1981-01-01

    This handbook describes a methodology for reliability analysis of complex systems such as those which comprise the engineered safety features of nuclear power generating stations. After an initial overview of the available system analysis approaches, the handbook focuses on a description of the deductive method known as fault tree analysis. The following aspects of fault tree analysis are covered: basic concepts for fault tree analysis; basic elements of a fault tree; fault tree construction; probability, statistics, and Boolean algebra for the fault tree analyst; qualitative and quantitative fault tree evaluation techniques; and computer codes for fault tree evaluation. Also discussed are several example problems illustrating the basic concepts of fault tree construction and evaluation

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution

    Directory of Open Access Journals (Sweden)

    Liran Carmel

    2010-01-01

    Full Text Available Evolutionary binary characters are features of species or genes, indicating the absence (value zero or presence (value one of some property. Examples include eukaryotic gene architecture (the presence or absence of an intron in a particular locus, gene content, and morphological characters. In many studies, the acquisition of such binary characters is assumed to represent a rare evolutionary event, and consequently, their evolution is analyzed using various flavors of parsimony. However, when gain and loss of the character are not rare enough, a probabilistic analysis becomes essential. Here, we present a comprehensive probabilistic model to describe the evolution of binary characters on a bifurcating phylogenetic tree. A fast software tool, EREM, is provided, using maximum likelihood to estimate the parameters of the model and to reconstruct ancestral states (presence and absence in internal nodes and events (gain and loss events along branches.

  14. EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution.

    Science.gov (United States)

    Carmel, Liran; Wolf, Yuri I; Rogozin, Igor B; Koonin, Eugene V

    2010-01-01

    Evolutionary binary characters are features of species or genes, indicating the absence (value zero) or presence (value one) of some property. Examples include eukaryotic gene architecture (the presence or absence of an intron in a particular locus), gene content, and morphological characters. In many studies, the acquisition of such binary characters is assumed to represent a rare evolutionary event, and consequently, their evolution is analyzed using various flavors of parsimony. However, when gain and loss of the character are not rare enough, a probabilistic analysis becomes essential. Here, we present a comprehensive probabilistic model to describe the evolution of binary characters on a bifurcating phylogenetic tree. A fast software tool, EREM, is provided, using maximum likelihood to estimate the parameters of the model and to reconstruct ancestral states (presence and absence in internal nodes) and events (gain and loss events along branches).

  15. Covering tree with stars

    DEFF Research Database (Denmark)

    Baumbach, Jan; Guo, Jiong; Ibragimov, Rashid

    2015-01-01

    We study the tree edit distance problem with edge deletions and edge insertions as edit operations. We reformulate a special case of this problem as Covering Tree with Stars (CTS): given a tree T and a set of stars, can we connect the stars in by adding edges between them such that the resulting...... tree is isomorphic to T? We prove that in the general setting, CST is NP-complete, which implies that the tree edit distance considered here is also NP-hard, even when both input trees having diameters bounded by 10. We also show that, when the number of distinct stars is bounded by a constant k, CTS...

  16. 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.

  17. 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.

  18. Bipartite Bell Inequality and Maximal Violation

    International Nuclear Information System (INIS)

    Li Ming; Fei Shaoming; Li-Jost Xian-Qing

    2011-01-01

    We present new bell inequalities for arbitrary dimensional bipartite quantum systems. The maximal violation of the inequalities is computed. The Bell inequality is capable of detecting quantum entanglement of both pure and mixed quantum states more effectively. (general)

  19. HEALTH INSURANCE: CONTRIBUTIONS AND REIMBURSEMENT MAXIMAL

    CERN Document Server

    HR Division

    2000-01-01

    Affected by both the salary adjustment index on 1.1.2000 and the evolution of the staff members and fellows population, the average reference salary, which is used as an index for fixed contributions and reimbursement maximal, has changed significantly. An adjustment of the amounts of the reimbursement maximal and the fixed contributions is therefore necessary, as from 1 January 2000.Reimbursement maximalThe revised reimbursement maximal will appear on the leaflet summarising the benefits for the year 2000, which will soon be available from the divisional secretariats and from the AUSTRIA office at CERN.Fixed contributionsThe fixed contributions, applicable to some categories of voluntarily insured persons, are set as follows (amounts in CHF for monthly contributions):voluntarily insured member of the personnel, with complete coverage:815,- (was 803,- in 1999)voluntarily insured member of the personnel, with reduced coverage:407,- (was 402,- in 1999)voluntarily insured no longer dependent child:326,- (was 321...

  20. Maximal Inequalities for Dependent Random Variables

    DEFF Research Database (Denmark)

    Hoffmann-Jorgensen, Jorgen

    2016-01-01

    Maximal inequalities play a crucial role in many probabilistic limit theorem; for instance, the law of large numbers, the law of the iterated logarithm, the martingale limit theorem and the central limit theorem. Let X-1, X-2,... be random variables with partial sums S-k = X-1 + ... + X-k. Then a......Maximal inequalities play a crucial role in many probabilistic limit theorem; for instance, the law of large numbers, the law of the iterated logarithm, the martingale limit theorem and the central limit theorem. Let X-1, X-2,... be random variables with partial sums S-k = X-1 + ... + X......-k. Then a maximal inequality gives conditions ensuring that the maximal partial sum M-n = max(1) (...

  1. Maximizing Function through Intelligent Robot Actuator Control

    Data.gov (United States)

    National Aeronautics and Space Administration — Maximizing Function through Intelligent Robot Actuator Control Successful missions to Mars and beyond will only be possible with the support of high-performance...

  2. An ethical justification of profit maximization

    DEFF Research Database (Denmark)

    Koch, Carsten Allan

    2010-01-01

    In much of the literature on business ethics and corporate social responsibility, it is more or less taken for granted that attempts to maximize profits are inherently unethical. The purpose of this paper is to investigate whether an ethical argument can be given in support of profit maximizing...... behaviour. It is argued that some form of consequential ethics must be applied, and that both profit seeking and profit maximization can be defended from a rule-consequential point of view. It is noted, however, that the result does not apply unconditionally, but requires that certain form of profit (and...... utility) maximizing actions are ruled out, e.g., by behavioural norms or formal institutions....

  3. A definition of maximal CP-violation

    International Nuclear Information System (INIS)

    Roos, M.

    1985-01-01

    The unitary matrix of quark flavour mixing is parametrized in a general way, permitting a mathematically natural definition of maximal CP violation. Present data turn out to violate this definition by 2-3 standard deviations. (orig.)

  4. A cosmological problem for maximally symmetric supergravity

    International Nuclear Information System (INIS)

    German, G.; Ross, G.G.

    1986-01-01

    Under very general considerations it is shown that inflationary models of the universe based on maximally symmetric supergravity with flat potentials are unable to resolve the cosmological energy density (Polonyi) problem. (orig.)

  5. Insulin resistance and maximal oxygen uptake

    DEFF Research Database (Denmark)

    Seibaek, Marie; Vestergaard, Henrik; Burchardt, Hans

    2003-01-01

    BACKGROUND: Type 2 diabetes, coronary atherosclerosis, and physical fitness all correlate with insulin resistance, but the relative importance of each component is unknown. HYPOTHESIS: This study was undertaken to determine the relationship between insulin resistance, maximal oxygen uptake......, and the presence of either diabetes or ischemic heart disease. METHODS: The study population comprised 33 patients with and without diabetes and ischemic heart disease. Insulin resistance was measured by a hyperinsulinemic euglycemic clamp; maximal oxygen uptake was measured during a bicycle exercise test. RESULTS......: There was a strong correlation between maximal oxygen uptake and insulin-stimulated glucose uptake (r = 0.7, p = 0.001), and maximal oxygen uptake was the only factor of importance for determining insulin sensitivity in a model, which also included the presence of diabetes and ischemic heart disease. CONCLUSION...

  6. Maximal supergravities and the E10 model

    International Nuclear Information System (INIS)

    Kleinschmidt, Axel; Nicolai, Hermann

    2006-01-01

    The maximal rank hyperbolic Kac-Moody algebra e 10 has been conjectured to play a prominent role in the unification of duality symmetries in string and M theory. We review some recent developments supporting this conjecture

  7. Gaussian maximally multipartite-entangled states

    Science.gov (United States)

    Facchi, Paolo; Florio, Giuseppe; Lupo, Cosmo; Mancini, Stefano; Pascazio, Saverio

    2009-12-01

    We study maximally multipartite-entangled states in the context of Gaussian continuous variable quantum systems. By considering multimode Gaussian states with constrained energy, we show that perfect maximally multipartite-entangled states, which exhibit the maximum amount of bipartite entanglement for all bipartitions, only exist for systems containing n=2 or 3 modes. We further numerically investigate the structure of these states and their frustration for n≤7 .

  8. Gaussian maximally multipartite-entangled states

    International Nuclear Information System (INIS)

    Facchi, Paolo; Florio, Giuseppe; Pascazio, Saverio; Lupo, Cosmo; Mancini, Stefano

    2009-01-01

    We study maximally multipartite-entangled states in the context of Gaussian continuous variable quantum systems. By considering multimode Gaussian states with constrained energy, we show that perfect maximally multipartite-entangled states, which exhibit the maximum amount of bipartite entanglement for all bipartitions, only exist for systems containing n=2 or 3 modes. We further numerically investigate the structure of these states and their frustration for n≤7.

  9. Neutrino mass textures with maximal CP violation

    International Nuclear Information System (INIS)

    Aizawa, Ichiro; Kitabayashi, Teruyuki; Yasue, Masaki

    2005-01-01

    We show three types of neutrino mass textures, which give maximal CP violation as well as maximal atmospheric neutrino mixing. These textures are described by six real mass parameters: one specified by two complex flavor neutrino masses and two constrained ones and the others specified by three complex flavor neutrino masses. In each texture, we calculate mixing angles and masses, which are consistent with observed data, as well as Majorana CP phases

  10. Why firms should not always maximize profits

    OpenAIRE

    Kolstad, Ivar

    2006-01-01

    Though corporate social responsibility (CSR) is on the agenda of most major corporations, corporate executives still largely support the view that corporations should maximize the returns to their owners. There are two lines of defence for this position. One is the Friedmanian view that maximizing owner returns is the corporate social responsibility of corporations. The other is a position voiced by many executives, that CSR and profits go together. This paper argues that the first position i...

  11. Maximally Informative Observables and Categorical Perception

    OpenAIRE

    Tsiang, Elaine

    2012-01-01

    We formulate the problem of perception in the framework of information theory, and prove that categorical perception is equivalent to the existence of an observable that has the maximum possible information on the target of perception. We call such an observable maximally informative. Regardless whether categorical perception is real, maximally informative observables can form the basis of a theory of perception. We conclude with the implications of such a theory for the problem of speech per...

  12. Trees and highway safety.

    Science.gov (United States)

    2011-03-01

    To minimize the severity of run-off-road collisions of vehicles with trees, departments of transportation (DOTs) : commonly establish clear zones for trees and other fixed objects. Caltrans clear zone on freeways is 30 feet : minimum (40 feet pref...

  13. Decision-Tree Program

    Science.gov (United States)

    Buntine, Wray

    1994-01-01

    IND computer program introduces Bayesian and Markov/maximum-likelihood (MML) methods and more-sophisticated methods of searching in growing trees. Produces more-accurate class-probability estimates important in applications like diagnosis. Provides range of features and styles with convenience for casual user, fine-tuning for advanced user or for those interested in research. Consists of four basic kinds of routines: data-manipulation, tree-generation, tree-testing, and tree-display. Written in C language.

  14. Pareto-optimal phylogenetic tree reconciliation.

    Science.gov (United States)

    Libeskind-Hadas, Ran; Wu, Yi-Chieh; Bansal, Mukul S; Kellis, Manolis

    2014-06-15

    Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is generally understood that reconciliations are sensitive to event costs, but little is understood about the relationship between event costs and solutions. Moreover, choosing appropriate event costs is a notoriously difficult problem. We address this problem by giving an efficient algorithm for computing Pareto-optimal sets of reconciliations, thus providing the first systematic method for understanding the relationship between event costs and reconciliations. This, in turn, results in new techniques for computing event support values and, for cophylogenetic analyses, performing robust statistical tests. We provide new software tools and demonstrate their use on a number of datasets from evolutionary genomic and cophylogenetic studies. Our Python tools are freely available at www.cs.hmc.edu/∼hadas/xscape. . © The Author 2014. Published by Oxford University Press.

  15. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  16. Minnesota's Forest Trees. Revised.

    Science.gov (United States)

    Miles, William R.; Fuller, Bruce L.

    This bulletin describes 46 of the more common trees found in Minnesota's forests and windbreaks. The bulletin contains two tree keys, a summer key and a winter key, to help the reader identify these trees. Besides the two keys, the bulletin includes an introduction, instructions for key use, illustrations of leaf characteristics and twig…

  17. D2-tree

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Sioutas, Spyros; Pantazos, Kostas

    2015-01-01

    We present a new overlay, called the Deterministic Decentralized tree (D2-tree). The D2-tree compares favorably to other overlays for the following reasons: (a) it provides matching and better complexities, which are deterministic for the supported operations; (b) the management of nodes (peers...

  18. Covering tree with stars

    DEFF Research Database (Denmark)

    Baumbach, Jan; Guo, Jian-Ying; Ibragimov, Rashid

    2013-01-01

    We study the tree edit distance problem with edge deletions and edge insertions as edit operations. We reformulate a special case of this problem as Covering Tree with Stars (CTS): given a tree T and a set of stars, can we connect the stars in by adding edges between them such that the resulting ...

  19. Winter Birch Trees

    Science.gov (United States)

    Sweeney, Debra; Rounds, Judy

    2011-01-01

    Trees are great inspiration for artists. Many art teachers find themselves inspired and maybe somewhat obsessed with the natural beauty and elegance of the lofty tree, and how it changes through the seasons. One such tree that grows in several regions and always looks magnificent, regardless of the time of year, is the birch. In this article, the…

  20. Total well dominated trees

    DEFF Research Database (Denmark)

    Finbow, Arthur; Frendrup, Allan; Vestergaard, Preben D.

    cardinality then G is a total well dominated graph. In this paper we study composition and decomposition of total well dominated trees. By a reversible process we prove that any total well dominated tree can both be reduced to and constructed from a family of three small trees....

  1. Shareholder, stakeholder-owner or broad stakeholder maximization

    OpenAIRE

    Mygind, Niels

    2004-01-01

    With reference to the discussion about shareholder versus stakeholder maximization it is argued that the normal type of maximization is in fact stakeholder-owner maxi-mization. This means maximization of the sum of the value of the shares and stake-holder benefits belonging to the dominating stakeholder-owner. Maximization of shareholder value is a special case of owner-maximization, and only under quite re-strictive assumptions shareholder maximization is larger or equal to stakeholder-owner...

  2. TreePics: visualizing trees with pictures

    Directory of Open Access Journals (Sweden)

    Nicolas Puillandre

    2017-09-01

    Full Text Available While many programs are available to edit phylogenetic trees, associating pictures with branch tips in an efficient and automatic way is not an available option. Here, we present TreePics, a standalone software that uses a web browser to visualize phylogenetic trees in Newick format and that associates pictures (typically, pictures of the voucher specimens to the tip of each branch. Pictures are visualized as thumbnails and can be enlarged by a mouse rollover. Further, several pictures can be selected and displayed in a separate window for visual comparison. TreePics works either online or in a full standalone version, where it can display trees with several thousands of pictures (depending on the memory available. We argue that TreePics can be particularly useful in a preliminary stage of research, such as to quickly detect conflicts between a DNA-based phylogenetic tree and morphological variation, that may be due to contamination that needs to be removed prior to final analyses, or the presence of species complexes.

  3. 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

  4. Vacua of maximal gauged D=3 supergravities

    International Nuclear Information System (INIS)

    Fischbacher, T; Nicolai, H; Samtleben, H

    2002-01-01

    We analyse the scalar potentials of maximal gauged three-dimensional supergravities which reveal a surprisingly rich structure. In contrast to maximal supergravities in dimensions D≥4, all these theories possess a maximally supersymmetric (N=16) ground state with negative cosmological constant Λ 2 gauged theory, whose maximally supersymmetric groundstate has Λ = 0. We compute the mass spectra of bosonic and fermionic fluctuations around these vacua and identify the unitary irreducible representations of the relevant background (super)isometry groups to which they belong. In addition, we find several stationary points which are not maximally supersymmetric, and determine their complete mass spectra as well. In particular, we show that there are analogues of all stationary points found in higher dimensions, among them are de Sitter (dS) vacua in the theories with noncompact gauge groups SO(5, 3) 2 and SO(4, 4) 2 , as well as anti-de Sitter (AdS) vacua in the compact gauged theory preserving 1/4 and 1/8 of the supersymmetries. All the dS vacua have tachyonic instabilities, whereas there do exist nonsupersymmetric AdS vacua which are stable, again in contrast to the D≥4 theories

  5. Spectra of chemical trees

    International Nuclear Information System (INIS)

    Balasubramanian, K.

    1982-01-01

    A method is developed for obtaining the spectra of trees of NMR and chemical interests. The characteristic polynomials of branched trees can be obtained in terms of the characteristic polynomials of unbranched trees and branches by pruning the tree at the joints. The unbranched trees can also be broken down further until a tree containing just two vertices is obtained. The effectively reduces the order of the secular determinant of the tree used at the beginning to determinants of orders atmost equal to the number of vertices in the branch containing the largest number of vertices. An illustrative example of a NMR graph is given for which the 22 x 22 secular determinant is reduced to determinants of orders atmost 4 x 4 in just the second step of the algorithm. The tree pruning algorithm can be applied even to trees with no symmetry elements and such a factoring can be achieved. Methods developed here can be elegantly used to find if two trees are cospectral and to construct cospectral trees

  6. Refining discordant gene trees.

    Science.gov (United States)

    Górecki, Pawel; Eulenstein, Oliver

    2014-01-01

    Evolutionary studies are complicated by discordance between gene trees and the species tree in which they evolved. Dealing with discordant trees often relies on comparison costs between gene and species trees, including the well-established Robinson-Foulds, gene duplication, and deep coalescence costs. While these costs have provided credible results for binary rooted gene trees, corresponding cost definitions for non-binary unrooted gene trees, which are frequently occurring in practice, are challenged by biological realism. We propose a natural extension of the well-established costs for comparing unrooted and non-binary gene trees with rooted binary species trees using a binary refinement model. For the duplication cost we describe an efficient algorithm that is based on a linear time reduction and also computes an optimal rooted binary refinement of the given gene tree. Finally, we show that similar reductions lead to solutions for computing the deep coalescence and the Robinson-Foulds costs. Our binary refinement of Robinson-Foulds, gene duplication, and deep coalescence costs for unrooted and non-binary gene trees together with the linear time reductions provided here for computing these costs significantly extends the range of trees that can be incorporated into approaches dealing with discordance.

  7. Breeding strategies for north central tree improvement programs

    Science.gov (United States)

    Ronald P. Overton; Hyun Kang

    1985-01-01

    The rationales and concepts of long-term tree breeding are discussed and compared with those for short-term breeding. A model breeding program is reviewed which maximizes short-term genetic gain for currently important traits and provides genetic resources that can be used effectively in future short-term breeding. The resources of the north-central region are examined...

  8. An information maximization model of eye movements

    Science.gov (United States)

    Renninger, Laura Walker; Coughlan, James; Verghese, Preeti; Malik, Jitendra

    2005-01-01

    We propose a sequential information maximization model as a general strategy for programming eye movements. The model reconstructs high-resolution visual information from a sequence of fixations, taking into account the fall-off in resolution from the fovea to the periphery. From this framework we get a simple rule for predicting fixation sequences: after each fixation, fixate next at the location that minimizes uncertainty (maximizes information) about the stimulus. By comparing our model performance to human eye movement data and to predictions from a saliency and random model, we demonstrate that our model is best at predicting fixation locations. Modeling additional biological constraints will improve the prediction of fixation sequences. Our results suggest that information maximization is a useful principle for programming eye movements.

  9. Utility Maximization in Nonconvex Wireless Systems

    CERN Document Server

    Brehmer, Johannes

    2012-01-01

    This monograph formulates a framework for modeling and solving utility maximization problems in nonconvex wireless systems. First, a model for utility optimization in wireless systems is defined. The model is general enough to encompass a wide array of system configurations and performance objectives. Based on the general model, a set of methods for solving utility maximization problems is developed. The development is based on a careful examination of the properties that are required for the application of each method. The focus is on problems whose initial formulation does not allow for a solution by standard convex methods. Solution approaches that take into account the nonconvexities inherent to wireless systems are discussed in detail. The monograph concludes with two case studies that demonstrate the application of the proposed framework to utility maximization in multi-antenna broadcast channels.

  10. Maximizing band gaps in plate structures

    DEFF Research Database (Denmark)

    Halkjær, Søren; Sigmund, Ole; Jensen, Jakob Søndergaard

    2006-01-01

    periodic plate using Bloch theory, which conveniently reduces the maximization problem to that of a single base cell. Secondly, we construct a finite periodic plate using a number of the optimized base cells in a postprocessed version. The dynamic properties of the finite plate are investigated......Band gaps, i.e., frequency ranges in which waves cannot propagate, can be found in elastic structures for which there is a certain periodic modulation of the material properties or structure. In this paper, we maximize the band gap size for bending waves in a Mindlin plate. We analyze an infinite...... theoretically and experimentally and the issue of finite size effects is addressed....

