Recrafting the Neighbor-Joining Method
Mailund; Brodal, Gerth Stølting; Fagerberg, Rolf;
2006-01-01
Background: The neighbor-joining method by Saitou and Nei is a widely used method for constructing phylogenetic trees. The formulation of the method gives rise to a canonical Θ(n3) algorithm upon which all existing implementations are based. Methods: In this paper we present techniques for speeding...... up the canonical neighbor-joining method. Our algorithms construct the same phylogenetic trees as the canonical neighbor-joining method. The best-case running time of our algorithms are O(n2) but the worst-case remains O(n3). We empirically evaluate the performance of our algoritms on distance...... neighbor-joining method. Conclusions: The experiments show that our algorithms also yield a significant speed-up, already for medium sized instances....
Direct maximum parsimony phylogeny reconstruction from genotype data
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.
PTree: pattern-based, stochastic search for maximum parsimony phylogenies
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/.
Mixed integer linear programming for maximum-parsimony phylogeny inference.
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.
The effect of natural selection on the performance of maximum parsimony
Ofria Charles
2007-06-01
Full Text Available Abstract Background Maximum parsimony is one of the most commonly used and extensively studied phylogeny reconstruction methods. While current evaluation methodologies such as computer simulations provide insight into how well maximum parsimony reconstructs phylogenies, they tell us little about how well maximum parsimony performs on taxa drawn from populations of organisms that evolved subject to natural selection in addition to the random factors of drift and mutation. It is clear that natural selection has a significant impact on Among Site Rate Variation (ASRV and the rate of accepted substitutions; that is, accepted mutations do not occur with uniform probability along the genome and some substitutions are more likely to occur than other substitutions. However, little is know about how ASRV and non-uniform character substitutions impact the performance of reconstruction methods such as maximum parsimony. To gain insight into these issues, we study how well maximum parsimony performs with data generated by Avida, a digital life platform where populations of digital organisms evolve subject to natural selective pressures. Results We first identify conditions where natural selection does affect maximum parsimony's reconstruction accuracy. In general, as we increase the probability that a significant adaptation will occur in an intermediate ancestor, the performance of maximum parsimony improves. In fact, maximum parsimony can correctly reconstruct small 4 taxa trees on data that have received surprisingly many mutations if the intermediate ancestor has received a significant adaptation. We demonstrate that this improved performance of maximum parsimony is attributable more to ASRV than to non-uniform character substitutions. Conclusion Maximum parsimony, as well as most other phylogeny reconstruction methods, may perform significantly better on actual biological data than is currently suggested by computer simulation studies because of natural
On the optimality of the neighbor-joining algorithm
Pachter Lior
2008-04-01
Full Text Available Abstract The popular neighbor-joining (NJ algorithm used in phylogenetics is a greedy algorithm for finding the balanced minimum evolution (BME tree associated to a dissimilarity map. From this point of view, NJ is "optimal" when the algorithm outputs the tree which minimizes the balanced minimum evolution criterion. We use the fact that the NJ tree topology and the BME tree topology are determined by polyhedral subdivisions of the spaces of dissimilarity maps R+(n2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaWenfgDOvwBHrxAJfwnHbqeg0uy0HwzTfgDPnwy1aaceaGae83gHi1aa0baaSqaaiabgUcaRaqaamaabmaabaqbaeqabiqaaaqaaiabd6gaUbqaaiabikdaYaaaaiaawIcacaGLPaaaaaaaaa@3BA1@ to study the optimality of the neighbor-joining algorithm. In particular, we investigate and compare the polyhedral subdivisions for n ≤ 8. This requires the measurement of volumes of spherical polytopes in high dimension, which we obtain using a combination of Monte Carlo methods and polyhedral algorithms. Our results include a demonstration that highly unrelated trees can be co-optimal in BME reconstruction, and that NJ regions are not convex. We obtain the l2 radius for neighbor-joining for n = 5 and we conjecture that the ability of the neighbor-joining algorithm to recover the BME tree depends on the diameter of the BME tree.
The behavior of admixed populations in neighbor-joining inference of population trees.
Kopelman, Naama M; Stone, Lewi; Gascuel, Olivier; Rosenberg, Noah A
2013-01-01
Neighbor-joining is one of the most widely used methods for constructing evolutionary trees. This approach from phylogenetics is often employed in population genetics, where distance matrices obtained from allele frequencies are used to produce a representation of population relationships in the form of a tree. In phylogenetics, the utility of neighbor-joining derives partly from a result that for a class of distance matrices including those that are additive or tree-like-generated by summing weights over the edges connecting pairs of taxa in a tree to obtain pairwise distances-application of neighbor-joining recovers exactly the underlying tree. For populations within a species, however, migration and admixture can produce distance matrices that reflect more complex processes than those obtained from the bifurcating trees typical in the multispecies context. Admixed populations-populations descended from recent mixture of groups that have long been separated-have been observed to be located centrally in inferred neighbor-joining trees, with short external branches incident to the path connecting their source populations. Here, using a simple model, we explore mathematically the behavior of an admixed population under neighbor-joining. We show that with an additive distance matrix, a population admixed among two source populations necessarily lies on the path between the sources. Relaxing the additivity requirement, we examine the smallest nontrivial case-four populations, one of which is admixed between two of the other three-showing that the two source populations never merge with each other before one of them merges with the admixed population. Furthermore, the distance on the constructed tree between the admixed population and either source population is always smaller than the distance between the source populations, and the external branch for the admixed population is always incident to the path connecting the sources. We define three properties that hold
The Geometry of the Neighbor-Joining Algorithm for Small Trees
Eickmeyer, Kord
2009-01-01
In 2007, Eickmeyer et al. showed that the tree topologies outputted by the Neighbor-Joining (NJ) algorithm and the balanced minimum evolution (BME) method for phylogenetic reconstruction are each determined by a polyhedral subdivision of the space of dissimilarity maps ${\\R}^{n \\choose 2}$, where $n$ is the number of taxa. In this paper, we will analyze the behavior of the Neighbor-Joining algorithm on five and six taxa and study the geometry and combinatorics of the polyhedral subdivision of the space of dissimilarity maps for six taxa as well as hyperplane representations of each polyhedral subdivision. We also study simulations for one of the questions stated by Eickmeyer et al., that is, the robustness of the NJ algorithm to small perturbations of tree metrics, with tree models which are known to be hard to be reconstructed via the NJ algorithm.
Maximum Parsimony and the Skewness Test: A Simulation Study of the Limits of Applicability
Määttä, Jussi; Roos, Teemu
2016-01-01
The maximum parsimony (MP) method for inferring phylogenies is widely used, but little is known about its limitations in non-asymptotic situations. This study employs large-scale computations with simulated phylogenetic data to estimate the probability that MP succeeds in finding the true phylogeny for up to twelve taxa and 256 characters. The set of candidate phylogenies are taken to be unrooted binary trees; for each simulated data set, the tree lengths of all (2n − 5)!! candidates are computed to evaluate quantities related to the performance of MP, such as the probability of finding the true phylogeny, the probability that the tree with the shortest length is unique, the probability that the true phylogeny has the shortest tree length, and the expected inverse of the number of trees sharing the shortest length. The tree length distributions are also used to evaluate and extend the skewness test of Hillis for distinguishing between random and phylogenetic data. The results indicate, for example, that the critical point after which MP achieves a success probability of at least 0.9 is roughly around 128 characters. The skewness test is found to perform well on simulated data and the study extends its scope to up to twelve taxa. PMID:27035667
Haseeb A. Khan
2008-01-01
Full Text Available 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 com- paring 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.
Holden, Clare Janaki
2002-04-22
Linguistic divergence occurs after speech communities divide, in a process similar to speciation among isolated biological populations. The resulting languages are hierarchically related, like genes or species. Phylogenetic methods developed in evolutionary biology can thus be used to infer language trees, with the caveat that 'borrowing' of linguistic elements between languages also occurs, to some degree. Maximum-parsimony trees for 75 Bantu and Bantoid African languages were constructed using 92 items of basic vocabulary. The level of character fit on the trees was high (consistency index was 0.65), indicating that a tree model fits Bantu language evolution well, at least for the basic vocabulary. The Bantu language tree reflects the spread of farming across this part of sub-Saharan Africa between ca. 3000 BC and AD 500. Modern Bantu subgroups, defined by clades on parsimony trees, mirror the earliest farming traditions both geographically and temporally. This suggests that the major subgroups of modern Bantu stem from the Neolithic and Early Iron Age, with little subsequent movement by speech communities.
Smith, J F
2000-06-01
Generic relationships within Episcieae were assessed using ITS and ndhF sequences. Previous analyses of this tribe have focussed only on ndhF data and have excluded two genera, Rhoogeton and Oerstedina, which are included in this analysis. Data were analyzed using both parsimony and maximum-likelihood methods. Results from partition homogeneity tests imply that the two data sets are significantly incongruent, but when Rhoogeton is removed from the analysis, the data sets are not significantly different. The combined data sets reveal greater strength of relationships within the tribe with the exception of the position of Rhoogeton. Poorly or unresolved relationships based exclusively on ndhF data are more fully resolved with ITS data. These resolved clades include the monophyly of the genera Columnea and Paradrymonia and the sister-group relationship of Nematanthus and Codonanthe. A closer affinity between Neomortonia nummularia and N. rosea than has previously been seen is apparent from these data, although these two species are not monophyletic in any tree. Lastly, Capanea appears to be a member of Gloxinieae, although C. grandiflora remains within Episcieae. Evolution of fruit type, epiphytic habit, and presence of tubers is re-examined with the new data presented here.
Pure Parsimony Xor Haplotyping
Bonizzoni, Paola; Dondi, Riccardo; Pirola, Yuri; Rizzi, Romeo
2010-01-01
The haplotype resolution from xor-genotype data has been recently formulated as a new model for genetic studies. The xor-genotype data is a cheaply obtainable type of data distinguishing heterozygous from homozygous sites without identifying the homozygous alleles. In this paper we propose a formulation based on a well-known model used in haplotype inference: pure parsimony. We exhibit exact solutions of the problem by providing polynomial time algorithms for some restricted cases and a fixed-parameter algorithm for the general case. These results are based on some interesting combinatorial properties of a graph representation of the solutions. Furthermore, we show that the problem has a polynomial time k-approximation, where k is the maximum number of xor-genotypes containing a given SNP. Finally, we propose a heuristic and produce an experimental analysis showing that it scales to real-world large instances taken from the HapMap project.
Pure parsimony xor haplotyping.
Bonizzoni, Paola; Della Vedova, Gianluca; Dondi, Riccardo; Pirola, Yuri; Rizzi, Romeo
2010-01-01
The haplotype resolution from xor-genotype data has been recently formulated as a new model for genetic studies. The xor-genotype data is a cheaply obtainable type of data distinguishing heterozygous from homozygous sites without identifying the homozygous alleles. In this paper, we propose a formulation based on a well-known model used in haplotype inference: pure parsimony. We exhibit exact solutions of the problem by providing polynomial time algorithms for some restricted cases and a fixed-parameter algorithm for the general case. These results are based on some interesting combinatorial properties of a graph representation of the solutions. Furthermore, we show that the problem has a polynomial time k-approximation, where k is the maximum number of xor-genotypes containing a given single nucleotide polymorphisms (SNP). Finally, we propose a heuristic and produce an experimental analysis showing that it scales to real-world large instances taken from the HapMap project.
Parsimonious Language Models for Information Retrieval
Hiemstra, Djoerd; Robertson, Stephen; Zaragoza, Hugo
2004-01-01
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,
Parsimonious Refraction Interferometry and Tomography
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.
Nor, Igor; Charlat, Sylvain; Engelstadter, Jan; Reuter, Max; Duron, Olivier; Sagot, Marie-France
2010-01-01
We address in this paper a new computational biology problem that aims at understanding a mechanism that could potentially be used to genetically manipulate natural insect populations infected by inherited, intra-cellular parasitic bacteria. In this problem, that we denote by \\textsc{Mod/Resc Parsimony Inference}, we are given a boolean matrix and the goal is to find two other boolean matrices with a minimum number of columns such that an appropriately defined operation on these matrices gives back the input. We show that this is formally equivalent to the \\textsc{Bipartite Biclique Edge Cover} problem and derive some complexity results for our problem using this equivalence. We provide a new, fixed-parameter tractability approach for solving both that slightly improves upon a previously published algorithm for the \\textsc{Bipartite Biclique Edge Cover}. Finally, we present experimental results where we applied some of our techniques to a real-life data set.
Statistical parsimony networks and species assemblages in Cephalotrichid nemerteans (nemertea).
Chen, Haixia; Strand, Malin; Norenburg, Jon L; Sun, Shichun; Kajihara, Hiroshi; Chernyshev, Alexey V; Maslakova, Svetlana A; Sundberg, Per
2010-09-21
It has been suggested that statistical parsimony network analysis could be used to get an indication of species represented in a set of nucleotide data, and the approach has been used to discuss species boundaries in some taxa. Based on 635 base pairs of the mitochondrial protein-coding gene cytochrome c oxidase I (COI), we analyzed 152 nemertean specimens using statistical parsimony network analysis with the connection probability set to 95%. The analysis revealed 15 distinct networks together with seven singletons. Statistical parsimony yielded three networks supporting the species status of Cephalothrix rufifrons, C. major and C. spiralis as they currently have been delineated by morphological characters and geographical location. Many other networks contained haplotypes from nearby geographical locations. Cladistic structure by maximum likelihood analysis overall supported the network analysis, but indicated a false positive result where subnetworks should have been connected into one network/species. This probably is caused by undersampling of the intraspecific haplotype diversity. Statistical parsimony network analysis provides a rapid and useful tool for detecting possible undescribed/cryptic species among cephalotrichid nemerteans based on COI gene. It should be combined with phylogenetic analysis to get indications of false positive results, i.e., subnetworks that would have been connected with more extensive haplotype sampling.
Statistical parsimony networks and species assemblages in Cephalotrichid nemerteans (nemertea.
Haixia Chen
Full Text Available BACKGROUND: It has been suggested that statistical parsimony network analysis could be used to get an indication of species represented in a set of nucleotide data, and the approach has been used to discuss species boundaries in some taxa. METHODOLOGY/PRINCIPAL FINDINGS: Based on 635 base pairs of the mitochondrial protein-coding gene cytochrome c oxidase I (COI, we analyzed 152 nemertean specimens using statistical parsimony network analysis with the connection probability set to 95%. The analysis revealed 15 distinct networks together with seven singletons. Statistical parsimony yielded three networks supporting the species status of Cephalothrix rufifrons, C. major and C. spiralis as they currently have been delineated by morphological characters and geographical location. Many other networks contained haplotypes from nearby geographical locations. Cladistic structure by maximum likelihood analysis overall supported the network analysis, but indicated a false positive result where subnetworks should have been connected into one network/species. This probably is caused by undersampling of the intraspecific haplotype diversity. CONCLUSIONS/SIGNIFICANCE: Statistical parsimony network analysis provides a rapid and useful tool for detecting possible undescribed/cryptic species among cephalotrichid nemerteans based on COI gene. It should be combined with phylogenetic analysis to get indications of false positive results, i.e., subnetworks that would have been connected with more extensive haplotype sampling.
Optimized ancestral state reconstruction using Sankoff parsimony
Valiente Gabriel
2009-02-01
Full Text Available Abstract Background Parsimony methods are widely used in molecular evolution to estimate the most plausible phylogeny for a set of characters. Sankoff parsimony determines the minimum number of changes required in a given phylogeny when a cost is associated to transitions between character states. Although optimizations exist to reduce the computations in the number of taxa, the original algorithm takes time O(n2 in the number of states, making it impractical for large values of n. Results In this study we introduce an optimization of Sankoff parsimony for the reconstruction of ancestral states when ultrametric or additive cost matrices are used. We analyzed its performance for randomly generated matrices, Jukes-Cantor and Kimura's two-parameter models of DNA evolution, and in the reconstruction of elongation factor-1α and ancestral metabolic states of a group of eukaryotes, showing that in all cases the execution time is significantly less than with the original implementation. Conclusion The algorithms here presented provide a fast computation of Sankoff parsimony for a given phylogeny. Problems where the number of states is large, such as reconstruction of ancestral metabolism, are particularly adequate for this optimization. Since we are reducing the computations required to calculate the parsimony cost of a single tree, our method can be combined with optimizations in the number of taxa that aim at finding the most parsimonious tree.
Dianfeng Liu; Zimei Dong; Yanze Gu; Lingxia Tao
2008-01-01
We studied patterns of distribution and relationships among distributional areas of Tetrigidae insects in China using parsimony analysis of endemism (PAE). We constructed a matrix based on distribution data for Chinese Tetrigidae insects and an area cladogram using northeastern China area as an outgroup. Exhaustivesearches were conducted under the maximum parsimony criterion. Cluster analysis divided eight biogeographic areas into four groups; group 1 was composed of northeast China, group 2 ...
Parsimonious catchment and river flow modelling
Khatibi, R.H.; Moore, R.J.; Booij, Martijn J.; Cadman, D.; Boyce, G.; Rizzoli, A.E.; Jakeman, A.J.
2002-01-01
It is increasingly the case that models are being developed as “evolving” products rather than one-off application tools, such that auditable modelling versus ad hoc treatment of models becomes a pivotal issue. Auditable modelling is particularly vital to “parsimonious modelling” aimed at meeting
Multiple 3D RNA Structure Superposition Using Neighbor Joining.
Hoksza, David; Svozil, Daniel
2015-01-01
Recent advances in RNA research and the steady growth of available RNA structures call for bioinformatics methods for handling and analyzing RNA structural data. Recently, we introduced SETTER-a fast and accurate method for RNA pairwise structure alignment. In this paper, we describe MultiSETTER, SETTER extension for multiple RNA structure alignment. MultiSETTER combines SETTER's decomposition of RNA structures into non-overlapping structural subunits with the multiple sequence alignment algorithm ClustalW adapted for the structure alignment. The accuracy of MultiSETTER was assessed by the automatic classification of RNA structures and its comparison to SCOR annotations. In addition, MultiSETTER classification was also compared to multiple sequence alignment-based and secondary structure alignment-based classifications provided by LocARNA and RNADistance tools, respectively. MultiSETTER precompiled Windows libraries, as well as the C++ source code, are freely available from http://siret.cz/multisetter.
Parsimonious modeling with information filtering networks
Barfuss, Wolfram; Massara, Guido Previde; Di Matteo, T.; Aste, Tomaso
2016-12-01
We introduce a methodology to construct parsimonious probabilistic models. This method makes use of information filtering networks to produce a robust estimate of the global sparse inverse covariance from a simple sum of local inverse covariances computed on small subparts of the network. Being based on local and low-dimensional inversions, this method is computationally very efficient and statistically robust, even for the estimation of inverse covariance of high-dimensional, noisy, and short time series. Applied to financial data our method results are computationally more efficient than state-of-the-art methodologies such as Glasso producing, in a fraction of the computation time, models that can have equivalent or better performances but with a sparser inference structure. We also discuss performances with sparse factor models where we notice that relative performances decrease with the number of factors. The local nature of this approach allows us to perform computations in parallel and provides a tool for dynamical adaptation by partial updating when the properties of some variables change without the need of recomputing the whole model. This makes this approach particularly suitable to handle big data sets with large numbers of variables. Examples of practical application for forecasting, stress testing, and risk allocation in financial systems are also provided.
Parsimonious Ways to Use Vision for Navigation
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.
Quality Quandaries- Time Series Model Selection and Parsimony
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....
Quality Quandaries- Time Series Model Selection and Parsimony
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....
A temporal extension to the parsimonious covering theory.
Wainer, J; Rezende, A de M
1997-07-01
In this paper, parsimonious covering theory is extended in such a way that temporal knowledge can be accommodated. In addition to causally associating possible manifestations with disorders, temporal relationships about duration and the time elapsed before a manifestation comes into existence can be represented by a graph. Precise definitions of the solution of a temporal diagnostic problem as well as algorithms to compute the solutions are provided. The medical suitability of the extended parsimonious cover theory is studied in the domain of food-borne disease.
Parsimonious extreme learning machine using recursive orthogonal least squares.
Wang, Ning; Er, Meng Joo; Han, Min
2014-10-01
Novel constructive and destructive parsimonious extreme learning machines (CP- and DP-ELM) are proposed in this paper. By virtue of the proposed ELMs, parsimonious structure and excellent generalization of multiinput-multioutput single hidden-layer feedforward networks (SLFNs) are obtained. The proposed ELMs are developed by innovative decomposition of the recursive orthogonal least squares procedure into sequential partial orthogonalization (SPO). The salient features of the proposed approaches are as follows: 1) Initial hidden nodes are randomly generated by the ELM methodology and recursively orthogonalized into an upper triangular matrix with dramatic reduction in matrix size; 2) the constructive SPO in the CP-ELM focuses on the partial matrix with the subcolumn of the selected regressor including nonzeros as the first column while the destructive SPO in the DP-ELM operates on the partial matrix including elements determined by the removed regressor; 3) termination criteria for CP- and DP-ELM are simplified by the additional residual error reduction method; and 4) the output weights of the SLFN need not be solved in the model selection procedure and is derived from the final upper triangular equation by backward substitution. Both single- and multi-output real-world regression data sets are used to verify the effectiveness and superiority of the CP- and DP-ELM in terms of parsimonious architecture and generalization accuracy. Innovative applications to nonlinear time-series modeling demonstrate superior identification results.
A Parsimonious and Universal Description of Turbulent Velocity Increments
Barndorff-Nielsen, O.E.; Blæsild, P.; Schmiegel, J.
This paper proposes a reformulation and extension of the concept of Extended Self-Similarity. In support of this new hypothesis, we discuss an analysis of the probability density function (pdf) of turbulent velocity increments based on the class of normal inverse Gaussian distributions. It allows...... for a parsimonious description of velocity increments that covers the whole range of amplitudes and all accessible scales from the finest resolution up to the integral scale. The analysis is performed for three different data sets obtained from a wind tunnel experiment, a free-jet experiment and an atmospheric...
Parsimony analysis of endemicity of enchodontoid fishes from the Cenomanian
Da Silva, Hilda,; GALLO,VALÉRIA
2007-01-01
8 pages; International audience; Parsimony analysis of endemicity was applied to analyze the distribution of enchodontoid fishes occurring strictly in the Cenomanian. The analysis was carried out using the computer program PAUP* 4.0b10, based on a data matrix built with 17 taxa and 12 areas. The rooting was made on an hypothetical all-zero outgroup. Applying the exact algorithm branch and bound, 47 trees were obtained with 26 steps, a consistency index of 0.73, and a retention index of 0.50. ...
A Parsimonious Bootstrap Method to Model Natural Inflow Energy Series
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.
Exactly computing the parsimony scores on phylogenetic networks using dynamic programming.
Kannan, Lavanya; Wheeler, Ward C
2014-04-01
Scoring a given phylogenetic network is the first step that is required in searching for the best evolutionary framework for a given dataset. Using the principle of maximum parsimony, we can score phylogenetic networks based on the minimum number of state changes across a subset of edges of the network for each character that are required for a given set of characters to realize the input states at the leaves of the networks. Two such subsets of edges of networks are interesting in light of studying evolutionary histories of datasets: (i) the set of all edges of the network, and (ii) the set of all edges of a spanning tree that minimizes the score. The problems of finding the parsimony scores under these two criteria define slightly different mathematical problems that are both NP-hard. In this article, we show that both problems, with scores generalized to adding substitution costs between states on the endpoints of the edges, can be solved exactly using dynamic programming. We show that our algorithms require O(m(p)k) storage at each vertex (per character), where k is the number of states the character can take, p is the number of reticulate vertices in the network, m = k for the problem with edge set (i), and m = 2 for the problem with edge set (ii). This establishes an O(nm(p)k(2)) algorithm for both the problems (n is the number of leaves in the network), which are extensions of Sankoff's algorithm for finding the parsimony scores for phylogenetic trees. We will discuss improvements in the complexities and show that for phylogenetic networks whose underlying undirected graphs have disjoint cycles, the storage at each vertex can be reduced to O(mk), thus making the algorithm polynomial for this class of networks. We will present some properties of the two approaches and guidance on choosing between the criteria, as well as traverse through the network space using either of the definitions. We show that our methodology provides an effective means to
A Practical pedestrian approach to parsimonious regression with inaccurate inputs
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.
Danforth, B N; Sauquet, H; Packer, L
1999-12-01
We investigated higher-level phylogenetic relationships within the genus Halictus based on parsimony and maximum likelihood (ML) analysis of elongation factor-1alpha DNA sequence data. Our data set includes 41 OTUs representing 35 species of halictine bees from a diverse sample of outgroup genera and from the three widely recognized subgenera of Halictus (Halictus s.s., Seladonia, and Vestitohalictus). We analyzed 1513 total aligned nucleotide sites spanning three exons and two introns. Equal-weights parsimony analysis of the overall data set yielded 144 equally parsimonious trees. Major conclusions supported in this analysis (and in all subsequent analyses) included the following: (1) Thrincohalictus is the sister group to Halictus s.l., (2) Halictus s.l. is monophyletic, (3) Vestitohalictus renders Seladonia paraphyletic but together Seladonia + Vestitohalictus is monophyletic, (4) Michener's Groups 1 and 3 are monophyletic, and (5) Michener's Group 1 renders Group 2 paraphyletic. In order to resolve basal relationships within Halictus we applied various weighting schemes under parsimony (successive approximations character weighting and implied weights) and employed ML under 17 models of sequence evolution. Weighted parsimony yielded conflicting results but, in general, supported the hypothesis that Seladonia + Vestitohalictus is sister to Michener's Group 3 and renders Halictus s.s. paraphyletic. ML analyses using the GTR model with site-specific rates supported an alternative hypothesis: Seladonia + Vestitohalictus is sister to Halictus s.s. We mapped social behavior onto trees obtained under ML and parsimony in order to reconstruct the likely historical pattern of social evolution. Our results are unambiguous: the ancestral state for the genus Halictus is eusociality. Reversal to solitary behavior has occurred at least four times among the species included in our analysis. Copyright 1999 Academic Press.
Hansen, Gert; Daugbjerg, Niels; Henriksen, Peter
2000-01-01
were nearly identical in all isolates, and molecular analyses using maximum likelihood, parsimony, and neighbor joining showed the geographical isolates as an unresolved clade. Based on the available data it is concluded that the European isolates, formerly identified as Gyrodinium aureolum, Gyrodinium...... cf. aureolum, or Gymnodinium cf. nagasakiense, are conspecific with the Japanese Gymnodinium mikimotoi. An isolate from the Pettaquamscutt River, USA, is suggested to represent what Hulburt (1957) described as Gyrodinium aureolum. The LSU rDNA sequence data and ultrastructural characters...
Pengintegrasian Model Leadership Menuju Model yang Lebih Komprhensip dan Parsimoni
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.
SEAPODYM-LTL: a parsimonious zooplankton dynamic biomass model
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.
Rahmann Sven
2004-06-01
Full Text Available Abstract Background In phylogenetic analysis we face the problem that several subclade topologies are known or easily inferred and well supported by bootstrap analysis, but basal branching patterns cannot be unambiguously estimated by the usual methods (maximum parsimony (MP, neighbor-joining (NJ, or maximum likelihood (ML, nor are they well supported. We represent each subclade by a sequence profile and estimate evolutionary distances between profiles to obtain a matrix of distances between subclades. Results Our estimator of profile distances generalizes the maximum likelihood estimator of sequence distances. The basal branching pattern can be estimated by any distance-based method, such as neighbor-joining. Our method (profile neighbor-joining, PNJ then inherits the accuracy and robustness of profiles and the time efficiency of neighbor-joining. Conclusions Phylogenetic analysis of Chlorophyceae with traditional methods (MP, NJ, ML and MrBayes reveals seven well supported subclades, but the methods disagree on the basal branching pattern. The tree reconstructed by our method is better supported and can be confirmed by known morphological characters. Moreover the accuracy is significantly improved as shown by parametric bootstrap.
Efficient K-Nearest Neighbor Join Algorithms for High Dimensional Sparse Data
Wang, Jijie; Huang, Ting; Wang, Jingjing; He, Zengyou
2010-01-01
The K-Nearest Neighbor (KNN) join is an expensive but important operation in many data mining algorithms. Several recent applications need to perform KNN join for high dimensional sparse data. Unfortunately, all existing KNN join algorithms are designed for low dimensional data. To fulfill this void, we investigate the KNN join problem for high dimensional sparse data. In this paper, we propose three KNN join algorithms: a brute force (BF) algorithm, an inverted index-based(IIB) algorithm and an improved inverted index-based(IIIB) algorithm. Extensive experiments on both synthetic and real-world datasets were conducted to demonstrate the effectiveness of our algorithms for high dimensional sparse data.
Predicting protein interactions via parsimonious network history inference.
Patro, Rob; Kingsford, Carl
2013-07-01
Reconstruction of the network-level evolutionary history of protein-protein interactions provides a principled way to relate interactions in several present-day networks. Here, we present a general framework for inferring such histories and demonstrate how it can be used to determine what interactions existed in the ancestral networks, which present-day interactions we might expect to exist based on evolutionary evidence and what information extant networks contain about the order of ancestral protein duplications. Our framework characterizes the space of likely parsimonious network histories. It results in a structure that can be used to find probabilities for a number of events associated with the histories. The framework is based on a directed hypergraph formulation of dynamic programming that we extend to enumerate many optimal and near-optimal solutions. The algorithm is applied to reconstructing ancestral interactions among bZIP transcription factors, imputing missing present-day interactions among the bZIPs and among proteins from five herpes viruses, and determining relative protein duplication order in the bZIP family. Our approach more accurately reconstructs ancestral interactions than existing approaches. In cross-validation tests, we find that our approach ranks the majority of the left-out present-day interactions among the top 2 and 17% of possible edges for the bZIP and herpes networks, respectively, making it a competitive approach for edge imputation. It also estimates relative bZIP protein duplication orders, using only interaction data and phylogenetic tree topology, which are significantly correlated with sequence-based estimates. The algorithm is implemented in C++, is open source and is available at http://www.cs.cmu.edu/ckingsf/software/parana2. Supplementary data are available at Bioinformatics online.
Parsimony score of phylogenetic networks: hardness results and a linear-time heuristic.
Jin, Guohua; Nakhleh, Luay; Snir, Sagi; Tuller, Tamir
2009-01-01
Phylogenies-the evolutionary histories of groups of organisms-play a major role in representing the interrelationships among biological entities. Many methods for reconstructing and studying such phylogenies have been proposed, almost all of which assume that the underlying history of a given set of species can be represented by a binary tree. Although many biological processes can be effectively modeled and summarized in this fashion, others cannot: recombination, hybrid speciation, and horizontal gene transfer result in networks of relationships rather than trees of relationships. In previous works, we formulated a maximum parsimony (MP) criterion for reconstructing and evaluating phylogenetic networks, and demonstrated its quality on biological as well as synthetic data sets. In this paper, we provide further theoretical results as well as a very fast heuristic algorithm for the MP criterion of phylogenetic networks. In particular, we provide a novel combinatorial definition of phylogenetic networks in terms of "forbidden cycles," and provide detailed hardness and hardness of approximation proofs for the "small" MP problem. We demonstrate the performance of our heuristic in terms of time and accuracy on both biological and synthetic data sets. Finally, we explain the difference between our model and a similar one formulated by Nguyen et al., and describe the implications of this difference on the hardness and approximation results.
Kinkhabwala, Ali
2013-01-01
The most fundamental problem in statistics is the inference of an unknown probability distribution from a finite number of samples. For a specific observed data set, answers to the following questions would be desirable: (1) Estimation: Which candidate distribution provides the best fit to the observed data?, (2) Goodness-of-fit: How concordant is this distribution with the observed data?, and (3) Uncertainty: How concordant are other candidate distributions with the observed data? A simple unified approach for univariate data that addresses these traditionally distinct statistical notions is presented called "maximum fidelity". Maximum fidelity is a strict frequentist approach that is fundamentally based on model concordance with the observed data. The fidelity statistic is a general information measure based on the coordinate-independent cumulative distribution and critical yet previously neglected symmetry considerations. An approximation for the null distribution of the fidelity allows its direct conversi...
Parsimonious Hydrologic and Nitrate Response Models For Silver Springs, Florida
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
Reed, David L; Carpenter, Kent E; deGravelle, Martin J
2002-06-01
The Carangidae represent a diverse family of marine fishes that include both ecologically and economically important species. Currently, there are four recognized tribes within the family, but phylogenetic relationships among them based on morphology are not resolved. In addition, the tribe Carangini contains species with a variety of body forms and no study has tried to interpret the evolution of this diversity. We used DNA sequences from the mitochondrial cytochrome b gene to reconstruct the phylogenetic history of 50 species from each of the four tribes of Carangidae and four carangoid outgroup taxa. We found support for the monophyly of three tribes within the Carangidae (Carangini, Naucratini, and Trachinotini); however, monophyly of the fourth tribe (Scomberoidini) remains questionable. A sister group relationship between the Carangini and the Naucratini is well supported. This clade is apparently sister to the Trachinotini plus Scomberoidini but there is uncertain support for this relationship. Additionally, we examined the evolution of body form within the tribe Carangini and determined that each of the predominant clades has a distinct evolutionary trend in body form. We tested three methods of phylogenetic inference, parsimony, maximum-likelihood, and Bayesian inference. Whereas the three analyses produced largely congruent hypotheses, they differed in several important relationships. Maximum-likelihood and Bayesian methods produced hypotheses with higher support values for deep branches. The Bayesian analysis was computationally much faster and yet produced phylogenetic hypotheses that were very similar to those of the maximum-likelihood analysis. (c) 2002 Elsevier Science (USA).
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...
Wei Wu; James Clark; James Vose
2010-01-01
Hierarchical Bayesian (HB) modeling allows for multiple sources of uncertainty by factoring complex relationships into conditional distributions that can be used to draw inference and make predictions. We applied an HB model to estimate the parameters and state variables of a parsimonious hydrological model â GR4J â by coherently assimilating the uncertainties from the...
Frederick H. Sheldon
2013-03-01
Full Text Available Insertion/deletion (indel mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP and a simple maximum likelihood (ML framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.
Salas-Leiva, Dayana E; Meerow, Alan W; Calonje, Michael; Griffith, M Patrick; Francisco-Ortega, Javier; Nakamura, Kyoko; Stevenson, Dennis W; Lewis, Carl E; Namoff, Sandra
2013-11-01
Despite a recent new classification, a stable phylogeny for the cycads has been elusive, particularly regarding resolution of Bowenia, Stangeria and Dioon. In this study, five single-copy nuclear genes (SCNGs) are applied to the phylogeny of the order Cycadales. The specific aim is to evaluate several gene tree-species tree reconciliation approaches for developing an accurate phylogeny of the order, to contrast them with concatenated parsimony analysis and to resolve the erstwhile problematic phylogenetic position of these three genera. DNA sequences of five SCNGs were obtained for 20 cycad species representing all ten genera of Cycadales. These were analysed with parsimony, maximum likelihood (ML) and three Bayesian methods of gene tree-species tree reconciliation, using Cycas as the outgroup. A calibrated date estimation was developed with Bayesian methods, and biogeographic analysis was also conducted. Concatenated parsimony, ML and three species tree inference methods resolve exactly the same tree topology with high support at most nodes. Dioon and Bowenia are the first and second branches of Cycadales after Cycas, respectively, followed by an encephalartoid clade (Macrozamia-Lepidozamia-Encephalartos), which is sister to a zamioid clade, of which Ceratozamia is the first branch, and in which Stangeria is sister to Microcycas and Zamia. A single, well-supported phylogenetic hypothesis of the generic relationships of the Cycadales is presented. However, massive extinction events inferred from the fossil record that eliminated broader ancestral distributions within Zamiaceae compromise accurate optimization of ancestral biogeographical areas for that hypothesis. While major lineages of Cycadales are ancient, crown ages of all modern genera are no older than 12 million years, supporting a recent hypothesis of mostly Miocene radiations. This phylogeny can contribute to an accurate infrafamilial classification of Zamiaceae.
Equally parsimonious pathways through an RNA sequence space are not equally likely
Lee, Y. H.; DSouza, L. M.; Fox, G. E.
1997-01-01
An experimental system for determining the potential ability of sequences resembling 5S ribosomal RNA (rRNA) to perform as functional 5S rRNAs in vivo in the Escherichia coli cellular environment was devised previously. Presumably, the only 5S rRNA sequences that would have been fixed by ancestral populations are ones that were functionally valid, and hence the actual historical paths taken through RNA sequence space during 5S rRNA evolution would have most likely utilized valid sequences. Herein, we examine the potential validity of all sequence intermediates along alternative equally parsimonious trajectories through RNA sequence space which connect two pairs of sequences that had previously been shown to behave as valid 5S rRNAs in E. coli. The first trajectory requires a total of four changes. The 14 sequence intermediates provide 24 apparently equally parsimonious paths by which the transition could occur. The second trajectory involves three changes, six intermediate sequences, and six potentially equally parsimonious paths. In total, only eight of the 20 sequence intermediates were found to be clearly invalid. As a consequence of the position of these invalid intermediates in the sequence space, seven of the 30 possible paths consisted of exclusively valid sequences. In several cases, the apparent validity/invalidity of the intermediate sequences could not be anticipated on the basis of current knowledge of the 5S rRNA structure. This suggests that the interdependencies in RNA sequence space may be more complex than currently appreciated. If ancestral sequences predicted by parsimony are to be regarded as actual historical sequences, then the present results would suggest that they should also satisfy a validity requirement and that, in at least limited cases, this conjecture can be tested experimentally.
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 ...
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...
Casabianca, Jodi M.; Lewis, Charles
2015-01-01
Loglinear smoothing (LLS) estimates the latent trait distribution while making fewer assumptions about its form and maintaining parsimony, thus leading to more precise item response theory (IRT) item parameter estimates than standard marginal maximum likelihood (MML). This article provides the expectation-maximization algorithm for MML estimation…
Dallolio Laura
2006-08-01
Full Text Available Abstract Background Cesarean section rates is often used as an indicator of quality of care in maternity hospitals. The assumption is that lower rates reflect in developed countries more appropriate clinical practice and general better performances. Hospitals are thus often ranked on the basis of caesarean section rates. The aim of this study is to assess whether the adjustment for clinical and sociodemographic variables of the mother and the fetus is necessary for inter-hospital comparisons of cesarean section (c-section rates and to assess whether a risk adjustment model based on a limited number of variables could be identified and used. Methods Discharge abstracts of labouring women without prior cesarean were linked with abstracts of newborns discharged from 29 hospitals of the Emilia-Romagna Region (Italy from 2003 to 2004. Adjusted ORs of cesarean by hospital were estimated by using two logistic regression models: 1 a full model including the potential confounders selected by a backward procedure; 2 a parsimonious model including only actual confounders identified by the "change-in-estimate" procedure. Hospital rankings, based on ORs were examined. Results 24 risk factors for c-section were included in the full model and 7 (marital status, maternal age, infant weight, fetopelvic disproportion, eclampsia or pre-eclampsia, placenta previa/abruptio placentae, malposition/malpresentation in the parsimonious model. Hospital ranking using the adjusted ORs from both models was different from that obtained using the crude ORs. The correlation between the rankings of the two models was 0.92. The crude ORs were smaller than ORs adjusted by both models, with the parsimonious ones producing more precise estimates. Conclusion Risk adjustment is necessary to compare hospital c-section rates, it shows differences in rankings and highlights inappropriateness of some hospitals. By adjusting for only actual confounders valid and more precise estimates
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.
Noro, M; Masuda, R; Dubrovo, I A; Yoshida, M C; Kato, M
1998-03-01
Complete sequences of cytochrome b (1,137 bases) and 12S ribosomal RNA (961 bases) genes in mitochondrial DNA were successfully determined from the woolly mammoth (Mammuthus primigenius), African elephant (Loxodonta africana), and Asian elephant (Elephas maximus). From these sequence data, phylogenetic relationships among three genera were examined. Molecular phylogenetic trees reconstructed by the neighbor-joining and the maximum parsimony methods provided an identical topology both for cytochrome b and 12S rRNA genes. These results support the "Mammuthus-Loxodonta" clade, which is contrary to some previous morphological reports that Mammuthus is more closely related to Elephas than to Loxodonta.
Phylogeny of protostome worms derived from 18S rRNA sequences.
Winnepenninckx, B; Backeljau, T; De Wachter, R
1995-07-01
The phylogenetic relationships of protostome worms were studied by comparing new complete 18S rRNA sequences of Vestimentifera, Pogonophora, Sipuncula, Echiura, Nemertea, and Annelida with existing 18S rRNA sequences of Mollusca, Arthropoda, Chordata, and Platyhelminthes. Phylogenetic trees were inferred via neighbor-joining and maximum parsimony analyses. These suggest that (1) Sipuncula and Echiura are not sister groups; (2) Nemertea are protostomes; (3) Vestimentifera and Pogonophora are protostomes that have a common ancestor with Echiura; and (4) Vestimentifera and Pogonophora are a monophyletic clade.
Commitment to Sport and Exercise: Re-examining the Literature for a Practical and Parsimonious Model
2013-01-01
A commitment to physical activity is necessary for personal health, and is a primary goal of physical activity practitioners. Effective practitioners rely on theory and research as a guide to best practices. Thus, sound theory, which is both practical and parsimonious, is a key to effective practice. The purpose of this paper is to review the literature in search of such a theory - one that applies to and explains commitment to physical activity in the form of sport and exercise for youths and adults. The Sport Commitment Model has been commonly used to study commitment to sport and has more recently been applied to the exercise context. In this paper, research using the Sport Commitment Model is reviewed relative to its utility in both the sport and exercise contexts. Through this process, the relevance of the Investment Model for study of physical activity commitment emerged, and a more parsimonious framework for studying of commitment to physical activity is suggested. Lastly, links between the models of commitment and individuals' participation motives in physical activity are suggested and practical implications forwarded. PMID:23412904
Williams, Lavon
2013-01-01
A commitment to physical activity is necessary for personal health, and is a primary goal of physical activity practitioners. Effective practitioners rely on theory and research as a guide to best practices. Thus, sound theory, which is both practical and parsimonious, is a key to effective practice. The purpose of this paper is to review the literature in search of such a theory - one that applies to and explains commitment to physical activity in the form of sport and exercise for youths and adults. The Sport Commitment Model has been commonly used to study commitment to sport and has more recently been applied to the exercise context. In this paper, research using the Sport Commitment Model is reviewed relative to its utility in both the sport and exercise contexts. Through this process, the relevance of the Investment Model for study of physical activity commitment emerged, and a more parsimonious framework for studying of commitment to physical activity is suggested. Lastly, links between the models of commitment and individuals' participation motives in physical activity are suggested and practical implications forwarded.
Parsimonious wave-equation travel-time inversion for refraction waves
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.
Chen, Shuo; Kang, Jian; Xing, Yishi; Wang, Guoqing
2015-12-01
Group-level functional connectivity analyses often aim to detect the altered connectivity patterns between subgroups with different clinical or psychological experimental conditions, for example, comparing cases and healthy controls. We present a new statistical method to detect differentially expressed connectivity networks with significantly improved power and lower false-positive rates. The goal of our method was to capture most differentially expressed connections within networks of constrained numbers of brain regions (by the rule of parsimony). By virtue of parsimony, the false-positive individual connectivity edges within a network are effectively reduced, whereas the informative (differentially expressed) edges are allowed to borrow strength from each other to increase the overall power of the network. We develop a test statistic for each network in light of combinatorics graph theory, and provide p-values for the networks (in the weak sense) by using permutation test with multiple-testing adjustment. We validate and compare this new approach with existing methods, including false discovery rate and network-based statistic, via simulation studies and a resting-state functional magnetic resonance imaging case-control study. The results indicate that our method can identify differentially expressed connectivity networks, whereas existing methods are limited.
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.
Van Meter, Kimberly J; Basu, Nandita B
2015-01-01
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.
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.
Singular Spectrum Analysis for astronomical time series: constructing a parsimonious hypothesis test
Greco, G; Kobayashi, S; Ghil, M; Branchesi, M; Guidorzi, C; Stratta, G; Ciszak, M; Marino, F; Ortolan, A
2015-01-01
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 $1/f^{\\beta}$ 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.
State space parsimonious reconstruction of attractor produced by an electronic oscillator
Aguirre, Luis A.; Freitas, Ubiratan S.; Letellier, Christophe; Sceller, Lois Le; Maquet, Jean
2000-02-01
This work discusses the reconstruction, from a set of real data, of a chaotic attractor produced by a well-known electronic oscillator, Chua's circuit. The mathematical representation used is a nonlinear differential equation of the polynomial type. One of the contributions of the present study is that structure selection techniques have been applied to help determine the regressors in the model. Models of the chaotic attractor obtained with and without structure selection were compared. The main differences between structure-selected models and complete structure models are: i) the former are more parsimonious that the latter, ii) fixed-point symmetry is guaranteed for the former, iii) for structure-selected models a trivial fixed point is also guaranteed, and iv) the former set of models produce attractors that are topologically closer to the original attractor than those produced by the complete structure models.
Roth, Bradley J.
2017-01-01
The strength-interval curve plays a major role in understanding how cardiac tissue responds to an electrical stimulus. This complex behavior has been studied previously using the bidomain formulation incorporating the Beeler-Reuter and Luo-Rudy dynamic ionic current models. The complexity of these models renders the interpretation and extrapolation of simulation results problematic. Here we utilize a recently developed parsimonious ionic current model with only two currents—a sodium current that activates rapidly upon depolarization INa and a time-independent inwardly rectifying repolarization current IK—which reproduces many experimentally measured action potential waveforms. Bidomain tissue simulations with this ionic current model reproduce the distinctive dip in the anodal (but not cathodal) strength-interval curve. Studying model variants elucidates the necessary and sufficient physiological conditions to predict the polarity dependent dip: a voltage and time dependent INa, a nonlinear rectifying repolarization current, and bidomain tissue with unequal anisotropy ratios. PMID:28222136
Distribution patterns of Neotropical primates (Platyrrhini based on Parsimony Analysis of Endemicity
A. Goldani
Full Text Available The Parsimony Analysis of Endemicity (PAE is a method of historical biogeography that is used for detecting and connecting areas of endemism. Based on data on the distribution of Neotropical primates, we constructed matrices using quadrats, interfluvial regions and pre-determinated areas of endemism described for avians as Operative Geographic Units (OGUs. We codified the absence of a species from an OGU as 0 (zero and its presence as 1 (one. A hypothetical area with a complete absence of primate species was used as outgroup to root the trees. All three analyses resulted in similar groupings of areas of endemism, which match the distribution of biomes in the Neotropical region. One area includes Central America and the extreme Northwest of South America, other the Amazon basin, and another the Atlantic Forest, Caatinga, Cerrado and Chaco.
Goldani, A; Carvalho, G S; Bicca-Marques, J C
2006-02-01
The Parsimony Analysis of Endemicity (PAE) is a method of historical biogeography that is used for detecting and connecting areas of endemism. Based on data on the distribution of Neotropical primates, we constructed matrices using quadrats, interfluvial regions and pre-determinated areas of endemism described for avians as Operative Geographic Units (OGUs). We codified the absence of a species from an OGU as 0 (zero) and its presence as 1 (one). A hypothetical area with a complete absence of primate species was used as outgroup to root the trees. All three analyses resulted in similar groupings of areas of endemism, which match the distribution of biomes in the Neotropical region. One area includes Central America and the extreme Northwest of South America, other the Amazon basin, and another the Atlantic Forest, Caatinga, Cerrado and Chaco.
Satisfiability Parsimoniously Reduces to the Tantrix(TM) Rotation Puzzle Problem
Baumeister, Dorothea
2007-01-01
Holzer and Holzer (Discrete Applied Mathematics 144(3):345--358, 2004) proved that the Tantrix(TM) rotation puzzle problem is NP-complete. They also showed that for infinite rotation puzzles, this problem becomes undecidable. We study the counting version and the unique version of this problem. We prove that the satisfiability problem parsimoniously reduces to the Tantrix(TM) rotation puzzle problem. In particular, this reduction preserves the uniqueness of the solution, which implies that the unique Tantrix(TM) rotation puzzle problem is as hard as the unique satisfiability problem, and so is DP-complete under polynomial-time randomized reductions, where DP is the second level of the boolean hierarchy over NP.
Time-Lapse Monitoring of Subsurface Fluid Flow using Parsimonious Seismic Interferometry
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.
Michael Seifert
2012-01-01
Full Text Available Array-based comparative genomic hybridization (Array-CGH is an important technology in molecular biology for the detection of DNA copy number polymorphisms between closely related genomes. Hidden Markov Models (HMMs are popular tools for the analysis of Array-CGH data, but current methods are only based on first-order HMMs having constrained abilities to model spatial dependencies between measurements of closely adjacent chromosomal regions. Here, we develop parsimonious higher-order HMMs enabling the interpolation between a mixture model ignoring spatial dependencies and a higher-order HMM exhaustively modeling spatial dependencies. We apply parsimonious higher-order HMMs to the analysis of Array-CGH data of the accessions C24 and Col-0 of the model plant Arabidopsis thaliana. We compare these models against first-order HMMs and other existing methods using a reference of known deletions and sequence deviations. We find that parsimonious higher-order HMMs clearly improve the identification of these polymorphisms. Moreover, we perform a functional analysis of identified polymorphisms revealing novel details of genomic differences between C24 and Col-0. Additional model evaluations are done on widely considered Array-CGH data of human cell lines indicating that parsimonious HMMs are also well-suited for the analysis of non-plant specific data. All these results indicate that parsimonious higher-order HMMs are useful for Array-CGH analyses. An implementation of parsimonious higher-order HMMs is available as part of the open source Java library Jstacs (www.jstacs.de/index.php/PHHMM.
Seifert, Michael; Gohr, André; Strickert, Marc; Grosse, Ivo
2012-01-01
Array-based comparative genomic hybridization (Array-CGH) is an important technology in molecular biology for the detection of DNA copy number polymorphisms between closely related genomes. Hidden Markov Models (HMMs) are popular tools for the analysis of Array-CGH data, but current methods are only based on first-order HMMs having constrained abilities to model spatial dependencies between measurements of closely adjacent chromosomal regions. Here, we develop parsimonious higher-order HMMs enabling the interpolation between a mixture model ignoring spatial dependencies and a higher-order HMM exhaustively modeling spatial dependencies. We apply parsimonious higher-order HMMs to the analysis of Array-CGH data of the accessions C24 and Col-0 of the model plant Arabidopsis thaliana. We compare these models against first-order HMMs and other existing methods using a reference of known deletions and sequence deviations. We find that parsimonious higher-order HMMs clearly improve the identification of these polymorphisms. Moreover, we perform a functional analysis of identified polymorphisms revealing novel details of genomic differences between C24 and Col-0. Additional model evaluations are done on widely considered Array-CGH data of human cell lines indicating that parsimonious HMMs are also well-suited for the analysis of non-plant specific data. All these results indicate that parsimonious higher-order HMMs are useful for Array-CGH analyses. An implementation of parsimonious higher-order HMMs is available as part of the open source Java library Jstacs (www.jstacs.de/index.php/PHHMM).
Parsimony and goodness-of-fit in multi-dimensional NMR inversion
Babak, Petro; Kryuchkov, Sergey; Kantzas, Apostolos
2017-01-01
Multi-dimensional nuclear magnetic resonance (NMR) experiments are often used for study of molecular structure and dynamics of matter in core analysis and reservoir evaluation. Industrial applications of multi-dimensional NMR involve a high-dimensional measurement dataset with complicated correlation structure and require rapid and stable inversion algorithms from the time domain to the relaxation rate and/or diffusion domains. In practice, applying existing inverse algorithms with a large number of parameter values leads to an infinite number of solutions with a reasonable fit to the NMR data. The interpretation of such variability of multiple solutions and selection of the most appropriate solution could be a very complex problem. In most cases the characteristics of materials have sparse signatures, and investigators would like to distinguish the most significant relaxation and diffusion values of the materials. To produce an easy to interpret and unique NMR distribution with the finite number of the principal parameter values, we introduce a new method for NMR inversion. The method is constructed based on the trade-off between the conventional goodness-of-fit approach to multivariate data and the principle of parsimony guaranteeing inversion with the least number of parameter values. We suggest performing the inversion of NMR data using the forward stepwise regression selection algorithm. To account for the trade-off between goodness-of-fit and parsimony, the objective function is selected based on Akaike Information Criterion (AIC). The performance of the developed multi-dimensional NMR inversion method and its comparison with conventional methods are illustrated using real data for samples with bitumen, water and clay.
无
2006-01-01
The complete small subunit rRNA (SSrRNA) gene sequence of a marine ciliate, Dysteria derouxi Gong and Song, 2004, was determined to be of 1 708 nucleotides. The phylogenetic position of this species within the class Phyllopharyngea was deduced using distance matrix, maximum parsimony and maximum likelihood methods. Dysteria derouxi, together with other available ciliates of the class Phyllopharyngea, forms a monophyletic clade with strong bootstrap support in the distance matrix, maximum parsimony and likelihood tree construction methods, while the dysterids are, as a monophyletic group, phylogenetically close to the clade of chlamydodontids [values of 100% LS(least-squares), 100% NJ(neighbor-joining)]. In addition, the trees indicate that dysteriids may be a higher or specialized group within the class, which corresponds well to the morphology and infraciliature.
Maximum Autocorrelation Factorial Kriging
Nielsen, Allan Aasbjerg; Conradsen, Knut; Pedersen, John L.
2000-01-01
This paper describes maximum autocorrelation factor (MAF) analysis, maximum autocorrelation factorial kriging, and its application to irregularly sampled stream sediment geochemical data from South Greenland. Kriged MAF images are compared with kriged images of varimax rotated factors from...
Leaf carbon assimilation and molecular phylogeny in Cattleya species (Orchidaceae).