  11. Singularity Structure of Maximally Supersymmetric Scattering Amplitudes

    DEFF Research Database (Denmark)

    Arkani-Hamed, Nima; Bourjaily, Jacob L.; Cachazo, Freddy

    2014-01-01

    We present evidence that loop amplitudes in maximally supersymmetric (N=4) Yang-Mills theory (SYM) beyond the planar limit share some of the remarkable structures of the planar theory. In particular, we show that through two loops, the four-particle amplitude in full N=4 SYM has only logarithmic ...... singularities and is free of any poles at infinity—properties closely related to uniform transcendentality and the UV finiteness of the theory. We also briefly comment on implications for maximal (N=8) supergravity theory (SUGRA)....

  12. Learning curves for mutual information maximization

    International Nuclear Information System (INIS)

    Urbanczik, R.

    2003-01-01

    An unsupervised learning procedure based on maximizing the mutual information between the outputs of two networks receiving different but statistically dependent inputs is analyzed [S. Becker and G. Hinton, Nature (London) 355, 161 (1992)]. For a generic data model, I show that in the large sample limit the structure in the data is recognized by mutual information maximization. For a more restricted model, where the networks are similar to perceptrons, I calculate the learning curves for zero-temperature Gibbs learning. These show that convergence can be rather slow, and a way of regularizing the procedure is considered

  13. Finding Maximal Pairs with Bounded Gap

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Lyngsø, Rune B.; Pedersen, Christian N. S.

    1999-01-01

    . In this paper we present methods for finding all maximal pairs under various constraints on the gap. In a string of length n we can find all maximal pairs with gap in an upper and lower bounded interval in time O(n log n+z) where z is the number of reported pairs. If the upper bound is removed the time reduces...... to O(n+z). Since a tandem repeat is a pair where the gap is zero, our methods can be seen as a generalization of finding tandem repeats. The running time of our methods equals the running time of well known methods for finding tandem repeats....

  14. Maximizing the Range of a Projectile.

    Science.gov (United States)

    Brown, Ronald A.

    1992-01-01

    Discusses solutions to the problem of maximizing the range of a projectile. Presents three references that solve the problem with and without the use of calculus. Offers a fourth solution suitable for introductory physics courses that relies more on trigonometry and the geometry of the problem. (MDH)

  15. Robust Utility Maximization Under Convex Portfolio Constraints

    International Nuclear Information System (INIS)

    Matoussi, Anis; Mezghani, Hanen; Mnif, Mohamed

    2015-01-01

    We study a robust maximization problem from terminal wealth and consumption under a convex constraints on the portfolio. We state the existence and the uniqueness of the consumption–investment strategy by studying the associated quadratic backward stochastic differential equation. We characterize the optimal control by using the duality method and deriving a dynamic maximum principle

  16. Ehrenfest's Lottery--Time and Entropy Maximization

    Science.gov (United States)

    Ashbaugh, Henry S.

    2010-01-01

    Successful teaching of the Second Law of Thermodynamics suffers from limited simple examples linking equilibrium to entropy maximization. I describe a thought experiment connecting entropy to a lottery that mixes marbles amongst a collection of urns. This mixing obeys diffusion-like dynamics. Equilibrium is achieved when the marble distribution is…

  17. Reserve design to maximize species persistence

    Science.gov (United States)

    Robert G. Haight; Laurel E. Travis

    2008-01-01

    We develop a reserve design strategy to maximize the probability of species persistence predicted by a stochastic, individual-based, metapopulation model. Because the population model does not fit exact optimization procedures, our strategy involves deriving promising solutions from theory, obtaining promising solutions from a simulation optimization heuristic, and...

  18. Maximal indecomposable past sets and event horizons

    International Nuclear Information System (INIS)

    Krolak, A.

    1984-01-01

    The existence of maximal indecomposable past sets MIPs is demonstrated using the Kuratowski-Zorn lemma. A criterion for the existence of an absolute event horizon in space-time is given in terms of MIPs and a relation to black hole event horizon is shown. (author)

  19. Maximization of eigenvalues using topology optimization

    DEFF Research Database (Denmark)

    Pedersen, Niels Leergaard

    2000-01-01

    to localized modes in low density areas. The topology optimization problem is formulated using the SIMP method. Special attention is paid to a numerical method for removing localized eigenmodes in low density areas. The method is applied to numerical examples of maximizing the first eigenfrequency, One example...

  20. Maximizing Resource Utilization in Video Streaming Systems

    Science.gov (United States)

    Alsmirat, Mohammad Abdullah

    2013-01-01

    Video streaming has recently grown dramatically in popularity over the Internet, Cable TV, and wire-less networks. Because of the resource demanding nature of video streaming applications, maximizing resource utilization in any video streaming system is a key factor to increase the scalability and decrease the cost of the system. Resources to…

  1. A THEORY OF MAXIMIZING SENSORY INFORMATION

    NARCIS (Netherlands)

    Hateren, J.H. van

    1992-01-01

    A theory is developed on the assumption that early sensory processing aims at maximizing the information rate in the channels connecting the sensory system to more central parts of the brain, where it is assumed that these channels are noisy and have a limited dynamic range. Given a stimulus power

  2. Maximizing scientific knowledge from randomized clinical trials

    DEFF Research Database (Denmark)

    Gustafsson, Finn; Atar, Dan; Pitt, Bertram

    2010-01-01

    Trialists have an ethical and financial responsibility to plan and conduct clinical trials in a manner that will maximize the scientific knowledge gained from the trial. However, the amount of scientific information generated by randomized clinical trials in cardiovascular medicine is highly vari...

  3. A Model of College Tuition Maximization

    Science.gov (United States)

    Bosshardt, Donald I.; Lichtenstein, Larry; Zaporowski, Mark P.

    2009-01-01

    This paper develops a series of models for optimal tuition pricing for private colleges and universities. The university is assumed to be a profit maximizing, price discriminating monopolist. The enrollment decision of student's is stochastic in nature. The university offers an effective tuition rate, comprised of stipulated tuition less financial…

  4. Logit Analysis for Profit Maximizing Loan Classification

    OpenAIRE

    Watt, David L.; Mortensen, Timothy L.; Leistritz, F. Larry

    1988-01-01

    Lending criteria and loan classification methods are developed. Rating system breaking points are analyzed to present a method to maximize loan revenues. Financial characteristics of farmers are used as determinants of delinquency in a multivariate logistic model. Results indicate that debt-to-asset and operating ration are most indicative of default.

  5. Developing maximal neuromuscular power: Part 1--biological basis of maximal power production.

    Science.gov (United States)

    Cormie, Prue; McGuigan, Michael R; Newton, Robert U

    2011-01-01

    This series of reviews focuses on the most important neuromuscular function in many sport performances, the ability to generate maximal muscular power. Part 1 focuses on the factors that affect maximal power production, while part 2, which will follow in a forthcoming edition of Sports Medicine, explores the practical application of these findings by reviewing the scientific literature relevant to the development of training programmes that most effectively enhance maximal power production. The ability of the neuromuscular system to generate maximal power is affected by a range of interrelated factors. Maximal muscular power is defined and limited by the force-velocity relationship and affected by the length-tension relationship. The ability to generate maximal power is influenced by the type of muscle action involved and, in particular, the time available to develop force, storage and utilization of elastic energy, interactions of contractile and elastic elements, potentiation of contractile and elastic filaments as well as stretch reflexes. Furthermore, maximal power production is influenced by morphological factors including fibre type contribution to whole muscle area, muscle architectural features and tendon properties as well as neural factors including motor unit recruitment, firing frequency, synchronization and inter-muscular coordination. In addition, acute changes in the muscle environment (i.e. alterations resulting from fatigue, changes in hormone milieu and muscle temperature) impact the ability to generate maximal power. Resistance training has been shown to impact each of these neuromuscular factors in quite specific ways. Therefore, an understanding of the biological basis of maximal power production is essential for developing training programmes that effectively enhance maximal power production in the human.

  6. Understanding Violations of Gricean Maxims in Preschoolers and Adults

    Directory of Open Access Journals (Sweden)

    Mako eOkanda

    2015-07-01

    Full Text Available This study used a revised Conversational Violations Test to examine Gricean maxim violations in 4- to 6-year-old Japanese children and adults. Participants’ understanding of the following maxims was assessed: be informative (first maxim of quantity, avoid redundancy (second maxim of quantity, be truthful (maxim of quality, be relevant (maxim of relation, avoid ambiguity (second maxim of manner, and be polite (maxim of politeness. Sensitivity to violations of Gricean maxims increased with age: 4-year-olds’ understanding of maxims was near chance, 5-year-olds understood some maxims (first maxim of quantity and maxims of quality, relation, and manner, and 6-year-olds and adults understood all maxims. Preschoolers acquired the maxim of relation first and had the greatest difficulty understanding the second maxim of quantity. Children and adults differed in their comprehension of the maxim of politeness. The development of the pragmatic understanding of Gricean maxims and implications for the construction of developmental tasks from early childhood to adulthood are discussed.

  7. The valuative tree

    CERN Document Server

    Favre, Charles

    2004-01-01

    This volume is devoted to a beautiful object, called the valuative tree and designed as a powerful tool for the study of singularities in two complex dimensions. Its intricate yet manageable structure can be analyzed by both algebraic and geometric means. Many types of singularities, including those of curves, ideals, and plurisubharmonic functions, can be encoded in terms of positive measures on the valuative tree. The construction of these measures uses a natural tree Laplace operator of independent interest.

  8. Exploring the relationship between sequence similarity and accurate phylogenetic trees.

    Science.gov (United States)

    Cantarel, Brandi L; Morrison, Hilary G; Pearson, William

    2006-11-01

    We have characterized the relationship between accurate phylogenetic reconstruction and sequence similarity, testing whether high levels of sequence similarity can consistently produce accurate evolutionary trees. We generated protein families with known phylogenies using a modified version of the PAML/EVOLVER program that produces insertions and deletions as well as substitutions. Protein families were evolved over a range of 100-400 point accepted mutations; at these distances 63% of the families shared significant sequence similarity. Protein families were evolved using balanced and unbalanced trees, with ancient or recent radiations. In families sharing statistically significant similarity, about 60% of multiple sequence alignments were 95% identical to true alignments. To compare recovered topologies with true topologies, we used a score that reflects the fraction of clades that were correctly clustered. As expected, the accuracy of the phylogenies was greatest in the least divergent families. About 88% of phylogenies clustered over 80% of clades in families that shared significant sequence similarity, using Bayesian, parsimony, distance, and maximum likelihood methods. However, for protein families with short ancient branches (ancient radiation), only 30% of the most divergent (but statistically significant) families produced accurate phylogenies, and only about 70% of the second most highly conserved families, with median expectation values better than 10(-60), produced accurate trees. These values represent upper bounds on expected tree accuracy for sequences with a simple divergence history; proteins from 700 Giardia families, with a similar range of sequence similarities but considerably more gaps, produced much less accurate trees. For our simulated insertions and deletions, correct multiple sequence alignments did not perform much better than those produced by T-COFFEE, and including sequences with expressed sequence tag-like sequencing errors did not

  9. Coded Splitting Tree Protocols

    DEFF Research Database (Denmark)

    Sørensen, Jesper Hemming; Stefanovic, Cedomir; Popovski, Petar

    2013-01-01

    This paper presents a novel approach to multiple access control called coded splitting tree protocol. The approach builds on the known tree splitting protocols, code structure and successive interference cancellation (SIC). Several instances of the tree splitting protocol are initiated, each...... instance is terminated prematurely and subsequently iterated. The combined set of leaves from all the tree instances can then be viewed as a graph code, which is decodable using belief propagation. The main design problem is determining the order of splitting, which enables successful decoding as early...

  10. Morocco - Fruit Tree Productivity

    Data.gov (United States)

    Millennium Challenge Corporation — Date Tree Irrigation Project: The specific objectives of this evaluation are threefold: - Performance evaluation of project activities, like the mid-term evaluation,...

  11. Are trees long-lived?

    Science.gov (United States)

    Kevin T. Smith

    2009-01-01

    Trees and tree care can capture the best of people's motivations and intentions. Trees are living memorials that help communities heal at sites of national tragedy, such as Oklahoma City and the World Trade Center. We mark the places of important historical events by the trees that grew nearby even if the original tree, such as the Charter Oak in Connecticut or...

  12. Refined reservoir description to maximize oil recovery

    International Nuclear Information System (INIS)

    Flewitt, W.E.

    1975-01-01

    To assure maximized oil recovery from older pools, reservoir description has been advanced by fully integrating original open-hole logs and the recently introduced interpretive techniques made available through cased-hole wireline saturation logs. A refined reservoir description utilizing normalized original wireline porosity logs has been completed in the Judy Creek Beaverhill Lake ''A'' Pool, a reefal carbonate pool with current potential productivity of 100,000 BOPD and 188 active wells. Continuous porosity was documented within a reef rim and cap while discontinuous porous lenses characterized an interior lagoon. With the use of pulsed neutron logs and production data a separate water front and pressure response was recognized within discrete environmental units. The refined reservoir description aided in reservoir simulation model studies and quantifying pool performance. A pattern water flood has now replaced the original peripheral bottom water drive to maximize oil recovery

  13. Maximal frustration as an immunological principle.

    Science.gov (United States)

    de Abreu, F Vistulo; Mostardinha, P

    2009-03-06

    A fundamental problem in immunology is that of understanding how the immune system selects promptly which cells to kill without harming the body. This problem poses an apparent paradox. Strong reactivity against pathogens seems incompatible with perfect tolerance towards self. We propose a different view on cellular reactivity to overcome this paradox: effector functions should be seen as the outcome of cellular decisions which can be in conflict with other cells' decisions. We argue that if cellular systems are frustrated, then extensive cross-reactivity among the elements in the system can decrease the reactivity of the system as a whole and induce perfect tolerance. Using numerical and mathematical analyses, we discuss two simple models that perform optimal pathogenic detection with no autoimmunity if cells are maximally frustrated. This study strongly suggests that a principle of maximal frustration could be used to build artificial immune systems. It would be interesting to test this principle in the real adaptive immune system.

  14. Derivative pricing based on local utility maximization

    OpenAIRE

    Jan Kallsen

    2002-01-01

    This paper discusses a new approach to contingent claim valuation in general incomplete market models. We determine the neutral derivative price which occurs if investors maximize their local utility and if derivative demand and supply are balanced. We also introduce the sensitivity process of a contingent claim. This process quantifies the reliability of the neutral derivative price and it can be used to construct price bounds. Moreover, it allows to calibrate market models in order to be co...

  15. Control of Shareholders’ Wealth Maximization in Nigeria

    OpenAIRE

    A. O. Oladipupo; C. O. Okafor

    2014-01-01

    This research focuses on who controls shareholder’s wealth maximization and how does this affect firm’s performance in publicly quoted non-financial companies in Nigeria. The shareholder fund was the dependent while explanatory variables were firm size (proxied by log of turnover), retained earning (representing management control) and dividend payment (representing measure of shareholders control). The data used for this study were obtained from the Nigerian Stock Exchange [NSE] fact book an...

  16. Definable maximal discrete sets in forcing extensions

    DEFF Research Database (Denmark)

    Törnquist, Asger Dag; Schrittesser, David

    2018-01-01

    Let  be a Σ11 binary relation, and recall that a set A is -discrete if no two elements of A are related by . We show that in the Sacks and Miller forcing extensions of L there is a Δ12 maximal -discrete set. We use this to answer in the negative the main question posed in [5] by showing...

  17. Dynamic Convex Duality in Constrained Utility Maximization

    OpenAIRE

    Li, Yusong; Zheng, Harry

    2016-01-01

    In this paper, we study a constrained utility maximization problem following the convex duality approach. After formulating the primal and dual problems, we construct the necessary and sufficient conditions for both the primal and dual problems in terms of FBSDEs plus additional conditions. Such formulation then allows us to explicitly characterize the primal optimal control as a function of the adjoint process coming from the dual FBSDEs in a dynamic fashion and vice versa. Moreover, we also...

  18. Fragmentation of random trees

    International Nuclear Information System (INIS)

    Kalay, Z; Ben-Naim, E

    2015-01-01

    We study fragmentation of a random recursive tree into a forest by repeated removal of nodes. The initial tree consists of N nodes and it is generated by sequential addition of nodes with each new node attaching to a randomly-selected existing node. As nodes are removed from the tree, one at a time, the tree dissolves into an ensemble of separate trees, namely, a forest. We study statistical properties of trees and nodes in this heterogeneous forest, and find that the fraction of remaining nodes m characterizes the system in the limit N→∞. We obtain analytically the size density ϕ s of trees of size s. The size density has power-law tail ϕ s ∼s −α with exponent α=1+(1/m). Therefore, the tail becomes steeper as further nodes are removed, and the fragmentation process is unusual in that exponent α increases continuously with time. We also extend our analysis to the case where nodes are added as well as removed, and obtain the asymptotic size density for growing trees. (paper)

  19. The tree BVOC index

    Science.gov (United States)

    J.R. Simpson; E.G. McPherson

    2011-01-01

    Urban trees can produce a number of benefits, among them improved air quality. Biogenic volatile organic compounds (BVOCs) emitted by some species are ozone precursors. Modifying future tree planting to favor lower-emitting species can reduce these emissions and aid air management districts in meeting federally mandated emissions reductions for these compounds. Changes...

  20. Tree growth visualization

    Science.gov (United States)

    L. Linsen; B.J. Karis; E.G. McPherson; B. Hamann

    2005-01-01

    In computer graphics, models describing the fractal branching structure of trees typically exploit the modularity of tree structures. The models are based on local production rules, which are applied iteratively and simultaneously to create a complex branching system. The objective is to generate three-dimensional scenes of often many realistic- looking and non-...

  1. Flowering T Flowering Trees

    Indian Academy of Sciences (India)

    Adansonia digitata L. ( The Baobab Tree) of Bombacaceae is a tree with swollen trunk that attains a dia. of 10m. Leaves are digitately compound with leaflets up to 18cm. long. Flowers are large, solitary, waxy white, and open at dusk. They open in 30 seconds and are bat pollinated. Stamens are many. Fruit is about 30 cm ...

  2. Fault tree graphics

    International Nuclear Information System (INIS)

    Bass, L.; Wynholds, H.W.; Porterfield, W.R.

    1975-01-01

    Described is an operational system that enables the user, through an intelligent graphics terminal, to construct, modify, analyze, and store fault trees. With this system, complex engineering designs can be analyzed. This paper discusses the system and its capabilities. Included is a brief discussion of fault tree analysis, which represents an aspect of reliability and safety modeling

  3. Tree biology and dendrochemistry

    Science.gov (United States)

    Kevin T. Smith; Walter C. Shortle

    1996-01-01

    Dendrochemistry, the interpretation of elemental analysis of dated tree rings, can provide a temporal record of environmental change. Using the dendrochemical record requires an understanding of tree biology. In this review, we pose four questions concerning assumptions that underlie recent dendrochemical research: 1) Does the chemical composition of the wood directly...

  4. Individual tree control

    Science.gov (United States)

    Harvey A. Holt

    1989-01-01

    Controlling individual unwanted trees in forest stands is a readily accepted method for improving the value of future harvests. The practice is especially important in mixed hardwood forests where species differ considerably in value and within species individual trees differ in quality. Individual stem control is a mechanical or chemical weeding operation that...

  5. Trees and Climate Change

    OpenAIRE

    Dettenmaier, Megan; Kuhns, Michael; Unger, Bethany; McAvoy, Darren

    2017-01-01

    This fact sheet describes the complex relationship between forests and climate change based on current research. It explains ways that trees can mitigate some of the risks associated with climate change. It details the impacts that forests are having on the changing climate and discuss specific ways that trees can be used to reduce or counter carbon emissions directly and indirectly.

  6. Structural Equation Model Trees

    Science.gov (United States)

    Brandmaier, Andreas M.; von Oertzen, Timo; McArdle, John J.; Lindenberger, Ulman

    2013-01-01

    In the behavioral and social sciences, structural equation models (SEMs) have become widely accepted as a modeling tool for the relation between latent and observed variables. SEMs can be seen as a unification of several multivariate analysis techniques. SEM Trees combine the strengths of SEMs and the decision tree paradigm by building tree…

  7. Matching Subsequences in Trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li

    2009-01-01

    Given two rooted, labeled trees P and T the tree path subsequence problem is to determine which paths in P are subsequences of which paths in T. Here a path begins at the root and ends at a leaf. In this paper we propose this problem as a useful query primitive for XML data, and provide new...

  8. Single maximal versus combination punch kinematics.

    Science.gov (United States)

    Piorkowski, Barry A; Lees, Adrian; Barton, Gabor J

    2011-03-01

    The aim of this study was to determine the influence of punch type (Jab, Cross, Lead Hook and Reverse Hook) and punch modality (Single maximal, 'In-synch' and 'Out of synch' combination) on punch speed and delivery time. Ten competition-standard volunteers performed punches with markers placed on their anatomical landmarks for 3D motion capture with an eight-camera optoelectronic system. Speed and duration between key moments were computed. There were significant differences in contact speed between punch types (F(2,18,84.87) = 105.76, p = 0.001) with Lead and Reverse Hooks developing greater speed than Jab and Cross. There were significant differences in contact speed between punch modalities (F(2,64,102.87) = 23.52, p = 0.001) with the Single maximal (M+/- SD: 9.26 +/- 2.09 m/s) higher than 'Out of synch' (7.49 +/- 2.32 m/s), 'In-synch' left (8.01 +/- 2.35 m/s) or right lead (7.97 +/- 2.53 m/s). Delivery times were significantly lower for Jab and Cross than Hook. Times were significantly lower 'In-synch' than a Single maximal or 'Out of synch' combination mode. It is concluded that a defender may have more evasion-time than previously reported. This research could be of use to performers and coaches when considering training preparations.

  9. Formation Control for the MAXIM Mission

    Science.gov (United States)

    Luquette, Richard J.; Leitner, Jesse; Gendreau, Keith; Sanner, Robert M.