Andrade-Souza, V; Almeida, A-A F; Corrêa, R X; Costa, M A; Mielke, M S; Gomes, F P
2009-08-11
We examined leaf CO(2) assimilation and how it varied among species within the orchid genus Cattleya. Measurements of CO(2) assimilation and maximum quantum yield of PS II (Fv/Fm) were made for mature leaves of nine species using a portable system for photosynthesis measurement and a portable fluorometer. Leaf area was measured with an area meter, and the specific leaf mass was determined. DNA of nine Cattleya species and two species of Hadrolaelia was extracted using the CTAB protocol. Each sample was amplified and sequenced using primers for the trnL gene. The phylogenetic analyses, using neighbor-joining and maximum parsimony methods, retrieved a group that included Cattleya and Hadrolaelia species, in which the unifoliate species were separated from the bifoliates. The topologies of the two cladograms showed some similarities. However, C. guttata (bifoliate) was placed in the unifoliate clade in the neighbor-joining tree, while C. warneri (unifoliate) was not placed in this clade in the maximum parsimony tree. Most Cattleya species keep the leaf stomata closed from 6 am to 4 pm. We suggest that C. elongata, C. tigrina and C. tenuis have C(3)-crassulacean acid metabolism since they open their stomata around 12 am. The Fv/Fm values remained relatively constant during the measurements of CO(2) assimilation. The same was observed for the specific leaf mass values, although great variations were found in the leaf area values. When the species were grouped using molecular data in the neighbor-joining analysis, no relation was observed with CO(2) assimilation.
Urban water quality modelling: a parsimonious holistic approach for a complex real case study.
Freni, Gabriele; Mannina, Giorgio; Viviani, Gaspare
2010-01-01
In the past three decades, scientific research has focused on the preservation of water resources, and in particular, on the polluting impact of urban areas on natural water bodies. One approach to this research has involved the development of tools to describe the phenomena that take place on the urban catchment during both wet and dry periods. Research has demonstrated the importance of the integrated analysis of all the transformation phases that characterise the delivery and treatment of urban water pollutants from source to outfall. With this aim, numerous integrated urban drainage models have been developed to analyse the fate of pollution from urban catchments to the final receiving waters, simulating several physical and chemical processes. Such modelling approaches require calibration, and for this reason, researchers have tried to address two opposing needs: the need for reliable representation of complex systems, and the need to employ parsimonious approaches to cope with the usually insufficient, especially for urban sources, water quality data. The present paper discusses the application of a be-spoke model to a complex integrated catchment: the Nocella basin (Italy). This system is characterised by two main urban areas served by two wastewater treatment plants, and has a small river as the receiving water body. The paper describes the monitoring approach that was used for model calibration, presents some interesting considerations about the monitoring needs for integrated modelling applications, and provides initial results useful for identifying the most relevant polluting sources.
A data parsimonious model for capturing snapshots of groundwater pollution sources.
Chaubey, Jyoti; Kashyap, Deepak
2017-02-01
Presented herein is a data parsimonious model for identification of regional and local groundwater pollution sources at a reference time employing corresponding fields of head, concentration and its time derivative. The regional source flux, assumed to be uniformly distributed, is viewed as the causative factor for the widely prevalent background concentration. The localized concentration-excesses are attributed to flux from local sources distributed around the respective centroids. The groundwater pollution is parameterized by flux from regional and local sources, and distribution parameters of the latter. These parameters are estimated by minimizing the sum of squares of differences between the observed and simulated concentration fields. The concentration field is simulated by a numerical solution of the transient solute transport equation. The equation is solved assuming the temporal derivative term to be known a priori and merging it with the sink term. This strategy circumvents the requirement of dynamic concentration data. The head field is generated using discrete point head data employing a specially devised interpolator that controls the numerical-differentiation errors and simultaneously ensures micro-level mass balance. This measure eliminates the requirement of flow modeling without compromising the sanctity of head field. The model after due verification has been illustrated employing available and simulated data from an area lying between two rivers Yamuna and Krishni in India. Copyright © 2016 Elsevier B.V. All rights reserved.
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.
B. P. Weissling
2007-01-01
Full Text Available Soil moisture condition plays a vital role in a watershed's hydrologic response to a precipitation event and is thus parameterized in most, if not all, rainfall-runoff models. Yet the soil moisture condition antecedent to an event has proven difficult to quantify both spatially and temporally. This study assesses the potential to parameterize a parsimonious streamflow prediction model solely utilizing precipitation records and multi-temporal remotely sensed biophysical variables (i.e.~from Moderate Resolution Imaging Spectroradiometer (MODIS/Terra satellite. This study is conducted on a 1420 km^{2} rural watershed in the Guadalupe River basin of southcentral Texas, a basin prone to catastrophic flooding from convective precipitation events. A multiple regression model, accounting for 78% of the variance of observed streamflow for calendar year 2004, was developed based on gauged precipitation, land surface temperature, and enhanced vegetation Index (EVI, on an 8-day interval. These results compared favorably with streamflow estimations utilizing the Natural Resources Conservation Service (NRCS curve number method and the 5-day antecedent moisture model. This approach has great potential for developing near real-time predictive models for flood forecasting and can be used as a tool for flood management in any region for which similar remotely sensed data are available.
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.
Weissling, B. P.; Xie, H.; Murray, K. E.
2007-01-01
Soil moisture condition plays a vital role in a watershed's hydrologic response to a precipitation event and is thus parameterized in most, if not all, rainfall-runoff models. Yet the soil moisture condition antecedent to an event has proven difficult to quantify both spatially and temporally. This study assesses the potential to parameterize a parsimonious streamflow prediction model solely utilizing precipitation records and multi-temporal remotely sensed biophysical variables (i.e.~from Moderate Resolution Imaging Spectroradiometer (MODIS)/Terra satellite). This study is conducted on a 1420 km2 rural watershed in the Guadalupe River basin of southcentral Texas, a basin prone to catastrophic flooding from convective precipitation events. A multiple regression model, accounting for 78% of the variance of observed streamflow for calendar year 2004, was developed based on gauged precipitation, land surface temperature, and enhanced vegetation Index (EVI), on an 8-day interval. These results compared favorably with streamflow estimations utilizing the Natural Resources Conservation Service (NRCS) curve number method and the 5-day antecedent moisture model. This approach has great potential for developing near real-time predictive models for flood forecasting and can be used as a tool for flood management in any region for which similar remotely sensed data are available.
Catalano, S A; Goloboff, P A
2012-05-01
All methods proposed to date for mapping landmark configurations on a phylogenetic tree start from an alignment generated by methods that make no use of phylogenetic information, usually by superimposing all configurations against a consensus configuration. In order to properly interpret differences between landmark configurations along the tree as changes in shape, the metric chosen to define the ancestral assignments should also form the basis to superimpose the configurations. Thus, we present here a method that merges both steps, map and align, into a single procedure that (for the given tree) produces a multiple alignment and ancestral assignments such that the sum of the Euclidean distances between the corresponding landmarks along tree nodes is minimized. This approach is an extension of the method proposed by Catalano et al. (2010. Phylogenetic morphometrics (I): the use of landmark data in a phylogenetic framework. Cladistics. 26:539-549) for mapping landmark data with parsimony as optimality criterion. In the context of phylogenetics, this method allows maximizing the degree to which similarity in landmark positions can be accounted for by common ancestry. In the context of morphometrics, this approach guarantees (heuristics aside) that all the transformations inferred on the tree represent changes in shape. The performance of the method was evaluated on different data sets, indicating that the method produces marked improvements in tree score (up to 5% compared with generalized superimpositions, up to 11% compared with ordinary superimpositions). These empirical results stress the importance of incorporating the phylogenetic information into the alignment step.
Komatitsch, Dimitri; Bozdag, Ebru; de Andrade, Elliott Sales; Peter, Daniel B; 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 $K_\\alpha$ 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-dispersi...
Gopal, Judy; Muthu, Manikandan; Chun, Sechul
2016-07-28
The development of thin film coatings has been a very important development in materials science for the modification of native material surface properties. Thin film coatings are enabled through the use of sophisticated instruments and technologies that demand expertise and huge initial and running costs. Nano-thin films are yet a furtherance of thin films which require more expertise and much more sophistication. In this work for the first time we present a one-pot straightforward carbon thin film coating methodology for glass substrates. There is novelty in every single aspect of the method, with the carbon used in the nanofilm being obtained from turmeric soot, the coating technique consisting of a basic immersion technique, a dip-dry method, in combination with the phytosoot-derived carbon's inherent ability to self-assemble to form a uniform and continuous stable coating. The carbon nanofilm has been characterized using field emission scanning electron microscopy (FESEM), Energy Dispersive X-ray (EDAX) analysis, a goniometer and X-ray diffraction (XRD). This study for the first time opens a new school of thought of using such naturally available free nanomaterials as eco-friendly green coatings. The amorphous porous carbon film can be coated on any hydrophilic substrate and is not substrate specific. Its added advantages of being transparent and antibacterial in spite of being green and parsimonious are meant to realize its utility as ideal choices for solar panels, medical implants and other construction applications.
Diodato, Nazzareno; Borrelli, Pasquale; Fiener, Peter; Bellocchi, Gianni; Romano, Nunzio
2017-01-01
An in-depth analysis of the interannual variability of storms is required to detect changes in soil erosive power of rainfall, which can also result in severe on-site and off-site damages. Evaluating long-term rainfall erosivity is a challenging task, mainly because of the paucity of high-resolution historical precipitation observations that are generally reported at coarser temporal resolutions (e.g., monthly to annual totals). In this paper we suggest overcoming this limitation through an analysis of long-term processes governing rainfall erosivity with an application to datasets available the central Ruhr region (Western Germany) for the period 1701-2011. Based on a parsimonious interpretation of seasonal rainfall-related processes (from spring to autumn), a model was derived using 5-min erosivity data from 10 stations covering the period 1937-2002, and then used to reconstruct a long series of annual rainfall erosivity values. Change-points in the evolution of rainfall erosivity are revealed over the 1760s and the 1920s that mark three sub-periods characterized by increasing mean values. The results indicate that the erosive hazard tends to increase as a consequence of an increased frequency of extreme precipitation events occurred during the last decades, characterized by short-rain events regrouped into prolonged wet spells.
A data parsimonious model for capturing snapshots of groundwater pollution sources
Chaubey, Jyoti; Kashyap, Deepak
2017-02-01
Presented herein is a data parsimonious model for identification of regional and local groundwater pollution sources at a reference time employing corresponding fields of head, concentration and its time derivative. The regional source flux, assumed to be uniformly distributed, is viewed as the causative factor for the widely prevalent background concentration. The localized concentration-excesses are attributed to flux from local sources distributed around the respective centroids. The groundwater pollution is parameterized by flux from regional and local sources, and distribution parameters of the latter. These parameters are estimated by minimizing the sum of squares of differences between the observed and simulated concentration fields. The concentration field is simulated by a numerical solution of the transient solute transport equation. The equation is solved assuming the temporal derivative term to be known a priori and merging it with the sink term. This strategy circumvents the requirement of dynamic concentration data. The head field is generated using discrete point head data employing a specially devised interpolator that controls the numerical-differentiation errors and simultaneously ensures micro-level mass balance. This measure eliminates the requirement of flow modeling without compromising the sanctity of head field. The model after due verification has been illustrated employing available and simulated data from an area lying between two rivers Yamuna and Krishni in India.
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.
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
Rota, Emilia; Martin, Patrick; Erséus, Christer
2001-01-01
To re-evaluate the various hypotheses on the systematic position of Parergodrilus heideri Reisinger, 1925 and Hrabeiella periglandulata Pizl & Chalupský, 1984, the sole truly terrestrial non-clitellate annelids known to date, their phylogenetic relationships were investigated using a data set of new
Rota, Emilia; Martin, Patrick; Erséus, Christer
2001-01-01
To re-evaluate the various hypotheses on the systematic position of Parergodrilus heideri Reisinger, 1925 and Hrabeiella periglandulata Pizl & Chalupský, 1984, the sole truly terrestrial non-clitellate annelids known to date, their phylogenetic relationships were investigated using a data set of new
A comparison of phylogenetic network methods using computer simulation.
Steven M Woolley
Full Text Available BACKGROUND: We present a series of simulation studies that explore the relative performance of several phylogenetic network approaches (statistical parsimony, split decomposition, union of maximum parsimony trees, neighbor-net, simulated history recombination upper bound, median-joining, reduced median joining and minimum spanning network compared to standard tree approaches, (neighbor-joining and maximum parsimony in the presence and absence of recombination. PRINCIPAL FINDINGS: In the absence of recombination, all methods recovered the correct topology and branch lengths nearly all of the time when the substitution rate was low, except for minimum spanning networks, which did considerably worse. At a higher substitution rate, maximum parsimony and union of maximum parsimony trees were the most accurate. With recombination, the ability to infer the correct topology was halved for all methods and no method could accurately estimate branch lengths. CONCLUSIONS: Our results highlight the need for more accurate phylogenetic network methods and the importance of detecting and accounting for recombination in phylogenetic studies. Furthermore, we provide useful information for choosing a network algorithm and a framework in which to evaluate improvements to existing methods and novel algorithms developed in the future.
Fossils impact as hard as living taxa in parsimony analyses of morphology.
Cobbett, Andrea; Wilkinson, Mark; Wills, Matthew A
2007-10-01
Systematists disagree whether data from fossils should be included in parsimony analyses. In a handful of well-documented cases, the addition of fossil data radically overturns a hypothesis of relationships based on extant taxa alone. Fossils can break up long branches and preserve character combinations closer in time to deep splitting events. However, fossils usually require more interpretation than extant taxa, introducing greater potential for spurious codings. Moreover, because fossils often have more "missing" codings, they are frequently accused of increasing numbers of MPTs, frustrating resolution and reducing support. Despite the controversy, remarkably little is known about the effects of fossils more generally. Here we provide the first systematic study, investigating empirically the behavior of fossil and extant taxa in 45 published morphological data sets. First-order jackknifing is used to determine the effects that each terminal has on inferred relationships, on the number of MPTs, and on CI' and RI as measures of homoplasy. Bootstrap leaf stabilities provide a proxy for the contribution of individual taxa to the branch support in the rest of the tree. There is no significant difference in the impact of fossil versus extant taxa on relationships, numbers of MPTs, and CI' or RI. However, adding individual fossil taxa is more likely to reduce the total branch support of the tree than adding extant taxa. This must be weighed against the superior taxon sampling afforded by including judiciously coded fossils, providing data from otherwise unsampled regions of the tree. We therefore recommend that investigators should include fossils, in the absence of compelling and case specific reasons for their exclusion.
Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles.
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
Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles.
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 provides a
Douglas D Gaffin
Full Text Available The navigation of bees and ants from hive to food and back has captivated people for more than a century. Recently, the Navigation by Scene Familiarity Hypothesis (NSFH has been proposed as a parsimonious approach that is congruent with the limited neural elements of these insects' brains. In the NSFH approach, an agent completes an initial training excursion, storing images along the way. To retrace the path, the agent scans the area and compares the current scenes to those previously experienced. By turning and moving to minimize the pixel-by-pixel differences between encountered and stored scenes, the agent is guided along the path without having memorized the sequence. An important premise of the NSFH is that the visual information of the environment is adequate to guide navigation without aliasing. Here we demonstrate that an image landscape of an indoor setting possesses ample navigational information. We produced a visual landscape of our laboratory and part of the adjoining corridor consisting of 2816 panoramic snapshots arranged in a grid at 12.7-cm centers. We show that pixel-by-pixel comparisons of these images yield robust translational and rotational visual information. We also produced a simple algorithm that tracks previously experienced routes within our lab based on an insect-inspired scene familiarity approach and demonstrate that adequate visual information exists for an agent to retrace complex training routes, including those where the path's end is not visible from its origin. We used this landscape to systematically test the interplay of sensor morphology, angles of inspection, and similarity threshold with the recapitulation performance of the agent. Finally, we compared the relative information content and chance of aliasing within our visually rich laboratory landscape to scenes acquired from indoor corridors with more repetitive scenery.
Gaffin, Douglas D; Brayfield, Brad P
2016-01-01
The navigation of bees and ants from hive to food and back has captivated people for more than a century. Recently, the Navigation by Scene Familiarity Hypothesis (NSFH) has been proposed as a parsimonious approach that is congruent with the limited neural elements of these insects' brains. In the NSFH approach, an agent completes an initial training excursion, storing images along the way. To retrace the path, the agent scans the area and compares the current scenes to those previously experienced. By turning and moving to minimize the pixel-by-pixel differences between encountered and stored scenes, the agent is guided along the path without having memorized the sequence. An important premise of the NSFH is that the visual information of the environment is adequate to guide navigation without aliasing. Here we demonstrate that an image landscape of an indoor setting possesses ample navigational information. We produced a visual landscape of our laboratory and part of the adjoining corridor consisting of 2816 panoramic snapshots arranged in a grid at 12.7-cm centers. We show that pixel-by-pixel comparisons of these images yield robust translational and rotational visual information. We also produced a simple algorithm that tracks previously experienced routes within our lab based on an insect-inspired scene familiarity approach and demonstrate that adequate visual information exists for an agent to retrace complex training routes, including those where the path's end is not visible from its origin. We used this landscape to systematically test the interplay of sensor morphology, angles of inspection, and similarity threshold with the recapitulation performance of the agent. Finally, we compared the relative information content and chance of aliasing within our visually rich laboratory landscape to scenes acquired from indoor corridors with more repetitive scenery.
Maximum Autocorrelation Factorial Kriging
Nielsen, Allan Aasbjerg; Conradsen, Knut; Pedersen, John L.; Steenfelt, Agnete
2000-01-01
This paper describes maximum autocorrelation factor (MAF) analysis, maximum autocorrelation factorial kriging, and its application to irregularly sampled stream sediment geochemical data from South Greenland. Kriged MAF images are compared with kriged images of varimax rotated factors from an ordinary non-spatial factor analysis, and they are interpreted in a geological context. It is demonstrated that MAF analysis contrary to ordinary non-spatial factor analysis gives an objective discrimina...
First molecular evidence for the existence of a Tardigrada + Arthropoda clade.
Giribet, G; Carranza, S; Baguñà, J; Riutort, M; Ribera, C
1996-01-01
The complete 18S rDNA gene sequence of Macrobiotus group hufelandi (Tardigrada) was obtained and aligned with 18S rDNA and rRNA gene sequences of 24 metazoans (mainly protostomes). Discrete character (maximum-parsimony) and distance (neighbor-joining) methods were used to infer their phylogeny. The evolution of bootstrap proportions with sequence length (pattern of resolved nodes, PRN) was studied to test the resolution of the nodes in neighbor-joining trees. The results show that arthropods are monophyletic. Tardigrades represent the sister group of arthropods (in parsimony analyses) or they are related with crustaceans (distance analysis and PRN). Arthropoda are divided into two main evolutionary lines, the Hexapoda + Crustacea line (weakly supported), and the Myriapoda + Chelicerata line. The Hexapoda + Crustacea line includes Pentastomida, but the internal resolution is far from clear. The Insecta (Ectognatha) are monophyletic, but no evidence for the monophyly of Hexapoda is found. The Chelicerata are a monophyletic group and the Myriapoda cluster close to Arachnida. Overall, the results obtained represent the first molecular evidence for a Tardigrada + Arthropoda clade. In addition, the congruence between molecular phylogenies of the Arthropoda from other authors and this obtained here indicates the need to review those obtained solely on morphological characters.
Predicting in ungauged basins using a parsimonious rainfall-runoff model
Skaugen, Thomas; Olav Peerebom, Ivar; Nilsson, Anna
2015-04-01
Prediction in ungauged basins is a demanding, but necessary test for hydrological model structures. Ideally, the relationship between model parameters and catchment characteristics (CC) should be hydrologically justifiable. Many studies, however, report on failure to obtain significant correlations between model parameters and CCs. Under the hypothesis that the lack of correlations stems from non-identifiability of model parameters caused by overparameterization, the relatively new parameter parsimonious DDD (Distance Distribution Dynamics) model was tested for predictions in ungauged basins in Norway. In DDD, the capacity of the subsurface water reservoir M is the only parameter to be calibrated whereas the runoff dynamics is completely parameterised from observed characteristics derived from GIS and runoff recession analysis. Water is conveyed through the soils to the river network by waves with celerities determined by the level of saturation in the catchment. The distributions of distances between points in the catchment to the nearest river reach and of the river network give, together with the celerities, distributions of travel times, and, consequently unit hydrographs. DDD has 6 parameters less to calibrate in the runoff module than, for example, the well-known Swedish HBV model. In this study, multiple regression equations relating CCs and model parameters were trained from 84 calibrated catchments located all over Norway and all model parameters showed significant correlations with catchment characteristics. The significant correlation coefficients (with p- value < 0.05) ranged from 0.22-0.55. The suitability of DDD for predictions in ungauged basins was tested for 17 catchments not used to estimate the multiple regression equations. For 10 of the 17 catchments, deviations in Nash-Suthcliffe Efficiency (NSE) criteria between the calibrated and regionalised model were less than 0.1. The median NSE for the regionalised DDD for the 17 catchments, for two
Urban micro-scale flood risk estimation with parsimonious hydraulic modelling and census data
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
A search for model parsimony in a real time flood forecasting system
Grossi, G.; Balistrocchi, M.
2009-04-01
As regards the hydrological simulation of flood events, a physically based distributed approach is the most appealing one, especially in those areas where the spatial variability of the soil hydraulic properties as well as of the meteorological forcing cannot be left apart, such as in mountainous regions. On the other hand, dealing with real time flood forecasting systems, less detailed models requiring a minor number of parameters may be more convenient, reducing both the computational costs and the calibration uncertainty. In fact in this case a precise quantification of the entire hydrograph pattern is not necessary, while the expected output of a real time flood forecasting system is just an estimate of the peak discharge, the time to peak and in some cases the flood volume. In this perspective a parsimonious model has to be found in order to increase the efficiency of the system. A suitable case study was identified in the northern Apennines: the Taro river is a right tributary to the Po river and drains about 2000 km2 of mountains, hills and floodplain, equally distributed . The hydrometeorological monitoring of this medium sized watershed is managed by ARPA Emilia Romagna through a dense network of uptodate gauges (about 30 rain gauges and 10 hydrometers). Detailed maps of the surface elevation, land use and soil texture characteristics are also available. Five flood events were recorded by the new monitoring network in the years 2003-2007: during these events the peak discharge was higher than 1000 m3/s, which is actually quite a high value when compared to the mean discharge rate of about 30 m3/s. The rainfall spatial patterns of such storms were analyzed in previous works by means of geostatistical tools and a typical semivariogram was defined, with the aim of establishing a typical storm structure leading to flood events in the Taro river. The available information was implemented into a distributed flood event model with a spatial resolution of 90m
Salas-Leiva, Dayana E; Meerow, Alan W; Calonje, Michael; Griffith, M Patrick; Francisco-Ortega, Javier; Nakamura, Kyoko; Stevenson, Dennis W; Lewis, Carl E; Namoff, Sandra
2013-01-01
.... The specific aim is to evaluate several gene tree-species tree reconciliation approaches for developing an accurate phylogeny of the order, to contrast them with concatenated parsimony analysis...
Maximum likely scale estimation
Loog, Marco; Pedersen, Kim Steenstrup; Markussen, Bo
2005-01-01
A maximum likelihood local scale estimation principle is presented. An actual implementation of the estimation principle uses second order moments of multiple measurements at a fixed location in the image. These measurements consist of Gaussian derivatives possibly taken at several scales and/or ...
Maximum information photoelectron metrology
Hockett, P; Wollenhaupt, M; Baumert, T
2015-01-01
Photoelectron interferograms, manifested in photoelectron angular distributions (PADs), are a high-information, coherent observable. In order to obtain the maximum information from angle-resolved photoionization experiments it is desirable to record the full, 3D, photoelectron momentum distribution. Here we apply tomographic reconstruction techniques to obtain such 3D distributions from multiphoton ionization of potassium atoms, and fully analyse the energy and angular content of the 3D data. The PADs obtained as a function of energy indicate good agreement with previous 2D data and detailed analysis [Hockett et. al., Phys. Rev. Lett. 112, 223001 (2014)] over the main spectral features, but also indicate unexpected symmetry-breaking in certain regions of momentum space, thus revealing additional continuum interferences which cannot otherwise be observed. These observations reflect the presence of additional ionization pathways and, most generally, illustrate the power of maximum information measurements of th...
Maximum Likelihood Associative Memories
Gripon, Vincent; Rabbat, Michael
2013-01-01
Associative memories are structures that store data in such a way that it can later be retrieved given only a part of its content -- a sort-of error/erasure-resilience property. They are used in applications ranging from caches and memory management in CPUs to database engines. In this work we study associative memories built on the maximum likelihood principle. We derive minimum residual error rates when the data stored comes from a uniform binary source. Second, we determine the minimum amo...
Maximum likely scale estimation
Loog, Marco; Pedersen, Kim Steenstrup; Markussen, Bo
2005-01-01
A maximum likelihood local scale estimation principle is presented. An actual implementation of the estimation principle uses second order moments of multiple measurements at a fixed location in the image. These measurements consist of Gaussian derivatives possibly taken at several scales and....../or having different derivative orders. Although the principle is applicable to a wide variety of image models, the main focus here is on the Brownian model and its use for scale selection in natural images. Furthermore, in the examples provided, the simplifying assumption is made that the behavior...... of the measurements is completely characterized by all moments up to second order....
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.
F. TopsÃƒÂ¸e
2001-09-01
Full Text Available Abstract: In its modern formulation, the Maximum Entropy Principle was promoted by E.T. Jaynes, starting in the mid-fifties. The principle dictates that one should look for a distribution, consistent with available information, which maximizes the entropy. However, this principle focuses only on distributions and it appears advantageous to bring information theoretical thinking more prominently into play by also focusing on the "observer" and on coding. This view was brought forward by the second named author in the late seventies and is the view we will follow-up on here. It leads to the consideration of a certain game, the Code Length Game and, via standard game theoretical thinking, to a principle of Game Theoretical Equilibrium. This principle is more basic than the Maximum Entropy Principle in the sense that the search for one type of optimal strategies in the Code Length Game translates directly into the search for distributions with maximum entropy. In the present paper we offer a self-contained and comprehensive treatment of fundamentals of both principles mentioned, based on a study of the Code Length Game. Though new concepts and results are presented, the reading should be instructional and accessible to a rather wide audience, at least if certain mathematical details are left aside at a rst reading. The most frequently studied instance of entropy maximization pertains to the Mean Energy Model which involves a moment constraint related to a given function, here taken to represent "energy". This type of application is very well known from the literature with hundreds of applications pertaining to several different elds and will also here serve as important illustration of the theory. But our approach reaches further, especially regarding the study of continuity properties of the entropy function, and this leads to new results which allow a discussion of models with so-called entropy loss. These results have tempted us to speculate over
Regularized maximum correntropy machine
Wang, Jim Jing-Yan
2015-02-12
In this paper we investigate the usage of regularized correntropy framework for learning of classifiers from noisy labels. The class label predictors learned by minimizing transitional loss functions are sensitive to the noisy and outlying labels of training samples, because the transitional loss functions are equally applied to all the samples. To solve this problem, we propose to learn the class label predictors by maximizing the correntropy between the predicted labels and the true labels of the training samples, under the regularized Maximum Correntropy Criteria (MCC) framework. Moreover, we regularize the predictor parameter to control the complexity of the predictor. The learning problem is formulated by an objective function considering the parameter regularization and MCC simultaneously. By optimizing the objective function alternately, we develop a novel predictor learning algorithm. The experiments on two challenging pattern classification tasks show that it significantly outperforms the machines with transitional loss functions.
Casewell, Nicholas R; Wagstaff, Simon C; Harrison, Robert A; Wüster, Wolfgang
2011-03-01
The proliferation of gene data from multiple loci of large multigene families has been greatly facilitated by considerable recent advances in sequence generation. The evolution of such gene families, which often undergo complex histories and different rates of change, combined with increases in sequence data, pose complex problems for traditional phylogenetic analyses, and in particular, those that aim to successfully recover species relationships from gene trees. Here, we implement gene tree parsimony analyses on multicopy gene family data sets of snake venom proteins for two separate groups of taxa, incorporating Bayesian posterior distributions as a rigorous strategy to account for the uncertainty present in gene trees. Gene tree parsimony largely failed to infer species trees congruent with each other or with species phylogenies derived from mitochondrial and single-copy nuclear sequences. Analysis of four toxin gene families from a large expressed sequence tag data set from the viper genus Echis failed to produce a consistent topology, and reanalysis of a previously published gene tree parsimony data set, from the family Elapidae, suggested that species tree topologies were predominantly unsupported. We suggest that gene tree parsimony failure in the family Elapidae is likely the result of unequal and/or incomplete sampling of paralogous genes and demonstrate that multiple parallel gene losses are likely responsible for the significant species tree conflict observed in the genus Echis. These results highlight the potential for gene tree parsimony analyses to be undermined by rapidly evolving multilocus gene families under strong natural selection.
Equalized near maximum likelihood detector
2012-01-01
This paper presents new detector that is used to mitigate intersymbol interference introduced by bandlimited channels. This detector is named equalized near maximum likelihood detector which combines nonlinear equalizer and near maximum likelihood detector. Simulation results show that the performance of equalized near maximum likelihood detector is better than the performance of nonlinear equalizer but worse than near maximum likelihood detector.
Cheeseman, Peter; Stutz, John
2005-01-01
A long standing mystery in using Maximum Entropy (MaxEnt) is how to deal with constraints whose values are uncertain. This situation arises when constraint values are estimated from data, because of finite sample sizes. One approach to this problem, advocated by E.T. Jaynes [1], is to ignore this uncertainty, and treat the empirically observed values as exact. We refer to this as the classic MaxEnt approach. Classic MaxEnt gives point probabilities (subject to the given constraints), rather than probability densities. We develop an alternative approach that assumes that the uncertain constraint values are represented by a probability density {e.g: a Gaussian), and this uncertainty yields a MaxEnt posterior probability density. That is, the classic MaxEnt point probabilities are regarded as a multidimensional function of the given constraint values, and uncertainty on these values is transmitted through the MaxEnt function to give uncertainty over the MaXEnt probabilities. We illustrate this approach by explicitly calculating the generalized MaxEnt density for a simple but common case, then show how this can be extended numerically to the general case. This paper expands the generalized MaxEnt concept introduced in a previous paper [3].
Carlos Alberto Gonçalves
2013-09-01
Full Text Available This work aims to presents the settings and the degree of intensity on the Organizational Performance based on significant antecedents in two sectors categorized as manufacturing and service. It is present measurements of the effects and combinations set composed by Managerial Factors, External Environment, Internal Organizational efforts, Strategy Process in the Organizational Performance. The research used data collection by interview, survey research and it was made statistical analysis by of Structural Equation Modeling methods and Qualitative Comparative Analysis - ACQ. It can be seen that the construct Strategy Process is the most important in explaining Organizational Performance in relation to other reports. It was also observed that the industry and service sectors have different sets parsimonious explanation for the Organizational Performance.
Xiao-Lei Huang
2010-05-01
Full Text Available Parsimony analysis of endemicity (PAE was used to identify areas of endemism (AOEs for Chinese birds at the subregional level. Four AOEs were identified based on a distribution database of 105 endemic species and using 18 avifaunal subregions as the operating geographical units (OGUs. The four AOEs are the Qinghai-Zangnan Subregion, the Southwest Mountainous Subregion, the Hainan Subregion and the Taiwan Subregion. Cladistic analysis of subregions generally supports the division of China’s avifauna into Palaearctic and Oriental realms. Two PAE area trees were produced from two different distribution datasets (year 1976 and 2007. The 1976 topology has four distinct subregional branches; however, the 2007 topology has three distinct branches. Moreover, three Palaearctic subregions in the 1976 tree clustered together with the Oriental subregions in the 2007 tree. Such topological differences may reflect changes in the distribution of bird species through circa three decades.
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.
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
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.
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
Phylogenetic relationship of Podocopida (Ostracoda: Podocopa) based on 18S ribosomal DNA sequences
YU Na; ZHAO Meiying; CHEN Liqiao; YANG Pin
2006-01-01
Nucleotide sequences from 18S rDNA of 11 ostracodes, which represent four suborders and six superfamilies ofpodocopidan, were determined. The phylogenetic relationships were analyzed based on three kinds of methods (maximum-likelihood, maximum-parsimony,and neighbor-joining), and the three topologies gained were basically similar. The results have showed that (1) a monophyletic Podocopida was supported strongly; (2) the phylogenetic relationships of four suborders were (Darwinulocopina plus (Bairdiocopina plus (Cytherocopina plus Cypridocopina))), which indicated that a close relationship between Cytherocopina and Cypridocopina, and Darwinulocopina had separated early from the main podocopinan; (3) Cypridocopinan formed a monophyletic group, among which the phylogenetic relationship of three superfamilies was (Cypridoidea plus (Macrocypridoidea plus Pontocypridoidea)).
LI Junbing; WANG Xuzhen; HE Shunping; CHEN Yiyu
2005-01-01
The mitochondrial 16S ribosomal RNA gene is sequenced from 24 ingroups taxa, including 18 species from Labeoninae grouped in 13 genera. Phylogenetic analyses are subjected to neighbor joining, maximum parsimony, maximum likelihood and Bayesian analyses. Phylogenetic analysis indicates that Labeoninae is basically a monophyletic assemblage and can be divided into 2 major clades: one comprising the genera Cirrhinus, Crossocheilus and Garra; and the other consisting of the genera Labeo, Sinilabeo, Osteochilus, Pseudoorossocheilus, Parasinilabeo, Ptychidio, Semilabeo, Pseudogyricheilus, Rectori and Discogobio. According to our present analysis,the features such as the presence of the adhesive disc on the chin and the pharyngeal teeth in 2 rows used in the traditional taxonomy of Labeoninae provide scarce information for phylogeny of labeonine fishes.
Rimantas Rakauskas
2013-07-01
Full Text Available Forty three European population samples of mealy aphids from various winter and summer host plants were attributed to respective species of Hyalopterus by means of their partial sequences of mitochondrial COI gene. Used Hyalopterus samples emerged as monophyletic relative to outgroup and formed three major clades representing three host specific mealy aphid species in the Neighbor joining, Maximum parsimony, Maximum likelihood and Bayesian inference trees. H. pruni and H. persikonus emerged as a sister species, whilst H. amygdali was located basally. Samples representing different clades in the molecular trees were used for canonical discrimination analysis based on twenty two morphological characters. Length of the median dorsal head hair enabled a 97.3 % separation of H. amygdali from the remaining two species. No single character enabled satisfactory discrimination between apterous viviparous females of H. pruni and H. persikonus. A modified key for the morphological identification of Hyalopterus species is suggested and their taxonomic status discussed.
无
2005-01-01
A 605 bp section of mitochondrial 16S rRNA gene from Paralichthys olivaceus, Pseudorhombus cinnamomeus, Psetta maxima and Kareius bicoloratus, which represent 3 families of Order Pleuronectiformes was amplified by PCR and sequenced to show the molecular systematics of Pleuronectiformes for comparison with related gene sequences of other 6 flatfish downloaded from GenBank. Phylogenetic analysis based on genetic distance from related gene sequences of 10 flatfish showed that this method was ideal to explore the relationship between species, genera and families. Phylogenetic trees set-up is based on neighbor-joining, maximum parsimony and maximum likelihood methods that accords to the general rule of Pleuronectiformes evolution. But they also resulted in some confusion. Unlike data from morphological characters, P. olivaceus clustered with K.bicoloratus, but P. cinnamomeus did not cluster with P. olivaceus, which is worth further studying.
Rakauskas, Rimantas; Havelka, Jekaterina; Zaremba, Audrius
2013-01-01
Forty three European population samples of mealy aphids from various winter and summer host plants were attributed to respective species of Hyalopterus by means of their partial sequences of mitochondrial COI gene. Used Hyalopterus samples emerged as monophyletic relative to outgroup and formed three major clades representing three host specific mealy aphid species in the Neighbor joining, Maximum parsimony, Maximum likelihood and Bayesian inference trees. Hyalopterus pruni and Hyalopterus persikonus emerged as a sister species, whilst Hyalopterus amygdali was located basally. Samples representing different clades in the molecular trees were used for canonical discrimination analysis based on twenty two morphological characters. Length of the median dorsal head hair enabled a 97.3 % separation of Hyalopterus amygdali from the remaining two species. No single character enabled satisfactory discrimination between apterous viviparous females of Hyalopterus pruni and Hyalopterus persikonus. A modified key for the morphological identification of Hyalopterus species is suggested and their taxonomic status discussed.
Sundberg, P; Saur, M
1998-12-01
The 16S rRNA mitochondrial gene was used to reconstruct the relationships among 10 heteronemertean species (subclass Heteronemertea, phylum Nemertea); Lineus ruber and L. viridis are represented by more than one specimen to assess intraspecific variation in these enigmatic species, and the analysis includes in total 14 terminal taxa incorporating one palaeonemertean species (Tubulanus annulatus) for outgroup rooting. The aligned sequences were subjected to maximum parsimony, maximum-likelihood, and neighbor-joining analyses to estimate the phylogenetic relationship of the species. The results were concordant from all analyses and indicate that neither Lineus nor Micrura are monophyletic taxa, and that there is no support from a phylogenetic point of view to establish the monotypic genus Riseriellus. Copyright 1998 Academic Press.
Jorge Ramirez
2011-07-01
Full Text Available The genera Bostryx and Scutalus (Orthalicidae: Bulimulinae are endemics from South America. They are mainly distributed on the western slopes of the Peruvian Andes. The goal of the present work was to assess their evolutionary position among the stylommatophoran gastropods based on the 16S rRNA mitochondrial marker. Four sequences were obtained, and along with 28 sequences of other Stylommatophora retrieved from the GenBank, were aligned with ClustalX. The phylogenetic reconstruction was carried out using the methods of Neighbor-Joining, Maximum Parsimony, Maximum Likelihood and Bayesian inference. The multiple sequence alignment had 371 sites, with indels. The two genera of the family Orthalicidae for the first time included in a molecular phylogeny (Bostryx and Scutalus, formed a monophyletic group along with another member of the superfamily Orthalicoidea (Placostylus, result that is comparable with that obtained with nuclear markers. Their evolutionary relationship with other land snails is also discussed.
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.
Matthews, Luke J; Rosenberger, Alfred L
2008-11-01
The classifications of primates, in general, and platyrrhine primates, in particular, have been greatly revised subsequent to the rationale for taxonomic decisions shifting from one rooted in the biological species concept to one rooted solely in phylogenetic affiliations. Given the phylogenetic justification provided for revised taxonomies, the scientific validity of taxonomic distinctions can be rightly judged by the robusticity of the phylogenetic results supporting them. In this study, we empirically investigated taxonomic-sampling effects on a cladogram previously inferred from craniodental data for the woolly monkeys (Lagothrix). We conducted the study primarily through much greater sampling of species-level taxa (OTUs) after improving some character codings and under a variety of outgroup choices. The results indicate that alternative selections of species subsets from within genera produce various tree topologies. These results stand even after adjusting the character set and considering the potential role of interobserver disagreement. We conclude that specific taxon combinations, in this case, generic or species pairings, of the primary study group has a biasing effect in parsimony analysis, and that the cladistic rationale for resurrecting the Oreonax generic distinction for the yellow-tailed woolly monkey (Lagothrix flavicauda) is based on an artifact of idiosyncratic sampling within the study group below the genus level. Some recommendations to minimize the problem, which is prevalent in all cladistic analyses, are proposed.
Sporothrix globosa, a pathogenic fungus with widespread geographical distribution.
Madrid, Hugo; Cano, Josep; Gené, Josepa; Bonifaz, Alexandro; Toriello, Conchita; Guarro, Josep
2009-09-30
Sporothrix globosa, reported from the USA, Europe, and Asia, is a recently described pathogenic species morphologically similar to Sporothrix schenckii. In this study, the phylogenetic affinities of 32 clinical and environmental isolates morphologically identified as S. schenckii, from Mexico, Guatemala, and Colombia, were assessed by cladistic analysis of partial sequences of the calmodulin gene using the maximum parsimony and neighbor-joining methods. The study revealed that one out of 25 isolates from Mexico (4%), one out of three isolates from Guatemala (33.3%), and two out of four isolates from Colombia (50%) belonged to S. globosa, while the other isolates belonged to S. schenckii sensu stricto. This is the first record of S. globosa from Mexico, and Central and South America.
Molecular Systematics of Polygonum minus Huds. Based on ITS Sequences
Normah Mohd Noor
2011-11-01
Full Text Available Plastid trnL-trnF and nuclear ribosomal ITS sequences were obtained from selected wild-type individuals of Polygonum minus Huds. in Peninsular Malaysia. The 380 bp trnL-trnF sequences of the Polygonum minus accessions were identical. Therefore, the trnL-trnF failed to distinguish between the Polygonum minus accessions. However, the divergence of ITS sequences (650 bp among the Polygonum minus accessions was 1%, indicating that these accessions could be distinguished by the ITS sequences. A phylogenetic relationship based on the ITS sequences was inferred using neighbor-joining, maximum parsimony and Bayesian inference. All of the tree topologies indicated that Polygonum minus from Peninsular Malaysia is unique and different from the synonymous Persicaria minor (Huds. Opiz and Polygonum kawagoeanum Makino.
First larval record of Mesocestoides in carnivora of Tenerife (Canary Islands).
Foronda, Pilar; Pérez Rivero, Alfredo; Santana Morales, María A; Kabdur, Alicia; González, Ana C; Quispe Ricalde, M Antonieta; Feliu, Carlos; Valladares, Basilio
2007-02-01
Larvae of Mesocestoides sp. were recovered in Tenerife (Canary Islands) in 2004 from the peritoneal cavities of 2 domestic dogs and a domestic cat. Morphological and molecular identification were carried out. Mesocestoides litteratus from Vulpes vulpes was sequenced for the first time using the ITS-2 region (18S rDNA), and was included in the phylogenetic analysis to compare the sequence variability among these and other Mesocestoides spp. belonging to different carnivores. Phylogenetic studies were carried out based on maximum parsimony and neighbor-joining analysis. The results showed the relationships between these and other previously published Mesocestoides species. Moreover, it is demonstrated that Mesocestoides sp. from Tenerife comprises a previously unreported sequence. This is the first larval record of Mesocestoides sp. in domestic animals from Tenerife, Canary Islands, Spain.
Molecular evolution of the period gene in sandflies.
Mazzoni, C J; Gomes, C A; Souza, N A; de Queiroz, R G; Justiniano, S C B; Ward, R D; Kyriacou, C P; Peixoto, A A
2002-11-01
The molecular evolution of the clock gene period was studied in Phlebotomine sandflies (Diptera: Psychodidae). Comparison of the synonymous and nonsynonymous substitution rates between sandflies and Drosophila revealed a significantly higher evolutionary rate in the latter in three of the four regions analyzed. The differences in rate were higher in the sequences flanking the Thr-Gly repetitive domain, a region that has expanded in Drosophila but remained stable and short in sandflies, a result consistent with the coevolutionary scenario proposed for this region of the gene. An initial phylogenetic analysis including eight neotropical sandfly species and one from the Old World was also carried out. The results showed that only the subgenus Nyssomyia is well supported by distance (neighbor-joining) and maximum parsimony analysis. The grouping of the other species from the subgenus Lutzomyia and Migonei group shows very low bootstrap values and is not entirely consistent with classical morphological systematics of the genus Lutzomyia.
HAO Jiasheng; LI Chunxiang; SUN Xiaoyan; YANG Qun
2005-01-01
The mitochondrial 16S rDNA sequences of 40 species of cheilostome bryozoans including those of 24 species newly determined were used to reconstruct the phylogenetic tree using neighboring-joining and maximum-parsimony methods. By applying molecular clock technique on the basis of the appropriate phylogeny and the fossil record, the divergence times of the two main cheilostome groups, Anasca and Ascophora sensu stricto, were estimated. The results show that the molecular phylogeny of the higher taxonomic groups (superfamilies and higher taxa) of cheilostome bryozoans is mostly in conflict with the morphology-based phylogenetic trees; the divergence of the extant groups of Anasca and those of Ascophora sensu stricto is estimated to have happened about 263 Ma (Permian Guadalupian Epoch) and 183 Ma (Early Jurassic), respectively.
Cloning and sequence analysis of the partial sequence of the rbcL from Bryopsis hypnoides
无
2005-01-01
The partial sequence of the rbcL from Bryopsis hypnoides, including the sequences of the upstream, extron and partial intron, was amplified by PCR and their sequences were determined. With Spinacia oleracea as the outgroup, neighbor-joining method and maximum parsimony method were used respectively to build phylogenetic trees according to the rbcL exon sequence among 13species that were the typical species of six phyla. Two kinds of trees showed clearly that there were two groups among those species,the green lineage and the non-green lineage. And the relationships of algae in the green lineage were similar in the two trees but those in the non-green lineage were not consistent. Analysis of codon preference indicated that the codon preference of the rbcL exon of Bryopsis hypnoides distinctly differed from that of the relevant sequence of photosynthetic bacteria.
Schminkey, Donna L; von Oertzen, Timo; Bullock, Linda
2016-08-01
With increasing access to population-based data and electronic health records for secondary analysis, missing data are common. In the social and behavioral sciences, missing data frequently are handled with multiple imputation methods or full information maximum likelihood (FIML) techniques, but healthcare researchers have not embraced these methodologies to the same extent and more often use either traditional imputation techniques or complete case analysis, which can compromise power and introduce unintended bias. This article is a review of options for handling missing data, concluding with a case study demonstrating the utility of multilevel structural equation modeling using full information maximum likelihood (MSEM with FIML) to handle large amounts of missing data. MSEM with FIML is a parsimonious and hypothesis-driven strategy to cope with large amounts of missing data without compromising power or introducing bias. This technique is relevant for nurse researchers faced with ever-increasing amounts of electronic data and decreasing research budgets. © 2016 Wiley Periodicals, Inc.
Meij, E.; Trieschnigg, D.; Rijke, M.de; Kraaij, W.
2008-01-01
In many collections, documents are annotated using concepts from a structured knowledge source such as an ontology or thesaurus. Examples include the news domain [7], where each news item is categorized according to the nature of the event that took place, and Wikipedia, with its per-article categor
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.
Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment?
Hartmann Stefanie
2008-03-01
Full Text Available Abstract Background While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood and studied ways to improve the accuracy of trees obtained from such datasets. Results We found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25% to 40% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences. Conclusion These results demonstrate that partial gene
OECD Maximum Residue Limit Calculator
With the goal of harmonizing the calculation of maximum residue limits (MRLs) across the Organisation for Economic Cooperation and Development, the OECD has developed an MRL Calculator. View the calculator.
Baumeister, Dorothea
2007-01-01
Holzer and Holzer (Discrete Applied Mathematics 144(3):345--358, 2004) proved the Tantrix(TM) rotation puzzle problem with four colors NP-complete. Baumeister and Rothe (MCU 2007) modified their construction to achieve a parsimonious reduction from satisfiability to this problem. Since parsimonious reductions preserve the number of solutions, it follows that the unique version of the four-color Tantrix(TM) rotation puzzle problem is DP-complete under randomized reductions. In this paper, we study the three-color and the two-color Tantrix(TM) rotation puzzle problem. Restricting the number of allowed colors to three (respectively, to two) reduces the set of available Tantrix(TM) tiles from 56 to 14 (respectively, to 8). We prove that both the three-color and the two-color Tantrix(TM) rotation puzzle problem is NP-complete, which answers a question raised by Holzer and Holzer in the affirmative. Since both these reductions are parsimonious, it follows that both the unique three-color and the unique two-color Ta...
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
Maximum margin Bayesian network classifiers.
Pernkopf, Franz; Wohlmayr, Michael; Tschiatschek, Sebastian
2012-03-01
We present a maximum margin parameter learning algorithm for Bayesian network classifiers using a conjugate gradient (CG) method for optimization. In contrast to previous approaches, we maintain the normalization constraints on the parameters of the Bayesian network during optimization, i.e., the probabilistic interpretation of the model is not lost. This enables us to handle missing features in discriminatively optimized Bayesian networks. In experiments, we compare the classification performance of maximum margin parameter learning to conditional likelihood and maximum likelihood learning approaches. Discriminative parameter learning significantly outperforms generative maximum likelihood estimation for naive Bayes and tree augmented naive Bayes structures on all considered data sets. Furthermore, maximizing the margin dominates the conditional likelihood approach in terms of classification performance in most cases. We provide results for a recently proposed maximum margin optimization approach based on convex relaxation. While the classification results are highly similar, our CG-based optimization is computationally up to orders of magnitude faster. Margin-optimized Bayesian network classifiers achieve classification performance comparable to support vector machines (SVMs) using fewer parameters. Moreover, we show that unanticipated missing feature values during classification can be easily processed by discriminatively optimized Bayesian network classifiers, a case where discriminative classifiers usually require mechanisms to complete unknown feature values in the data first.
Maximum Entropy in Drug Discovery
Chih-Yuan Tseng
2014-07-01
Full Text Available Drug discovery applies multidisciplinary approaches either experimentally, computationally or both ways to identify lead compounds to treat various diseases. While conventional approaches have yielded many US Food and Drug Administration (FDA-approved drugs, researchers continue investigating and designing better approaches to increase the success rate in the discovery process. In this article, we provide an overview of the current strategies and point out where and how the method of maximum entropy has been introduced in this area. The maximum entropy principle has its root in thermodynamics, yet since Jaynes’ pioneering work in the 1950s, the maximum entropy principle has not only been used as a physics law, but also as a reasoning tool that allows us to process information in hand with the least bias. Its applicability in various disciplines has been abundantly demonstrated. We give several examples of applications of maximum entropy in different stages of drug discovery. Finally, we discuss a promising new direction in drug discovery that is likely to hinge on the ways of utilizing maximum entropy.
Skaugen, Thomas; Haddeland, Ingjerd
2014-05-01
A new parameter-parsimonious rainfall-runoff model, DDD (Distance Distribution Dynamics) has been run operationally at the Norwegian Flood Forecasting Service for approximately a year. DDD has been calibrated for, altogether, 104 catchments throughout Norway, and provide runoff forecasts 8 days ahead on a daily temporal resolution driven by precipitation and temperature from the meteorological forecast models AROME (48 hrs) and EC (192 hrs). The current version of DDD differs from the standard model used for flood forecasting in Norway, the HBV model, in its description of the subsurface and runoff dynamics. In DDD, the capacity of the subsurface water reservoir M, is the only parameter to be calibrated whereas the runoff dynamics is completely parameterised from observed characteristics derived from GIS and runoff recession analysis. Water is conveyed through the soils to the river network by waves with celerities determined by the level of saturation in the catchment. The distributions of distances between points in the catchment to the nearest river reach and of the river network give, together with the celerities, distributions of travel times, and, consequently unit hydrographs. DDD has 6 parameters less to calibrate in the runoff module than the HBV model. Experiences using DDD show that especially the timing of flood peaks has improved considerably and in a comparison between DDD and HBV, when assessing timeseries of 64 years for 75 catchments, DDD had a higher hit rate and a lower false alarm rate than HBV. For flood peaks higher than the mean annual flood the median hit rate is 0.45 and 0.41 for the DDD and HBV models respectively. Corresponding number for the false alarm rate is 0.62 and 0.75 For floods over the five year return interval, the median hit rate is 0.29 and 0.28 for the DDD and HBV models, respectively with false alarm rates equal to 0.67 and 0.80. During 2014 the Norwegian flood forecasting service will run DDD operationally at a 3h temporal
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 (R^{2} > 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
The molecular phylogenetic signature of Bali cattle revealed by maternal and paternal markers.
Syed-Shabthar, S M F; Rosli, M K A; Mohd-Zin, N A A; Romaino, S M N; Fazly-Ann, Z A; Mahani, M C; Abas-Mazni, O; Zainuddin, R; Yaakop, S; Md-Zain, B M
2013-08-01
Bali cattle is a domestic cattle breed that can be found in Malaysia. It is a domestic cattle that was purely derived from a domestication event in Banteng (Bos javanicus) around 3,500 BC in Indonesia. This research was conducted to portray the phylogenetic relationships of the Bali cattle with other cattle species in Malaysia based on maternal and paternal lineage. We analyzed the cytochrome c oxidase I (COI) mitochondrial gene and SRY of Y chromosome obtained from five species of the Bos genus (B. javanicus, Bos gaurus, Bos indicus, Bos taurus, and Bos grunniens). The water buffalo (Bubalus bubalis) was used as an outgroup. The phylogenetic relationships were observed by employing several algorithms: Neighbor-Joining (PAUP version 4.0), Maximum parsimony (PAUP version 4.0) and Bayesian inference (MrBayes 3.1). Results from the maternal data showed that the Bali cattle formed a monophyletic clade, and together with the B. gaurus clade formed a wild cattle clade. Results were supported by high bootstrap and posterior probability values together with genetic distance data. For the paternal lineage, the sequence variation is low (with parsimony informative characters: 2/660) resulting an unresolved Neighbor-Joining tree. However, Bali cattle and other domestic cattle appear in two monophyletic clades distinct from yak, gaur and selembu. This study expresses the potential of the COI gene in portraying the phylogenetic relationships between several Bos species which is important for conservation efforts especially in decision making since cattle is highly bred and hybrid breeds are often formed. Genetic conservation for this high quality beef cattle breed is important by maintaining its genetic characters to prevent extinction or even decreased the genetic quality.
Greenslade, Thomas B., Jr.
1985-01-01
Discusses a series of experiments performed by Thomas Hope in 1805 which show the temperature at which water has its maximum density. Early data cast into a modern form as well as guidelines and recent data collected from the author provide background for duplicating Hope's experiments in the classroom. (JN)
Abolishing the maximum tension principle
Dabrowski, Mariusz P
2015-01-01
We find the series of example theories for which the relativistic limit of maximum tension $F_{max} = c^2/4G$ represented by the entropic force can be abolished. Among them the varying constants theories, some generalized entropy models applied both for cosmological and black hole horizons as well as some generalized uncertainty principle models.
Abolishing the maximum tension principle
Mariusz P. Da̧browski
2015-09-01
Full Text Available We find the series of example theories for which the relativistic limit of maximum tension Fmax=c4/4G represented by the entropic force can be abolished. Among them the varying constants theories, some generalized entropy models applied both for cosmological and black hole horizons as well as some generalized uncertainty principle models.
Maximum Genus of Strong Embeddings
Er-ling Wei; Yan-pei Liu; Han Ren
2003-01-01
The strong embedding conjecture states that any 2-connected graph has a strong embedding on some surface. It implies the circuit double cover conjecture: Any 2-connected graph has a circuit double cover.Conversely, it is not true. But for a 3-regular graph, the two conjectures are equivalent. In this paper, a characterization of graphs having a strong embedding with exactly 3 faces, which is the strong embedding of maximum genus, is given. In addition, some graphs with the property are provided. More generally, an upper bound of the maximum genus of strong embeddings of a graph is presented too. Lastly, it is shown that the interpolation theorem is true to planar Halin graph.