    2004-01-01

    Over the next twenty years, a wave of change is occurring in the space-based scientific remote sensing community. While the fundamental limits in the spatial and angular resolution achievable in spacecraft have been reached, based on today s technology, an expansive new technology base has appeared over the past decade in the area of Distributed Space Systems (DSS). A key subset of the DSS technology area is that which covers precision formation flying of space vehicles. Through precision formation flying, the baselines, previously defined by the largest monolithic structure which could fit in the largest launch vehicle fairing, are now virtually unlimited. Several missions including the Micro-Arcsecond X-ray Imaging Mission (MAXIM), and the Stellar Imager will drive the formation flying challenges to achieve unprecedented baselines for high resolution, extended-scene, interferometry in the ultraviolet and X-ray regimes. This paper focuses on establishing the feasibility for the formation control of the MAXIM mission. MAXIM formation flying requirements are on the order of microns, while Stellar Imager mission requirements are on the order of nanometers. This paper specifically addresses: (1) high-level science requirements for these missions and how they evolve into engineering requirements; and (2) the development of linearized equations of relative motion for a formation operating in an n-body gravitational field. Linearized equations of motion provide the ground work for linear formation control designs.

  10. Gradient Dynamics and Entropy Production Maximization

    Science.gov (United States)

    Janečka, Adam; Pavelka, Michal

    2018-01-01

    We compare two methods for modeling dissipative processes, namely gradient dynamics and entropy production maximization. Both methods require similar physical inputs-how energy (or entropy) is stored and how it is dissipated. Gradient dynamics describes irreversible evolution by means of dissipation potential and entropy, it automatically satisfies Onsager reciprocal relations as well as their nonlinear generalization (Maxwell-Onsager relations), and it has statistical interpretation. Entropy production maximization is based on knowledge of free energy (or another thermodynamic potential) and entropy production. It also leads to the linear Onsager reciprocal relations and it has proven successful in thermodynamics of complex materials. Both methods are thermodynamically sound as they ensure approach to equilibrium, and we compare them and discuss their advantages and shortcomings. In particular, conditions under which the two approaches coincide and are capable of providing the same constitutive relations are identified. Besides, a commonly used but not often mentioned step in the entropy production maximization is pinpointed and the condition of incompressibility is incorporated into gradient dynamics.

  11. Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees.

    Science.gov (United States)

    Stolzer, Maureen; Lai, Han; Xu, Minli; Sathaye, Deepa; Vernot, Benjamin; Durand, Dannie

    2012-09-15

    Gene duplication (D), transfer (T), loss (L) and incomplete lineage sorting (I) are crucial to the evolution of gene families and the emergence of novel functions. The history of these events can be inferred via comparison of gene and species trees, a process called reconciliation, yet current reconciliation algorithms model only a subset of these evolutionary processes. We present an algorithm to reconcile a binary gene tree with a nonbinary species tree under a DTLI parsimony criterion. This is the first reconciliation algorithm to capture all four evolutionary processes driving tree incongruence and the first to reconcile non-binary species trees with a transfer model. Our algorithm infers all optimal solutions and reports complete, temporally feasible event histories, giving the gene and species lineages in which each event occurred. It is fixed-parameter tractable, with polytime complexity when the maximum species outdegree is fixed. Application of our algorithms to prokaryotic and eukaryotic data show that use of an incomplete event model has substantial impact on the events inferred and resulting biological conclusions. Our algorithms have been implemented in Notung, a freely available phylogenetic reconciliation software package, available at http://www.cs.cmu.edu/~durand/Notung. mstolzer@andrew.cmu.edu.

  12. Environmental tritium in trees

    International Nuclear Information System (INIS)

    Brown, R.M.

    1979-01-01

    The distribution of environmental tritium in the free water and organically bound hydrogen of trees growing in the vicinity of the Chalk River Nuclear Laboratories (CRNL) has been studied. The regional dispersal of HTO in the atmosphere has been observed by surveying the tritium content of leaf moisture. Measurement of the distribution of organically bound tritium in the wood of tree ring sequences has given information on past concentrations of HTO taken up by trees growing in the CRNL Liquid Waste Disposal Area. For samples at background environmental levels, cellulose separation and analysis was done. The pattern of bomb tritium in precipitation of 1955-68 was observed to be preserved in the organically bound tritium of a tree ring sequence. Reactor tritium was discernible in a tree growing at a distance of 10 km from CRNL. These techniques provide convenient means of monitoring dispersal of HTO from nuclear facilities. (author)

  13. Dynamics of investor spanning trees around dot-com bubble.

    Directory of Open Access Journals (Sweden)

    Sindhuja Ranganathan

    Full Text Available We identify temporal investor networks for Nokia stock by constructing networks from correlations between investor-specific net-volumes and analyze changes in the networks around dot-com bubble. The analysis is conducted separately for households, financial, and non-financial institutions. Our results indicate that spanning tree measures for households reflected the boom and crisis: the maximum spanning tree measures had a clear upward tendency in the bull markets when the bubble was building up, and, even more importantly, the minimum spanning tree measures pre-reacted the burst of the bubble. At the same time, we find less clear reactions in the minimal and maximal spanning trees of non-financial and financial institutions around the bubble, which suggests that household investors can have a greater herding tendency around bubbles.

  14. Dynamics of investor spanning trees around dot-com bubble.

    Science.gov (United States)

    Ranganathan, Sindhuja; Kivelä, Mikko; Kanniainen, Juho

    2018-01-01

    We identify temporal investor networks for Nokia stock by constructing networks from correlations between investor-specific net-volumes and analyze changes in the networks around dot-com bubble. The analysis is conducted separately for households, financial, and non-financial institutions. Our results indicate that spanning tree measures for households reflected the boom and crisis: the maximum spanning tree measures had a clear upward tendency in the bull markets when the bubble was building up, and, even more importantly, the minimum spanning tree measures pre-reacted the burst of the bubble. At the same time, we find less clear reactions in the minimal and maximal spanning trees of non-financial and financial institutions around the bubble, which suggests that household investors can have a greater herding tendency around bubbles.

  15. Generalising tree traversals and tree transformations to DAGs

    DEFF Research Database (Denmark)

    Bahr, Patrick; Axelsson, Emil

    2017-01-01

    We present a recursion scheme based on attribute grammars that can be transparently applied to trees and acyclic graphs. Our recursion scheme allows the programmer to implement a tree traversal or a tree transformation and then apply it to compact graph representations of trees instead. The resul......We present a recursion scheme based on attribute grammars that can be transparently applied to trees and acyclic graphs. Our recursion scheme allows the programmer to implement a tree traversal or a tree transformation and then apply it to compact graph representations of trees instead...... as the complementing theory with a number of examples....

  16. Cardiorespiratory Coordination in Repeated Maximal Exercise

    Directory of Open Access Journals (Sweden)

    Sergi Garcia-Retortillo

    2017-06-01

    Full Text Available Increases in cardiorespiratory coordination (CRC after training with no differences in performance and physiological variables have recently been reported using a principal component analysis approach. However, no research has yet evaluated the short-term effects of exercise on CRC. The aim of this study was to delineate the behavior of CRC under different physiological initial conditions produced by repeated maximal exercises. Fifteen participants performed 2 consecutive graded and maximal cycling tests. Test 1 was performed without any previous exercise, and Test 2 6 min after Test 1. Both tests started at 0 W and the workload was increased by 25 W/min in males and 20 W/min in females, until they were not able to maintain the prescribed cycling frequency of 70 rpm for more than 5 consecutive seconds. A principal component (PC analysis of selected cardiovascular and cardiorespiratory variables (expired fraction of O2, expired fraction of CO2, ventilation, systolic blood pressure, diastolic blood pressure, and heart rate was performed to evaluate the CRC defined by the number of PCs in both tests. In order to quantify the degree of coordination, the information entropy was calculated and the eigenvalues of the first PC (PC1 were compared between tests. Although no significant differences were found between the tests with respect to the performed maximal workload (Wmax, maximal oxygen consumption (VO2 max, or ventilatory threshold (VT, an increase in the number of PCs and/or a decrease of eigenvalues of PC1 (t = 2.95; p = 0.01; d = 1.08 was found in Test 2 compared to Test 1. Moreover, entropy was significantly higher (Z = 2.33; p = 0.02; d = 1.43 in the last test. In conclusion, despite the fact that no significant differences were observed in the conventionally explored maximal performance and physiological variables (Wmax, VO2 max, and VT between tests, a reduction of CRC was observed in Test 2. These results emphasize the interest of CRC

  17. 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.

  18. A recursive algorithm for trees and forests

    OpenAIRE

    Guo, Song; Guo, Victor J. W.

    2017-01-01

    Trees or rooted trees have been generously studied in the literature. A forest is a set of trees or rooted trees. Here we give recurrence relations between the number of some kind of rooted forest with $k$ roots and that with $k+1$ roots on $\\{1,2,\\ldots,n\\}$. Classical formulas for counting various trees such as rooted trees, bipartite trees, tripartite trees, plane trees, $k$-ary plane trees, $k$-edge colored trees follow immediately from our recursive relations.

  19. Phylogenetic trees in bioinformatics

    Energy Technology Data Exchange (ETDEWEB)

    Burr, Tom L [Los Alamos National Laboratory

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  20. Skewed Binary Search Trees

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Moruz, Gabriel

    2006-01-01

    It is well-known that to minimize the number of comparisons a binary search tree should be perfectly balanced. Previous work has shown that a dominating factor over the running time for a search is the number of cache faults performed, and that an appropriate memory layout of a binary search tree...... can reduce the number of cache faults by several hundred percent. Motivated by the fact that during a search branching to the left or right at a node does not necessarily have the same cost, e.g. because of branch prediction schemes, we in this paper study the class of skewed binary search trees....... For all nodes in a skewed binary search tree the ratio between the size of the left subtree and the size of the tree is a fixed constant (a ratio of 1/2 gives perfect balanced trees). In this paper we present an experimental study of various memory layouts of static skewed binary search trees, where each...

  1. Species trees from consensus single nucleotide polymorphism (SNP) data: Testing phylogenetic approaches with simulated and empirical data.

    Science.gov (United States)

    Schmidt-Lebuhn, Alexander N; Aitken, Nicola C; Chuah, Aaron

    2017-11-01

    Datasets of hundreds or thousands of SNPs (Single Nucleotide Polymorphisms) from multiple individuals per species are increasingly used to study population structure, species delimitation and shallow phylogenetics. The principal software tool to infer species or population trees from SNP data is currently the BEAST template SNAPP which uses a Bayesian coalescent analysis. However, it is computationally extremely demanding and tolerates only small amounts of missing data. We used simulated and empirical SNPs from plants (Australian Craspedia, Asteraceae, and Pelargonium, Geraniaceae) to compare species trees produced (1) by SNAPP, (2) using SVD quartets, and (3) using Bayesian and parsimony analysis with several different approaches to summarising data from multiple samples into one set of traits per species. Our aims were to explore the impact of tree topology and missing data on the results, and to test which data summarising and analyses approaches would best approximate the results obtained from SNAPP for empirical data. SVD quartets retrieved the correct topology from simulated data, as did SNAPP except in the case of a very unbalanced phylogeny. Both methods failed to retrieve the correct topology when large amounts of data were missing. Bayesian analysis of species level summary data scoring the two alleles of each SNP as independent characters and parsimony analysis of data scoring each SNP as one character produced trees with branch length distributions closest to the true trees on which SNPs were simulated. For empirical data, Bayesian inference and Dollo parsimony analysis of data scored allele-wise produced phylogenies most congruent with the results of SNAPP. In the case of study groups divergent enough for missing data to be phylogenetically informative (because of additional mutations preventing amplification of genomic fragments or bioinformatic establishment of homology), scoring of SNP data as a presence/absence matrix irrespective of allele

  2. Postactivation potentiation biases maximal isometric strength assessment.

    Science.gov (United States)

    Lima, Leonardo Coelho Rabello; Oliveira, Felipe Bruno Dias; Oliveira, Thiago Pires; Assumpção, Claudio de Oliveira; Greco, Camila Coelho; Cardozo, Adalgiso Croscato; Denadai, Benedito Sérgio

    2014-01-01

    Postactivation potentiation (PAP) is known to enhance force production. Maximal isometric strength assessment protocols usually consist of two or more maximal voluntary isometric contractions (MVCs). The objective of this study was to determine if PAP would influence isometric strength assessment. Healthy male volunteers (n = 23) performed two five-second MVCs separated by a 180-seconds interval. Changes in isometric peak torque (IPT), time to achieve it (tPTI), contractile impulse (CI), root mean square of the electromyographic signal during PTI (RMS), and rate of torque development (RTD), in different intervals, were measured. Significant increases in IPT (240.6 ± 55.7 N·m versus 248.9 ± 55.1 N·m), RTD (746 ± 152 N·m·s(-1) versus 727 ± 158 N·m·s(-1)), and RMS (59.1 ± 12.2% RMSMAX  versus 54.8 ± 9.4% RMSMAX) were found on the second MVC. tPTI decreased significantly on the second MVC (2373 ± 1200 ms versus 2784 ± 1226 ms). We conclude that a first MVC leads to PAP that elicits significant enhancements in strength-related variables of a second MVC performed 180 seconds later. If disconsidered, this phenomenon might bias maximal isometric strength assessment, overestimating some of these variables.

  3. Gain maximization in a probabilistic entanglement protocol

    Science.gov (United States)

    di Lorenzo, Antonio; Esteves de Queiroz, Johnny Hebert

    Entanglement is a resource. We can therefore define gain as a monotonic function of entanglement G (E) . If a pair with entanglement E is produced with probability P, the net gain is N = PG (E) - (1 - P) C , where C is the cost of a failed attempt. We study a protocol where a pair of quantum systems is produced in a maximally entangled state ρm with probability Pm, while it is produced in a partially entangled state ρp with the complementary probability 1 -Pm . We mix a fraction w of the partially entangled pairs with the maximally entangled ones, i.e. we take the state to be ρ = (ρm + wUlocρpUloc+) / (1 + w) , where Uloc is an appropriate unitary local operation designed to maximize the entanglement of ρ. This procedure on one hand reduces the entanglement E, and hence the gain, but on the other hand it increases the probability of success to P =Pm + w (1 -Pm) , therefore the net gain N may increase. There may be hence, a priori, an optimal value for w, the fraction of failed attempts that we mix in. We show that, in the hypothesis of a linear gain G (E) = E , even assuming a vanishing cost C -> 0 , the net gain N is increasing with w, therefore the best strategy is to always mix the partially entangled states. Work supported by CNPq, Conselho Nacional de Desenvolvimento Científico e Tecnológico, proc. 311288/2014-6, and by FAPEMIG, Fundação de Amparo à Pesquisa de Minas Gerais, proc. IC-FAPEMIG2016-0269 and PPM-00607-16.

  4. The gravity apple tree

    International Nuclear Information System (INIS)

    Aldama, Mariana Espinosa

    2015-01-01

    The gravity apple tree is a genealogical tree of the gravitation theories developed during the past century. The graphic representation is full of information such as guides in heuristic principles, names of main proponents, dates and references for original articles (See under Supplementary Data for the graphic representation). This visual presentation and its particular classification allows a quick synthetic view for a plurality of theories, many of them well validated in the Solar System domain. Its diachronic structure organizes information in a shape of a tree following similarities through a formal concept analysis. It can be used for educational purposes or as a tool for philosophical discussion. (paper)

  5. Visualizing phylogenetic tree landscapes.

    Science.gov (United States)

    Wilgenbusch, James C; Huang, Wen; Gallivan, Kyle A

    2017-02-02

    Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented. Curvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D

  6. Does biodiversity make a difference? Relationships between species richness, evolutionary diversity, and aboveground live tree biomass across US forests

    Science.gov (United States)

    Kevin M. Potter; Christopher W. Woodall

    2014-01-01

    Biodiversity conveys numerous functional benefits to forested ecosystems, including community stability and resilience. In the context of managing forests for climate change mitigation/adaptation, maximizing and/or maintaining aboveground biomass will require understanding the interactions between tree biodiversity, site productivity, and the stocking of live trees....

  7. Maximizing percentage depletion in solid minerals

    International Nuclear Information System (INIS)

    Tripp, J.; Grove, H.D.; McGrath, M.

    1982-01-01

    This article develops a strategy for maximizing percentage depletion deductions when extracting uranium or other solid minerals. The goal is to avoid losing percentage depletion deductions by staying below the 50% limitation on taxable income from the property. The article is divided into two major sections. The first section is comprised of depletion calculations that illustrate the problem and corresponding solutions. The last section deals with the feasibility of applying the strategy and complying with the Internal Revenue Code and appropriate regulations. Three separate strategies or appropriate situations are developed and illustrated. 13 references, 3 figures, 7 tables

  8. What currency do bumble bees maximize?

    Directory of Open Access Journals (Sweden)

    Nicholas L Charlton

    2010-08-01

    Full Text Available In modelling bumble bee foraging, net rate of energetic intake has been suggested as the appropriate currency. The foraging behaviour of honey bees is better predicted by using efficiency, the ratio of energetic gain to expenditure, as the currency. We re-analyse several studies of bumble bee foraging and show that efficiency is as good a currency as net rate in terms of predicting behaviour. We suggest that future studies of the foraging of bumble bees should be designed to distinguish between net rate and efficiency maximizing behaviour in an attempt to discover which is the more appropriate currency.

  9. New Maximal Two-distance Sets

    DEFF Research Database (Denmark)

    Lisonek, Petr

    1996-01-01

    A two-distance set in E^d is a point set X inthe d-dimensional Euclidean spacesuch that the distances between distinct points in Xassume only two different non-zero values. Based on results from classical distance geometry, we developan algorithm to classify, for a given dimension, all maximal...... (largest possible)two-distance sets in E^d.Using this algorithm we have completed the full classificationfor all dimensions less than or equal to 7, andwe have found one set in E^8 whosemaximality follows from Blokhuis' upper bound on sizes of s-distance sets.While in the dimensions less than or equal to 6...

  10. Maximizing policy learning in international committees

    DEFF Research Database (Denmark)

    Nedergaard, Peter

    2007-01-01

    , this article demonstrates that valuable lessons can be learned about policy learning, in practice and theoretically, by analysing the cooperation in the OMC committees. Using the Advocacy Coalition Framework as the starting point of analysis, 15 hypotheses on policy learning are tested. Among other things......, it is concluded that in order to maximize policy learning in international committees, empirical data should be made available to committees and provided by sources close to the participants (i.e. the Commission). In addition, the work in the committees should be made prestigious in order to attract well...

  11. Pouliot type duality via a-maximization

    International Nuclear Information System (INIS)

    Kawano, Teruhiko; Ookouchi, Yutaka; Tachikawa, Yuji; Yagi, Futoshi

    2006-01-01

    We study four-dimensional N=1Spin(10) gauge theory with a single spinor and N Q vectors at the superconformal fixed point via the electric-magnetic duality and a-maximization. When gauge invariant chiral primary operators hit the unitarity bounds, we find that the theory with no superpotential is identical to the one with some superpotential at the infrared fixed point. The auxiliary field method in the electric theory offers a satisfying description of the infrared fixed point, which is consistent with the better picture in the magnetic theory. In particular, it gives a clear description of the emergence of new massless degrees of freedom in the electric theory

  12. Developing maximal neuromuscular power: part 2 - training considerations for improving maximal power production.

    Science.gov (United States)

    Cormie, Prue; McGuigan, Michael R; Newton, Robert U

    2011-02-01

    This series of reviews focuses on the most important neuromuscular function in many sport performances: the ability to generate maximal muscular power. Part 1, published in an earlier issue of Sports Medicine, focused on the factors that affect maximal power production while part 2 explores the practical application of these findings by reviewing the scientific literature relevant to the development of training programmes that most effectively enhance maximal power production. The ability to generate maximal power during complex motor skills is of paramount importance to successful athletic performance across many sports. A crucial issue faced by scientists and coaches is the development of effective and efficient training programmes that improve maximal power production in dynamic, multi-joint movements. Such training is referred to as 'power training' for the purposes of this review. Although further research is required in order to gain a deeper understanding of the optimal training techniques for maximizing power in complex, sports-specific movements and the precise mechanisms underlying adaptation, several key conclusions can be drawn from this review. First, a fundamental relationship exists between strength and power, which dictates that an individual cannot possess a high level of power without first being relatively strong. Thus, enhancing and maintaining maximal strength is essential when considering the long-term development of power. Second, consideration of movement pattern, load and velocity specificity is essential when designing power training programmes. Ballistic, plyometric and weightlifting exercises can be used effectively as primary exercises within a power training programme that enhances maximal power. The loads applied to these exercises will depend on the specific requirements of each particular sport and the type of movement being trained. The use of ballistic exercises with loads ranging from 0% to 50% of one-repetition maximum (1RM) and

  13. Tree-growth analyses to estimate tree species' drought tolerance

    NARCIS (Netherlands)

    Eilmann, B.; Rigling, A.

    2012-01-01

    Climate change is challenging forestry management and practices. Among other things, tree species with the ability to cope with more extreme climate conditions have to be identified. However, while environmental factors may severely limit tree growth or even cause tree death, assessing a tree

  14. Big trees, old trees, and growth factor tables

    Science.gov (United States)

    Kevin T. Smith

    2018-01-01

    The potential for a tree to reach a great size and to live a long life frequently captures the public's imagination. Sometimes the desire to know the age of an impressively large tree is simple curiosity. For others, the date-of-tree establishment can make a big diff erence for management, particularly for trees at historic sites or those mentioned in property...