Remizov, Ivan D
2009-01-01
In this note, we represent a subdifferential of a maximum functional defined on the space of all real-valued continuous functions on a given metric compact set. For a given argument, $f$ it coincides with the set of all probability measures on the set of points maximizing $f$ on the initial compact set. This complete characterization lies in the heart of several important identities in microeconomics, such as Roy's identity, Sheppard's lemma, as well as duality theory in production and linear programming.
The Testability of Maximum Magnitude
Clements, R.; Schorlemmer, D.; Gonzalez, A.; Zoeller, G.; Schneider, M.
2012-12-01
Recent disasters caused by earthquakes of unexpectedly large magnitude (such as Tohoku) illustrate the need for reliable assessments of the seismic hazard. Estimates of the maximum possible magnitude M at a given fault or in a particular zone are essential parameters in probabilistic seismic hazard assessment (PSHA), but their accuracy remains untested. In this study, we discuss the testability of long-term and short-term M estimates and the limitations that arise from testing such rare events. Of considerable importance is whether or not those limitations imply a lack of testability of a useful maximum magnitude estimate, and whether this should have any influence on current PSHA methodology. We use a simple extreme value theory approach to derive a probability distribution for the expected maximum magnitude in a future time interval, and we perform a sensitivity analysis on this distribution to determine if there is a reasonable avenue available for testing M estimates as they are commonly reported today: devoid of an appropriate probability distribution of their own and estimated only for infinite time (or relatively large untestable periods). Our results imply that any attempt at testing such estimates is futile, and that the distribution is highly sensitive to M estimates only under certain optimal conditions that are rarely observed in practice. In the future we suggest that PSHA modelers be brutally honest about the uncertainty of M estimates, or must find a way to decrease its influence on the estimated hazard.
Alternative Multiview Maximum Entropy Discrimination.
Chao, Guoqing; Sun, Shiliang
2016-07-01
Maximum entropy discrimination (MED) is a general framework for discriminative estimation based on maximum entropy and maximum margin principles, and can produce hard-margin support vector machines under some assumptions. Recently, the multiview version of MED multiview MED (MVMED) was proposed. In this paper, we try to explore a more natural MVMED framework by assuming two separate distributions p1( Θ1) over the first-view classifier parameter Θ1 and p2( Θ2) over the second-view classifier parameter Θ2 . We name the new MVMED framework as alternative MVMED (AMVMED), which enforces the posteriors of two view margins to be equal. The proposed AMVMED is more flexible than the existing MVMED, because compared with MVMED, which optimizes one relative entropy, AMVMED assigns one relative entropy term to each of the two views, thus incorporating a tradeoff between the two views. We give the detailed solving procedure, which can be divided into two steps. The first step is solving our optimization problem without considering the equal margin posteriors from two views, and then, in the second step, we consider the equal posteriors. Experimental results on multiple real-world data sets verify the effectiveness of the AMVMED, and comparisons with MVMED are also reported.
Cacti with maximum Kirchhoff index
Wang, Wen-Rui; Pan, Xiang-Feng
2015-01-01
The concept of resistance distance was first proposed by Klein and Randi\\'c. The Kirchhoff index $Kf(G)$ of a graph $G$ is the sum of resistance distance between all pairs of vertices in $G$. A connected graph $G$ is called a cactus if each block of $G$ is either an edge or a cycle. Let $Cat(n;t)$ be the set of connected cacti possessing $n$ vertices and $t$ cycles, where $0\\leq t \\leq \\lfloor\\frac{n-1}{2}\\rfloor$. In this paper, the maximum kirchhoff index of cacti are characterized, as well...
Generic maximum likely scale selection
Pedersen, Kim Steenstrup; Loog, Marco; Markussen, Bo
2007-01-01
The fundamental problem of local scale selection is addressed by means of a novel principle, which is based on maximum likelihood estimation. The principle is generally applicable to a broad variety of image models and descriptors, and provides a generic scale estimation methodology. The focus...... on second order moments of multiple measurements outputs at a fixed location. These measurements, which reflect local image structure, consist in the cases considered here of Gaussian derivatives taken at several scales and/or having different derivative orders....
Economics and Maximum Entropy Production
Lorenz, R. D.
2003-04-01
Price differentials, sales volume and profit can be seen as analogues of temperature difference, heat flow and work or entropy production in the climate system. One aspect in which economic systems exhibit more clarity than the climate is that the empirical and/or statistical mechanical tendency for systems to seek a maximum in production is very evident in economics, in that the profit motive is very clear. Noting the common link between 1/f noise, power laws and Self-Organized Criticality with Maximum Entropy Production, the power law fluctuations in security and commodity prices is not inconsistent with the analogy. There is an additional thermodynamic analogy, in that scarcity is valued. A commodity concentrated among a few traders is valued highly by the many who do not have it. The market therefore encourages via prices the spreading of those goods among a wider group, just as heat tends to diffuse, increasing entropy. I explore some empirical price-volume relationships of metals and meteorites in this context.
Objects of maximum electromagnetic chirality
Fernandez-Corbaton, Ivan
2015-01-01
We introduce a definition of the electromagnetic chirality of an object and show that it has an upper bound. The upper bound is attained if and only if the object is transparent for fields of one handedness (helicity). Additionally, electromagnetic duality symmetry, i.e. helicity preservation upon scattering, turns out to be a necessary condition for reciprocal scatterers to attain the upper bound. We use these results to provide requirements for the design of such extremal scatterers. The requirements can be formulated as constraints on the polarizability tensors for dipolar scatterers or as material constitutive relations. We also outline two applications for objects of maximum electromagnetic chirality: A twofold resonantly enhanced and background free circular dichroism measurement setup, and angle independent helicity filtering glasses.
Maximum mutual information regularized classification
Wang, Jim Jing-Yan
2014-09-07
In this paper, a novel pattern classification approach is proposed by regularizing the classifier learning to maximize mutual information between the classification response and the true class label. We argue that, with the learned classifier, the uncertainty of the true class label of a data sample should be reduced by knowing its classification response as much as possible. The reduced uncertainty is measured by the mutual information between the classification response and the true class label. To this end, when learning a linear classifier, we propose to maximize the mutual information between classification responses and true class labels of training samples, besides minimizing the classification error and reducing the classifier complexity. An objective function is constructed by modeling mutual information with entropy estimation, and it is optimized by a gradient descend method in an iterative algorithm. Experiments on two real world pattern classification problems show the significant improvements achieved by maximum mutual information regularization.
The strong maximum principle revisited
Pucci, Patrizia; Serrin, James
In this paper we first present the classical maximum principle due to E. Hopf, together with an extended commentary and discussion of Hopf's paper. We emphasize the comparison technique invented by Hopf to prove this principle, which has since become a main mathematical tool for the study of second order elliptic partial differential equations and has generated an enormous number of important applications. While Hopf's principle is generally understood to apply to linear equations, it is in fact also crucial in nonlinear theories, such as those under consideration here. In particular, we shall treat and discuss recent generalizations of the strong maximum principle, and also the compact support principle, for the case of singular quasilinear elliptic differential inequalities, under generally weak assumptions on the quasilinear operators and the nonlinearities involved. Our principal interest is in necessary and sufficient conditions for the validity of both principles; in exposing and simplifying earlier proofs of corresponding results; and in extending the conclusions to wider classes of singular operators than previously considered. The results have unexpected ramifications for other problems, as will develop from the exposition, e.g. two point boundary value problems for singular quasilinear ordinary differential equations (Sections 3 and 4); the exterior Dirichlet boundary value problem (Section 5); the existence of dead cores and compact support solutions, i.e. dead cores at infinity (Section 7); Euler-Lagrange inequalities on a Riemannian manifold (Section 9); comparison and uniqueness theorems for solutions of singular quasilinear differential inequalities (Section 10). The case of p-regular elliptic inequalities is briefly considered in Section 11.
Naushad, Sohail; Barkema, Herman W.; Luby, Christopher; Condas, Larissa A. Z.; Nobrega, Diego B.; Carson, Domonique A.; De Buck, Jeroen
2016-01-01
Non-aureus staphylococci (NAS), a heterogeneous group of a large number of species and subspecies, are the most frequently isolated pathogens from intramammary infections in dairy cattle. Phylogenetic relationships among bovine NAS species are controversial and have mostly been determined based on single-gene trees. Herein, we analyzed phylogeny of bovine NAS species using whole-genome sequencing (WGS) of 441 distinct isolates. In addition, evolutionary relationships among bovine NAS were estimated from multilocus data of 16S rRNA, hsp60, rpoB, sodA, and tuf genes and sequences from these and numerous other single genes/proteins. All phylogenies were created with FastTree, Maximum-Likelihood, Maximum-Parsimony, and Neighbor-Joining methods. Regardless of methodology, WGS-trees clearly separated bovine NAS species into five monophyletic coherent clades. Furthermore, there were consistent interspecies relationships within clades in all WGS phylogenetic reconstructions. Except for the Maximum-Parsimony tree, multilocus data analysis similarly produced five clades. There were large variations in determining clades and interspecies relationships in single gene/protein trees, under different methods of tree constructions, highlighting limitations of using single genes for determining bovine NAS phylogeny. However, based on WGS data, we established a robust phylogeny of bovine NAS species, unaffected by method or model of evolutionary reconstructions. Therefore, it is now possible to determine associations between phylogeny and many biological traits, such as virulence, antimicrobial resistance, environmental niche, geographical distribution, and host specificity. PMID:28066335
Zhang, Z; Green, B R; Cavalier-Smith, T
2000-07-01
Complete chloroplast 23S rRNA and psbA genes from five peridinin-containing dinoflagellates (Heterocapsa pygmaea, Heterocapsa niei, Heterocapsa rotun-data, Amphidinium carterae, and Protoceratium reticulatum) were amplified by PCR and sequenced; partial sequences were obtained from Thoracosphaera heimii and Scrippsiella trochoidea. Comparison with chloroplast 23S rRNA and psbA genes of other organisms shows that dinoflagellate chloroplast genes are the most divergent and rapidly evolving of all. Quartet puzzling, maximum likelihood, maximum parsimony, neighbor joining, and LogDet trees were constructed. Intersite rate variation and invariant sites were allowed for with quartet puzzling and neighbor joining. All psbA and 23S rRNA trees showed peridinin-containing dinoflagellate chloroplasts as monophyletic. In psbA trees they are related to those of chromists and red algae. In 23S rRNA trees, dinoflagellates are always the sisters of Sporozoa (apicomplexans); maximum likelihood analysis of Heterocapsa triquetra 16S rRNA also groups the dinoflagellate and sporozoan sequences, but the other methods were inconsistent. Thus, dinoflagellate chloroplasts may actually be related to sporozoan plastids, but the possibility of reproducible long-branch artifacts cannot be strongly ruled out. The results for all three genes fit the idea that dinoflagellate chloroplasts originated from red algae by a secondary endosymbiosis, possibly the same one as for chromists and Sporozoa. The marked disagreement between 16S rRNA trees using different phylogenetic algorithms indicates that this is a rather poor molecule for elucidating overall chloroplast phylogeny. We discuss possible reasons why both plastid and mitochondrial genomes of alveolates (Dinozoa, Sporozoa and Ciliophora) have ultra-rapid substitution rates and a proneness to unique genomic rearrangements.
Voss, C. I.; Soliman, S. M.; Aggarwal, P. K.
2013-12-01
Important information for management of large aquifer systems can be obtained via a parsimonious approach to groundwater modeling, in part, employing isotope-interpreted groundwater ages. ';Parsimonious' modeling implies active avoidance of overly-complex representations when constructing models. This approach is essential for evaluation of aquifer systems that lack informative hydrogeologic databases. Even in the most remote aquifers, despite lack of typical data, groundwater ages can be interpreted from isotope samples at only a few downstream locations. These samples incorporate hydrogeologic information from the entire upstream groundwater flowpath; thus, interpreted ages are among the most-effective information sources for groundwater model development. This approach is applied to the world's largest non-renewable aquifer, the transboundary Nubian Aquifer System (NAS) of Chad, Egypt, Libya and Sudan. In the NAS countries, water availability is a critical problem and NAS can reliably serve as a water supply for an extended future period. However, there are national concerns about transboundary impacts of water use by neighbors. These concerns include excessive depletion of shared groundwater by individual countries and the spread of water-table drawdown across borders, where neighboring country near-border shallow wells and oases may dry. Development of a parsimonious groundwater flow model, based on limited available NAS hydrogeologic data and on 81Kr groundwater ages below oases in Egypt, is a key step in providing a technical basis for international discussion concerning management of this non-renewable water resource. Simply-structured model analyses, undertaken as part of an IAEA/UNDP/GEF project, show that although the main transboundary issue is indeed drawdown crossing national boundaries, given the large scale of NAS and its plausible ranges of aquifer parameter values, the magnitude of transboundary drawdown will likely be small and may not be a
Maximum entropy production in daisyworld
Maunu, Haley A.; Knuth, Kevin H.
2012-05-01
Daisyworld was first introduced in 1983 by Watson and Lovelock as a model that illustrates how life can influence a planet's climate. These models typically involve modeling a planetary surface on which black and white daisies can grow thus influencing the local surface albedo and therefore also the temperature distribution. Since then, variations of daisyworld have been applied to study problems ranging from ecological systems to global climate. Much of the interest in daisyworld models is due to the fact that they enable one to study self-regulating systems. These models are nonlinear, and as such they exhibit sensitive dependence on initial conditions, and depending on the specifics of the model they can also exhibit feedback loops, oscillations, and chaotic behavior. Many daisyworld models are thermodynamic in nature in that they rely on heat flux and temperature gradients. However, what is not well-known is whether, or even why, a daisyworld model might settle into a maximum entropy production (MEP) state. With the aim to better understand these systems, this paper will discuss what is known about the role of MEP in daisyworld models.
Maximum stellar iron core mass
F W Giacobbe
2003-03-01
An analytical method of estimating the mass of a stellar iron core, just prior to core collapse, is described in this paper. The method employed depends, in part, upon an estimate of the true relativistic mass increase experienced by electrons within a highly compressed iron core, just prior to core collapse, and is signiﬁcantly different from a more typical Chandrasekhar mass limit approach. This technique produced a maximum stellar iron core mass value of 2.69 × 1030 kg (1.35 solar masses). This mass value is very near to the typical mass values found for neutron stars in a recent survey of actual neutron star masses. Although slightly lower and higher neutron star masses may also be found, lower mass neutron stars are believed to be formed as a result of enhanced iron core compression due to the weight of non-ferrous matter overlying the iron cores within large stars. And, higher mass neutron stars are likely to be formed as a result of fallback or accretion of additional matter after an initial collapse event involving an iron core having a mass no greater than 2.69 × 1030 kg.
Maximum Matchings via Glauber Dynamics
Jindal, Anant; Pal, Manjish
2011-01-01
In this paper we study the classic problem of computing a maximum cardinality matching in general graphs $G = (V, E)$. The best known algorithm for this problem till date runs in $O(m \\sqrt{n})$ time due to Micali and Vazirani \\cite{MV80}. Even for general bipartite graphs this is the best known running time (the algorithm of Karp and Hopcroft \\cite{HK73} also achieves this bound). For regular bipartite graphs one can achieve an $O(m)$ time algorithm which, following a series of papers, has been recently improved to $O(n \\log n)$ by Goel, Kapralov and Khanna (STOC 2010) \\cite{GKK10}. In this paper we present a randomized algorithm based on the Markov Chain Monte Carlo paradigm which runs in $O(m \\log^2 n)$ time, thereby obtaining a significant improvement over \\cite{MV80}. We use a Markov chain similar to the \\emph{hard-core model} for Glauber Dynamics with \\emph{fugacity} parameter $\\lambda$, which is used to sample independent sets in a graph from the Gibbs Distribution \\cite{V99}, to design a faster algori...
2011-01-10
...: Establishing Maximum Allowable Operating Pressure or Maximum Operating Pressure Using Record Evidence, and... facilities of their responsibilities, under Federal integrity management (IM) regulations, to perform... system, especially when calculating Maximum Allowable Operating Pressure (MAOP) or Maximum Operating...
A. Townsend Peterson
2008-12-01
Full Text Available Parsimony analysis of endemism (PAE has become a popular analytical approach in efforts to map the biogeography of Mexican biotas. Although attractive, the technique has serious drawbacks that make correct inferences of biogeographic history unlikely, which has been noted amply in the broader literature.El PAE se ha convertido en un método popular en los esfuerzos por resumir, en forma de mapas, la biogeografía de la biota de México. A pesar de su atractivo, la técnica tiene problemas serios que impiden que las conclusiones resultantes sean las correctas. Estos problemas se han hecho ampliamente evidentes en la literatura sobre este campo.
The Sherpa Maximum Likelihood Estimator
Nguyen, D.; Doe, S.; Evans, I.; Hain, R.; Primini, F.
2011-07-01
A primary goal for the second release of the Chandra Source Catalog (CSC) is to include X-ray sources with as few as 5 photon counts detected in stacked observations of the same field, while maintaining acceptable detection efficiency and false source rates. Aggressive source detection methods will result in detection of many false positive source candidates. Candidate detections will then be sent to a new tool, the Maximum Likelihood Estimator (MLE), to evaluate the likelihood that a detection is a real source. MLE uses the Sherpa modeling and fitting engine to fit a model of a background and source to multiple overlapping candidate source regions. A background model is calculated by simultaneously fitting the observed photon flux in multiple background regions. This model is used to determine the quality of the fit statistic for a background-only hypothesis in the potential source region. The statistic for a background-plus-source hypothesis is calculated by adding a Gaussian source model convolved with the appropriate Chandra point spread function (PSF) and simultaneously fitting the observed photon flux in each observation in the stack. Since a candidate source may be located anywhere in the field of view of each stacked observation, a different PSF must be used for each observation because of the strong spatial dependence of the Chandra PSF. The likelihood of a valid source being detected is a function of the two statistics (for background alone, and for background-plus-source). The MLE tool is an extensible Python module with potential for use by the general Chandra user.
Vestige: Maximum likelihood phylogenetic footprinting
Maxwell Peter
2005-05-01
Full Text Available Abstract Background Phylogenetic footprinting is the identification of functional regions of DNA by their evolutionary conservation. This is achieved by comparing orthologous regions from multiple species and identifying the DNA regions that have diverged less than neutral DNA. Vestige is a phylogenetic footprinting package built on the PyEvolve toolkit that uses probabilistic molecular evolutionary modelling to represent aspects of sequence evolution, including the conventional divergence measure employed by other footprinting approaches. In addition to measuring the divergence, Vestige allows the expansion of the definition of a phylogenetic footprint to include variation in the distribution of any molecular evolutionary processes. This is achieved by displaying the distribution of model parameters that represent partitions of molecular evolutionary substitutions. Examination of the spatial incidence of these effects across regions of the genome can identify DNA segments that differ in the nature of the evolutionary process. Results Vestige was applied to a reference dataset of the SCL locus from four species and provided clear identification of the known conserved regions in this dataset. To demonstrate the flexibility to use diverse models of molecular evolution and dissect the nature of the evolutionary process Vestige was used to footprint the Ka/Ks ratio in primate BRCA1 with a codon model of evolution. Two regions of putative adaptive evolution were identified illustrating the ability of Vestige to represent the spatial distribution of distinct molecular evolutionary processes. Conclusion Vestige provides a flexible, open platform for phylogenetic footprinting. Underpinned by the PyEvolve toolkit, Vestige provides a framework for visualising the signatures of evolutionary processes across the genome of numerous organisms simultaneously. By exploiting the maximum-likelihood statistical framework, the complex interplay between mutational
Alstrup, Jan; Jørgensen, Mikkel; Medford, Andrew James
2010-01-01
itself takes less than 4−8 min and requires 15−30 mg each of donor and acceptor material. The optimum donor−acceptor composition of P3HT and PCBM was found to be a broad maximum centered on a 1:1 ratio. We demonstrate how the optimal thickness of the active layer can be found by the same method...... and materials usage by variation of the layer thickness in small steps of 1.5−4 nm. Contrary to expectation we did not find oscillatory variation of the device performance with device thickness because of optical interference. We ascribe this to the nature of the solar cell type explored in this example...... that employs nonreflective or semitransparent printed electrodes. We further found that very thick active layers on the order of 1 μm can be prepared without loss in performance and estimate the active layer thickness could easily approach 4−5 μm while maintaining photovoltaic properties....
Modelling and Simulation of Seasonal Rainfall Using the Principle of Maximum Entropy
Jonathan Borwein
2014-02-01
Full Text Available We use the principle of maximum entropy to propose a parsimonious model for the generation of simulated rainfall during the wettest three-month season at a typical location on the east coast of Australia. The model uses a checkerboard copula of maximum entropy to model the joint probability distribution for total seasonal rainfall and a set of two-parameter gamma distributions to model each of the marginal monthly rainfall totals. The model allows us to match the grade correlation coefficients for the checkerboard copula to the observed Spearman rank correlation coefficients for the monthly rainfalls and, hence, provides a model that correctly describes the mean and variance for each of the monthly totals and also for the overall seasonal total. Thus, we avoid the need for a posteriori adjustment of simulated monthly totals in order to correctly simulate the observed seasonal statistics. Detailed results are presented for the modelling and simulation of seasonal rainfall in the town of Kempsey on the mid-north coast of New South Wales. Empirical evidence from extensive simulations is used to validate this application of the model. A similar analysis for Sydney is also described.
Receiver function estimated by maximum entropy deconvolution
吴庆举; 田小波; 张乃铃; 李卫平; 曾融生
2003-01-01
Maximum entropy deconvolution is presented to estimate receiver function, with the maximum entropy as the rule to determine auto-correlation and cross-correlation functions. The Toeplitz equation and Levinson algorithm are used to calculate the iterative formula of error-predicting filter, and receiver function is then estimated. During extrapolation, reflective coefficient is always less than 1, which keeps maximum entropy deconvolution stable. The maximum entropy of the data outside window increases the resolution of receiver function. Both synthetic and real seismograms show that maximum entropy deconvolution is an effective method to measure receiver function in time-domain.
Maximum Power from a Solar Panel
Michael Miller
2010-01-01
Full Text Available Solar energy has become a promising alternative to conventional fossil fuel sources. Solar panels are used to collect solar radiation and convert it into electricity. One of the techniques used to maximize the effectiveness of this energy alternative is to maximize the power output of the solar collector. In this project the maximum power is calculated by determining the voltage and the current of maximum power. These quantities are determined by finding the maximum value for the equation for power using differentiation. After the maximum values are found for each time of day, each individual quantity, voltage of maximum power, current of maximum power, and maximum power is plotted as a function of the time of day.
Kassian, Alexei
2015-01-01
A lexicostatistical classification is proposed for 20 languages and dialects of the Lezgian group of the North Caucasian family, based on meticulously compiled 110-item wordlists, published as part of the Global Lexicostatistical Database project. The lexical data have been subsequently analyzed with the aid of the principal phylogenetic methods, both distance-based and character-based: Starling neighbor joining (StarlingNJ), Neighbor joining (NJ), Unweighted pair group method with arithmetic mean (UPGMA), Bayesian Markov chain Monte Carlo (MCMC), Unweighted maximum parsimony (UMP). Cognation indexes within the input matrix were marked by two different algorithms: traditional etymological approach and phonetic similarity, i.e., the automatic method of consonant classes (Levenshtein distances). Due to certain reasons (first of all, high lexicographic quality of the wordlists and a consensus about the Lezgian phylogeny among Caucasologists), the Lezgian database is a perfect testing area for appraisal of phylogenetic methods. For the etymology-based input matrix, all the phylogenetic methods, with the possible exception of UMP, have yielded trees that are sufficiently compatible with each other to generate a consensus phylogenetic tree of the Lezgian lects. The obtained consensus tree agrees with the traditional expert classification as well as some of the previously proposed formal classifications of this linguistic group. Contrary to theoretical expectations, the UMP method has suggested the least plausible tree of all. In the case of the phonetic similarity-based input matrix, the distance-based methods (StarlingNJ, NJ, UPGMA) have produced the trees that are rather close to the consensus etymology-based tree and the traditional expert classification, whereas the character-based methods (Bayesian MCMC, UMP) have yielded less likely topologies.
Alexei Kassian
Full Text Available A lexicostatistical classification is proposed for 20 languages and dialects of the Lezgian group of the North Caucasian family, based on meticulously compiled 110-item wordlists, published as part of the Global Lexicostatistical Database project. The lexical data have been subsequently analyzed with the aid of the principal phylogenetic methods, both distance-based and character-based: Starling neighbor joining (StarlingNJ, Neighbor joining (NJ, Unweighted pair group method with arithmetic mean (UPGMA, Bayesian Markov chain Monte Carlo (MCMC, Unweighted maximum parsimony (UMP. Cognation indexes within the input matrix were marked by two different algorithms: traditional etymological approach and phonetic similarity, i.e., the automatic method of consonant classes (Levenshtein distances. Due to certain reasons (first of all, high lexicographic quality of the wordlists and a consensus about the Lezgian phylogeny among Caucasologists, the Lezgian database is a perfect testing area for appraisal of phylogenetic methods. For the etymology-based input matrix, all the phylogenetic methods, with the possible exception of UMP, have yielded trees that are sufficiently compatible with each other to generate a consensus phylogenetic tree of the Lezgian lects. The obtained consensus tree agrees with the traditional expert classification as well as some of the previously proposed formal classifications of this linguistic group. Contrary to theoretical expectations, the UMP method has suggested the least plausible tree of all. In the case of the phonetic similarity-based input matrix, the distance-based methods (StarlingNJ, NJ, UPGMA have produced the trees that are rather close to the consensus etymology-based tree and the traditional expert classification, whereas the character-based methods (Bayesian MCMC, UMP have yielded less likely topologies.
Dao-Chuan Zhang; Hong-Yan Han; Hong Yin; Xin-Jiang Li; Zhan Yin; Xiang-Chu Yin
2011-01-01
Phylogenetic relationships of Pamphagidae were examined using cytochrome oxidase subunit Ⅱ (COII) mtDNA sequences (684 bp). Twenty-seven species of Acridoidea from 20 genera were sequenced to obtain mtDNA data, along with four species from the GenBank nucleotide database. The purpose of this study was analyzing the phylogenetic relationships among subfamilies within Pamphagidae and interpreting the phylogenetic position of this family within the Acridoidea superfamily. Phylogenetic trees were reconstructed using neighbor-joining (NJ), maximum parsimony (MP) and Bayesian inference (BI) methods. The 684 bp analyzed fragment included 126 parsimony informative sites. Sequences diverged 1.0%-l1.1% between genera within subfamilies, and 8.8%-12.3% between subfamilies. Amino acid sequence diverged 0-6.1% between genera within subfamilies, and 0.4%-7.5% between subfamilies. Our phylogenetic trees revealed the monophyly of Pamphagidae and three distinct major groups within this family. Moreover, several well supported and stable clades were found in Pamphagidae. The global clustering results were similar to that obtained through classical morphological classification: Prionotropisinae, Thrinchinae and Pamphaginae were monophyletic groups. However, the current genus Filchnerella (Prionotropisinae) was not a monophyletic group and the genus Asiotmethis (Prionotropisinae) was a sister group of the genus Thrinchus (Thrinchinae). Further molecular and morphological studies are required to clarify the phylogenetic relationships of the genera Filchnerella and Asiotmethis.
Gardner Benjamin
2012-08-01
Full Text Available Abstract Background The twelve-item Self-Report Habit Index (SRHI is the most popular measure of energy-balance related habits. This measure characterises habit by automatic activation, behavioural frequency, and relevance to self-identity. Previous empirical research suggests that the SRHI may be abbreviated with no losses in reliability or predictive utility. Drawing on recent theorising suggesting that automaticity is the ‘active ingredient’ of habit-behaviour relationships, we tested whether an automaticity-specific SRHI subscale could capture habit-based behaviour patterns in self-report data. Methods A content validity task was undertaken to identify a subset of automaticity indicators within the SRHI. The reliability, convergent validity and predictive validity of the automaticity item subset was subsequently tested in secondary analyses of all previous SRHI applications, identified via systematic review, and in primary analyses of four raw datasets relating to energy‐balance relevant behaviours (inactive travel, active travel, snacking, and alcohol consumption. Results A four-item automaticity subscale (the ‘Self-Report Behavioural Automaticity Index’; ‘SRBAI’ was found to be reliable and sensitive to two hypothesised effects of habit on behaviour: a habit-behaviour correlation, and a moderating effect of habit on the intention-behaviour relationship. Conclusion The SRBAI offers a parsimonious measure that adequately captures habitual behaviour patterns. The SRBAI may be of particular utility in predicting future behaviour and in studies tracking habit formation or disruption.
Voss, Clifford I.; Soliman, Safaa M.
2014-01-01
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.
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.
Toda, M.; Yokozawa, M.; Richardson, A. D.; Kohyama, T.
2011-12-01
The effects of wind disturbance on interannual variability in ecosystem CO2 exchange have been assessed in two forests in northern Japan, i.e., a young, even-aged, monocultured, deciduous forest and an uneven-aged mixed forest of evergreen and deciduous trees, including some over 200 years old using eddy covariance (EC) measurements during 2004-2008. The EC measurements have indicated that photosynthetic recovery of trees after a huge typhoon occurred during early September in 2004 activated annual carbon uptake of both forests due to changes in physiological response of tree leaves during their growth stages. However, little have been resolved about what biotic and abiotic factors regulated interannual variability in heat, water and carbon exchange between an atmosphere and forests. In recent years, an inverse modeling analysis has been utilized as a powerful tool to estimate biotic and abiotic parameters that might affect heat, water and CO2 exchange between the atmosphere and forest of a parsimonious physiologically based model. We conducted the Bayesian inverse model analysis for the model with the EC measurements. The preliminary result showed that the above model-derived NEE values were consistent with observed ones on the hourly basis with optimized parameters by Baysian inversion. In the presentation, we would examine interannual variability in biotic and abiotic parameters related to heat, water and carbon exchange between the atmosphere and forests after disturbance by typhoon.
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.
The inverse maximum dynamic flow problem
BAGHERIAN; Mehri
2010-01-01
We consider the inverse maximum dynamic flow (IMDF) problem.IMDF problem can be described as: how to change the capacity vector of a dynamic network as little as possible so that a given feasible dynamic flow becomes a maximum dynamic flow.After discussing some characteristics of this problem,it is converted to a constrained minimum dynamic cut problem.Then an efficient algorithm which uses two maximum dynamic flow algorithms is proposed to solve the problem.
Maximum permissible voltage of YBCO coated conductors
Wen, J.; Lin, B.; Sheng, J.; Xu, J.; Jin, Z. [Department of Electrical Engineering, Shanghai Jiao Tong University, Shanghai (China); Hong, Z., E-mail: zhiyong.hong@sjtu.edu.cn [Department of Electrical Engineering, Shanghai Jiao Tong University, Shanghai (China); Wang, D.; Zhou, H.; Shen, X.; Shen, C. [Qingpu Power Supply Company, State Grid Shanghai Municipal Electric Power Company, Shanghai (China)
2014-06-15
Highlights: • We examine three kinds of tapes’ maximum permissible voltage. • We examine the relationship between quenching duration and maximum permissible voltage. • Continuous I{sub c} degradations under repetitive quenching where tapes reaching maximum permissible voltage. • The relationship between maximum permissible voltage and resistance, temperature. - Abstract: Superconducting fault current limiter (SFCL) could reduce short circuit currents in electrical power system. One of the most important thing in developing SFCL is to find out the maximum permissible voltage of each limiting element. The maximum permissible voltage is defined as the maximum voltage per unit length at which the YBCO coated conductors (CC) do not suffer from critical current (I{sub c}) degradation or burnout. In this research, the time of quenching process is changed and voltage is raised until the I{sub c} degradation or burnout happens. YBCO coated conductors test in the experiment are from American superconductor (AMSC) and Shanghai Jiao Tong University (SJTU). Along with the quenching duration increasing, the maximum permissible voltage of CC decreases. When quenching duration is 100 ms, the maximum permissible of SJTU CC, 12 mm AMSC CC and 4 mm AMSC CC are 0.72 V/cm, 0.52 V/cm and 1.2 V/cm respectively. Based on the results of samples, the whole length of CCs used in the design of a SFCL can be determined.
Nikoh, N; Hayase, N; Iwabe, N; Kuma, K; Miyata, T
1994-09-01
The phylogenetic relationship among the kingdoms Animalia, Plantae, and Fungi remains uncertain, because of lack of solid fossil evidence. In spite of the extensive molecular phylogenetic analyses since the early report, this problem is a longstanding controversy; the proposed phylogenetic relationships differ for different authors, depending on the molecules and methods that they use. To settle this problem, we have accumulated 23 different protein species from the three kingdoms and have inferred the phylogenetic trees by three different methods--the maximum-likelihood method, the neighbor-joining method, and the maximum-parsimony method--for each data set. Although inferred tree topologies differ for different protein species and methods used, both the maximum-likelihood analysis based on the difference (delta l) between the total log-likelihood of a tree and that of the maximum-likelihood tree and bootstrap probability (P) of 23 proteins consisting of 10,051 amino acid sites in total have shown that a tree ((A,F),P), in which Plantae (P) is an outgroup to an Animalia (A)-Fungi (F) clade, is the maximum-likelihood tree; the delta l (= 0.0) and P (94%) of ((A,F),P) are significantly larger than those of ((A,P),F) (delta l = -54.4 +/- 36.3; and P = 6%) and ((F,P),A) (delta l = -141.1 +/- 30.9; and P = 0%).(ABSTRACT TRUNCATED AT 250 WORDS)
Generalised maximum entropy and heterogeneous technologies
Oude Lansink, A.G.J.M.
1999-01-01
Generalised maximum entropy methods are used to estimate a dual model of production on panel data of Dutch cash crop farms over the period 1970-1992. The generalised maximum entropy approach allows a coherent system of input demand and output supply equations to be estimated for each farm in the sam
20 CFR 229.48 - Family maximum.
2010-04-01
... month on one person's earnings record is limited. This limited amount is called the family maximum. The family maximum used to adjust the social security overall minimum rate is based on the employee's Overall..., when any of the persons entitled to benefits on the insured individual's compensation would, except...
The maximum rotation of a galactic disc
Bottema, R
1997-01-01
The observed stellar velocity dispersions of galactic discs show that the maximum rotation of a disc is on average 63% of the observed maximum rotation. This criterion can, however, not be applied to small or low surface brightness (LSB) galaxies because such systems show, in general, a continuously
Duality of Maximum Entropy and Minimum Divergence
Shinto Eguchi
2014-06-01
Full Text Available We discuss a special class of generalized divergence measures by the use of generator functions. Any divergence measure in the class is separated into the difference between cross and diagonal entropy. The diagonal entropy measure in the class associates with a model of maximum entropy distributions; the divergence measure leads to statistical estimation via minimization, for arbitrarily giving a statistical model. The dualistic relationship between the maximum entropy model and the minimum divergence estimation is explored in the framework of information geometry. The model of maximum entropy distributions is characterized to be totally geodesic with respect to the linear connection associated with the divergence. A natural extension for the classical theory for the maximum likelihood method under the maximum entropy model in terms of the Boltzmann-Gibbs-Shannon entropy is given. We discuss the duality in detail for Tsallis entropy as a typical example.
Matthew R. Borths
2016-11-01
the topologies 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.
Kirkpatrick Mark
2005-01-01
Full Text Available Abstract Principal component analysis is a widely used 'dimension reduction' technique, albeit generally at a phenotypic level. It is shown that we can estimate genetic principal components directly through a simple reparameterisation of the usual linear, mixed model. This is applicable to any analysis fitting multiple, correlated genetic effects, whether effects for individual traits or sets of random regression coefficients to model trajectories. Depending on the magnitude of genetic correlation, a subset of the principal component generally suffices to capture the bulk of genetic variation. Corresponding estimates of genetic covariance matrices are more parsimonious, have reduced rank and are smoothed, with the number of parameters required to model the dispersion structure reduced from k(k + 1/2 to m(2k - m + 1/2 for k effects and m principal components. Estimation of these parameters, the largest eigenvalues and pertaining eigenvectors of the genetic covariance matrix, via restricted maximum likelihood using derivatives of the likelihood, is described. It is shown that reduced rank estimation can reduce computational requirements of multivariate analyses substantially. An application to the analysis of eight traits recorded via live ultrasound scanning of beef cattle is given.
A dual method for maximum entropy restoration
Smith, C. B.
1979-01-01
A simple iterative dual algorithm for maximum entropy image restoration is presented. The dual algorithm involves fewer parameters than conventional minimization in the image space. Minicomputer test results for Fourier synthesis with inadequate phantom data are given.
Maximum Throughput in Multiple-Antenna Systems
Zamani, Mahdi
2012-01-01
The point-to-point multiple-antenna channel is investigated in uncorrelated block fading environment with Rayleigh distribution. The maximum throughput and maximum expected-rate of this channel are derived under the assumption that the transmitter is oblivious to the channel state information (CSI), however, the receiver has perfect CSI. First, we prove that in multiple-input single-output (MISO) channels, the optimum transmission strategy maximizing the throughput is to use all available antennas and perform equal power allocation with uncorrelated signals. Furthermore, to increase the expected-rate, multi-layer coding is applied. Analogously, we establish that sending uncorrelated signals and performing equal power allocation across all available antennas at each layer is optimum. A closed form expression for the maximum continuous-layer expected-rate of MISO channels is also obtained. Moreover, we investigate multiple-input multiple-output (MIMO) channels, and formulate the maximum throughput in the asympt...
Photoemission spectromicroscopy with MAXIMUM at Wisconsin
Ng, W.; Ray-Chaudhuri, A.K.; Cole, R.K.; Wallace, J.; Crossley, S.; Crossley, D.; Chen, G.; Green, M.; Guo, J.; Hansen, R.W.C.; Cerrina, F.; Margaritondo, G. (Dept. of Electrical Engineering, Dept. of Physics and Synchrotron Radiation Center, Univ. of Wisconsin, Madison (USA)); Underwood, J.H.; Korthright, J.; Perera, R.C.C. (Center for X-ray Optics, Accelerator and Fusion Research Div., Lawrence Berkeley Lab., CA (USA))
1990-06-01
We describe the development of the scanning photoemission spectromicroscope MAXIMUM at the Wisoncsin Synchrotron Radiation Center, which uses radiation from a 30-period undulator. The article includes a discussion of the first tests after the initial commissioning. (orig.).
Maximum-likelihood method in quantum estimation
Paris, M G A; Sacchi, M F
2001-01-01
The maximum-likelihood method for quantum estimation is reviewed and applied to the reconstruction of density matrix of spin and radiation as well as to the determination of several parameters of interest in quantum optics.
The maximum entropy technique. System's statistical description
Belashev, B Z
2002-01-01
The maximum entropy technique (MENT) is applied for searching the distribution functions of physical values. MENT takes into consideration the demand of maximum entropy, the characteristics of the system and the connection conditions, naturally. It is allowed to apply MENT for statistical description of closed and open systems. The examples in which MENT had been used for the description of the equilibrium and nonequilibrium states and the states far from the thermodynamical equilibrium are considered
19 CFR 114.23 - Maximum period.
2010-04-01
... 19 Customs Duties 1 2010-04-01 2010-04-01 false Maximum period. 114.23 Section 114.23 Customs... CARNETS Processing of Carnets § 114.23 Maximum period. (a) A.T.A. carnet. No A.T.A. carnet with a period of validity exceeding 1 year from date of issue shall be accepted. This period of validity cannot be...
Maximum-Likelihood Detection Of Noncoherent CPM
Divsalar, Dariush; Simon, Marvin K.
1993-01-01
Simplified detectors proposed for use in maximum-likelihood-sequence detection of symbols in alphabet of size M transmitted by uncoded, full-response continuous phase modulation over radio channel with additive white Gaussian noise. Structures of receivers derived from particular interpretation of maximum-likelihood metrics. Receivers include front ends, structures of which depends only on M, analogous to those in receivers of coherent CPM. Parts of receivers following front ends have structures, complexity of which would depend on N.
SEXUAL DIMORPHISM OF MAXIMUM FEMORAL LENGTH
Pandya A M
2011-04-01
Full Text Available Sexual identification from the skeletal parts has medico legal and anthropological importance. Present study aims to obtain values of maximum femoral length and to evaluate its possible usefulness in determining correct sexual identification. Study sample consisted of 184 dry, normal, adult, human femora (136 male & 48 female from skeletal collections of Anatomy department, M. P. Shah Medical College, Jamnagar, Gujarat. Maximum length of femur was considered as maximum vertical distance between upper end of head of femur and the lowest point on femoral condyle, measured with the osteometric board. Mean Values obtained were, 451.81 and 417.48 for right male and female, and 453.35 and 420.44 for left male and female respectively. Higher value in male was statistically highly significant (P< 0.001 on both sides. Demarking point (D.P. analysis of the data showed that right femora with maximum length more than 476.70 were definitely male and less than 379.99 were definitely female; while for left bones, femora with maximum length more than 484.49 were definitely male and less than 385.73 were definitely female. Maximum length identified 13.43% of right male femora, 4.35% of right female femora, 7.25% of left male femora and 8% of left female femora. [National J of Med Res 2011; 1(2.000: 67-70
The maximum rotation of a galactic disc
Bottema, R
1997-01-01
The observed stellar velocity dispersions of galactic discs show that the maximum rotation of a disc is on average 63% of the observed maximum rotation. This criterion can, however, not be applied to small or low surface brightness (LSB) galaxies because such systems show, in general, a continuously rising rotation curve until the outermost measured radial position. That is why a general relation has been derived, giving the maximum rotation for a disc depending on the luminosity, surface brightness, and colour of the disc. As a physical basis of this relation serves an adopted fixed mass-to-light ratio as a function of colour. That functionality is consistent with results from population synthesis models and its absolute value is determined from the observed stellar velocity dispersions. The derived maximum disc rotation is compared with a number of observed maximum rotations, clearly demonstrating the need for appreciable amounts of dark matter in the disc region and even more so for LSB galaxies. Matters h...
Maximum permissible voltage of YBCO coated conductors
Wen, J.; Lin, B.; Sheng, J.; Xu, J.; Jin, Z.; Hong, Z.; Wang, D.; Zhou, H.; Shen, X.; Shen, C.
2014-06-01
Superconducting fault current limiter (SFCL) could reduce short circuit currents in electrical power system. One of the most important thing in developing SFCL is to find out the maximum permissible voltage of each limiting element. The maximum permissible voltage is defined as the maximum voltage per unit length at which the YBCO coated conductors (CC) do not suffer from critical current (Ic) degradation or burnout. In this research, the time of quenching process is changed and voltage is raised until the Ic degradation or burnout happens. YBCO coated conductors test in the experiment are from American superconductor (AMSC) and Shanghai Jiao Tong University (SJTU). Along with the quenching duration increasing, the maximum permissible voltage of CC decreases. When quenching duration is 100 ms, the maximum permissible of SJTU CC, 12 mm AMSC CC and 4 mm AMSC CC are 0.72 V/cm, 0.52 V/cm and 1.2 V/cm respectively. Based on the results of samples, the whole length of CCs used in the design of a SFCL can be determined.
Computing Rooted and Unrooted Maximum Consistent Supertrees
van Iersel, Leo
2009-01-01
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary trees on four leaves. We give exact algorithms constructing rooted and unrooted maximum consistent supertrees in time O(2^n n^5 m^2 log(m)) for a set of m triplets (quartets), each one distinctly leaf-labeled by some subset of n labels. The algorithms extend to weighted triplets (quartets). We further present fast exact algorithms for constructing rooted and unrooted maximum consistent trees in polynomial space. Finally, for a set T of m rooted or unrooted trees with maximum degree D and distinctly leaf-labeled by some subset of a set L of n labels, we compute, in O(2^{mD} n^m m^5 n^6 log(m)) time, a tree distinctly leaf-labeled by a maximum-size subset X of L that all trees in T, when restricted to X, are consistent with.
Maximum magnitude earthquakes induced by fluid injection
McGarr, Arthur F.
2014-01-01
Analysis of numerous case histories of earthquake sequences induced by fluid injection at depth reveals that the maximum magnitude appears to be limited according to the total volume of fluid injected. Similarly, the maximum seismic moment seems to have an upper bound proportional to the total volume of injected fluid. Activities involving fluid injection include (1) hydraulic fracturing of shale formations or coal seams to extract gas and oil, (2) disposal of wastewater from these gas and oil activities by injection into deep aquifers, and (3) the development of enhanced geothermal systems by injecting water into hot, low-permeability rock. Of these three operations, wastewater disposal is observed to be associated with the largest earthquakes, with maximum magnitudes sometimes exceeding 5. To estimate the maximum earthquake that could be induced by a given fluid injection project, the rock mass is assumed to be fully saturated, brittle, to respond to injection with a sequence of earthquakes localized to the region weakened by the pore pressure increase of the injection operation and to have a Gutenberg-Richter magnitude distribution with a b value of 1. If these assumptions correctly describe the circumstances of the largest earthquake, then the maximum seismic moment is limited to the volume of injected liquid times the modulus of rigidity. Observations from the available case histories of earthquakes induced by fluid injection are consistent with this bound on seismic moment. In view of the uncertainties in this analysis, however, this should not be regarded as an absolute physical limit.
Maximum magnitude earthquakes induced by fluid injection
McGarr, A.
2014-02-01
Analysis of numerous case histories of earthquake sequences induced by fluid injection at depth reveals that the maximum magnitude appears to be limited according to the total volume of fluid injected. Similarly, the maximum seismic moment seems to have an upper bound proportional to the total volume of injected fluid. Activities involving fluid injection include (1) hydraulic fracturing of shale formations or coal seams to extract gas and oil, (2) disposal of wastewater from these gas and oil activities by injection into deep aquifers, and (3) the development of enhanced geothermal systems by injecting water into hot, low-permeability rock. Of these three operations, wastewater disposal is observed to be associated with the largest earthquakes, with maximum magnitudes sometimes exceeding 5. To estimate the maximum earthquake that could be induced by a given fluid injection project, the rock mass is assumed to be fully saturated, brittle, to respond to injection with a sequence of earthquakes localized to the region weakened by the pore pressure increase of the injection operation and to have a Gutenberg-Richter magnitude distribution with a b value of 1. If these assumptions correctly describe the circumstances of the largest earthquake, then the maximum seismic moment is limited to the volume of injected liquid times the modulus of rigidity. Observations from the available case histories of earthquakes induced by fluid injection are consistent with this bound on seismic moment. In view of the uncertainties in this analysis, however, this should not be regarded as an absolute physical limit.
Maximum Multiflow in Wireless Network Coding
Zhou, Jin-Yi; Jiang, Yong; Zheng, Hai-Tao
2012-01-01
In a multihop wireless network, wireless interference is crucial to the maximum multiflow (MMF) problem, which studies the maximum throughput between multiple pairs of sources and sinks. In this paper, we observe that network coding could help to decrease the impacts of wireless interference, and propose a framework to study the MMF problem for multihop wireless networks with network coding. Firstly, a network model is set up to describe the new conflict relations modified by network coding. Then, we formulate a linear programming problem to compute the maximum throughput and show its superiority over one in networks without coding. Finally, the MMF problem in wireless network coding is shown to be NP-hard and a polynomial approximation algorithm is proposed.
The Wiener maximum quadratic assignment problem
Cela, Eranda; Woeginger, Gerhard J
2011-01-01
We investigate a special case of the maximum quadratic assignment problem where one matrix is a product matrix and the other matrix is the distance matrix of a one-dimensional point set. We show that this special case, which we call the Wiener maximum quadratic assignment problem, is NP-hard in the ordinary sense and solvable in pseudo-polynomial time. Our approach also yields a polynomial time solution for the following problem from chemical graph theory: Find a tree that maximizes the Wiener index among all trees with a prescribed degree sequence. This settles an open problem from the literature.
Maximum confidence measurements via probabilistic quantum cloning
Zhang Wen-Hai; Yu Long-Bao; Cao Zhuo-Liang; Ye Liu
2013-01-01
Probabilistic quantum cloning (PQC) cannot copy a set of linearly dependent quantum states.In this paper,we show that if incorrect copies are allowed to be produced,linearly dependent quantum states may also be cloned by the PQC.By exploiting this kind of PQC to clone a special set of three linearly dependent quantum states,we derive the upper bound of the maximum confidence measure of a set.An explicit transformation of the maximum confidence measure is presented.
Maximum floodflows in the conterminous United States
Crippen, John R.; Bue, Conrad D.
1977-01-01
Peak floodflows from thousands of observation sites within the conterminous United States were studied to provide a guide for estimating potential maximum floodflows. Data were selected from 883 sites with drainage areas of less than 10,000 square miles (25,900 square kilometers) and were grouped into regional sets. Outstanding floods for each region were plotted on graphs, and envelope curves were computed that offer reasonable limits for estimates of maximum floods. The curves indicate that floods may occur that are two to three times greater than those known for most streams.
Revealing the Maximum Strength in Nanotwinned Copper
Lu, L.; Chen, X.; Huang, Xiaoxu
2009-01-01
The strength of polycrystalline materials increases with decreasing grain size. Below a critical size, smaller grains might lead to softening, as suggested by atomistic simulations. The strongest size should arise at a transition in deformation mechanism from lattice dislocation activities to grain...... boundary–related processes. We investigated the maximum strength of nanotwinned copper samples with different twin thicknesses. We found that the strength increases with decreasing twin thickness, reaching a maximum at 15 nanometers, followed by a softening at smaller values that is accompanied by enhanced...
The Maximum Resource Bin Packing Problem
Boyar, J.; Epstein, L.; Favrholdt, L.M.
2006-01-01
Usually, for bin packing problems, we try to minimize the number of bins used or in the case of the dual bin packing problem, maximize the number or total size of accepted items. This paper presents results for the opposite problems, where we would like to maximize the number of bins used...... algorithms, First-Fit-Increasing and First-Fit-Decreasing for the maximum resource variant of classical bin packing. For the on-line variant, we define maximum resource variants of classical and dual bin packing. For dual bin packing, no on-line algorithm is competitive. For classical bin packing, we find...
Maximum entropy analysis of EGRET data
Pohl, M.; Strong, A.W.
1997-01-01
EGRET data are usually analysed on the basis of the Maximum-Likelihood method \\cite{ma96} in a search for point sources in excess to a model for the background radiation (e.g. \\cite{hu97}). This method depends strongly on the quality of the background model, and thus may have high systematic unce...... uncertainties in region of strong and uncertain background like the Galactic Center region. Here we show images of such regions obtained by the quantified Maximum-Entropy method. We also discuss a possible further use of MEM in the analysis of problematic regions of the sky....
Revealing the Maximum Strength in Nanotwinned Copper
Lu, L.; Chen, X.; Huang, Xiaoxu
2009-01-01
The strength of polycrystalline materials increases with decreasing grain size. Below a critical size, smaller grains might lead to softening, as suggested by atomistic simulations. The strongest size should arise at a transition in deformation mechanism from lattice dislocation activities to grain...... boundary–related processes. We investigated the maximum strength of nanotwinned copper samples with different twin thicknesses. We found that the strength increases with decreasing twin thickness, reaching a maximum at 15 nanometers, followed by a softening at smaller values that is accompanied by enhanced...
Maximum phytoplankton concentrations in the sea
Jackson, G.A.; Kiørboe, Thomas
2008-01-01
A simplification of plankton dynamics using coagulation theory provides predictions of the maximum algal concentration sustainable in aquatic systems. These predictions have previously been tested successfully against results from iron fertilization experiments. We extend the test to data collected...... in the North Atlantic as part of the Bermuda Atlantic Time Series program as well as data collected off Southern California as part of the Southern California Bight Study program. The observed maximum particulate organic carbon and volumetric particle concentrations are consistent with the predictions...
Analysis of Photovoltaic Maximum Power Point Trackers
Veerachary, Mummadi
The photovoltaic generator exhibits a non-linear i-v characteristic and its maximum power point (MPP) varies with solar insolation. An intermediate switch-mode dc-dc converter is required to extract maximum power from the photovoltaic array. In this paper buck, boost and buck-boost topologies are considered and a detailed mathematical analysis, both for continuous and discontinuous inductor current operation, is given for MPP operation. The conditions on the connected load values and duty ratio are derived for achieving the satisfactory maximum power point operation. Further, it is shown that certain load values, falling out of the optimal range, will drive the operating point away from the true maximum power point. Detailed comparison of various topologies for MPPT is given. Selection of the converter topology for a given loading is discussed. Detailed discussion on circuit-oriented model development is given and then MPPT effectiveness of various converter systems is verified through simulations. Proposed theory and analysis is validated through experimental investigations.
On maximum cycle packings in polyhedral graphs
Peter Recht
2014-04-01
Full Text Available This paper addresses upper and lower bounds for the cardinality of a maximum vertex-/edge-disjoint cycle packing in a polyhedral graph G. Bounds on the cardinality of such packings are provided, that depend on the size, the order or the number of faces of G, respectively. Polyhedral graphs are constructed, that attain these bounds.
Hard graphs for the maximum clique problem
Hoede, Cornelis
1988-01-01
The maximum clique problem is one of the NP-complete problems. There are graphs for which a reduction technique exists that transforms the problem for these graphs into one for graphs with specific properties in polynomial time. The resulting graphs do not grow exponentially in order and number. Gra
Maximum Likelihood Estimation of Search Costs
J.L. Moraga-Gonzalez (José Luis); M.R. Wildenbeest (Matthijs)
2006-01-01
textabstractIn a recent paper Hong and Shum (forthcoming) present a structural methodology to estimate search cost distributions. We extend their approach to the case of oligopoly and present a maximum likelihood estimate of the search cost distribution. We apply our method to a data set of online p
Weak Scale From the Maximum Entropy Principle
Hamada, Yuta; Kawana, Kiyoharu
2015-01-01
The theory of multiverse and wormholes suggests that the parameters of the Standard Model are fixed in such a way that the radiation of the $S^{3}$ universe at the final stage $S_{rad}$ becomes maximum, which we call the maximum entropy principle. Although it is difficult to confirm this principle generally, for a few parameters of the Standard Model, we can check whether $S_{rad}$ actually becomes maximum at the observed values. In this paper, we regard $S_{rad}$ at the final stage as a function of the weak scale ( the Higgs expectation value ) $v_{h}$, and show that it becomes maximum around $v_{h}={\\cal{O}}(300\\text{GeV})$ when the dimensionless couplings in the Standard Model, that is, the Higgs self coupling, the gauge couplings, and the Yukawa couplings are fixed. Roughly speaking, we find that the weak scale is given by \\begin{equation} v_{h}\\sim\\frac{T_{BBN}^{2}}{M_{pl}y_{e}^{5}},\
Weak scale from the maximum entropy principle
Hamada, Yuta; Kawai, Hikaru; Kawana, Kiyoharu
2015-03-01
The theory of the multiverse and wormholes suggests that the parameters of the Standard Model (SM) are fixed in such a way that the radiation of the S3 universe at the final stage S_rad becomes maximum, which we call the maximum entropy principle. Although it is difficult to confirm this principle generally, for a few parameters of the SM, we can check whether S_rad actually becomes maximum at the observed values. In this paper, we regard S_rad at the final stage as a function of the weak scale (the Higgs expectation value) vh, and show that it becomes maximum around vh = {{O}} (300 GeV) when the dimensionless couplings in the SM, i.e., the Higgs self-coupling, the gauge couplings, and the Yukawa couplings are fixed. Roughly speaking, we find that the weak scale is given by vh ˜ T_{BBN}2 / (M_{pl}ye5), where ye is the Yukawa coupling of electron, T_BBN is the temperature at which the Big Bang nucleosynthesis starts, and M_pl is the Planck mass.