  15. A bijection between phylogenetic trees and plane oriented recursive trees

    OpenAIRE

    Prodinger, Helmut

    2017-01-01

    Phylogenetic trees are binary nonplanar trees with labelled leaves, and plane oriented recursive trees are planar trees with an increasing labelling. Both families are enumerated by double factorials. A bijection is constructed, using the respective representations a 2-partitions and trapezoidal words.

  16. A Suffix Tree Or Not a Suffix Tree?

    DEFF Research Database (Denmark)

    Starikovskaya, Tatiana; Vildhøj, Hjalte Wedel

    2015-01-01

    In this paper we study the structure of suffix trees. Given an unlabeled tree r on n nodes and suffix links of its internal nodes, we ask the question “Is r a suffix tree?”, i.e., is there a string S whose suffix tree has the same topological structure as r? We place no restrictions on S, in part...

  17. Tree-level amplitudes and dual superconformal symmetry

    Energy Technology Data Exchange (ETDEWEB)

    Drummond, J M, E-mail: drummond@lapp.in2p3.fr [PH-TH Division, CERN, CH-1211, Geneva 23 (Switzerland); LAPTH, Universite de Savoie, CNRS, B.P. 110, F-74941 Annecy-le-Vieux Cedex (France)

    2011-11-11

    We review the structure of gauge theory scattering amplitudes at tree level and describe how a compact expression can be found which encodes all the tree-level amplitudes in the maximally supersymmetric N=4 theory. The expressions for the amplitudes reveal a dual superconformal symmetry. We describe how these ideas can be extended to leading singularities and the loop integrand in the planar theory and discuss the appearance of dual conformal symmetry in higher-dimensional gauge theories. This paper is an invited review for a special issue of Journal of Physics A: Mathematical and Theoretical devoted to 'Scattering amplitudes in gauge theories'. (review)

  18. NLCD 2001 - Tree Canopy

    Data.gov (United States)

    Minnesota Department of Natural Resources — The National Land Cover Database 2001 tree canopy layer for Minnesota (mapping zones 39-42, 50-51) was produced through a cooperative project conducted by the...

  19. Trees for future forests

    DEFF Research Database (Denmark)

    Lobo, Albin

    Climate change creates new challenges in forest management. The increase in temperature may in the long run be beneficial for the forests in the northern latitudes, but the high rate at which climate change is predicted to proceed will make adaptation difficult because trees are long living sessile...... organisms. The aim of the present thesis is therefore to explore genetic resilience and phenotypic plasticity mechanisms that allows trees to adapt and evolve with changing climates. The thesis focus on the abiotic factors associated with climate change, especially raised temperatures and lack...... age of these tree species and the uncertainty around the pace and effect of climate, it remains an open question if the native populations can respond fast enough. Phenotypic plasticity through epigenetic regulation of spring phenology is found to be present in a tree species which might act...

  20. Value tree analysis

    International Nuclear Information System (INIS)

    Keeney, R.; Renn, O.; Winterfeldt, D. von; Kotte, U.

    1985-01-01

    What are the targets and criteria on which national energy policy should be based. What priorities should be set, and how can different social interests be matched. To answer these questions, a new instrument of decision theory is presented which has been applied with good results to controversial political issues in the USA. The new technique is known under the name of value tree analysis. Members of important West German organisations (BDI, VDI, RWE, the Catholic and Protestant Church, Deutscher Naturschutzring, and ecological research institutions) were asked about the goals of their organisations. These goals were then ordered systematically and arranged in a hierarchical tree structure. The value trees of different groups can be combined into a catalogue of social criteria of acceptability and policy assessment. The authors describe the philosophy and methodology of value tree analysis and give an outline of its application in the development of a socially acceptable energy policy. (orig.) [de

  1. Maximization techniques for oilfield development profits

    International Nuclear Information System (INIS)

    Lerche, I.

    1999-01-01

    In 1981 Nind provided a quantitative procedure for estimating the optimum number of development wells to emplace on an oilfield to maximize profit. Nind's treatment assumed that there was a steady selling price, that all wells were placed in production simultaneously, and that each well's production profile was identical and a simple exponential decline with time. This paper lifts these restrictions to allow for price fluctuations, variable with time emplacement of wells, and production rates that are more in line with actual production records than is a simple exponential decline curve. As a consequence, it is possible to design production rate strategies, correlated with price fluctuations, so as to maximize the present-day worth of a field. For price fluctuations that occur on a time-scale rapid compared to inflation rates it is appropriate to have production rates correlate directly with such price fluctuations. The same strategy does not apply for price fluctuations occurring on a time-scale long compared to inflation rates where, for small amplitudes in the price fluctuations, it is best to sell as much product as early as possible to overcome inflation factors, while for large amplitude fluctuations the best strategy is to sell product as early as possible but to do so mainly on price upswings. Examples are provided to show how these generalizations of Nind's (1981) formula change the complexion of oilfield development optimization. (author)

  2. Multiscale singularity trees

    DEFF Research Database (Denmark)

    Somchaipeng, Kerawit; Sporring, Jon; Johansen, Peter

    2007-01-01

    We propose MultiScale Singularity Trees (MSSTs) as a structure to represent images, and we propose an algorithm for image comparison based on comparing MSSTs. The algorithm is tested on 3 public image databases and compared to 2 state-of-theart methods. We conclude that the computational complexity...... of our algorithm only allows for the comparison of small trees, and that the results of our method are comparable with state-of-the-art using much fewer parameters for image representation....

  3. Type extension trees

    DEFF Research Database (Denmark)

    Jaeger, Manfred

    2006-01-01

    We introduce type extension trees as a formal representation language for complex combinatorial features of relational data. Based on a very simple syntax this language provides a unified framework for expressing features as diverse as embedded subgraphs on the one hand, and marginal counts...... of attribute values on the other. We show by various examples how many existing relational data mining techniques can be expressed as the problem of constructing a type extension tree and a discriminant function....

  4. Tree felling 2014

    CERN Multimedia

    2014-01-01

    With a view to creating new landscapes and making its population of trees safer and healthier, this winter CERN will complete the tree-felling campaign started in 2010.   Tree felling will take place between 15 and 22 November on the Swiss part of the Meyrin site. This work is being carried out above all for safety reasons. The trees to be cut down are at risk of falling as they are too old and too tall to withstand the wind. In addition, the roots of poplar trees are very powerful and spread widely, potentially damaging underground networks, pavements and roadways. Compensatory tree planting campaigns will take place in the future, subject to the availability of funding, with the aim of creating coherent landscapes while also respecting the functional constraints of the site. These matters are being considered in close collaboration with the Geneva nature and countryside directorate (Direction générale de la nature et du paysage, DGNP). GS-SE Group

  5. Benefit-based tree valuation

    Science.gov (United States)

    E.G. McPherson

    2007-01-01

    Benefit-based tree valuation provides alternative estimates of the fair and reasonable value of trees while illustrating the relative contribution of different benefit types. This study compared estimates of tree value obtained using cost- and benefit-based approaches. The cost-based approach used the Council of Landscape and Tree Appraisers trunk formula method, and...

  6. Attack Trees with Sequential Conjunction

    NARCIS (Netherlands)

    Jhawar, Ravi; Kordy, Barbara; Mauw, Sjouke; Radomirović, Sasa; Trujillo-Rasua, Rolando

    2015-01-01

    We provide the first formal foundation of SAND attack trees which are a popular extension of the well-known attack trees. The SAND at- tack tree formalism increases the expressivity of attack trees by intro- ducing the sequential conjunctive operator SAND. This operator enables the modeling of

  7. Tree manipulation experiment

    Science.gov (United States)

    Nishina, K.; Takenaka, C.; Ishizuka, S.; Hashimoto, S.; Yagai, Y.

    2012-12-01

    Some forest operations such as thinning and harvesting management could cause changes in N cycling and N2O emission from soils, since thinning and harvesting managements are accompanied with changes in aboveground environments such as an increase of slash falling and solar radiation on the forest floor. However, a considerable uncertainty exists in effects of thinning and harvesting on N2O fluxes regarding changes in belowground environments by cutting trees. To focus on the effect of changes in belowground environments on the N2O emissions from soils, we conducted a tree manipulation experiment in Japanese cedar (Cryptomeria japonica) stand without soil compaction and slash falling near the chambers and measured N2O flux at 50 cm and 150 cm distances from the tree trunk (stump) before and after cutting. We targeted 5 trees for the manipulation and established the measurement chambers to the 4 directions around each targeted tree relative to upper slope (upper, left, right, lower positions). We evaluated the effect of logging on the emission by using hierarchical Bayesian model. HB model can evaluate the variability in observed data and their uncertainties in the estimation with various probability distributions. Moreover, the HB model can easily accommodate the non-linear relationship among the N2O emissions and the environmental factors, and explicitly take non-independent data (nested structure of data) for the estimation into account by using random effects in the model. Our results showed tree cutting stimulated N2O emission from soils, and also that the increase of N2O flux depended on the distance from the trunk (stump): the increase of N2O flux at 50 cm from the trunk (stump) was greater than that of 150 cm from the trunk. The posterior simulation of the HB model indicated that the stimulation of N2O emission by tree cut- ting could reach up to 200 cm in our experimental plot. By tree cutting, the estimated N2O emission at 0-40 cm from the trunk doubled

  8. Shareholder, stakeholder-owner or broad stakeholder maximization

    DEFF Research Database (Denmark)

    Mygind, Niels

    2004-01-01

    With reference to the discussion about shareholder versus stakeholder maximization it is argued that the normal type of maximization is in fact stakeholder-owner maxi-mization. This means maximization of the sum of the value of the shares and stake-holder benefits belonging to the dominating...... including the shareholders of a company. Although it may be the ultimate goal for Corporate Social Responsibility to achieve this kind of maximization, broad stakeholder maximization is quite difficult to give a precise definition. There is no one-dimensional measure to add different stakeholder benefits...... not traded on the mar-ket, and therefore there is no possibility for practical application. Broad stakeholder maximization instead in practical applications becomes satisfying certain stakeholder demands, so that the practical application will be stakeholder-owner maximization un-der constraints defined...

  9. Pylogeny: an open-source Python framework for phylogenetic tree reconstruction and search space heuristics

    Directory of Open Access Journals (Sweden)

    Alexander Safatli

    2015-06-01

    Full Text Available Summary. Pylogeny is a cross-platform library for the Python programming language that provides an object-oriented application programming interface for phylogenetic heuristic searches. Its primary function is to permit both heuristic search and analysis of the phylogenetic tree search space, as well as to enable the design of novel algorithms to search this space. To this end, the framework supports the structural manipulation of phylogenetic trees, in particular using rearrangement operators such as NNI, SPR, and TBR, the scoring of trees using parsimony and likelihood methods, the construction of a tree search space graph, and the programmatic execution of a few existing heuristic programs. The library supports a range of common phylogenetic file formats and can be used for both nucleotide and protein data. Furthermore, it is also capable of supporting GPU likelihood calculation on nucleotide character data through the BEAGLE library.Availability. Existing development and source code is available for contribution and for download by the public from GitHub (http://github.com/AlexSafatli/Pylogeny. A stable release of this framework is available for download through PyPi (Python Package Index at http://pypi.python.org/pypi/pylogeny.

  10. 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.

  11. Maximizing Lumen Gain With Directional Atherectomy.

    Science.gov (United States)

    Stanley, Gregory A; Winscott, John G

    2016-08-01

    To describe the use of a low-pressure balloon inflation (LPBI) technique to delineate intraluminal plaque and guide directional atherectomy in order to maximize lumen gain and achieve procedure success. The technique is illustrated in a 77-year-old man with claudication who underwent superficial femoral artery revascularization using a HawkOne directional atherectomy catheter. A standard angioplasty balloon was inflated to 1 to 2 atm during live fluoroscopy to create a 3-dimensional "lumenogram" of the target lesion. Directional atherectomy was performed only where plaque impinged on the balloon at a specific fluoroscopic orientation. The results of the LPBI technique were corroborated with multimodality diagnostic imaging, including digital subtraction angiography, intravascular ultrasound, and intra-arterial pressure measurements. With the LPBI technique, directional atherectomy can routinely achieve <10% residual stenosis, as illustrated in this case, thereby broadly supporting a no-stent approach to lower extremity endovascular revascularization. © The Author(s) 2016.

  12. Primordial two-component maximally symmetric inflation

    Science.gov (United States)

    Enqvist, K.; Nanopoulos, D. V.; Quirós, M.; Kounnas, C.

    1985-12-01

    We propose a two-component inflation model, based on maximally symmetric supergravity, where the scales of reheating and the inflation potential at the origin are decoupled. This is possible because of the second-order phase transition from SU(5) to SU(3)×SU(2)×U(1) that takes place when φ≅φcinflation at the global minimum, and leads to a reheating temperature TR≅(1015-1016) GeV. This makes it possible to generate baryon asymmetry in the conventional way without any conflict with experimental data on proton lifetime. The mass of the gravitinos is m3/2≅1012 GeV, thus avoiding the gravitino problem. Monopoles are diluted by residual inflation in the broken phase below the cosmological bounds if φcUSA.

  13. Distributed-Memory Fast Maximal Independent Set

    Energy Technology Data Exchange (ETDEWEB)

    Kanewala Appuhamilage, Thejaka Amila J.; Zalewski, Marcin J.; Lumsdaine, Andrew

    2017-09-13

    The Maximal Independent Set (MIS) graph problem arises in many applications such as computer vision, information theory, molecular biology, and process scheduling. The growing scale of MIS problems suggests the use of distributed-memory hardware as a cost-effective approach to providing necessary compute and memory resources. Luby proposed four randomized algorithms to solve the MIS problem. All those algorithms are designed focusing on shared-memory machines and are analyzed using the PRAM model. These algorithms do not have direct efficient distributed-memory implementations. In this paper, we extend two of Luby’s seminal MIS algorithms, “Luby(A)” and “Luby(B),” to distributed-memory execution, and we evaluate their performance. We compare our results with the “Filtered MIS” implementation in the Combinatorial BLAS library for two types of synthetic graph inputs.

  14. Quench dynamics of topological maximally entangled states.

    Science.gov (United States)

    Chung, Ming-Chiang; Jhu, Yi-Hao; Chen, Pochung; Mou, Chung-Yu

    2013-07-17

    We investigate the quench dynamics of the one-particle entanglement spectra (OPES) for systems with topologically nontrivial phases. By using dimerized chains as an example, it is demonstrated that the evolution of OPES for the quenched bipartite systems is governed by an effective Hamiltonian which is characterized by a pseudospin in a time-dependent pseudomagnetic field S(k,t). The existence and evolution of the topological maximally entangled states (tMESs) are determined by the winding number of S(k,t) in the k-space. In particular, the tMESs survive only if nontrivial Berry phases are induced by the winding of S(k,t). In the infinite-time limit the equilibrium OPES can be determined by an effective time-independent pseudomagnetic field Seff(k). Furthermore, when tMESs are unstable, they are destroyed by quasiparticles within a characteristic timescale in proportion to the system size.

  15. Maximizing policy learning in international committees

    DEFF Research Database (Denmark)

    Nedergaard, Peter

    2007-01-01

    , this article demonstrates that valuable lessons can be learned about policy learning, in practice and theoretically, by analysing the cooperation in the OMC committees. Using the Advocacy Coalition Framework as the starting point of analysis, 15 hypotheses on policy learning are tested. Among other things......In the voluminous literature on the European Union's open method of coordination (OMC), no one has hitherto analysed on the basis of scholarly examination the question of what contributes to the learning processes in the OMC committees. On the basis of a questionnaire sent to all participants......, it is concluded that in order to maximize policy learning in international committees, empirical data should be made available to committees and provided by sources close to the participants (i.e. the Commission). In addition, the work in the committees should be made prestigious in order to attract well...

  16. Lovelock black holes with maximally symmetric horizons

    Energy Technology Data Exchange (ETDEWEB)

    Maeda, Hideki; Willison, Steven; Ray, Sourya, E-mail: hideki@cecs.cl, E-mail: willison@cecs.cl, E-mail: ray@cecs.cl [Centro de Estudios CientIficos (CECs), Casilla 1469, Valdivia (Chile)

    2011-08-21

    We investigate some properties of n( {>=} 4)-dimensional spacetimes having symmetries corresponding to the isometries of an (n - 2)-dimensional maximally symmetric space in Lovelock gravity under the null or dominant energy condition. The well-posedness of the generalized Misner-Sharp quasi-local mass proposed in the past study is shown. Using this quasi-local mass, we clarify the basic properties of the dynamical black holes defined by a future outer trapping horizon under certain assumptions on the Lovelock coupling constants. The C{sup 2} vacuum solutions are classified into four types: (i) Schwarzschild-Tangherlini-type solution; (ii) Nariai-type solution; (iii) special degenerate vacuum solution; and (iv) exceptional vacuum solution. The conditions for the realization of the last two solutions are clarified. The Schwarzschild-Tangherlini-type solution is studied in detail. We prove the first law of black-hole thermodynamics and present the expressions for the heat capacity and the free energy.

  17. MAXIMIZING THE BENEFITS OF ERP SYSTEMS

    Directory of Open Access Journals (Sweden)

    Paulo André da Conceição Menezes

    2010-04-01

    Full Text Available The ERP (Enterprise Resource Planning systems have been consolidated in companies with different sizes and sectors, allowing their real benefits to be definitively evaluated. In this study, several interactions have been studied in different phases, such as the strategic priorities and strategic planning defined as ERP Strategy; business processes review and the ERP selection in the pre-implementation phase, the project management and ERP adaptation in the implementation phase, as well as the ERP revision and integration efforts in the post-implementation phase. Through rigorous use of case study methodology, this research led to developing and to testing a framework for maximizing the benefits of the ERP systems, and seeks to contribute for the generation of ERP initiatives to optimize their performance.

  18. Maximal energy extraction under discrete diffusive exchange

    Energy Technology Data Exchange (ETDEWEB)

    Hay, M. J., E-mail: hay@princeton.edu [Department of Astrophysical Sciences, Princeton University, Princeton, New Jersey 08544 (United States); Schiff, J. [Department of Mathematics, Bar-Ilan University, Ramat Gan 52900 (Israel); Fisch, N. J. [Department of Astrophysical Sciences, Princeton University, Princeton, New Jersey 08544 (United States); Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543 (United States)

    2015-10-15

    Waves propagating through a bounded plasma can rearrange the densities of states in the six-dimensional velocity-configuration phase space. Depending on the rearrangement, the wave energy can either increase or decrease, with the difference taken up by the total plasma energy. In the case where the rearrangement is diffusive, only certain plasma states can be reached. It turns out that the set of reachable states through such diffusive rearrangements has been described in very different contexts. Building upon those descriptions, and making use of the fact that the plasma energy is a linear functional of the state densities, the maximal extractable energy under diffusive rearrangement can then be addressed through linear programming.

  19. Maximizing profitability in a hospital outpatient pharmacy.

    Science.gov (United States)

    Jorgenson, J A; Kilarski, J W; Malatestinic, W N; Rudy, T A

    1989-07-01

    This paper describes the strategies employed to increase the profitability of an existing ambulatory pharmacy operated by the hospital. Methods to generate new revenue including implementation of a home parenteral therapy program, a home enteral therapy program, a durable medical equipment service, and home care disposable sales are described. Programs to maximize existing revenue sources such as increasing the capture rate on discharge prescriptions, increasing "walk-in" prescription traffic and increasing HMO prescription volumes are discussed. A method utilized to reduce drug expenditures is also presented. By minimizing expenses and increasing the revenues for the ambulatory pharmacy operation, net profit increased from +26,000 to over +140,000 in one year.

  20. Maximizing the benefits of a dewatering system

    International Nuclear Information System (INIS)

    Matthews, P.; Iverson, T.S.

    1999-01-01

    The use of dewatering systems in the mining, industrial sludge and sewage waste treatment industries is discussed, also describing some of the problems that have been encountered while using drilling fluid dewatering technology. The technology is an acceptable drilling waste handling alternative but it has had problems associated with recycled fluid incompatibility, high chemical costs and system inefficiencies. This paper discussed the following five action areas that can maximize the benefits and help reduce costs of a dewatering project: (1) co-ordinate all services, (2) choose equipment that fits the drilling program, (3) match the chemical treatment with the drilling fluid types, (4) determine recycled fluid compatibility requirements, and (5) determine the disposal requirements before project start-up. 2 refs., 5 figs

  1. Mixtures of maximally entangled pure states

    Energy Technology Data Exchange (ETDEWEB)

    Flores, M.M., E-mail: mflores@nip.up.edu.ph; Galapon, E.A., E-mail: eric.galapon@gmail.com

    2016-09-15

    We study the conditions when mixtures of maximally entangled pure states remain entangled. We found that the resulting mixed state remains entangled when the number of entangled pure states to be mixed is less than or equal to the dimension of the pure states. For the latter case of mixing a number of pure states equal to their dimension, we found that the mixed state is entangled provided that the entangled pure states to be mixed are not equally weighted. We also found that one can restrict the set of pure states that one can mix from in order to ensure that the resulting mixed state is genuinely entangled. Also, we demonstrate how these results could be applied as a way to detect entanglement in mixtures of the entangled pure states with noise.