Global characterization of the Holocene Thermal Maximum
Renssen, H.; Seppä, H.; Crosta, X.; Goosse, H.; Roche, D.M.V.A.P.
2012-01-01
We analyze the global variations in the timing and magnitude of the Holocene Thermal Maximum (HTM) and their dependence on various forcings in transient simulations covering the last 9000 years (9 ka), performed with a global atmosphere-ocean-vegetation model. In these experiments, we consider the i
Instance Optimality of the Adaptive Maximum Strategy
L. Diening; C. Kreuzer; R. Stevenson
2016-01-01
In this paper, we prove that the standard adaptive finite element method with a (modified) maximum marking strategy is instance optimal for the total error, being the square root of the squared energy error plus the squared oscillation. This result will be derived in the model setting of Poisson’s e
Maximum phonation time: variability and reliability.
Speyer, Renée; Bogaardt, Hans C A; Passos, Valéria Lima; Roodenburg, Nel P H D; Zumach, Anne; Heijnen, Mariëlle A M; Baijens, Laura W J; Fleskens, Stijn J H M; Brunings, Jan W
2010-05-01
The objective of the study was to determine maximum phonation time reliability as a function of the number of trials, days, and raters in dysphonic and control subjects. Two groups of adult subjects participated in this reliability study: a group of outpatients with functional or organic dysphonia versus a group of healthy control subjects matched by age and gender. Over a period of maximally 6 weeks, three video recordings were made of five subjects' maximum phonation time trials. A panel of five experts were responsible for all measurements, including a repeated measurement of the subjects' first recordings. Patients showed significantly shorter maximum phonation times compared with healthy controls (on average, 6.6 seconds shorter). The averaged interclass correlation coefficient (ICC) over all raters per trial for the first day was 0.998. The averaged reliability coefficient per rater and per trial for repeated measurements of the first day's data was 0.997, indicating high intrarater reliability. The mean reliability coefficient per day for one trial was 0.939. When using five trials, the reliability increased to 0.987. The reliability over five trials for a single day was 0.836; for 2 days, 0.911; and for 3 days, 0.935. To conclude, the maximum phonation time has proven to be a highly reliable measure in voice assessment. A single rater is sufficient to provide highly reliable measurements.
Maximum Phonation Time: Variability and Reliability
R. Speyer; H.C.A. Bogaardt; V.L. Passos; N.P.H.D. Roodenburg; A. Zumach; M.A.M. Heijnen; L.W.J. Baijens; S.J.H.M. Fleskens; J.W. Brunings
2010-01-01
The objective of the study was to determine maximum phonation time reliability as a function of the number of trials, days, and raters in dysphonic and control subjects. Two groups of adult subjects participated in this reliability study: a group of outpatients with functional or organic dysphonia v
Maximum likelihood estimation of fractionally cointegrated systems
Lasak, Katarzyna
In this paper we consider a fractionally cointegrated error correction model and investigate asymptotic properties of the maximum likelihood (ML) estimators of the matrix of the cointe- gration relations, the degree of fractional cointegration, the matrix of the speed of adjustment...
Maximum likelihood estimation for integrated diffusion processes
Baltazar-Larios, Fernando; Sørensen, Michael
EM-algorithm to obtain maximum likelihood estimates of the parameters in the diffusion model. As part of the algorithm, we use a recent simple method for approximate simulation of diffusion bridges. In simulation studies for the Ornstein-Uhlenbeck process and the CIR process the proposed method works...
Maximum gain of Yagi-Uda arrays
Bojsen, J.H.; Schjær-Jacobsen, Hans; Nilsson, E.
1971-01-01
Numerical optimisation techniques have been used to find the maximum gain of some specific parasitic arrays. The gain of an array of infinitely thin, equispaced dipoles loaded with arbitrary reactances has been optimised. The results show that standard travelling-wave design methods are not optimum....... Yagi–Uda arrays with equal and unequal spacing have also been optimised with experimental verification....
Model Selection Through Sparse Maximum Likelihood Estimation
Banerjee, Onureena; D'Aspremont, Alexandre
2007-01-01
We consider the problem of estimating the parameters of a Gaussian or binary distribution in such a way that the resulting undirected graphical model is sparse. Our approach is to solve a maximum likelihood problem with an added l_1-norm penalty term. The problem as formulated is convex but the memory requirements and complexity of existing interior point methods are prohibitive for problems with more than tens of nodes. We present two new algorithms for solving problems with at least a thousand nodes in the Gaussian case. Our first algorithm uses block coordinate descent, and can be interpreted as recursive l_1-norm penalized regression. Our second algorithm, based on Nesterov's first order method, yields a complexity estimate with a better dependence on problem size than existing interior point methods. Using a log determinant relaxation of the log partition function (Wainwright & Jordan (2006)), we show that these same algorithms can be used to solve an approximate sparse maximum likelihood problem for...
Maximum-entropy description of animal movement.
Fleming, Chris H; Subaşı, Yiğit; Calabrese, Justin M
2015-03-01
We introduce a class of maximum-entropy states that naturally includes within it all of the major continuous-time stochastic processes that have been applied to animal movement, including Brownian motion, Ornstein-Uhlenbeck motion, integrated Ornstein-Uhlenbeck motion, a recently discovered hybrid of the previous models, and a new model that describes central-place foraging. We are also able to predict a further hierarchy of new models that will emerge as data quality improves to better resolve the underlying continuity of animal movement. Finally, we also show that Langevin equations must obey a fluctuation-dissipation theorem to generate processes that fall from this class of maximum-entropy distributions when the constraints are purely kinematic.
Pareto versus lognormal: a maximum entropy test.
Bee, Marco; Riccaboni, Massimo; Schiavo, Stefano
2011-08-01
It is commonly found that distributions that seem to be lognormal over a broad range change to a power-law (Pareto) distribution for the last few percentiles. The distributions of many physical, natural, and social events (earthquake size, species abundance, income and wealth, as well as file, city, and firm sizes) display this structure. We present a test for the occurrence of power-law tails in statistical distributions based on maximum entropy. This methodology allows one to identify the true data-generating processes even in the case when it is neither lognormal nor Pareto. The maximum entropy approach is then compared with other widely used methods and applied to different levels of aggregation of complex systems. Our results provide support for the theory that distributions with lognormal body and Pareto tail can be generated as mixtures of lognormally distributed units.
Maximum Variance Hashing via Column Generation
Lei Luo
2013-01-01
item search. Recently, a number of data-dependent methods have been developed, reflecting the great potential of learning for hashing. Inspired by the classic nonlinear dimensionality reduction algorithm—maximum variance unfolding, we propose a novel unsupervised hashing method, named maximum variance hashing, in this work. The idea is to maximize the total variance of the hash codes while preserving the local structure of the training data. To solve the derived optimization problem, we propose a column generation algorithm, which directly learns the binary-valued hash functions. We then extend it using anchor graphs to reduce the computational cost. Experiments on large-scale image datasets demonstrate that the proposed method outperforms state-of-the-art hashing methods in many cases.
The Maximum Resource Bin Packing Problem
Boyar, J.; Epstein, L.; Favrholdt, L.M.
2006-01-01
algorithms, First-Fit-Increasing and First-Fit-Decreasing for the maximum resource variant of classical bin packing. For the on-line variant, we define maximum resource variants of classical and dual bin packing. For dual bin packing, no on-line algorithm is competitive. For classical bin packing, we find......Usually, for bin packing problems, we try to minimize the number of bins used or in the case of the dual bin packing problem, maximize the number or total size of accepted items. This paper presents results for the opposite problems, where we would like to maximize the number of bins used...... the competitive ratio of various natural algorithms. We study the general versions of the problems as well as the parameterized versions where there is an upper bound of on the item sizes, for some integer k....
Nonparametric Maximum Entropy Estimation on Information Diagrams
Martin, Elliot A; Meinke, Alexander; Děchtěrenko, Filip; Davidsen, Jörn
2016-01-01
Maximum entropy estimation is of broad interest for inferring properties of systems across many different disciplines. In this work, we significantly extend a technique we previously introduced for estimating the maximum entropy of a set of random discrete variables when conditioning on bivariate mutual informations and univariate entropies. Specifically, we show how to apply the concept to continuous random variables and vastly expand the types of information-theoretic quantities one can condition on. This allows us to establish a number of significant advantages of our approach over existing ones. Not only does our method perform favorably in the undersampled regime, where existing methods fail, but it also can be dramatically less computationally expensive as the cardinality of the variables increases. In addition, we propose a nonparametric formulation of connected informations and give an illustrative example showing how this agrees with the existing parametric formulation in cases of interest. We furthe...
Zipf's law, power laws and maximum entropy
Visser, Matt
2013-04-01
Zipf's law, and power laws in general, have attracted and continue to attract considerable attention in a wide variety of disciplines—from astronomy to demographics to software structure to economics to linguistics to zoology, and even warfare. A recent model of random group formation (RGF) attempts a general explanation of such phenomena based on Jaynes' notion of maximum entropy applied to a particular choice of cost function. In the present paper I argue that the specific cost function used in the RGF model is in fact unnecessarily complicated, and that power laws can be obtained in a much simpler way by applying maximum entropy ideas directly to the Shannon entropy subject only to a single constraint: that the average of the logarithm of the observable quantity is specified.
Zipf's law, power laws, and maximum entropy
Visser, Matt
2012-01-01
Zipf's law, and power laws in general, have attracted and continue to attract considerable attention in a wide variety of disciplines - from astronomy to demographics to economics to linguistics to zoology, and even warfare. A recent model of random group formation [RGF] attempts a general explanation of such phenomena based on Jaynes' notion of maximum entropy applied to a particular choice of cost function. In the present article I argue that the cost function used in the RGF model is in fact unnecessarily complicated, and that power laws can be obtained in a much simpler way by applying maximum entropy ideas directly to the Shannon entropy subject only to a single constraint: that the average of the logarithm of the observable quantity is specified.
Regions of constrained maximum likelihood parameter identifiability
Lee, C.-H.; Herget, C. J.
1975-01-01
This paper considers the parameter identification problem of general discrete-time, nonlinear, multiple-input/multiple-output dynamic systems with Gaussian-white distributed measurement errors. Knowledge of the system parameterization is assumed to be known. Regions of constrained maximum likelihood (CML) parameter identifiability are established. A computation procedure employing interval arithmetic is proposed for finding explicit regions of parameter identifiability for the case of linear systems. It is shown that if the vector of true parameters is locally CML identifiable, then with probability one, the vector of true parameters is a unique maximal point of the maximum likelihood function in the region of parameter identifiability and the CML estimation sequence will converge to the true parameters.
A Maximum Radius for Habitable Planets.
Alibert, Yann
2015-09-01
We compute the maximum radius a planet can have in order to fulfill two constraints that are likely necessary conditions for habitability: 1- surface temperature and pressure compatible with the existence of liquid water, and 2- no ice layer at the bottom of a putative global ocean, that would prevent the operation of the geologic carbon cycle to operate. We demonstrate that, above a given radius, these two constraints cannot be met: in the Super-Earth mass range (1-12 Mearth), the overall maximum that a planet can have varies between 1.8 and 2.3 Rearth. This radius is reduced when considering planets with higher Fe/Si ratios, and taking into account irradiation effects on the structure of the gas envelope.
Maximum Profit Configurations of Commercial Engines
Yiran Chen
2011-01-01
An investigation of commercial engines with finite capacity low- and high-price economic subsystems and a generalized commodity transfer law [n ∝ Δ (P m)] in commodity flow processes, in which effects of the price elasticities of supply and demand are introduced, is presented in this paper. Optimal cycle configurations of commercial engines for maximum profit are obtained by applying optimal control theory. In some special cases, the eventual state—market equilibrium—is solely determined by t...
A stochastic maximum principle via Malliavin calculus
Øksendal, Bernt; Zhou, Xun Yu; Meyer-Brandis, Thilo
2008-01-01
This paper considers a controlled It\\^o-L\\'evy process where the information available to the controller is possibly less than the overall information. All the system coefficients and the objective performance functional are allowed to be random, possibly non-Markovian. Malliavin calculus is employed to derive a maximum principle for the optimal control of such a system where the adjoint process is explicitly expressed.
Tissue radiation response with maximum Tsallis entropy.
Sotolongo-Grau, O; Rodríguez-Pérez, D; Antoranz, J C; Sotolongo-Costa, Oscar
2010-10-08
The expression of survival factors for radiation damaged cells is currently based on probabilistic assumptions and experimentally fitted for each tumor, radiation, and conditions. Here, we show how the simplest of these radiobiological models can be derived from the maximum entropy principle of the classical Boltzmann-Gibbs expression. We extend this derivation using the Tsallis entropy and a cutoff hypothesis, motivated by clinical observations. The obtained expression shows a remarkable agreement with the experimental data found in the literature.
Maximum Estrada Index of Bicyclic Graphs
Wang, Long; Wang, Yi
2012-01-01
Let $G$ be a simple graph of order $n$, let $\\lambda_1(G),\\lambda_2(G),...,\\lambda_n(G)$ be the eigenvalues of the adjacency matrix of $G$. The Esrada index of $G$ is defined as $EE(G)=\\sum_{i=1}^{n}e^{\\lambda_i(G)}$. In this paper we determine the unique graph with maximum Estrada index among bicyclic graphs with fixed order.
Maximum privacy without coherence, zero-error
Leung, Debbie; Yu, Nengkun
2016-09-01
We study the possible difference between the quantum and the private capacities of a quantum channel in the zero-error setting. For a family of channels introduced by Leung et al. [Phys. Rev. Lett. 113, 030512 (2014)], we demonstrate an extreme difference: the zero-error quantum capacity is zero, whereas the zero-error private capacity is maximum given the quantum output dimension.
Automatic maximum entropy spectral reconstruction in NMR.
Mobli, Mehdi; Maciejewski, Mark W; Gryk, Michael R; Hoch, Jeffrey C
2007-10-01
Developments in superconducting magnets, cryogenic probes, isotope labeling strategies, and sophisticated pulse sequences together have enabled the application, in principle, of high-resolution NMR spectroscopy to biomolecular systems approaching 1 megadalton. In practice, however, conventional approaches to NMR that utilize the fast Fourier transform, which require data collected at uniform time intervals, result in prohibitively lengthy data collection times in order to achieve the full resolution afforded by high field magnets. A variety of approaches that involve nonuniform sampling have been proposed, each utilizing a non-Fourier method of spectrum analysis. A very general non-Fourier method that is capable of utilizing data collected using any of the proposed nonuniform sampling strategies is maximum entropy reconstruction. A limiting factor in the adoption of maximum entropy reconstruction in NMR has been the need to specify non-intuitive parameters. Here we describe a fully automated system for maximum entropy reconstruction that requires no user-specified parameters. A web-accessible script generator provides the user interface to the system.
Maximum entropy analysis of cosmic ray composition
Nosek, Dalibor; Vícha, Jakub; Trávníček, Petr; Nosková, Jana
2016-01-01
We focus on the primary composition of cosmic rays with the highest energies that cause extensive air showers in the Earth's atmosphere. A way of examining the two lowest order moments of the sample distribution of the depth of shower maximum is presented. The aim is to show that useful information about the composition of the primary beam can be inferred with limited knowledge we have about processes underlying these observations. In order to describe how the moments of the depth of shower maximum depend on the type of primary particles and their energies, we utilize a superposition model. Using the principle of maximum entropy, we are able to determine what trends in the primary composition are consistent with the input data, while relying on a limited amount of information from shower physics. Some capabilities and limitations of the proposed method are discussed. In order to achieve a realistic description of the primary mass composition, we pay special attention to the choice of the parameters of the sup...
A Maximum Resonant Set of Polyomino Graphs
Zhang Heping
2016-05-01
Full Text Available A polyomino graph P is a connected finite subgraph of the infinite plane grid such that each finite face is surrounded by a regular square of side length one and each edge belongs to at least one square. A dimer covering of P corresponds to a perfect matching. Different dimer coverings can interact via an alternating cycle (or square with respect to them. A set of disjoint squares of P is a resonant set if P has a perfect matching M so that each one of those squares is M-alternating. In this paper, we show that if K is a maximum resonant set of P, then P − K has a unique perfect matching. We further prove that the maximum forcing number of a polyomino graph is equal to the cardinality of a maximum resonant set. This confirms a conjecture of Xu et al. [26]. We also show that if K is a maximal alternating set of P, then P − K has a unique perfect matching.
The maximum rate of mammal evolution
Evans, Alistair R.; Jones, David; Boyer, Alison G.; Brown, James H.; Costa, Daniel P.; Ernest, S. K. Morgan; Fitzgerald, Erich M. G.; Fortelius, Mikael; Gittleman, John L.; Hamilton, Marcus J.; Harding, Larisa E.; Lintulaakso, Kari; Lyons, S. Kathleen; Okie, Jordan G.; Saarinen, Juha J.; Sibly, Richard M.; Smith, Felisa A.; Stephens, Patrick R.; Theodor, Jessica M.; Uhen, Mark D.
2012-03-01
How fast can a mammal evolve from the size of a mouse to the size of an elephant? Achieving such a large transformation calls for major biological reorganization. Thus, the speed at which this occurs has important implications for extensive faunal changes, including adaptive radiations and recovery from mass extinctions. To quantify the pace of large-scale evolution we developed a metric, clade maximum rate, which represents the maximum evolutionary rate of a trait within a clade. We applied this metric to body mass evolution in mammals over the last 70 million years, during which multiple large evolutionary transitions occurred in oceans and on continents and islands. Our computations suggest that it took a minimum of 1.6, 5.1, and 10 million generations for terrestrial mammal mass to increase 100-, and 1,000-, and 5,000-fold, respectively. Values for whales were down to half the length (i.e., 1.1, 3, and 5 million generations), perhaps due to the reduced mechanical constraints of living in an aquatic environment. When differences in generation time are considered, we find an exponential increase in maximum mammal body mass during the 35 million years following the Cretaceous-Paleogene (K-Pg) extinction event. Our results also indicate a basic asymmetry in macroevolution: very large decreases (such as extreme insular dwarfism) can happen at more than 10 times the rate of increases. Our findings allow more rigorous comparisons of microevolutionary and macroevolutionary patterns and processes.
Minimal Length, Friedmann Equations and Maximum Density
Awad, Adel
2014-01-01
Inspired by Jacobson's thermodynamic approach[gr-qc/9504004], Cai et al [hep-th/0501055,hep-th/0609128] have shown the emergence of Friedmann equations from the first law of thermodynamics. We extend Akbar--Cai derivation [hep-th/0609128] of Friedmann equations to accommodate a general entropy-area law. Studying the resulted Friedmann equations using a specific entropy-area law, which is motivated by the generalized uncertainty principle (GUP), reveals the existence of a maximum energy density closed to Planck density. Allowing for a general continuous pressure $p(\\rho,a)$ leads to bounded curvature invariants and a general nonsingular evolution. In this case, the maximum energy density is reached in a finite time and there is no cosmological evolution beyond this point which leaves the big bang singularity inaccessible from a spacetime prospective. The existence of maximum energy density and a general nonsingular evolution is independent of the equation of state and the spacial curvature $k$. As an example w...
Maximum saliency bias in binocular fusion
Lu, Yuhao; Stafford, Tom; Fox, Charles
2016-07-01
Subjective experience at any instant consists of a single ("unitary"), coherent interpretation of sense data rather than a "Bayesian blur" of alternatives. However, computation of Bayes-optimal actions has no role for unitary perception, instead being required to integrate over every possible action-percept pair to maximise expected utility. So what is the role of unitary coherent percepts, and how are they computed? Recent work provided objective evidence for non-Bayes-optimal, unitary coherent, perception and action in humans; and further suggested that the percept selected is not the maximum a posteriori percept but is instead affected by utility. The present study uses a binocular fusion task first to reproduce the same effect in a new domain, and second, to test multiple hypotheses about exactly how utility may affect the percept. After accounting for high experimental noise, it finds that both Bayes optimality (maximise expected utility) and the previously proposed maximum-utility hypothesis are outperformed in fitting the data by a modified maximum-salience hypothesis, using unsigned utility magnitudes in place of signed utilities in the bias function.
The maximum rate of mammal evolution
Evans, Alistair R.; Jones, David; Boyer, Alison G.; Brown, James H.; Costa, Daniel P.; Ernest, S. K. Morgan; Fitzgerald, Erich M. G.; Fortelius, Mikael; Gittleman, John L.; Hamilton, Marcus J.; Harding, Larisa E.; Lintulaakso, Kari; Lyons, S. Kathleen; Okie, Jordan G.; Saarinen, Juha J.; Sibly, Richard M.; Smith, Felisa A.; Stephens, Patrick R.; Theodor, Jessica M.; Uhen, Mark D.
2012-01-01
How fast can a mammal evolve from the size of a mouse to the size of an elephant? Achieving such a large transformation calls for major biological reorganization. Thus, the speed at which this occurs has important implications for extensive faunal changes, including adaptive radiations and recovery from mass extinctions. To quantify the pace of large-scale evolution we developed a metric, clade maximum rate, which represents the maximum evolutionary rate of a trait within a clade. We applied this metric to body mass evolution in mammals over the last 70 million years, during which multiple large evolutionary transitions occurred in oceans and on continents and islands. Our computations suggest that it took a minimum of 1.6, 5.1, and 10 million generations for terrestrial mammal mass to increase 100-, and 1,000-, and 5,000-fold, respectively. Values for whales were down to half the length (i.e., 1.1, 3, and 5 million generations), perhaps due to the reduced mechanical constraints of living in an aquatic environment. When differences in generation time are considered, we find an exponential increase in maximum mammal body mass during the 35 million years following the Cretaceous–Paleogene (K–Pg) extinction event. Our results also indicate a basic asymmetry in macroevolution: very large decreases (such as extreme insular dwarfism) can happen at more than 10 times the rate of increases. Our findings allow more rigorous comparisons of microevolutionary and macroevolutionary patterns and processes. PMID:22308461
Maximum-biomass prediction of homofermentative Lactobacillus.
Cui, Shumao; Zhao, Jianxin; Liu, Xiaoming; Chen, Yong Q; Zhang, Hao; Chen, Wei
2016-07-01
Fed-batch and pH-controlled cultures have been widely used for industrial production of probiotics. The aim of this study was to systematically investigate the relationship between the maximum biomass of different homofermentative Lactobacillus and lactate accumulation, and to develop a prediction equation for the maximum biomass concentration in such cultures. The accumulation of the end products and the depletion of nutrients by various strains were evaluated. In addition, the minimum inhibitory concentrations (MICs) of acid anions for various strains at pH 7.0 were examined. The lactate concentration at the point of complete inhibition was not significantly different from the MIC of lactate for all of the strains, although the inhibition mechanism of lactate and acetate on Lactobacillus rhamnosus was different from the other strains which were inhibited by the osmotic pressure caused by acid anions at pH 7.0. When the lactate concentration accumulated to the MIC, the strains stopped growing. The maximum biomass was closely related to the biomass yield per unit of lactate produced (YX/P) and the MIC (C) of lactate for different homofermentative Lactobacillus. Based on the experimental data obtained using different homofermentative Lactobacillus, a prediction equation was established as follows: Xmax - X0 = (0.59 ± 0.02)·YX/P·C.
The maximum rate of mammal evolution.
Evans, Alistair R; Jones, David; Boyer, Alison G; Brown, James H; Costa, Daniel P; Ernest, S K Morgan; Fitzgerald, Erich M G; Fortelius, Mikael; Gittleman, John L; Hamilton, Marcus J; Harding, Larisa E; Lintulaakso, Kari; Lyons, S Kathleen; Okie, Jordan G; Saarinen, Juha J; Sibly, Richard M; Smith, Felisa A; Stephens, Patrick R; Theodor, Jessica M; Uhen, Mark D
2012-03-13
How fast can a mammal evolve from the size of a mouse to the size of an elephant? Achieving such a large transformation calls for major biological reorganization. Thus, the speed at which this occurs has important implications for extensive faunal changes, including adaptive radiations and recovery from mass extinctions. To quantify the pace of large-scale evolution we developed a metric, clade maximum rate, which represents the maximum evolutionary rate of a trait within a clade. We applied this metric to body mass evolution in mammals over the last 70 million years, during which multiple large evolutionary transitions occurred in oceans and on continents and islands. Our computations suggest that it took a minimum of 1.6, 5.1, and 10 million generations for terrestrial mammal mass to increase 100-, and 1,000-, and 5,000-fold, respectively. Values for whales were down to half the length (i.e., 1.1, 3, and 5 million generations), perhaps due to the reduced mechanical constraints of living in an aquatic environment. When differences in generation time are considered, we find an exponential increase in maximum mammal body mass during the 35 million years following the Cretaceous-Paleogene (K-Pg) extinction event. Our results also indicate a basic asymmetry in macroevolution: very large decreases (such as extreme insular dwarfism) can happen at more than 10 times the rate of increases. Our findings allow more rigorous comparisons of microevolutionary and macroevolutionary patterns and processes.
Zardoya, R.; Meyer, A.
1997-01-01
The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3' end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNAs, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship. PMID:9215903
Zardoya, R; Meyer, A
1996-05-28
The origin of land vertebrates was one of the major transitions in the history of vertebrates. Yet, despite many studies that are based on either morphology or molecules, the phylogenetic relationships among tetrapods and the other two living groups of lobe-finned fishes, the coelacanth and the lungfishes, are still unresolved and debated. Knowledge of the relationships among these lineages, which originated back in the Devonian, has profound implications for the reconstruction of the evolutionary scenario of the conquest of land. We collected the largest molecular data set on this issue so far, about 3,500 base pairs from seven species of the large 28S nuclear ribosomal gene. All phylogenetic analyses (maximum parsimony, neighbor-joining, and maximum likelihood) point toward the hypothesis that lungfishes and coelacanths form a monophyletic group and are equally closely related to land vertebrates. This evolutionary hypothesis complicates the identification of morphological or physiological preadaptations that might have permitted the common ancestor of tetrapods to colonize land. This is because the reconstruction of its ancestral conditions would be hindered by the difficulty to separate uniquely derived characters from shared derived characters in the coelacanth/lungfish and tetrapod lineages. This molecular phylogeny aids in the reconstruction of morphological evolutionary steps by providing a framework; however, only paleontological evidence can determine the sequence of morphological acquisitions that allowed lobe-finned fishes to colonize land.