  2. Maximally reliable Markov chains under energy constraints.

    Science.gov (United States)

    Escola, Sean; Eisele, Michael; Miller, Kenneth; Paninski, Liam

    2009-07-01

    Signal-to-noise ratios in physical systems can be significantly degraded if the outputs of the systems are highly variable. Biological processes for which highly stereotyped signal generations are necessary features appear to have reduced their signal variabilities by employing multiple processing steps. To better understand why this multistep cascade structure might be desirable, we prove that the reliability of a signal generated by a multistate system with no memory (i.e., a Markov chain) is maximal if and only if the system topology is such that the process steps irreversibly through each state, with transition rates chosen such that an equal fraction of the total signal is generated in each state. Furthermore, our result indicates that by increasing the number of states, it is possible to arbitrarily increase the reliability of the system. In a physical system, however, an energy cost is associated with maintaining irreversible transitions, and this cost increases with the number of such transitions (i.e., the number of states). Thus, an infinite-length chain, which would be perfectly reliable, is infeasible. To model the effects of energy demands on the maximally reliable solution, we numerically optimize the topology under two distinct energy functions that penalize either irreversible transitions or incommunicability between states, respectively. In both cases, the solutions are essentially irreversible linear chains, but with upper bounds on the number of states set by the amount of available energy. We therefore conclude that a physical system for which signal reliability is important should employ a linear architecture, with the number of states (and thus the reliability) determined by the intrinsic energy constraints of the system.

  3. A Criterion to Identify Maximally Entangled Four-Qubit State

    International Nuclear Information System (INIS)

    Zha Xinwei; Song Haiyang; Feng Feng

    2011-01-01

    Paolo Facchi, et al. [Phys. Rev. A 77 (2008) 060304(R)] presented a maximally multipartite entangled state (MMES). Here, we give a criterion for the identification of maximally entangled four-qubit states. Using this criterion, we not only identify some existing maximally entangled four-qubit states in the literature, but also find several new maximally entangled four-qubit states as well. (general)

  4. Maximal lattice free bodies, test sets and the Frobenius problem

    DEFF Research Database (Denmark)

    Jensen, Anders Nedergaard; Lauritzen, Niels; Roune, Bjarke Hammersholt

    Maximal lattice free bodies are maximal polytopes without interior integral points. Scarf initiated the study of maximal lattice free bodies relative to the facet normals in a fixed matrix. In this paper we give an efficient algorithm for computing the maximal lattice free bodies of an integral m...... method is inspired by the novel algorithm by Einstein, Lichtblau, Strzebonski and Wagon and the Groebner basis approach by Roune....

  5. Steiner trees in industry

    CERN Document Server

    Du, Ding-Zhu

    2001-01-01

    This book is a collection of articles studying various Steiner tree prob­ lems with applications in industries, such as the design of electronic cir­ cuits, computer networking, telecommunication, and perfect phylogeny. The Steiner tree problem was initiated in the Euclidean plane. Given a set of points in the Euclidean plane, the shortest network interconnect­ ing the points in the set is called the Steiner minimum tree. The Steiner minimum tree may contain some vertices which are not the given points. Those vertices are called Steiner points while the given points are called terminals. The shortest network for three terminals was first studied by Fermat (1601-1665). Fermat proposed the problem of finding a point to minimize the total distance from it to three terminals in the Euclidean plane. The direct generalization is to find a point to minimize the total distance from it to n terminals, which is still called the Fermat problem today. The Steiner minimum tree problem is an indirect generalization. Sch...

  6. Visualization of Uncertain Contour Trees

    DEFF Research Database (Denmark)

    Kraus, Martin

    2010-01-01

    Contour trees can represent the topology of large volume data sets in a relatively compact, discrete data structure. However, the resulting trees often contain many thousands of nodes; thus, many graph drawing techniques fail to produce satisfactory results. Therefore, several visualization methods...... were proposed recently for the visualization of contour trees. Unfortunately, none of these techniques is able to handle uncertain contour trees although any uncertainty of the volume data inevitably results in partially uncertain contour trees. In this work, we visualize uncertain contour trees...... by combining the contour trees of two morphologically filtered versions of a volume data set, which represent the range of uncertainty. These two contour trees are combined and visualized within a single image such that a range of potential contour trees is represented by the resulting visualization. Thus...

  7. Fixed Parameter Evolutionary Algorithms and Maximum Leaf Spanning Trees: A Matter of Mutations

    DEFF Research Database (Denmark)

    Kratsch, Stefan; Lehre, Per Kristian; Neumann, Frank

    2011-01-01

    Evolutionary algorithms have been shown to be very successful for a wide range of NP-hard combinatorial optimization problems. We investigate the NP-hard problem of computing a spanning tree that has a maximal number of leaves by evolutionary algorithms in the context of fixed parameter tractabil...... two common mutation operators, we show that an operator related to spanning tree problems leads to an FPT running time in contrast to a general mutation operator that does not have this property....

  8. On maximal surfaces in asymptotically flat space-times

    International Nuclear Information System (INIS)

    Bartnik, R.; Chrusciel, P.T.; O Murchadha, N.

    1990-01-01

    Existence of maximal and 'almost maximal' hypersurfaces in asymptotically flat space-times is established under boundary conditions weaker than those considered previously. We show in particular that every vacuum evolution of asymptotically flat data for Einstein equations can be foliated by slices maximal outside a spatially compact set and that every (strictly) stationary asymptotically flat space-time can be foliated by maximal hypersurfaces. Amongst other uniqueness results, we show that maximal hypersurface can be used to 'partially fix' an asymptotic Poincare group. (orig.)

  9. Generic Ising trees

    DEFF Research Database (Denmark)

    Durhuus, Bergfinnur Jøgvan; Napolitano, George Maria

    2012-01-01

    The Ising model on a class of infinite random trees is defined as a thermodynamiclimit of finite systems. A detailed description of the corresponding distribution of infinite spin configurations is given. As an application, we study the magnetization properties of such systems and prove that they......The Ising model on a class of infinite random trees is defined as a thermodynamiclimit of finite systems. A detailed description of the corresponding distribution of infinite spin configurations is given. As an application, we study the magnetization properties of such systems and prove...... that they exhibit no spontaneous magnetization. Furthermore, the values of the Hausdorff and spectral dimensions of the underlying trees are calculated and found to be, respectively,¯dh =2 and¯ds = 4/3....

  10. ColorTree: a batch customization tool for phylogenic trees.

    Science.gov (United States)

    Chen, Wei-Hua; Lercher, Martin J

    2009-07-31

    Genome sequencing projects and comparative genomics studies typically aim to trace the evolutionary history of large gene sets, often requiring human inspection of hundreds of phylogenetic trees. If trees are checked for compatibility with an explicit null hypothesis (e.g., the monophyly of certain groups), this daunting task is greatly facilitated by an appropriate coloring scheme. In this note, we introduce ColorTree, a simple yet powerful batch customization tool for phylogenic trees. Based on pattern matching rules, ColorTree applies a set of customizations to an input tree file, e.g., coloring labels or branches. The customized trees are saved to an output file, which can then be viewed and further edited by Dendroscope (a freely available tree viewer). ColorTree runs on any Perl installation as a stand-alone command line tool, and its application can thus be easily automated. This way, hundreds of phylogenic trees can be customized for easy visual inspection in a matter of minutes. ColorTree allows efficient and flexible visual customization of large tree sets through the application of a user-supplied configuration file to multiple tree files.

  11. A parallel buffer tree

    DEFF Research Database (Denmark)

    Sitchinava, Nodar; Zeh, Norbert

    2012-01-01

    We present the parallel buffer tree, a parallel external memory (PEM) data structure for batched search problems. This data structure is a non-trivial extension of Arge's sequential buffer tree to a private-cache multiprocessor environment and reduces the number of I/O operations by the number of...... in the optimal OhOf(psortN + K/PB) parallel I/O complexity, where K is the size of the output reported in the process and psortN is the parallel I/O complexity of sorting N elements using P processors....

  12. A Note of Caution on Maximizing Entropy

    Directory of Open Access Journals (Sweden)

    Richard E. Neapolitan

    2014-07-01

    Full Text Available The Principle of Maximum Entropy is often used to update probabilities due to evidence instead of performing Bayesian updating using Bayes’ Theorem, and its use often has efficacious results. However, in some circumstances the results seem unacceptable and unintuitive. This paper discusses some of these cases, and discusses how to identify some of the situations in which this principle should not be used. The paper starts by reviewing three approaches to probability, namely the classical approach, the limiting frequency approach, and the Bayesian approach. It then introduces maximum entropy and shows its relationship to the three approaches. Next, through examples, it shows that maximizing entropy sometimes can stand in direct opposition to Bayesian updating based on reasonable prior beliefs. The paper concludes that if we take the Bayesian approach that probability is about reasonable belief based on all available information, then we can resolve the conflict between the maximum entropy approach and the Bayesian approach that is demonstrated in the examples.

  13. Optimal topologies for maximizing network transmission capacity

    Science.gov (United States)

    Chen, Zhenhao; Wu, Jiajing; Rong, Zhihai; Tse, Chi K.

    2018-04-01

    It has been widely demonstrated that the structure of a network is a major factor that affects its traffic dynamics. In this work, we try to identify the optimal topologies for maximizing the network transmission capacity, as well as to build a clear relationship between structural features of a network and the transmission performance in terms of traffic delivery. We propose an approach for designing optimal network topologies against traffic congestion by link rewiring and apply them on the Barabási-Albert scale-free, static scale-free and Internet Autonomous System-level networks. Furthermore, we analyze the optimized networks using complex network parameters that characterize the structure of networks, and our simulation results suggest that an optimal network for traffic transmission is more likely to have a core-periphery structure. However, assortative mixing and the rich-club phenomenon may have negative impacts on network performance. Based on the observations of the optimized networks, we propose an efficient method to improve the transmission capacity of large-scale networks.

  14. New features of the maximal abelian projection

    International Nuclear Information System (INIS)

    Bornyakov, V.G.; Polikarpov, M.I.; Syritsyn, S.N.; Schierholz, G.; Suzuki, T.

    2005-12-01

    After fixing the Maximal Abelian gauge in SU(2) lattice gauge theory we decompose the nonabelian gauge field into the so called monopole field and the modified nonabelian field with monopoles removed. We then calculate respective static potentials and find that the potential due to the modified nonabelian field is nonconfining while, as is well known, the monopole field potential is linear. Furthermore, we show that the sum of these potentials approximates the nonabelian static potential with 5% or higher precision at all distances considered. We conclude that at large distances the monopole field potential describes the classical energy of the hadronic string while the modified nonabelian field potential describes the string fluctuations. Similar decomposition was observed to work for the adjoint static potential. A check was also made of the center projection in the direct center gauge. Two static potentials, determined by projected Z 2 and by modified nonabelian field without Z 2 component were calculated. It was found that their sum is a substantially worse approximation of the SU(2) static potential than that found in the monopole case. It is further demonstrated that similar decomposition can be made for the flux tube action/energy density. (orig.)

  15. 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.

  16. Trees for tomorrow

    Science.gov (United States)

    Edward A. Johnson

    1980-01-01

    As coal production increases, forestry will become an increasingly important land use both before and after mining activity. New studies are needed to determine the long-range effect of mining in forested areas and to maximize the production of wood products on reclaimed areas.

  17. Embedding complete ternary tree in hypercubes using AVL trees

    NARCIS (Netherlands)

    S.A. Choudum; I. Raman (Indhumathi)

    2008-01-01

    htmlabstractA complete ternary tree is a tree in which every non-leaf vertex has exactly three children. We prove that a complete ternary tree of height h, TTh, is embeddable in a hypercube of dimension . This result coincides with the result of [2]. However, in this paper, the embedding utilizes

  18. Cladistic analysis of Bantu languages: a new tree based on combined lexical and grammatical data

    Science.gov (United States)

    Rexová, Kateřina; Bastin, Yvonne; Frynta, Daniel

    2006-04-01

    The phylogeny of the Bantu languages is reconstructed by application of the cladistic methodology to the combined lexical and grammatical data (87 languages, 144 characters). A maximum parsimony tree and Bayesian analysis supported some previously recognized clades, e.g., that of eastern and southern Bantu languages. Moreover, the results revealed that Bantu languages south and east of the equatorial forest are probably monophyletic. It suggests an unorthodox scenario of Bantu expansion including (after initial radiation in their homelands and neighboring territories) just a single passage through rainforest areas followed by a subsequent divergence into major clades. The likely localization of this divergence is in the area west of the Great Lakes. It conforms to the view that demographic expansion and dispersal throughout the dry-forests and savanna regions of subequatorial Africa was associated with the acquisition of new technologies (iron metallurgy and grain cultivation).

  19. Portraits of Tree Families

    NARCIS (Netherlands)

    Balgooy, van M.M.J.

    1998-01-01

    With the publication of the second volume of the series ‘Malesian Seed Plants’, entitled ‘Portraits of Tree Families’, I would like to refer to the Introduction of the first volume, ‘Spot-characters’ for a historical background and an explanation of the aims of this series. The present book treats

  20. P{owering 'Trees

    Indian Academy of Sciences (India)

    Melia dubia Cav. of Meliaceae is a large deciduous tree. Leaves are compound with toothed leaflets. Flowers are small, greenish-yellow in much-branched inflorescences. Fruits are green, ellipsoidal with a single seed covered by hard portion ( as in a mango fruit) and surrounded by fleshy pulp outside. The bark is bitter ...

  1. Programming macro tree transducers

    DEFF Research Database (Denmark)

    Bahr, Patrick; Day, Laurence E.

    2013-01-01

    transducers can be concisely represented in Haskell, and demonstrate the benefits of utilising such an approach with a number of examples. In particular, tree transducers afford a modular programming style as they can be easily composed and manipulated. Our Haskell representation generalises the original...

  2. Chapter 5 - Tree Mortality

    Science.gov (United States)

    Mark J. Ambrose

    2014-01-01

    Tree mortality is a natural process in all forest ecosystems. Extremely high mortality, however, can also be an indicator of forest health issues. On a regional scale, high mortality levels may indicate widespread insect or disease problems. High mortality may also occur if a large proportion of the forest in a particular region is made up of older, senescent stands....

  3. A Universal Phylogenetic Tree.

    Science.gov (United States)

    Offner, Susan

    2001-01-01

    Presents a universal phylogenetic tree suitable for use in high school and college-level biology classrooms. Illustrates the antiquity of life and that all life is related, even if it dates back 3.5 billion years. Reflects important evolutionary relationships and provides an exciting way to learn about the history of life. (SAH)

  4. Base tree property

    Czech Academy of Sciences Publication Activity Database

    Balcar, B.; Doucha, Michal; Hrušák, M.

    2015-01-01

    Roč. 32, č. 1 (2015), s. 69-81 ISSN 0167-8094 R&D Projects: GA AV ČR IAA100190902 Institutional support: RVO:67985840 Keywords : forcing * Boolean algebras * base tree Subject RIV: BA - General Mathematics Impact factor: 0.614, year: 2015 http://link.springer.com/article/10.1007/s11083-013-9316-2

  5. Multiquarks and Steiner trees

    International Nuclear Information System (INIS)

    Richard, Jean-Marc

    2010-01-01

    A brief review review is presented of models tentatively leading to stable multiquarks. A new attempt is presented, based on a Steiner-tree model of confinement, which is inspired by by QCD. It leads to more attraction than the empirical colour-additive model used in earlier multiquark calculations, and predict several multiquark states in configurations with different flavours.

  6. Tree Transduction Tools for Cdec

    Directory of Open Access Journals (Sweden)

    Austin Matthews

    2014-09-01

    Full Text Available We describe a collection of open source tools for learning tree-to-string and tree-to-tree transducers and the extensions to the cdec decoder that enable translation with these. Our modular, easy-to-extend tools extract rules from trees or forests aligned to strings and trees subject to different structural constraints. A fast, multithreaded implementation of the Cohn and Blunsom (2009 model for extracting compact tree-to-string rules is also included. The implementation of the tree composition algorithm used by cdec is described, and translation quality and decoding time results are presented. Our experimental results add to the body of evidence suggesting that tree transducers are a compelling option for translation, particularly when decoding speed and translation model size are important.

  7. Selecting Landscape Plants: Shade Trees

    OpenAIRE

    Relf, Diane; Appleton, Bonnie Lee, 1948-2012; Close, David

    2015-01-01

    Because of the permanency of trees and their importance in the landscape, care must be taken to select the best species for each situation. This publication goes over how to choose landscape trees that are shade tolerant.

  8. Value maximizing maintenance policies under general repair

    International Nuclear Information System (INIS)

    Marais, Karen B.

    2013-01-01

    One class of maintenance optimization problems considers the notion of general repair maintenance policies where systems are repaired or replaced on failure. In each case the optimality is based on minimizing the total maintenance cost of the system. These cost-centric optimizations ignore the value dimension of maintenance and can lead to maintenance strategies that do not maximize system value. This paper applies these ideas to the general repair optimization problem using a semi-Markov decision process, discounted cash flow techniques, and dynamic programming to identify the value-optimal actions for any given time and system condition. The impact of several parameters on maintenance strategy, such as operating cost and revenue, system failure characteristics, repair and replacement costs, and the planning time horizon, is explored. This approach provides a quantitative basis on which to base maintenance strategy decisions that contribute to system value. These decisions are different from those suggested by traditional cost-based approaches. The results show (1) how the optimal action for a given time and condition changes as replacement and repair costs change, and identifies the point at which these costs become too high for profitable system operation; (2) that for shorter planning horizons it is better to repair, since there is no time to reap the benefits of increased operating profit and reliability; (3) how the value-optimal maintenance policy is affected by the system's failure characteristics, and hence whether it is worthwhile to invest in higher reliability; and (4) the impact of the repair level on the optimal maintenance policy. -- Highlights: •Provides a quantitative basis for maintenance strategy decisions that contribute to system value. •Shows how the optimal action for a given condition changes as replacement and repair costs change. •Shows how the optimal policy is affected by the system's failure characteristics. •Shows when it is

  9. 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.

  10. 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.

  11. Adjustable chain trees for proteins

    DEFF Research Database (Denmark)

    Winter, Pawel; Fonseca, Rasmus

    2012-01-01

    A chain tree is a data structure for changing protein conformations. It enables very fast detection of clashes and free energy potential calculations. A modified version of chain trees that adjust themselves to the changing conformations of folding proteins is introduced. This results in much...... tighter bounding volume hierarchies and therefore fewer intersection checks. Computational results indicate that the efficiency of the adjustable chain trees is significantly improved compared to the traditional chain trees....

  12. Introduction to fault tree analysis

    International Nuclear Information System (INIS)

    Barlow, R.E.; Lambert, H.E.

    1975-01-01

    An elementary, engineering oriented introduction to fault tree analysis is presented. The basic concepts, techniques and applications of fault tree analysis, FTA, are described. The two major steps of FTA are identified as (1) the construction of the fault tree and (2) its evaluation. The evaluation of the fault tree can be qualitative or quantitative depending upon the scope, extensiveness and use of the analysis. The advantages, limitations and usefulness of FTA are discussed

  13. Inferring 'weak spots' in phylogenetic trees: application to mosasauroid nomenclature.

    Science.gov (United States)

    Madzia, Daniel; Cau, Andrea

    2017-01-01

    Mosasauroid squamates represented the apex predators within the Late Cretaceous marine and occasionally also freshwater ecosystems. Proper understanding of the origin of their ecological adaptations or paleobiogeographic dispersals requires adequate knowledge of their phylogeny. The studies assessing the position of mosasauroids on the squamate evolutionary tree and their origins have long given conflicting results. The phylogenetic relationships within Mosasauroidea, however, have experienced only little changes throughout the last decades. Considering the substantial improvements in the development of phylogenetic methodology that have undergone in recent years, resulting, among others, in numerous alterations in the phylogenetic hypotheses of other fossil amniotes, we test the robustness in our understanding of mosasauroid beginnings and their evolutionary history. We re-examined a data set that results from modifications assembled in the course of the last 20 years and performed multiple parsimony analyses and Bayesian tip-dating analysis. Following the inferred topologies and the 'weak spots' in the phylogeny of mosasauroids, we revise the nomenclature of the 'traditionally' recognized mosasauroid clades, to acknowledge the overall weakness among branches and the alternative topologies suggested previously, and discuss several factors that might have an impact on the differing phylogenetic hypotheses and their statistical support.

  14. The Re-Think Tree.

    Science.gov (United States)

    Gear, Jim

    1993-01-01

    The Re-Think Tree is a simple framework to help individuals assess and improve their behaviors related to environmental issues. The branches of the tree in order of priority are refuse, reduce, re-use, and recycle. Roots of the tree include such things as public opinion, education, and watchdog groups. (KS)

  15. The Hopi Fruit Tree Book.

    Science.gov (United States)

    Nyhuis, Jane

    Referring as often as possible to traditional Hopi practices and to materials readily available on the reservation, the illustrated booklet provides information on the care and maintenance of young fruit trees. An introduction to fruit trees explains the special characteristics of new trees, e.g., grafting, planting pits, and watering. The…

  16. Rectilinear Full Steiner Tree Generation

    DEFF Research Database (Denmark)

    Zachariasen, Martin

    1999-01-01

    The fastest exact algorithm (in practice) for the rectilinear Steiner tree problem in the plane uses a two-phase scheme: First, a small but sufficient set of full Steiner trees (FSTs) is generated and then a Steiner minimum tree is constructed from this set by using simple backtrack search, dynamic...

  17. Inferences from growing trees backwards

    Science.gov (United States)

    David W. Green; Kent A. McDonald

    1997-01-01

    The objective of this paper is to illustrate how longitudinal stress wave techniques can be useful in tracking the future quality of a growing tree. Monitoring the quality of selected trees in a plantation forest could provide early input to decisions on the effectiveness of management practices, or future utilization options, for trees in a plantation. There will...

  18. Genetic transformation of forest trees

    African Journals Online (AJOL)

    Admin

    In this review, the recent progress on genetic transformation of forest trees were discussed. Its described also, different applications of genetic engineering for improving forest trees or understanding the mechanisms governing genes expression in woody plants. Key words: Genetic transformation, transgenic forest trees, ...

  19. POLITENESS MAXIM OF MAIN CHARACTER IN SECRET FORGIVEN

    Directory of Open Access Journals (Sweden)

    Sang Ayu Isnu Maharani

    2017-06-01

    Full Text Available Maxim of Politeness is an interesting subject to be discussed, since politeness has been criticized from our childhood. We are obliques to be polite to anyone either in speaking or in acting. Somehow we are manage to show politeness in our spoken expression though our intention might be not so polite. For example we must appriciate others opinion although we feel objection toward the opinion. In this article the analysis of politeness is based on maxim proposes by Leech. He proposed six types of politeness maxim. The discussion shows that the main character (Kristen and Kami use all types of maxim in their conversation. The most commonly used are approbation maxim and agreement maxim

  20. TREE SELECTING AND TREE RING MEASURING IN DENDROCHRONOLOGICAL INVESTIGATIONS

    Directory of Open Access Journals (Sweden)

    Sefa Akbulut

    2004-04-01

    Full Text Available Dendrochronology is a method of dating which makes use of the annual nature of tree growth. Dendrochronology may be divided into a number of subfields, each of which covers one or more aspects of the use of tree ring data: dendroclimatology, dendrogeomorphology, dendrohydrology, dendroecology, dendroarchaelogy, and dendrogylaciology. Basic of all form the analysis of the tree rings. The wood or tree rings can aid to dating past events about climatology, ecology, geology, hydrology. Dendrochronological studies are conducted either on increment cores or on discs. It may be seen abnormalities on tree rings during the measurement like that false rings, missing rings, reaction wood. Like that situation, increment cores must be extracted from four different sides of each tree and be studied as more as on tree.

  1. Tree Colors: Color Schemes for Tree-Structured Data.

    Science.gov (United States)

    Tennekes, Martijn; de Jonge, Edwin

    2014-12-01

    We present a method to map tree structures to colors from the Hue-Chroma-Luminance color model, which is known for its well balanced perceptual properties. The Tree Colors method can be tuned with several parameters, whose effect on the resulting color schemes is discussed in detail. We provide a free and open source implementation with sensible parameter defaults. Categorical data are very common in statistical graphics, and often these categories form a classification tree. We evaluate applying Tree Colors to tree structured data with a survey on a large group of users from a national statistical institute. Our user study suggests that Tree Colors are useful, not only for improving node-link diagrams, but also for unveiling tree structure in non-hierarchical visualizations.

  2. Maximizers versus satisficers: Decision-making styles, competence, and outcomes

    OpenAIRE

    Andrew M. Parker; Wändi Bruine de Bruin; Baruch Fischhoff

    2007-01-01

    Our previous research suggests that people reporting a stronger desire to maximize obtain worse life outcomes (Bruine de Bruin et al., 2007). Here, we examine whether this finding may be explained by the decision-making styles of self-reported maximizers. Expanding on Schwartz et al.\\ (2002), we find that self-reported maximizers are more likely to show problematic decision-making styles, as evidenced by self-reports of less behavioral coping, greater dependence on others when making decision...

  3. Rate of tree carbon accumulation increases continuously with tree size.

    Science.gov (United States)

    Stephenson, N L; Das, A J; Condit, R; Russo, S E; Baker, P J; Beckman, N G; Coomes, D A; Lines, E R; Morris, W K; Rüger, N; Alvarez, E; Blundo, C; Bunyavejchewin, S; Chuyong, G; Davies, S J; Duque, A; Ewango, C N; Flores, O; Franklin, J F; Grau, H R; Hao, Z; Harmon, M E; Hubbell, S P; Kenfack, D; Lin, Y; Makana, J-R; Malizia, A; Malizia, L R; Pabst, R J; Pongpattananurak, N; Su, S-H; Sun, I-F; Tan, S; Thomas, D; van Mantgem, P J; Wang, X; Wiser, S K; Zavala, M A

    2014-03-06

    Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest carbon cycle--particularly net primary productivity and carbon storage--increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree's total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to undertand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence.

  4. Natural maximal νμ-ντ mixing

    International Nuclear Information System (INIS)

    Wetterich, C.

    1999-01-01

    The naturalness of maximal mixing between myon- and tau-neutrinos is investigated. A spontaneously broken nonabelian generation symmetry can explain a small parameter which governs the deviation from maximal mixing. In many cases all three neutrino masses are almost degenerate. Maximal ν μ -ν τ -mixing suggests that the leading contribution to the light neutrino masses arises from the expectation value of a heavy weak triplet rather than from the seesaw mechanism. In this scenario the deviation from maximal mixing is predicted to be less than about 1%. (Copyright (c) 1999 Elsevier Science B.V., Amsterdam. All rights reserved.)

  5. On the way towards a generalized entropy maximization procedure

    International Nuclear Information System (INIS)

    Bagci, G. Baris; Tirnakli, Ugur

    2009-01-01

    We propose a generalized entropy maximization procedure, which takes into account the generalized averaging procedures and information gain definitions underlying the generalized entropies. This novel generalized procedure is then applied to Renyi and Tsallis entropies. The generalized entropy maximization procedure for Renyi entropies results in the exponential stationary distribution asymptotically for q element of (0,1] in contrast to the stationary distribution of the inverse power law obtained through the ordinary entropy maximization procedure. Another result of the generalized entropy maximization procedure is that one can naturally obtain all the possible stationary distributions associated with the Tsallis entropies by employing either ordinary or q-generalized Fourier transforms in the averaging procedure.

  6. Violating Bell inequalities maximally for two d-dimensional systems

    International Nuclear Information System (INIS)

    Chen Jingling; Wu Chunfeng; Oh, C. H.; Kwek, L. C.; Ge Molin

    2006-01-01

    We show the maximal violation of Bell inequalities for two d-dimensional systems by using the method of the Bell operator. The maximal violation corresponds to the maximal eigenvalue of the Bell operator matrix. The eigenvectors corresponding to these eigenvalues are described by asymmetric entangled states. We estimate the maximum value of the eigenvalue for large dimension. A family of elegant entangled states |Ψ> app that violate Bell inequality more strongly than the maximally entangled state but are somewhat close to these eigenvectors is presented. These approximate states can potentially be useful for quantum cryptography as well as many other important fields of quantum information

  7. Fault tree analysis

    International Nuclear Information System (INIS)

    1981-09-01

    Suggestion are made concerning the method of the fault tree analysis, the use of certain symbols in the examination of system failures. This purpose of the fault free analysis is to find logical connections of component or subsystem failures leading to undesirable occurrances. The results of these examinations are part of the system assessment concerning operation and safety. The objectives of the analysis are: systematical identification of all possible failure combinations (causes) leading to a specific undesirable occurrance, finding of reliability parameters such as frequency of failure combinations, frequency of the undesirable occurrance or non-availability of the system when required. The fault tree analysis provides a near and reconstructable documentation of the examination. (orig./HP) [de

  8. Tree-level formalism

    International Nuclear Information System (INIS)

    Brandhuber, Andreas; Spence, Bill; Travaglini, Gabriele

    2011-01-01

    We review two novel techniques used to calculate tree-level scattering amplitudes efficiently: MHV diagrams, and on-shell recursion relations. For the MHV diagrams, we consider applications to tree-level amplitudes and focus in particular on the N=4 supersymmetric formulation. We also briefly describe the derivation of loop amplitudes using MHV diagrams. For the recursion relations, after presenting their general proof, we discuss several applications to massless theories with and without supersymmetry, to theories with massive particles, and to graviton amplitudes in general relativity. This article is an invited review for a special issue of Journal of Physics A: Mathematical and Theoretical devoted to 'Scattering amplitudes in gauge theories'. (review)

  9. Factors influencing bird foraging preferences among conspecific fruit trees

    Science.gov (United States)

    Foster, M.S.

    1990-01-01

    The rates at which birds visit fruiting individuals of Allophylus edulis (Sapindaceae) differ substantially among trees. Such avian feeding preferences are well-known, but usually involve fruits and trees of different species. Factors controlling avian preferences for particular trees in a population of conspecifics are generally undocumented. To address this issue, I attempted to correlate rates at which individual birds and species fed in trees of Allophylus with 27 fruit or plant characteristics. Birds that swallow fruits whole were considered separately from those that feed in other ways. Plant characters were selected on the basis of their potential influence on feeding efficiency or predation risk, assuming that birds would select feeding trees so as to maximize the net rate of energy or nutrient intake and to minimize predation. Correlations were found between feeding visits by some groups of birds and percent water in the pulp, milligrams of mineral ash in the pulp, and crop size. No character was correlated with feeding visits by all groups of birds in both years of the study. The correlations with water and mineral ash are unexplained and may be artifacts. The correlation with crop size may represent a tactic to minimize predation.

  10. Tree Rings: Timekeepers of the Past.

    Science.gov (United States)

    Phipps, R. L.; McGowan, J.

    One of a series of general interest publications on science issues, this booklet describes the uses of tree rings in historical and biological recordkeeping. Separate sections cover the following topics: dating of tree rings, dating with tree rings, tree ring formation, tree ring identification, sample collections, tree ring cross dating, tree…

  11. Wood for the trees

    Directory of Open Access Journals (Sweden)

    Rob Garbutt

    2013-10-01

    Full Text Available Our paper focuses on the materiality, cultural history and cultural relations of selected artworks in the exhibition Wood for the trees (Lismore Regional Gallery, New South Wales, Australia, 10 June – 17 July 2011. The title of the exhibition, intentionally misreading the aphorism “Can’t see the wood for the trees”, by reading the wood for the resource rather than the collective wood[s], implies conservation, preservation, and the need for sustaining the originating resource. These ideas have particular resonance on the NSW far north coast, a region once rich in rainforest. While the Indigenous population had sustainable practices of forest and land management, the colonists deployed felling and harvesting in order to convert the value of the local, abundant rainforest trees into high-value timber. By the late twentieth century, however, a new wave of settlers launched a protest movements against the proposed logging of remnant rainforest at Terania Creek and elsewhere in the region. Wood for the trees, curated by Gallery Director Brett Adlington, plays on this dynamic relationship between wood, trees and people. We discuss the way selected artworks give expression to the themes or concepts of productive labour, nature and culture, conservation and sustainability, and memory. The artworks include Watjinbuy Marrawilil’s (1980 Carved ancestral figure ceremonial pole, Elizabeth Stops’ (2009/10 Explorations into colonisation, Hossein Valamanesh’s (2008 Memory stick, and AñA Wojak’s (2008 Unread book (in a forgotten language. Our art writing on the works, a practice informed by Bal (2002, Muecke (2008 and Papastergiadis (2004, becomes a conversation between the works and the themes or concepts. As a form of material excess of the most productive kind (Grosz, 2008, p. 7, art seeds a response to that which is in the air waiting to be said of the past, present and future.

  12. Recursive Trees for Practical ORAM

    Directory of Open Access Journals (Sweden)

    Moataz Tarik

    2015-06-01

    Full Text Available We present a new, general data structure that reduces the communication cost of recent tree-based ORAMs. Contrary to ORAM trees with constant height and path lengths, our new construction r-ORAM allows for trees with varying shorter path length. Accessing an element in the ORAM tree results in different communication costs depending on the location of the element. The main idea behind r-ORAM is a recursive ORAM tree structure, where nodes in the tree are roots of other trees. While this approach results in a worst-case access cost (tree height at most as any recent tree-based ORAM, we show that the average cost saving is around 35% for recent binary tree ORAMs. Besides reducing communication cost, r-ORAM also reduces storage overhead on the server by 4% to 20% depending on the ORAM’s client memory type. To prove r-ORAM’s soundness, we conduct a detailed overflow analysis. r-ORAM’s recursive approach is general in that it can be applied to all recent tree ORAMs, both constant and poly-log client memory ORAMs. Finally, we implement and benchmark r-ORAM in a practical setting to back up our theoretical claims.

  13. Mathematical foundations of event trees

    International Nuclear Information System (INIS)

    Papazoglou, Ioannis A.

    1998-01-01

    A mathematical foundation from first principles of event trees is presented. The main objective of this formulation is to offer a formal basis for developing automated computer assisted construction techniques for event trees. The mathematical theory of event trees is based on the correspondence between the paths of the tree and the elements of the outcome space of a joint event. The concept of a basic cylinder set is introduced to describe joint event outcomes conditional on specific outcomes of basic events or unconditional on the outcome of basic events. The concept of outcome space partition is used to describe the minimum amount of information intended to be preserved by the event tree representation. These concepts form the basis for an algorithm for systematic search for and generation of the most compact (reduced) form of an event tree consistent with the minimum amount of information the tree should preserve. This mathematical foundation allows for the development of techniques for automated generation of event trees corresponding to joint events which are formally described through other types of graphical models. Such a technique has been developed for complex systems described by functional blocks and it is reported elsewhere. On the quantification issue of event trees, a formal definition of a probability space corresponding to the event tree outcomes is provided. Finally, a short discussion is offered on the relationship of the presented mathematical theory with the more general use of event trees in reliability analysis of dynamic systems

  14. Making CSB + -Trees Processor Conscious

    DEFF Research Database (Denmark)

    Samuel, Michael; Pedersen, Anders Uhl; Bonnet, Philippe

    2005-01-01

    of the CSB+-tree. We argue that it is necessary to consider a larger group of parameters in order to adapt CSB+-tree to processor architectures as different as Pentium and Itanium. We identify this group of parameters and study how it impacts the performance of CSB+-tree on Itanium 2. Finally, we propose......Cache-conscious indexes, such as CSB+-tree, are sensitive to the underlying processor architecture. In this paper, we focus on how to adapt the CSB+-tree so that it performs well on a range of different processor architectures. Previous work has focused on the impact of node size on the performance...... a systematic method for adapting CSB+-tree to new platforms. This work is a first step towards integrating CSB+-tree in MySQL’s heap storage manager....

  15. (Almost) practical tree codes

    KAUST Repository

    Khina, Anatoly

    2016-08-15

    We consider the problem of stabilizing an unstable plant driven by bounded noise over a digital noisy communication link, a scenario at the heart of networked control. To stabilize such a plant, one needs real-time encoding and decoding with an error probability profile that decays exponentially with the decoding delay. The works of Schulman and Sahai over the past two decades have developed the notions of tree codes and anytime capacity, and provided the theoretical framework for studying such problems. Nonetheless, there has been little practical progress in this area due to the absence of explicit constructions of tree codes with efficient encoding and decoding algorithms. Recently, linear time-invariant tree codes were proposed to achieve the desired result under maximum-likelihood decoding. In this work, we take one more step towards practicality, by showing that these codes can be efficiently decoded using sequential decoding algorithms, up to some loss in performance (and with some practical complexity caveats). We supplement our theoretical results with numerical simulations that demonstrate the effectiveness of the decoder in a control system setting.

  16. Acceptance and suitability of novel trees for Orthotomicus erosus, an exotic bark beetle in North America

    Science.gov (United States)

    A.J. Walter; R.C. Venette; S.A. Kells

    2010-01-01

    To predict whether an herbivorous pest insect will establish in a new area, the potential host plants must be known. For invading bark beetles, adults must recognize and accept trees suitable for larval development. The preference-performance hypothesis predicts that adults will select host species that maximize the fitness of their offspring. We tested five species of...

  17. Evaluation of anti-hyperglycemic effect of Actinidia kolomikta (Maxim. etRur.) Maxim. root extract.

    Science.gov (United States)

    Hu, Xuansheng; Cheng, Delin; Wang, Linbo; Li, Shuhong; Wang, Yuepeng; Li, Kejuan; Yang, Yingnan; Zhang, Zhenya

    2015-05-01

    This study aimed to evaluate the anti-hyperglycemic effect of ethanol extract from Actinidia kolomikta (Maxim. etRur.) Maxim. root (AKE).An in vitro evaluation was performed by using rat intestinal α-glucosidase (maltase and sucrase), the key enzymes linked with type 2 diabetes. And an in vivo evaluation was also performed by loading maltose, sucrose, glucose to normal rats. As a result, AKE showed concentration-dependent inhibition effects on rat intestinal maltase and rat intestinal sucrase with IC(50) values of 1.83 and 1.03mg/mL, respectively. In normal rats, after loaded with maltose, sucrose and glucose, administration of AKE significantly reduced postprandial hyperglycemia, which is similar to acarbose used as an anti-diabetic drug. High contents of total phenolics (80.49 ± 0.05mg GAE/g extract) and total flavonoids (430.69 ± 0.91mg RE/g extract) were detected in AKE. In conclusion, AKE possessed anti-hyperglycemic effects and the possible mechanisms were associated with its inhibition on α-glucosidase and the improvement on insulin release and/or insulin sensitivity as well. The anti-hyperglycemic activity possessed by AKE maybe attributable to its high contents of phenolic and flavonoid compounds.

  18. Trait acclimation mitigates mortality risks of tropical canopy trees under global warming

    Directory of Open Access Journals (Sweden)

    Frank eSterck

    2016-05-01

    Full Text Available There is a heated debate about the effect of global change on tropical forests. Many scientists predict large-scale tree mortality while others point to mitigating roles of CO2 fertilization and – the notoriously unknown – physiological trait acclimation of trees. In this opinion article we provided a first quantification of the potential of trait acclimation to mitigate the negative effects of warming on tropical canopy tree growth and survival. We applied a physiological tree growth model that incorporates trait acclimation through an optimization approach. Our model estimated the maximum effect of acclimation when trees optimize traits that are strongly plastic on a week to annual time scale (leaf photosynthetic capacity, total leaf area, stem sapwood area to maximize carbon gain. We simulated tree carbon gain for temperatures (25-35ºC and ambient CO2 concentrations (390-800 ppm predicted for the 21st century. Full trait acclimation increased simulated carbon gain by up to 10-20% and the maximum tolerated temperature by up to 2ºC, thus reducing risks of tree death under predicted warming. Functional trait acclimation may thus increase the resilience of tropical trees to warming, but cannot prevent tree death during extremely hot and dry years at current CO2 levels. We call for incorporating trait acclimation in field and experimental studies of plant functional traits, and in models that predict responses of tropical forests to climate change.

  19. Trait Acclimation Mitigates Mortality Risks of Tropical Canopy Trees under Global Warming

    Science.gov (United States)

    Sterck, Frank; Anten, Niels P. R.; Schieving, Feike; Zuidema, Pieter A.

    2016-01-01

    There is a heated debate about the effect of global change on tropical forests. Many scientists predict large-scale tree mortality while others point to mitigating roles of CO2 fertilization and – the notoriously unknown – physiological trait acclimation of trees. In this opinion article we provided a first quantification of the potential of trait acclimation to mitigate the negative effects of warming on tropical canopy tree growth and survival. We applied a physiological tree growth model that incorporates trait acclimation through an optimization approach. Our model estimated the maximum effect of acclimation when trees optimize traits that are strongly plastic on a week to annual time scale (leaf photosynthetic capacity, total leaf area, stem sapwood area) to maximize carbon gain. We simulated tree carbon gain for temperatures (25–35°C) and ambient CO2 concentrations (390–800 ppm) predicted for the 21st century. Full trait acclimation increased simulated carbon gain by up to 10–20% and the maximum tolerated temperature by up to 2°C, thus reducing risks of tree death under predicted warming. Functional trait acclimation may thus increase the resilience of tropical trees to warming, but cannot prevent tree death during extremely hot and dry years at current CO2 levels. We call for incorporating trait acclimation in field and experimental studies of plant functional traits, and in models that predict responses of tropical forests to climate change. PMID:27242814

  20. Alternative approaches to maximally supersymmetric field theories

    International Nuclear Information System (INIS)

    Broedel, Johannes

    2010-01-01

    The central objective of this work is the exploration and application of alternative possibilities to describe maximally supersymmetric field theories in four dimensions: N=4 super Yang-Mills theory and N=8 supergravity. While twistor string theory has been proven very useful in the context of N=4 SYM, no analogous formulation for N=8 supergravity is available. In addition to the part describing N=4 SYM theory, twistor string theory contains vertex operators corresponding to the states of N=4 conformal supergravity. Those vertex operators have to be altered in order to describe (non-conformal) Einstein supergravity. A modified version of the known open twistor string theory, including a term which breaks the conformal symmetry for the gravitational vertex operators, has been proposed recently. In a first part of the thesis structural aspects and consistency of the modified theory are discussed. Unfortunately, the majority of amplitudes can not be constructed, which can be traced back to the fact that the dimension of the moduli space of algebraic curves in twistor space is reduced in an inconsistent manner. The issue of a possible finiteness of N=8 supergravity is closely related to the question of the existence of valid counterterms in the perturbation expansion of the theory. In particular, the coefficient in front of the so-called R 4 counterterm candidate has been shown to vanish by explicit calculation. This behavior points into the direction of a symmetry not taken into account, for which the hidden on-shell E 7(7) symmetry is the prime candidate. The validity of the so-called double-soft scalar limit relation is a necessary condition for a theory exhibiting E 7(7) symmetry. By calculating the double-soft scalar limit for amplitudes derived from an N=8 supergravity action modified by an additional R 4 counterterm, one can test for possible constraints originating in the E 7(7) symmetry. In a second part of the thesis, the appropriate amplitudes are calculated

  1. Rate of tree carbon accumulation increases continuously with tree size

    Science.gov (United States)

    Stephenson, N.L.; Das, A.J.; Condit, R.; Russo, S.E.; Baker, P.J.; Beckman, N.G.; Coomes, D.A.; Lines, E.R.; Morris, W.K.; Rüger, N.; Álvarez, E.; Blundo, C.; Bunyavejchewin, S.; Chuyong, G.; Davies, S.J.; Duque, Á.; Ewango, C.N.; Flores, O.; Franklin, J.F.; Grau, H.R.; Hao, Z.; Harmon, M.E.; Hubbell, S.P.; Kenfack, D.; Lin, Y.; Makana, J.-R.; Malizia, A.; Malizia, L.R.; Pabst, R.J.; Pongpattananurak, N.; Su, S.-H.; Sun, I-F.; Tan, S.; Thomas, D.; van Mantgem, P.J.; Wang, X.; Wiser, S.K.; Zavala, M.A.

    2014-01-01

    Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest carbon cycle—particularly net primary productivity and carbon storage - increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree’s total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to understand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence.

  2. Constructal tree-shaped flow structures

    International Nuclear Information System (INIS)

    Bejan, A.; Lorente, S.

    2007-01-01

    This paper is an introduction to a new trend in the conceptual design of energy systems: the generation of flow configuration based on the 'constructal' principle that the global performance is maximized by balancing and arranging the various flow resistances (the irreversibilities) in a flow system that is free to morph. The paper focuses on distribution and collection, which are flows that connect one point (source, or sink) with an infinity of points (volume, area, curve). The flow configurations that emerge from this principle are tree-shaped, and the systems that employ them are 'vascularized'. The paper traces the most recent progress made on constructal vascularization. The direction is from large-scale applications toward microscales. The large-scale tree-shaped designs of electric power distribution systems and networks for natural gas and water are now invading small-scale designs such as fuel cells, heat exchangers and cooled packages of electronics. These flow configurations have several properties in common: freedom to morph, multiple scales, hierarchy, nonuniform (optimal) distribution of scales through the available volume, compactness and finite complexity

  3. Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses.

    Science.gov (United States)

    Jacox, Edwin; Weller, Mathias; Tannier, Eric; Scornavacca, Celine

    2017-04-01

    Gene trees reconstructed from sequence alignments contain poorly supported branches when the phylogenetic signal in the sequences is insufficient to determine them all. When a species tree is available, the signal of gains and losses of genes can be used to correctly resolve the unsupported parts of the gene history. However finding a most parsimonious binary resolution of a non-binary tree obtained by contracting the unsupported branches is NP-hard if transfer events are considered as possible gene scale events, in addition to gene origination, duplication and loss. We propose an exact, parameterized algorithm to solve this problem in single-exponential time, where the parameter is the number of connected branches of the gene tree that show low support from the sequence alignment or, equivalently, the maximum number of children of any node of the gene tree once the low-support branches have been collapsed. This improves on the best known algorithm by an exponential factor. We propose a way to choose among optimal solutions based on the available information. We show the usability of this principle on several simulated and biological datasets. The results are comparable in quality to several other tested methods having similar goals, but our approach provides a lower running time and a guarantee that the produced solution is optimal. Our algorithm has been integrated into the ecceTERA phylogeny package, available at http://mbb.univ-montp2.fr/MBB/download_sources/16__ecceTERA and which can be run online at http://mbb.univ-montp2.fr/MBB/subsection/softExec.php?soft=eccetera . celine.scornavacca@umontpellier.fr. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  4. Resolving the tips of the tree of life: How much mitochondrialdata doe we need?

    Energy Technology Data Exchange (ETDEWEB)

    Bonett, Ronald M.; Macey, J. Robert; Boore, Jeffrey L.; Chippindale, Paul T.

    2005-04-29

    Mitochondrial (mt) DNA sequences are used extensively to reconstruct evolutionary relationships among recently diverged animals,and have constituted the most widely used markers for species- and generic-level relationships for the last decade or more. However, most studies to date have employed relatively small portions of the mt-genome. In contrast, complete mt-genomes primarily have been used to investigate deep divergences, including several studies of the amount of mt sequence necessary to recover ancient relationships. We sequenced and analyzed 24 complete mt-genomes from a group of salamander species exhibiting divergences typical of those in many species-level studies. We present the first comprehensive investigation of the amount of mt sequence data necessary to consistently recover the mt-genome tree at this level, using parsimony and Bayesian methods. Both methods of phylogenetic analysis revealed extremely similar results. A surprising number of well supported, yet conflicting, relationships were found in trees based on fragments less than {approx}2000 nucleotides (nt), typical of the vast majority of the thousands of mt-based studies published to date. Large amounts of data (11,500+ nt) were necessary to consistently recover the whole mt-genome tree. Some relationships consistently were recovered with fragments of all sizes, but many nodes required the majority of the mt-genome to stabilize, particularly those associated with short internal branches. Although moderate amounts of data (2000-3000 nt) were adequate to recover mt-based relationships for which most nodes were congruent with the whole mt-genome tree, many thousands of nucleotides were necessary to resolve rapid bursts of evolution. Recent advances in genomics are making collection of large amounts of sequence data highly feasible, and our results provide the basis for comparative studies of other closely related groups to optimize mt sequence sampling and phylogenetic resolution at the &apos

  5. 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.

  6. 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.

  7. Kinetic theory in maximal-acceleration invariant phase space

    International Nuclear Information System (INIS)

    Brandt, H.E.

    1989-01-01

    A vanishing directional derivative of a scalar field along particle trajectories in maximal acceleration invariant phase space is identical in form to the ordinary covariant Vlasov equation in curved spacetime in the presence of both gravitational and nongravitational forces. A natural foundation is thereby provided for a covariant kinetic theory of particles in maximal-acceleration invariant phase space. (orig.)

  8. IIB solutions with N>28 Killing spinors are maximally supersymmetric

    International Nuclear Information System (INIS)

    Gran, U.; Gutowski, J.; Papadopoulos, G.; Roest, D.

    2007-01-01

    We show that all IIB supergravity backgrounds which admit more than 28 Killing spinors are maximally supersymmetric. In particular, we find that for all N>28 backgrounds the supercovariant curvature vanishes, and that the quotients of maximally supersymmetric backgrounds either preserve all 32 or N<29 supersymmetries

  9. Muscle mitochondrial capacity exceeds maximal oxygen delivery in humans

    DEFF Research Database (Denmark)

    Boushel, Robert Christopher; Gnaiger, Erich; Calbet, Jose A L

    2011-01-01

    Across a wide range of species and body mass a close matching exists between maximal conductive oxygen delivery and mitochondrial respiratory rate. In this study we investigated in humans how closely in-vivo maximal oxygen consumption (VO(2) max) is matched to state 3 muscle mitochondrial respira...

  10. Pace's Maxims for Homegrown Library Projects. Coming Full Circle

    Science.gov (United States)

    Pace, Andrew K.

    2005-01-01

    This article discusses six maxims by which to run library automation. The following maxims are discussed: (1) Solve only known problems; (2) Avoid changing data to fix display problems; (3) Aut viam inveniam aut faciam; (4) If you cannot make it yourself, buy something; (5) Kill the alligator closest to the boat; and (6) Just because yours is…

  11. MaxAlign: maximizing usable data in an alignment

    DEFF Research Database (Denmark)

    Oliveira, Rodrigo Gouveia; Sackett, Peter Wad; Pedersen, Anders Gorm

    2007-01-01

    Align. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS) that we consider useful for comparing tree topologies. CONCLUSION: We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also...

  12. On Determining if Tree-based Networks Contain Fixed Trees.

    Science.gov (United States)

    Anaya, Maria; Anipchenko-Ulaj, Olga; Ashfaq, Aisha; Chiu, Joyce; Kaiser, Mahedi; Ohsawa, Max Shoji; Owen, Megan; Pavlechko, Ella; St John, Katherine; Suleria, Shivam; Thompson, Keith; Yap, Corrine

    2016-05-01

    We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is N based on T? We show that it is [Formula: see text]-hard to decide, by reduction from 3-Dimensional Matching (3DM) and further that the problem is fixed-parameter tractable.

  13. Trees in the city: valuing street trees in Portland, Oregon

    Science.gov (United States)

    G.H. Donovan; D.T. Butry

    2010-01-01

    We use a hedonic price model to simultaneously estimate the effects of street trees on the sales price and the time-on-market (TOM) of houses in Portland. Oregon. On average, street trees add $8,870 to sales price and reduce TOM by 1.7 days. In addition, we found that the benefits of street trees spill over to neighboring houses. Because the provision and maintenance...

  14. Systolic trees and systolic language recognition by tree automata

    Energy Technology Data Exchange (ETDEWEB)

    Steinby, M

    1983-01-01

    K. Culik II, J. Gruska, A. Salomaa and D. Wood have studied the language recognition capabilities of certain types of systolically operating networks of processors (see research reports Cs-81-32, Cs-81-36 and Cs-82-01, Univ. of Waterloo, Ontario, Canada). In this paper, their model for systolic VLSI trees is formalised in terms of standard tree automaton theory, and the way in which some known facts about recognisable forests and tree transductions can be applied in VLSI tree theory is demonstrated. 13 references.

  15. Inquiry in bibliography some of the bustan`s maxim

    Directory of Open Access Journals (Sweden)

    sajjad rahmatian

    2016-12-01

    Full Text Available Sa`di is on of those poets who`s has placed a special position to preaching and guiding the people and among his works, allocated throughout the text of bustan to advice and maxim on legal and ethical various subjects. Surely, sa`di on the way of to compose this work and expression of its moral point, direct or indirect have been affected by some previous sources and possibly using their content. The main purpose of this article is that the pay review of basis and sources of bustan`s maxims and show that sa`di when expression the maxims of this work has been affected by which of the texts and works. For this purpose is tried to with search and research on the resources that have been allocated more or less to the aphorisms, to discover and extract traces of influence sa`di from their moral and didactic content. From the most important the finding of this study can be mentioned that indirect effect of some pahlavi books of maxim (like maxims of azarbad marespandan and bozorgmehr book of maxim and also noted sa`di directly influenced of moral and ethical works of poets and writers before him, and of this, sa`di`s influence from abo- shakur balkhi maxims, ferdowsi and keikavus is remarkable and noteworthy.

  16. Can monkeys make investments based on maximized pay-off?

    Directory of Open Access Journals (Sweden)

    Sophie Steelandt

    2011-03-01

    Full Text Available Animals can maximize benefits but it is not known if they adjust their investment according to expected pay-offs. We investigated whether monkeys can use different investment strategies in an exchange task. We tested eight capuchin monkeys (Cebus apella and thirteen macaques (Macaca fascicularis, Macaca tonkeana in an experiment where they could adapt their investment to the food amounts proposed by two different experimenters. One, the doubling partner, returned a reward that was twice the amount given by the subject, whereas the other, the fixed partner, always returned a constant amount regardless of the amount given. To maximize pay-offs, subjects should invest a maximal amount with the first partner and a minimal amount with the second. When tested with the fixed partner only, one third of monkeys learned to remove a maximal amount of food for immediate consumption before investing a minimal one. With both partners, most subjects failed to maximize pay-offs by using different decision rules with each partner' quality. A single Tonkean macaque succeeded in investing a maximal amount to one experimenter and a minimal amount to the other. The fact that only one of over 21 subjects learned to maximize benefits in adapting investment according to experimenters' quality indicates that such a task is difficult for monkeys, albeit not impossible.

  17. Tree felling: a necessary evil

    CERN Multimedia

    CERN Bulletin

    2013-01-01

    CERN started a campaign of tree felling in 2010 for safety reasons, and it will continue this year in various parts of the Meyrin site. As in previous years, the trees cut down in 2013 will be recycled and some will be replaced.   Diseased tree that had to be cut down on the Meyrin site. In association with the Geneva nature and countryside directorate (Direction générale de la nature et du paysage, DGNP), CERN commissioned the Geneva school of landscaping, engineering and architecture (Haute école du paysage, d’ingénierie et d’architecture, HEPIA) to compile an inventory of the trees on the Meyrin site. In total, 1285 trees (excluding poplars) were recorded. 75.5% of these trees were declared to be in a good state of health (i.e. 971 trees), 21.5% in a moderate state of health (276 trees) and 3% in a poor state of health (38 trees). As for the poplars, the 236 specimens recorded on the Meyrin site were judged to be too old, to...

  18. Human decision error (HUMDEE) trees

    International Nuclear Information System (INIS)

    Ostrom, L.T.

    1993-01-01

    Graphical presentations of human actions in incident and accident sequences have been used for many years. However, for the most part, human decision making has been underrepresented in these trees. This paper presents a method of incorporating the human decision process into graphical presentations of incident/accident sequences. This presentation is in the form of logic trees. These trees are called Human Decision Error Trees or HUMDEE for short. The primary benefit of HUMDEE trees is that they graphically illustrate what else the individuals involved in the event could have done to prevent either the initiation or continuation of the event. HUMDEE trees also present the alternate paths available at the operator decision points in the incident/accident sequence. This is different from the Technique for Human Error Rate Prediction (THERP) event trees. There are many uses of these trees. They can be used for incident/accident investigations to show what other courses of actions were available and for training operators. The trees also have a consequence component so that not only the decision can be explored, also the consequence of that decision

  19. Phylogenetic trees and Euclidean embeddings.

    Science.gov (United States)

    Layer, Mark; Rhodes, John A

    2017-01-01

    It was recently observed by de Vienne et al. (Syst Biol 60(6):826-832, 2011) that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on a diffusion model of continuous character evolution along the tree, here we give a direct and elementary explanation for it that provides substantial additional insight. We use this embedding to reinterpret the differences between the NJ and BIONJ tree building algorithms, providing one illustration of how this embedding reflects tree structures in data.

  20. Occurrence of leguminous trees

    Energy Technology Data Exchange (ETDEWEB)

    Kirkbride, J.H.; Arkcoll, D.B.A.; Turnbull, J.W.; Magalhaes, L.M.S.; Fernandes, N.P.

    1984-01-01

    Five papers from the symposium are presented. Kirkbride, J.H. Jr.; Legumes of the cerrado. pp 23-46 (Refs. 55) A review is given. Some 548 legume species in 59 genera are listed that have been reported from cerrado vegetation. Felker, P.; Legume trees in semi-arid and arid areas. pp 47-59 (Refs. 41) A review is given of worldwide research activities. Arkcoll, D.B.; A comparison of some fast growing species suitable for woodlots in the wet tropics. pp 61-68 (Refs. 9) Studies are described near Manaus on intensive silviculture (for fuelwood production) of Eucalyptus deglupta, Cedrelinga catanaeformis (catenaeformis), Jacaranda copaia, and Inga edulis. Turnbull, J.W.; Six phyllodinous Acacia species for planting in the humid tropical lowlands. pp 69-73 (Refs. 14) Distribution, ecology, growth, and utilization are described for A. auriculiformis, A. mangium, A. aulacocarpa, A. crassicarpa, A. cincinnata, and A. polystachya. Magalhaes, L.M.S., Fernandes, N.P.; Experimental stands of leguminous trees in the Manaus region. pp 75-79 (Refs. 8) Performance up to age 20 yr of Cedrelinga catenaeformis, Dalbergia nigra, Dinizia excelsa, Dipteryx odorata, Dipteryx sp., Diplotropis sp., Eperua bijuga, Pithecellobium racemosum, Vouacapoua pallidior, and Hymenaea sp. is described.

  1. The Steiner tree problem

    CERN Document Server

    Hwang, FK; Winter, P

    1992-01-01

    The Steiner problem asks for a shortest network which spans a given set of points. Minimum spanning networks have been well-studied when all connections are required to be between the given points. The novelty of the Steiner tree problem is that new auxiliary points can be introduced between the original points so that a spanning network of all the points will be shorter than otherwise possible. These new points are called Steiner points - locating them has proved problematic and research has diverged along many different avenues. This volume is devoted to the assimilation of the rich field of intriguing analyses and the consolidation of the fragments. A section has been given to each of the three major areas of interest which have emerged. The first concerns the Euclidean Steiner Problem, historically the original Steiner tree problem proposed by Jarník and Kössler in 1934. The second deals with the Steiner Problem in Networks, which was propounded independently by Hakimi and Levin and has enjoyed the most...

  2. Genealogy and gene trees.

    Science.gov (United States)

    Rasmuson, Marianne

    2008-02-01

    Heredity can be followed in persons or in genes. Persons can be identified only a few generations back, but simplified models indicate that universal ancestors to all now living persons have occurred in the past. Genetic variability can be characterized as variants of DNA sequences. Data are available only from living persons, but from the pattern of variation gene trees can be inferred by means of coalescence models. The merging of lines backwards in time leads to a MRCA (most recent common ancestor). The time and place of living for this inferred person can give insights in human evolutionary history. Demographic processes are incorporated in the model, but since culture and customs are known to influence demography the models used ought to be tested against available genealogy. The Icelandic data base offers a possibility to do so and points to some discrepancies. Mitochondrial DNA and Y chromosome patterns give a rather consistent view of human evolutionary history during the latest 100 000 years but the earlier epochs of human evolution demand gene trees with longer branches. The results of such studies reveal as yet unsolved problems about the sources of our genome.

  3. Distributed Merge Trees

    Energy Technology Data Exchange (ETDEWEB)

    Morozov, Dmitriy; Weber, Gunther

    2013-01-08

    Improved simulations and sensors are producing datasets whose increasing complexity exhausts our ability to visualize and comprehend them directly. To cope with this problem, we can detect and extract significant features in the data and use them as the basis for subsequent analysis. Topological methods are valuable in this context because they provide robust and general feature definitions. As the growth of serial computational power has stalled, data analysis is becoming increasingly dependent on massively parallel machines. To satisfy the computational demand created by complex datasets, algorithms need to effectively utilize these computer architectures. The main strength of topological methods, their emphasis on global information, turns into an obstacle during parallelization. We present two approaches to alleviate this problem. We develop a distributed representation of the merge tree that avoids computing the global tree on a single processor and lets us parallelize subsequent queries. To account for the increasing number of cores per processor, we develop a new data structure that lets us take advantage of multiple shared-memory cores to parallelize the work on a single node. Finally, we present experiments that illustrate the strengths of our approach as well as help identify future challenges.

  4. Gravitational collapse of charged dust shell and maximal slicing condition

    International Nuclear Information System (INIS)

    Maeda, Keiichi

    1980-01-01

    The maximal slicing condition is a good time coordinate condition qualitatively when pursuing the gravitational collapse by the numerical calculation. The analytic solution of the gravitational collapse under the maximal slicing condition is given in the case of a spherical charged dust shell and the behavior of time slices with this coordinate condition is investigated. It is concluded that under the maximal slicing condition we can pursue the gravitational collapse until the radius of the shell decreases to about 0.7 x (the radius of the event horizon). (author)

  5. Optimal quantum error correcting codes from absolutely maximally entangled states

    Science.gov (United States)

    Raissi, Zahra; Gogolin, Christian; Riera, Arnau; Acín, Antonio

    2018-02-01

    Absolutely maximally entangled (AME) states are pure multi-partite generalizations of the bipartite maximally entangled states with the property that all reduced states of at most half the system size are in the maximally mixed state. AME states are of interest for multipartite teleportation and quantum secret sharing and have recently found new applications in the context of high-energy physics in toy models realizing the AdS/CFT-correspondence. We work out in detail the connection between AME states of minimal support and classical maximum distance separable (MDS) error correcting codes and, in particular, provide explicit closed form expressions for AME states of n parties with local dimension \

  6. Breakdown of maximality conjecture in continuous phase transitions

    International Nuclear Information System (INIS)

    Mukamel, D.; Jaric, M.V.

    1983-04-01

    A Landau-Ginzburg-Wilson model associated with a single irreducible representation which exhibits an ordered phase whose symmetry group is not a maximal isotropy subgroup of the symmetry group of the disordered phase is constructed. This example disproves the maximality conjecture suggested in numerous previous studies. Below the (continuous) transition, the order parameter points along a direction which varies with the temperature and with the other parameters which define the model. An extension of the maximality conjecture to reducible representations was postulated in the context of Higgs symmetry breaking mechanism. Our model can also be extended to provide a counter example in these cases. (author)

  7. Two-loop ghost-antighost condensation for SU(2) Yang-Mills theories in the maximal abelian gauge

    International Nuclear Information System (INIS)

    Fazio, A.R.

    2004-01-01

    In the framework of the formalism of Cornwall et.al. for composite operators I study the ghost-antighost condensation in SU(2) Yang-Mills theories quantized in the Maximal Abelian Gauge and derive analytically a condensating effective potential at two ghost loops. I find that in this approximation the one-loop pairing ghost-antighost is not destroyed and no mass is generated if the ansatz for the propagator suggested by the tree level Hubbard-Stratonovich transformations is used

  8. Visualizing Individual Tree Differences in Tree-Ring Studies

    Directory of Open Access Journals (Sweden)

    Mario Trouillier

    2018-04-01

    Full Text Available Averaging tree-ring measurements from multiple individuals is one of the most common procedures in dendrochronology. It serves to filter out noise from individual differences between trees, such as competition, height, and micro-site effects, which ideally results in a site chronology sensitive to regional scale factors such as climate. However, the climate sensitivity of individual trees can be modulated by factors like competition, height, and nitrogen deposition, calling attention to whether average chronologies adequately assess climatic growth-control. In this study, we demonstrate four simple but effective methods to visually assess differences between individual trees. Using individual tree climate-correlations we: (1 employed jitter plots with superimposed metadata to assess potential causes for these differences; (2 plotted the frequency distributions of climate correlations over time as heat maps; (3 mapped the spatial distribution of climate sensitivity over time to assess spatio-temporal dynamics; and (4 used t-distributed Stochastic Neighborhood Embedding (t-SNE to assess which trees were generally more similar in terms of their tree-ring pattern and their correlation with climate variables. This suite of exploratory methods can indicate if individuals in tree-ring datasets respond differently to climate variability, and therefore, should not solely be explored with climate correlations of the mean population chronology.

  9. Tree Size Comparison of Some Important Street Trees Growing at ...

    African Journals Online (AJOL)

    PROF HORSFALL

    More research is needed on these trees for healthy environment of city. The present ..... use and CO2 emissions from power plants. Environ. Poll. .... Anna. Bot., 65:567-574. Kozlowski, T.T., 1971. Growth and Development of. Trees. Vol. 1.

  10. Relating phylogenetic trees to transmission trees of infectious disease outbreaks.

    Science.gov (United States)

    Ypma, Rolf J F; van Ballegooijen, W Marijn; Wallinga, Jacco

    2013-11-01

    Transmission events are the fundamental building blocks of the dynamics of any infectious disease. Much about the epidemiology of a disease can be learned when these individual transmission events are known or can be estimated. Such estimations are difficult and generally feasible only when detailed epidemiological data are available. The genealogy estimated from genetic sequences of sampled pathogens is another rich source of information on transmission history. Optimal inference of transmission events calls for the combination of genetic data and epidemiological data into one joint analysis. A key difficulty is that the transmission tree, which describes the transmission events between infected hosts, differs from the phylogenetic tree, which describes the ancestral relationships between pathogens sampled from these hosts. The trees differ both in timing of the internal nodes and in topology. These differences become more pronounced when a higher fraction of infected hosts is sampled. We show how the phylogenetic tree of sampled pathogens is related to the transmission tree of an outbreak of an infectious disease, by the within-host dynamics of pathogens. We provide a statistical framework to infer key epidemiological and mutational parameters by simultaneously estimating the phylogenetic tree and the transmission tree. We test the approach using simulations and illustrate its use on an outbreak of foot-and-mouth disease. The approach unifies existing methods in the emerging field of phylodynamics with transmission tree reconstruction methods that are used in infectious disease epidemiology.

  11. DIF Trees: Using Classification Trees to Detect Differential Item Functioning

    Science.gov (United States)

    Vaughn, Brandon K.; Wang, Qiu

    2010-01-01

    A nonparametric tree classification procedure is used to detect differential item functioning for items that are dichotomously scored. Classification trees are shown to be an alternative procedure to detect differential item functioning other than the use of traditional Mantel-Haenszel and logistic regression analysis. A nonparametric…

  12. Picking a tree: habitat use by the tree agama, Acanthocercus ...

    African Journals Online (AJOL)

    We studied tree agama (Acanthocercus a. atricollis) habitat use in the Magaliesberg mountain range in northern South Africa using sightings of marked individuals, and in a few cases, radio-telemetry. Acanthocercus a. atricollis preferentially selected thorn trees (46%; Acacia karroo), followed by common sugarbush (10%; ...

  13. On Profit-Maximizing Pricing for the Highway and Tollbooth Problems

    Science.gov (United States)

    Elbassioni, Khaled; Raman, Rajiv; Ray, Saurabh; Sitters, René

    In the tollbooth problem on trees, we are given a tree T= (V,E) with n edges, and a set of m customers, each of whom is interested in purchasing a path on the graph. Each customer has a fixed budget, and the objective is to price the edges of T such that the total revenue made by selling the paths to the customers that can afford them is maximized. An important special case of this problem, known as the highway problem, is when T is restricted to be a line. For the tollbooth problem, we present an O(logn)-approximation, improving on the current best O(logm)-approximation. We also study a special case of the tollbooth problem, when all the paths that customers are interested in purchasing go towards a fixed root of T. In this case, we present an algorithm that returns a (1 - ɛ)-approximation, for any ɛ> 0, and runs in quasi-polynomial time. On the other hand, we rule out the existence of an FPTAS by showing that even for the line case, the problem is strongly NP-hard. Finally, we show that in the discount model, when we allow some items to be priced below zero to improve the overall profit, the problem becomes even APX-hard.

  14. Reference Values for Maximal Inspiratory Pressure: A Systematic Review

    Directory of Open Access Journals (Sweden)

    Isabela MB Sclauser Pessoa

    2014-01-01

    Full Text Available BACKGROUND: Maximal inspiratory pressure (MIP is the most commonly used measure to evaluate inspiratory muscle strength. Normative values for MIP vary significantly among studies, which may reflect differences in participant demographics and technique of MIP measurement.

  15. Classification of conformal representations induced from the maximal cuspidal parabolic

    Energy Technology Data Exchange (ETDEWEB)

    Dobrev, V. K., E-mail: dobrev@inrne.bas.bg [Scuola Internazionale Superiore di Studi Avanzati (Italy)

    2017-03-15

    In the present paper we continue the project of systematic construction of invariant differential operators on the example of representations of the conformal algebra induced from the maximal cuspidal parabolic.

  16. Maximizing Your Investment in Building Automation System Technology.

    Science.gov (United States)

    Darnell, Charles

    2001-01-01

    Discusses how organizational issues and system standardization can be important factors that determine an institution's ability to fully exploit contemporary building automation systems (BAS). Further presented is management strategy for maximizing BAS investments. (GR)

  17. Eccentric exercise decreases maximal insulin action in humans

    DEFF Research Database (Denmark)

    Asp, Svend; Daugaard, J R; Kristiansen, S

    1996-01-01

    subjects participated in two euglycaemic clamps, performed in random order. One clamp was preceded 2 days earlier by one-legged eccentric exercise (post-eccentric exercise clamp (PEC)) and one was without the prior exercise (control clamp (CC)). 2. During PEC the maximal insulin-stimulated glucose uptake...... for all three clamp steps used (P maximal activity of glycogen synthase was identical in the two thighs for all clamp steps. 3. The glucose infusion rate (GIR......) necessary to maintain euglycaemia during maximal insulin stimulation was lower during PEC compared with CC (15.7%, 81.3 +/- 3.2 vs. 96.4 +/- 8.8 mumol kg-1 min-1, P maximal...

  18. Maximal slicing of D-dimensional spherically symmetric vacuum spacetime

    International Nuclear Information System (INIS)

    Nakao, Ken-ichi; Abe, Hiroyuki; Yoshino, Hirotaka; Shibata, Masaru

    2009-01-01

    We study the foliation of a D-dimensional spherically symmetric black-hole spacetime with D≥5 by two kinds of one-parameter families of maximal hypersurfaces: a reflection-symmetric foliation with respect to the wormhole slot and a stationary foliation that has an infinitely long trumpetlike shape. As in the four-dimensional case, the foliations by the maximal hypersurfaces avoid the singularity irrespective of the dimensionality. This indicates that the maximal slicing condition will be useful for simulating higher-dimensional black-hole spacetimes in numerical relativity. For the case of D=5, we present analytic solutions of the intrinsic metric, the extrinsic curvature, the lapse function, and the shift vector for the foliation by the stationary maximal hypersurfaces. These data will be useful for checking five-dimensional numerical-relativity codes based on the moving puncture approach.

  19. ICTs and Urban Micro Enterprises : Maximizing Opportunities for ...

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

    ICTs and Urban Micro Enterprises : Maximizing Opportunities for Economic Development ... the use of ICTs in micro enterprises and their role in reducing poverty. ... in its approach to technological connectivity but bottom-up in relation to.

  20. Real-time topic-aware influence maximization using preprocessing.

    Science.gov (United States)

    Chen, Wei; Lin, Tian; Yang, Cheng

    2016-01-01

    Influence maximization is the task of finding a set of seed nodes in a social network such that the influence spread of these seed nodes based on certain influence diffusion model is maximized. Topic-aware influence diffusion models have been recently proposed to address the issue that influence between a pair of users are often topic-dependent and information, ideas, innovations etc. being propagated in networks are typically mixtures of topics. In this paper, we focus on the topic-aware influence maximization task. In particular, we study preprocessing methods to avoid redoing influence maximization for each mixture from scratch. We explore two preprocessing algorithms with theoretical justifications. Our empirical results on data obtained in a couple of existing studies demonstrate that one of our algorithms stands out as a strong candidate providing microsecond online response time and competitive influence spread, with reasonable preprocessing effort.

  1. b-tree facets for the simple graph partitioning polytope

    DEFF Research Database (Denmark)

    Sørensen, Michael Malmros

    2004-01-01

    The simple graph partitioning problem is to partition an edge-weighted graph into mutually disjoint subgraphs, each consisting of no more than b nodes, such that the sum of the weights of all edges in the subgraphs is maximal. In this paper we introduce a large class of facet defining inequalities...... for the simple graph partitioning polytopes P_n(b), b >= 3, associated with the complete graph on n nodes. These inequalities are induced by a graph configuration which is built upon trees of cardinality b. We provide a closed-form theorem that states all necessary and sufficient conditions for the facet...... defining property of the inequalities. Udgivelsesdato: JUN...

  2. A framework for sensitivity analysis of decision trees.

    Science.gov (United States)

    Kamiński, Bogumił; Jakubczyk, Michał; Szufel, Przemysław

    2018-01-01

    In the paper, we consider sequential decision problems with uncertainty, represented as decision trees. Sensitivity analysis is always a crucial element of decision making and in decision trees it often focuses on probabilities. In the stochastic model considered, the user often has only limited information about the true values of probabilities. We develop a framework for performing sensitivity analysis of optimal strategies accounting for this distributional uncertainty. We design this robust optimization approach in an intuitive and not overly technical way, to make it simple to apply in daily managerial practice. The proposed framework allows for (1) analysis of the stability of the expected-value-maximizing strategy and (2) identification of strategies which are robust with respect to pessimistic/optimistic/mode-favoring perturbations of probabilities. We verify the properties of our approach in two cases: (a) probabilities in a tree are the primitives of the model and can be modified independently; (b) probabilities in a tree reflect some underlying, structural probabilities, and are interrelated. We provide a free software tool implementing the methods described.

  3. Nonadditive entropy maximization is inconsistent with Bayesian updating

    Science.gov (United States)

    Pressé, Steve

    2014-11-01

    The maximum entropy method—used to infer probabilistic models from data—is a special case of Bayes's model inference prescription which, in turn, is grounded in basic propositional logic. By contrast to the maximum entropy method, the compatibility of nonadditive entropy maximization with Bayes's model inference prescription has never been established. Here we demonstrate that nonadditive entropy maximization is incompatible with Bayesian updating and discuss the immediate implications of this finding. We focus our attention on special cases as illustrations.

  4. Sex differences in autonomic function following maximal exercise.

    Science.gov (United States)

    Kappus, Rebecca M; Ranadive, Sushant M; Yan, Huimin; Lane-Cordova, Abbi D; Cook, Marc D; Sun, Peng; Harvey, I Shevon; Wilund, Kenneth R; Woods, Jeffrey A; Fernhall, Bo

    2015-01-01

    Heart rate variability (HRV), blood pressure variability, (BPV) and heart rate recovery (HRR) are measures that provide insight regarding autonomic function. Maximal exercise can affect autonomic function, and it is unknown if there are sex differences in autonomic recovery following exercise. Therefore, the purpose of this study was to determine sex differences in several measures of autonomic function and the response following maximal exercise. Seventy-one (31 males and 40 females) healthy, nonsmoking, sedentary normotensive subjects between the ages of 18 and 35 underwent measurements of HRV and BPV at rest and following a maximal exercise bout. HRR was measured at minute one and two following maximal exercise. Males have significantly greater HRR following maximal exercise at both minute one and two; however, the significance between sexes was eliminated when controlling for VO2 peak. Males had significantly higher resting BPV-low-frequency (LF) values compared to females and did not significantly change following exercise, whereas females had significantly increased BPV-LF values following acute maximal exercise. Although males and females exhibited a significant decrease in both HRV-LF and HRV-high frequency (HF) with exercise, females had significantly higher HRV-HF values following exercise. Males had a significantly higher HRV-LF/HF ratio at rest; however, both males and females significantly increased their HRV-LF/HF ratio following exercise. Pre-menopausal females exhibit a cardioprotective autonomic profile compared to age-matched males due to lower resting sympathetic activity and faster vagal reactivation following maximal exercise. Acute maximal exercise is a sufficient autonomic stressor to demonstrate sex differences in the critical post-exercise recovery period.

  5. Power Converters Maximize Outputs Of Solar Cell Strings

    Science.gov (United States)

    Frederick, Martin E.; Jermakian, Joel B.

    1993-01-01

    Microprocessor-controlled dc-to-dc power converters devised to maximize power transferred from solar photovoltaic strings to storage batteries and other electrical loads. Converters help in utilizing large solar photovoltaic arrays most effectively with respect to cost, size, and weight. Main points of invention are: single controller used to control and optimize any number of "dumb" tracker units and strings independently; power maximized out of converters; and controller in system is microprocessor.

  6. Maximally flat radiation patterns of a circular aperture

    Science.gov (United States)

    Minkovich, B. M.; Mints, M. Ia.

    1989-08-01

    The paper presents an explicit solution to the problems of maximizing the area utilization coefficient and of obtaining the best approximation (on the average) of a sectorial Pi-shaped radiation pattern of an antenna with a circular aperture when Butterworth conditions are imposed on the approximating pattern with the aim of flattening it. Constraints on the choice of admissible minimum and maximum antenna dimensions are determined which make possible the synthesis of maximally flat patterns with small sidelobes.

  7. Design of optimal linear antennas with maximally flat radiation patterns

    Science.gov (United States)

    Minkovich, B. M.; Mints, M. Ia.

    1990-02-01

    The paper presents an explicit solution to the problem of maximizing the aperture area utilization coefficient and obtaining the best approximation in the mean of the sectorial U-shaped radiation pattern of a linear antenna, when Butterworth flattening constraints are imposed on the approximating pattern. Constraints are established on the choice of the smallest and large antenna dimensions that make it possible to obtain maximally flat patterns, having a low sidelobe level and free from pulsations within the main lobe.

  8. No Mikheyev-Smirnov-Wolfenstein Effect in Maximal Mixing

    OpenAIRE

    Harrison, P. F.; Perkins, D. H.; Scott, W. G.

    1996-01-01

    We investigate the possible influence of the MSW effect on the expectations for the solar neutrino experiments in the maximal mixing scenario suggested by the atmospheric neutrino data. A direct numerical calculation of matter induced effects in the Sun shows that the naive vacuum predictions are left completely undisturbed in the particular case of maximal mixing, so that the MSW effect turns out to be unobservable. We give a qualitative explanation of this result.

  9. A fractional optimal control problem for maximizing advertising efficiency

    OpenAIRE

    Igor Bykadorov; Andrea Ellero; Stefania Funari; Elena Moretti

    2007-01-01

    We propose an optimal control problem to model the dynamics of the communication activity of a firm with the aim of maximizing its efficiency. We assume that the advertising effort undertaken by the firm contributes to increase the firm's goodwill and that the goodwill affects the firm's sales. The aim is to find the advertising policies in order to maximize the firm's efficiency index which is computed as the ratio between "outputs" and "inputs" properly weighted; the outputs are represented...

  10. A New Augmentation Based Algorithm for Extracting Maximal Chordal Subgraphs.

    Science.gov (United States)

    Bhowmick, Sanjukta; Chen, Tzu-Yi; Halappanavar, Mahantesh

    2015-02-01

    A graph is chordal if every cycle of length greater than three contains an edge between non-adjacent vertices. Chordal graphs are of interest both theoretically, since they admit polynomial time solutions to a range of NP-hard graph problems, and practically, since they arise in many applications including sparse linear algebra, computer vision, and computational biology. A maximal chordal subgraph is a chordal subgraph that is not a proper subgraph of any other chordal subgraph. Existing algorithms for computing maximal chordal subgraphs depend on dynamically ordering the vertices, which is an inherently sequential process and therefore limits the algorithms' parallelizability. In this paper we explore techniques to develop a scalable parallel algorithm for extracting a maximal chordal subgraph. We demonstrate that an earlier attempt at developing a parallel algorithm may induce a non-optimal vertex ordering and is therefore not guaranteed to terminate with a maximal chordal subgraph. We then give a new algorithm that first computes and then repeatedly augments a spanning chordal subgraph. After proving that the algorithm terminates with a maximal chordal subgraph, we then demonstrate that this algorithm is more amenable to parallelization and that the parallel version also terminates with a maximal chordal subgraph. That said, the complexity of the new algorithm is higher than that of the previous parallel algorithm, although the earlier algorithm computes a chordal subgraph which is not guaranteed to be maximal. We experimented with our augmentation-based algorithm on both synthetic and real-world graphs. We provide scalability results and also explore the effect of different choices for the initial spanning chordal subgraph on both the running time and on the number of edges in the maximal chordal subgraph.

  11. On Maximally Dissipative Shock Waves in Nonlinear Elasticity

    OpenAIRE

    Knowles, James K.

    2010-01-01

    Shock waves in nonlinearly elastic solids are, in general, dissipative. We study the following question: among all plane shock waves that can propagate with a given speed in a given one-dimensional nonlinearly elastic bar, which one—if any—maximizes the rate of dissipation? We find that the answer to this question depends strongly on the qualitative nature of the stress-strain relation characteristic of the given material. When maximally dissipative shocks do occur, they propagate according t...

  12. Maximal near-field radiative heat transfer between two plates

    OpenAIRE

    Nefzaoui, Elyes; Ezzahri, Younès; Drevillon, Jérémie; Joulain, Karl

    2013-01-01

    International audience; Near-field radiative transfer is a promising way to significantly and simultaneously enhance both thermo-photovoltaic (TPV) devices power densities and efficiencies. A parametric study of Drude and Lorentz models performances in maximizing near-field radiative heat transfer between two semi-infinite planes separated by nanometric distances at room temperature is presented in this paper. Optimal parameters of these models that provide optical properties maximizing the r...

  13. Two Trees: Migrating Fault Trees to Decision Trees for Real Time Fault Detection on International Space Station

    Science.gov (United States)

    Lee, Charles; Alena, Richard L.; Robinson, Peter

    2004-01-01

    We started from ISS fault trees example to migrate to decision trees, presented a method to convert fault trees to decision trees. The method shows that the visualizations of root cause of fault are easier and the tree manipulating becomes more programmatic via available decision tree programs. The visualization of decision trees for the diagnostic shows a format of straight forward and easy understands. For ISS real time fault diagnostic, the status of the systems could be shown by mining the signals through the trees and see where it stops at. The other advantage to use decision trees is that the trees can learn the fault patterns and predict the future fault from the historic data. The learning is not only on the static data sets but also can be online, through accumulating the real time data sets, the decision trees can gain and store faults patterns in the trees and recognize them when they come.

  14. Softly Broken Lepton Numbers: an Approach to Maximal Neutrino Mixing

    International Nuclear Information System (INIS)

    Grimus, W.; Lavoura, L.

    2001-01-01

    We discuss models where the U(1) symmetries of lepton numbers are responsible for maximal neutrino mixing. We pay particular attention to an extension of the Standard Model (SM) with three right-handed neutrino singlets in which we require that the three lepton numbers L e , L μ , and L τ be separately conserved in the Yukawa couplings, but assume that they are softly broken by the Majorana mass matrix M R of the neutrino singlets. In this framework, where lepton-number breaking occurs at a scale much higher than the electroweak scale, deviations from family lepton number conservation are calculable, i.e., finite, and lepton mixing stems exclusively from M R . We show that in this framework either maximal atmospheric neutrino mixing or maximal solar neutrino mixing or both can be imposed by invoking symmetries. In this way those maximal mixings are stable against radiative corrections. The model which achieves maximal (or nearly maximal) solar neutrino mixing assumes that there are two different scales in M R and that the lepton number (dash)L=L e -L μ -L τ 1 is conserved in between them. We work out the difference between this model and the conventional scenario where (approximate) (dash)L invariance is imposed directly on the mass matrix of the light neutrinos. (author)

  15. Better trees through systematic breeding

    Science.gov (United States)

    Robert Z. Callaham

    1957-01-01

    Today I would like to tell you briefly about the efforts of forest geneticists to improve the quality of forest trees. What do we mean by quality? Here, the consumer has the first word. The trees we produce are primarily for timber production, and the timber growing and wood-using industries give us our guidelines. Nevertheless, many of the characteristics sought by...

  16. Tree physiology and bark beetles

    Science.gov (United States)

    Michael G. Ryan; Gerard Sapes; Anna Sala; Sharon Hood

    2015-01-01

    Irruptive bark beetles usually co-occur with their co-evolved tree hosts at very low (endemic) population densities. However, recent droughts and higher temperatures have promoted widespread tree mortality with consequences for forest carbon, fire and ecosystem services (Kurz et al., 2008; Raffa et al., 2008; Jenkins et al., 2012). In this issue of New Phytologist,...

  17. Tree Hydraulics: How Sap Rises

    Science.gov (United States)

    Denny, Mark

    2012-01-01

    Trees transport water from roots to crown--a height that can exceed 100 m. The physics of tree hydraulics can be conveyed with simple fluid dynamics based upon the Hagen-Poiseuille equation and Murray's law. Here the conduit structure is modelled as conical pipes and as branching pipes. The force required to lift sap is generated mostly by…

  18. Boosted decision trees and applications

    International Nuclear Information System (INIS)

    Coadou, Y.

    2013-01-01

    Decision trees are a machine learning technique more and more commonly used in high energy physics, while it has been widely used in the social sciences. After introducing the concepts of decision trees, this article focuses on its application in particle physics. (authors)

  19. Who pays for tree improvement?

    Science.gov (United States)

    Tom D. Byram; E. M. Raley

    2011-01-01

    Tree improvement has been one of the most successful collaborative research efforts in history, eliciting participation from a wide variety of players. This effort has included state forestry agencies, research universities, integrated forest industries, and the USDA Forest Service. Tree improvement was organized through cooperatives whose objectives were to distribute...

  20. Mean-field lattice trees

    NARCIS (Netherlands)

    Borgs, C.; Chayes, J.T.; Hofstad, van der R.W.; Slade, G.

    1999-01-01

    We introduce a mean-field model of lattice trees based on embeddings into d of abstract trees having a critical Poisson offspring distribution. This model provides a combinatorial interpretation for the self-consistent mean-field model introduced previously by Derbez and Slade [9], and provides an