Zardoya, R; Meyer, A
1997-07-01
The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3' end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNAs, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.
Zardoya, Rafael; Meyer, Axel
The phylogenetic position of tetrapods relative to the other two living sarcopterygian lineages (lungfishes and the coelacanth) has been subject to debate for many decades, yet remains unresolved. There are three possible alternatives for the phylogenetic relationships among these three living lineages of sarcopterygians, i.e., lungfish as living sister group of tetrapods, the coelacanth as closest living relative of tetrapods, and lungfish and coelacanth equally closely related to tetrapods. To resolve this important evolutionary question several molecular data sets have been collected in recent years, the largest being the almost complete 28S rRNA gene sequences (about 3500bp) and the complete mitochondrial genomes of the coelacanth and a lungfish (about 16500bp each). Phylogenetic analyses of several molecular data sets had not provided unequivocal support for any of the three hypotheses. However, a lungfish+tetrapod or a lungfish+coelacanth clade were predominantly favored over a coelacanth+tetrapod grouping when the entire mitochondrial genomes alone or in combination with the nuclear 28S rRNA gene data were analyzed with maximum parsimony, neighbor-joining, and maximum likelihood phylogenetic methods. Also, current paleontological and morphological data seem to concur with these molecular results. Therefore the currently available molecular data seems to rule out a coelacanth+tetrapod relationship, the traditional textbook hypothesis. These tentative molecular phylogenetic results point to the inherent difficulty in resolving relationships among lineages which apparently originated in rapid succession during the Devonian.
First report of Trichomonas tenax infections in the Philippines.
Dimasuay, Kris Genelyn B; Rivera, Windell L
2014-04-01
Recent studies have reported Trichomonas tenax as a cause of pleuropulmonary infections in humans. In this study, sputum and vaginal swab samples were collected from patients suffering from respiratory ailments in Rodriguez, Rizal and sex workers attending the social hygiene clinics in Angeles City in Pampanga, Mandaluyong City and Pasay City in Metro Manila, Philippines, respectively. DNA was extracted from samples and the 18S rRNA gene was amplified and sequenced. Phylogenetic trees were constructed using neighbor-joining, maximum-likelihood, maximum parsimony, and Bayesian inference analyses. Results showed that the new primer sets successfully amplified T. tenax from 14 sputum samples and Trichomonas vaginalis from 19 vaginal swab samples. Consequently, all isolates clustered with high bootstrap support and posterior probability values to their respective reference strains in the phylogenetic tree. Thus, the genus Trichomonas formed a highly supported clade with T. vaginalis in the first clade and T. tenax in the second clade. These findings conclude that T. vaginalis is solely present in the genito-urinary tract of females and that T. tenax can be found in the respiratory tract of humans. To our knowledge, this is the first report of detection and identification of T. tenax from sputum samples in the Philippines. However, further studies are still needed to determine the pathogenicity of this organism in humans. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.
Azevedo, Carlos; Abdel-Baki, Abdel-Azeem S; Rocha, Sónia; Al-Quraishy, Saleh; Casal, Graça
2016-02-01
A new microsporidian species, Glugea arabica n. sp., is reported infecting the intestinal wall of the marine teleost Epinephelus polyphekadion (=microdon) collected from the Red Sea coast off Saudi Arabia, and described on the basis of microscopic and molecular procedures. Spherical blackish xenomas formed parasitophorous vacuoles completely packed with several parasitic developmental stages, including spores. The nuclei were monokaryotic in all developmental stages. Spores were ellipsoidal to pyriform and measured 6.3 ± 0.3 (5.9-6.6) μm in length and 3.3 ± 0.4 (2.9-3.7) μm in width. A lamellar polaroplast surrounded the uncoiled portion of the polar filament, which extended into the spore's posterior pole and formed 27-29 coils organized in three or four rows. The posterior vacuole, located at the spore's posterior pole, appeared surrounded by the polar filament coils and displayed an irregular matrix composed of light material, in which was located the posterosome. Molecular analysis of the rRNA genes, including the ITS region, was performed using maximum parsimony, neighbor-joining and maximum likelihood methodologies. The ultrastructural features observed, in combination with the molecular data analysed, suggests the parasite to be a new species of the genus Glugea.
Rocha, S; Casal, G; Garcia, P; Matos, E; Al-Quraishy, S; Azevedo, C
2014-12-02
Microscopic and molecular procedures are used to describe a new myxosporean species, Henneguya carolina sp. nov., found infecting the intestine of the marine teleost fish Trachinotus carolinus on the southern Atlantic coast of Brazil. Spherical to ellipsoid cysts, measuring up to ~750 µm, display synchronous development. Mature myxospores are ellipsoidal with a bifurcated caudal process. Myxospore body length, width, and thickness are 12.7 ± 0.8 (12.0-13.4) µm, 8.8 ± 0.6 (7.5-9.6) µm, and 5.8 ± 0.4 (5.0-6.4) µm, respectively; 2 equal caudal processes are 16.8 ± 1.1 (15.9-18.0) µm long, and the total myxospore length is 29.4 ± 0.8 (28.4-30.4) µm. Two pyriform polar capsules measure 5.0 ± 0.5 (4.6-5.6) × 2.4 ± 0.4 (1.9-2.9) µm, and each contains a polar filament forming 3 to 4 coils. Sporoplasm is binucleated and presents a spherical vacuole surrounded by numerous globular sporoplasmosomes. Molecular analysis of the small subunit rRNA gene by maximum parsimony, neighbor joining, and maximum likelihood reveals the parasite clustering together with other myxobolids that are histozoic in marine fish of the order Perciformes, thereby strengthening the contention that the host phylogenetic relationships and aquatic environment are the strongest evolutionary signal for myxosporeans of the family Myxobolidae.
无
2007-01-01
The family Cyprinidae is widely distributed in East Asia, and has the important phylogenetic signifi- cance in the fish evolution. In this study, the 5′ end partial sequences (containing exon 1, exon 2 and indel 1) of S6K1 gene were obtained from 30 representative species in Cyprinidae and outgroup using PCR amplification and sequencing. The phylogenetic relationships of Cyprinidae were reconstructed with neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML), and Bayesian meth- ods. Myxocyprinus asiaticus (Catostomidae) was assigned to the outgroup taxon. Similar phylogenetic relationships within the family Cyprinidae were achieved with the four analyses. Leuciscini and Barbini were monophyletic lineages respectively with the high nodal supports. Leuciscini comprises Hypophthalmichthyinae, Xenocyprinae, Cultrinae, Gobioninae, Acheilognathinae and East Asian species of Leuciscinae and Danioninae. Monophyly of East Asian clade was supported with high nodal support. Barbini comprises Schizothoracinae, Barbinae, Cyprininae and Labeoninae. The monophyletic lineage consisting of Danio rerio, D. myersi, and Rasbora trilineata was basal in the tree. In addition, the large fragment indels in intron 1 were analyzed to improve the understanding of Cyprinidae relationships. The results showed that the large fragment indels were correlated with the relations among species. Some conserved regions in intron 1 were thought to be involved in the functional regulation. However, no correlation was found between sequence variations and species characteristic size.
无
2008-01-01
The phylogenetic relationships within the genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae) remain unresolved. Because of the use of Takifugu as model organisms, the resolution of these relationships is crucial for the interpretation of evolutionary trends in biology. Pufferfishes of this genus are comprised of a comparatively small number of species and are mainly distributed along the coastal region of the western part of the Sea of Japan and the coastline of China. Mitochondrial gene sequences were employed to test the phylogenetic hypotheses within the genus. Seventeen species of the genus were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, neighbor-joining, maximum likelihood and Bayesian methods. Our hypothesis of internal relationships within the genus differs from previous hypotheses. Our results indicate that (1) the genus Takifugu is a monophyletic assemblage; (2) the genus is divided into 6 subgroups based on the molecular data; and (3) there is low genetic diversity among the species within this genus. In addition,speciation within Takifugu appears to be driven by hybridization and isolation by distribution. Our resuits also suggested that the taxonomy in the genus should be clarified based on both molecular and morphological data.
Phylogenetic relationships among six species of Epistylis inferred from 18S-ITS1 sequences
MIAO; Wei(缪炜; ); YU; Yuhe(余育和); SHEN; Yunfen(沈韫芬); ZHANG; Xiyuan(张锡元)
2002-01-01
Phylogenetic relationships among six species of Epistylis (i. e. E. plicatilis, E. urceolata, E. chrysemydis, E. hentscheli, E. wenrichi, and E. galea) were investigated using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA). Amplified rDNA fragment sequences consisted of 215 or 217 bases of the flanking 18S and 5.8S regions, and the entire ITS-1 region (from 145 to 155 bases). There were more than 33 variable bases between E. galea and the other five species in both the 18S region and the ITS-1 region. The affiliation of them was assessed using Neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses. In all the NJ, MP and ML analyses E. galea, whose macronucleic position and shape are distinctly different from those of the other five species, was probably diverged from the ancestor of Epistylis earlier than the other five species. The topology in which E. plicatilis and E. hentscheli formed a strongly supported sister clade to E. urceolata, E. chrysemydis, and E. wenrichi was consistent with variations in the thickness of the peristomial lip. We concluded that the macronucleus and peristomial lip might be the important phylogenetic characteristics within the genus Epistylis.
HE; Shunping; LIU; Huanzhang; CHEN; Yiyu; Masayuki; Kuwah
2004-01-01
Complete mitochondrial cytochrome b sequences of 54 species, including 18 newly sequenced, were analyzed to infer the phylogenetic relationships within the family Cyprinidae in East Asia. Phylogenetic trees were generated using various tree-building methods, including Neighbor-joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods, with Myxocyprinus asiaticus (family Catostomidae) as the designated outgroup. The results from NJ and ML methods were mostly similar, supporting some existing subfamilies within Cyprinidae as monophyletic, such as Cultrinae, Xenocyprinae and Gobioninae (including Gobiobotinae). However, genera within the subfamily "Danioninae" did not form a monophyletic group. The subfamily Leuciscinae was divided into two unrelated groups: the "Leuciscinae" in East Asia forming as a monophyletic group together with Cultrinae and Xenocyprinae, while the Leuciscinae in Europe, Siberia, and North America as another monophyletic group. The monophyly of subfamily Cyprininae sensu Howes was supported by NJ and ML trees and is basal in the tree. The position of Acheilognathinae, a widely accepted monophyletic group represented by Rhodeus sericeus, was not resolved.
Aslak JØRGENSEN
2007-09-01
Full Text Available In the present study we investigate the genetic diversity within the asexually reproducing tardigrade Echiniscus testudo. The present study is the first to sample a tardigrade species for comparison of DNA sequence diversity between widely separated samples. Echiniscus testudo was sampled at 13 localities spanning three continents. DNA sequences of the mitochondrial COI gene and the nuclear ITS2 sequence were used to investigate the genetic diversity and phylogeographic structure of the various asexual lineages. Terrestrial tardigrades with the capability of entering a cryptobiotic state are assumed to have a high passive dispersal potential through airborne transport. Our results show moderate (ITS2 to high (COI haplotype diversity and low sequence diversity that indicate evolution of haplotypes within distinct asexual lineages and a high dispersal potential. No isolation by distance was detected by Mantel tests. Different phylogeny inference methods (neighbor-joining, maximum parsimony, maximum likelihood and Bayesian inference revealed little topological resolution, but minimum spanning networks showed some phylogeographic patterns. The COI and ITS2 minimum spanning networks show patterns that indicate dispersal of several haplotypes from founding populations. In conclusion our data show a low genetic diversity and a relatively high haplotype diversity indicating that E. testudo is a young species with a high dispersal potential.
Subtype Distribution of Blastocystis in Communities along the Chao Phraya River, Thailand.
Palasuwan, Attakorn; Palasuwan, Duangdao; Mahittikorn, Aongart; Chiabchalard, Rachatawan; Combes, Valery; Popruk, Supaluk
2016-08-01
Blastocystis is a common zoonotic enteric protozoan that has been classified into 17 distinct subtypes (STs). A cross-sectional study was conducted to determine the prevalence and subtype distributions of Blastocystis in villagers living along the Chao Phraya River, Ayutthaya Province, Thailand, and to assess the risk of zoonotic infection. In total, 220 stool samples were collected, and DNA was extracted. PCR and sequencing were performed with primers targeting the small-subunit ribosomal RNA (SSU rRNA) genes. Blastocystis was present in 5.9% (13/220) of samples, and ST3 (5.0%; 11/220) was the predominant subtype, followed by ST2 (0.45%; 1/220) and ST6 (0.45%; 1/220). Phylogenetic trees were constructed with the maximum-likelihood method based on the Hasegawa-Kishino-Yano + G + I model, neighbor-joining, and maximum parsimony methods. The percentage of bootstrapped trees in which the associated taxa clustered together was relatively high. All the sequences of the Blastocystis-positive samples (KU051524-KU051536) were closely related to those from animals (pig, cattle, and chicken), indicating a zoonotic risk. Therefore, the villagers require proper health education, especially regarding the prevention of parasitic infection, to improve their personal hygiene and community health. Further studies are required to investigate the Blastocystis STs in the animals living in these villages.
SHI Suhua; DU Yaqing; D. E. Boufford; GONG Xun; HUANG Yelin; HE Hanghang; ZHONG Yang
2003-01-01
The chloroplast gene matK and the internal transcribed spacers (ITS) of the nuclear ribosomal DNA from Schnabelia, a genus endemic to China, and 6 genera of Verbenaceae and 13 genera of Lamiaceae were sequenced. The phylogenetic signal and validity outgroups were measured and evaluated by means of the relatively apparent synapomorphy analysis (RASA). Independent and combined phylogenetic analyses for the matK and ITS sequences were performed using the maximum parsimony (MP), neighbor- joining (NJ) and maximum likelihood (ML) methods, indicating that Schnabelia oligophylla and Caryopteris terniflora form a sister-group relationship. The Caryopteris complex is not shown to be a monophyly because Trichostema, C. paniculata and C. forrestii are paraphyletic to the clade containing the remaining members of the complex. A monophyly of Ajugoideae proposed by Cantino et al., including 8 genera in this study, is strongly supported and the closest relatives of Schnabelia are in the Ajugoideae (Lamiaceae), especially near Caryopteris terniflora. The polygenetic analyses also showed that the genera of Lamiaceae and Verbenaceae sampled in this tudy are phylogenetically mixed and the genus Avicennia is distant to other genera of Verbenaceae. RASA and combined analysis can be used as effective approaches to determining the relationships among phylogenetically complex groups.
Rocha, Sónia; Casal, Graça; Velasco, Michele; Alves, Angela; Matos, Edilson; Al-Quraishy, Saleh; Azevedo, Carlos
2014-01-01
Thelohanellus marginatus n. sp., a new myxosporean parasite infecting the primary gill filaments of the teleost fish Hypophthalmus marginatus (Pimelodidae) in the Amazon River, is described on the basis of microscopic and molecular procedures. The parasite forms whitish and ellipsoidal cysts up to 250 μm in diam. Myxospores ellipsoidal with a slightly more pointed anterior end, measuring 17.1 ± 0.6 μm in length, 6.9 ± 0.4 μm in width, and 5.1 ± 0.5 μm in thickness. A single pyriform polar capsule, 9.0 ± 0.3 μm long and 6.1 ± 0.4 μm wide, positioned slightly right to the medial plane in valvular view, contains a polar filament arranged in 4-5 coils. Molecular analysis of the SSU rRNA gene by Maximum Parsimony, Neighbor-Joining, and Maximum Likelihood revealed the parasite clustering among other myxobolids, namely Henneguya and Myxobolus. Host affinity is supported as an important evolutionary signal for the phylogeny of myxobolids. The parasite here described represents the first record of the genus Thelohanellus Kudo, 1933 from the South American fauna. © 2014 The Author(s) Journal of Eukaryotic Microbiology © 2014 International Society of Protistologists.
Phylogenesis of relapsing fever Borrelia spp.
Ras, N M; Lascola, B; Postic, D; Cutler, S J; Rodhain, F; Baranton, G; Raoult, D
1996-10-01
The phylogenetic relationships of 20 relapsing fever (RF) Borrelia spp. were estimated on the basis of the sequences of rrs genes. Complete sequences were aligned and compared with previously published sequences, and the similarity values were found to be 97.7 to 99.9%. Phylogenetic trees were constructed by using the three neighbor-joining, maximum-parsimony, and maximum-likelihood methods. The results of the comparative phylogenetic analysis divided the RF Borrelia spp. into three major clusters. One cluster included Borrelia crocidurae, Borrelia duttonii, Borrelia recurrentis, and Borrelia hispanica. Another cluster comprised tow main branches with Borrelia coriaceae, Borrelia lonestari, and Borrelia miyamotoi on one side and Borrelia parkeri, Borrelia turicatae, and Borrelia hermsii on the other side. Borrelia anserina constituted the third cluster. The phylogenetic position of Borrelia persica was more uncertain. These results suggested that the taxonomy of these spirochetes should be revised. To overcome the problems of culturing the spirochetes, RF Borrelia primers were defined. Following PCR amplification of the rrs gene, restriction length fragment polymorphism could be used to distinguish between RF Borrelia strains.
Wang, Hai Tang; Yu, Xu; Liu, Yan; Liang, Cheng-Yuan; Li, Wei-Lin
2013-07-25
The genus Mentha comprises a group of aromatic plants with worldwide distribution. Because of frequent interspecific hybridization, the genetic relationships within the genus are not clearly understood. Limonene synthase, which catalyses the first committed step in the essential oil monoterpene biosynthetic pathway, is considered to be a possible rate limiting enzyme. With the homology-based cloning method, primers were designed according to cDNA sequence to amplify full-length DNA sequences in 13 Mentha samples from five species, using Perilla as an outgroup. Analyses of gene structure, length variation, GC-content, Ts/Tv ratio and evolutionary diversity were carried out. Consensus phylogenetic trees were obtained using maximum likelihood, neighbor-joining, and maximum parsimony, respectively, based on the full-length genomic DNA sequences, complete ORF coding sequences and predicted amino acid sequences. The results presented here based on the sequence of MhLS provide the first credibly supported genetic relationships for Mentha, which enables a basis for further mint taxonomy, cultivation and breeding.
A molecular phylogenetic investigation of zoothamnium (ciliophora, peritrichia, sessilida).
Clamp, John C; Williams, Daniel
2006-01-01
The gene coding for 18S small subunit ribosomal RNA (ssu rRNA) was sequenced in seven free-living, marine species of the sessiline peritrich genus Zoothamnium. These were Zoothamnium niveum, Zoothamnium alternans, Zoothamnium pelagicum, and four unidentified species. The ssu rRNA gene also was sequenced in Vorticella convallaria, Vorticella microstoma, and in an unidentified, freshwater species of Vorticella. Phylogenetic trees were constructed using these new sequences to test a previously published phylogenetic association between Zoothamnium arbuscula, currently in the family Zoothamniidae, and peritrichs in the family Vorticellidae. Trees constructed by means of neighbor-joining, maximum parsimony, maximum likelihood, and Bayesian inference methods all had similar topologies. The seven new sequences of Zoothamnium species grouped into three well-supported clades, each of which contained a diversity of morphological types. The three clades formed a poorly supported, larger clade that was deeply divergent from Z. arbuscula, which remained more closely associated with vorticellid peritrichs. It is apparent that Zoothamnium is a richly diverse genus and that a much more intensive investigation, involving both morphological and molecular data and a wider selection of species, will be necessary to resolve its phylogeny. A greater amount of molecular diversity than is predicted by morphological data exists within all major clades of sessiline peritrichs that have been included in molecular phylogenies, indicating that characteristics of stalk and peristomial structure traditionally used to differentiate taxa at the generic level and above may not be uniformly reliable.
Multiple sequence alignment accuracy and phylogenetic inference.
Ogden, T Heath; Rosenberg, Michael S
2006-04-01
Phylogenies are often thought to be more dependent upon the specifics of the sequence alignment rather than on the method of reconstruction. Simulation of sequences containing insertion and deletion events was performed in order to determine the role that alignment accuracy plays during phylogenetic inference. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (ultrametric equal branch length, ultrametric random branch length, nonultrametric random branch length). Comparisons between hypothesized alignments and true alignments enabled determination of two measures of alignment accuracy, that of the total data set and that of individual branches. In general, our results indicate that as alignment error increases, topological accuracy decreases. This trend was much more pronounced for data sets derived from more pectinate topologies. In contrast, for balanced, ultrametric, equal branch length tree shapes, alignment inaccuracy had little average effect on tree reconstruction. These conclusions are based on average trends of many analyses under different conditions, and any one specific analysis, independent of the alignment accuracy, may recover very accurate or inaccurate topologies. Maximum likelihood and Bayesian, in general, outperformed neighbor joining and maximum parsimony in terms of tree reconstruction accuracy. Results also indicated that as the length of the branch and of the neighboring branches increase, alignment accuracy decreases, and the length of the neighboring branches is the major factor in topological accuracy. Thus, multiple-sequence alignment can be an important factor in downstream effects on topological reconstruction.
Sang-Mi Sun
2016-01-01
Full Text Available Capsosiphon fulvescens is a filamentous green algae in the class Ulvophyceae. It has been consumed as food with unique flavor and soft texture to treat stomach disorders and hangovers, and its economic value justifies studying its nutritional and potential therapeutic effects. In contrast to these applications, only a few taxonomic studies have been conducted on C. fulvescens. In particular, classification and phylogenetic relationships of the C. fulvescens below the order level are controversial. To determine its phylogenetic position in the class, we used rbcL and 18S rDNA sequences as molecular markers to construct phylogenetic trees. The amplified rbcL and 18S rDNA sequences from 4 C. fulvescens isolates (Jindo, Jangheung, Wando, and Koheung, Korea were used for phylogenetic analysis by employing three different phylogenetic methods: neighbor joining (NJ, maximum parsimony (MP, and maximum likelihood (ML. The rbcL phylogenetic tree showed that all taxa in the order Ulvales were clustered as a monophyletic group and resolved the phylogenetic position of C. fulvescens in the order Ulotrichales. The significance of our study is that the 18S rDNA phylogenetic tree shows the detailed taxonomic position of C. fulvescens. In our result, C. fulvescens is inferred as a member of Ulotrichaceae, along with Urospora and Acrosiphonia.
Phylogeny and evolution of Cervidae based on complete mitochondrial genomes.
Zhang, W-Q; Zhang, M-H
2012-03-14
Mitochondrial DNA sequences can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We made phylogenetic analyses of 19 species of Cervidae, with Bos taurus as the outgroup. We used neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods on whole mitochondrial genome sequences. The consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Plesiometacarpalia and Telemetacarpalia, and four tribes, Cervinae, Muntiacinae, Hydropotinae, and Odocoileinae. The divergence times in these families were estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock method; the results were consistent with those of previous studies. We concluded that the evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; this method could be used broadly in phylogenetic evolutionary analysis of animal taxa.
Batishcheva, N M; Kartavtsev, Iu F; Bogutskaia, N G
2011-10-01
Molecular genetic analysis of Altai osmans of the genus Oreoleuciscus from two different parts of the range was carried out. In this study, based on the mitochondrial Co-1 gene sequence, a total of 25 fish specimens belonging to four genera were examined: (1) O. humilis, 2 specimens; O. potanini, 13 specimens; (2) Pseudaspius leptocephalus, 1 specimen; (3) Tribolodon brandtii, T. hakonensis, and T. sachalinensis from the GenBank database, 8 speciens; and (4) Leuciscus waleckii, 1 specimen (used as an outgroup). The p-distances were very low both within and between the species: (1) 0.20 +/- 0.03%; (2) 0.40 +/- 0.12%; and (1-2) 0.80 +/- 0.04%. To visualize the relationships among all of the species examined, the neighbor joining (NJ), maximum parsimony (MP), Bayesian (BA), and maximum likelihood (ML) trees were constructed. The results obtained using these methods were very similar. It was demonstrated that species assignment of the individuals (barcoding) with the help Co-1 gene was effective, despite of very low divergence of the two osman taxa, which was comparable with typical intraspecific values in other animal groups. Taxonomic status of O. potanini and O. humilis requires further investigation with paying attention to low genetic distances between these species along with the lack of material from sympatric parts of the ranges.
Zhang, W Q; Zhang, M H
2013-09-03
Many mitochondrial DNA sequences are used to estimate phylogenetic relationships among animal taxa and perform molecular phylogenetic evolution analysis. With the continuous development of sequencing technology, numerous mitochondrial sequences have been released in public databases, especially complete mitochondrial DNA sequences. Using multiple sequences is better than using single sequences for phylogenetic analysis of animals because multiple sequences have sufficient information for evolutionary process reconstruction. Therefore, we performed phylogenetic analyses of 14 species of Felidae based on complete mitochondrial genome sequences, with Canis familiaris as an outgroup, using neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods. The consensus phylogenetic trees supported the monophyly of Felidae, and the family could be divided into 2 subfamilies, Felinae and Pantherinae. The genus Panthera and species tigris were also studied in detail. Meanwhile, the divergence of this family was estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock, and the results shown were consistent with previous studies. In summary, the evolution of Felidae was reconstructed by phylogenetic analysis based on mitochondrial genome sequences. The described method may be broadly applicable for phylogenetic analyses of anima taxa.
Sharina, S N; Kartavtsev, Iu F
2010-03-01
Seventeen nucleotide sequences of Co-1 gene from 13 Pleuronectiformes species and 2 Perciformes species served as the outgroup were examined. For divergence comparison, the initial stage involved calculation of pairwise p-distances for all investigated sequences. This allowed to evaluate the nucleotide diversity on four phylogenetically different levels: (1) intraspecific, (2) intrageneric, (3) intrafamilial, and (4) intraordinal. The values of p-distances for the Co-1 gene for the four mentioned categories were (1) 0.93 +/- 0.73%, (2) 11.72 +/- 1.86%, (3) 12.10 +/- 1.10%, and (4) 20.20 +/- 0.22%, respectively. An increase in the level of genetic divergence along with an enhancement in taxon rank was previously reported for different species, which might be explained by prevalence of geographic speciation model in nature. Phylogenetic trees were constructed using four approaches: maximum parsimony, Bayesian, maximum likelihood, and neighbor-joining. These trees demonstrated similar results confirming the monophyletic origin of the families studied. The examined representatives of the flatfish species and genera were shown to be sufficiently divergent genetically.
Yuan-Miao FU; Wei-Mei JIANG; Cheng-Xin FU
2011-01-01
Many species of Tetrastigma (Miq.) Planch. (Vitaceae) have long been used as medicinal plants in China, and some are endangered due to overexploitation. Although adulterants are often added to traditional Chinese medicines, there is no reliable or practical method for identifying them. In this study, we used four markers (rbcL, matK, trnH-psbA and internal transcribed spacer [ITS]) as DNA barcodes to test their ability to distinguish species of Tetrastigma. The results indicated that the best barcode was ITS, which showed significant inter-specific genetic variability, and thus its potential as a DNA barcode for identifying Tetrastigma. Multiple loci provided a greater ability to distinguish species than single loci. We recommend using the combined rbcL+matK+ITS barcode for the genus. Phylogenetic trees from each barcode were compared. Analyses using the unweighted pair group method with arithmetic mean discriminated an equal or greater percentage of resolvable species than did neighbor joining, maximum likelihood, or maximum parsimony analyses. Additionally, five medicinal species of Tetrastigma, especially T. Hemsleyanum, could be identified precisely using DNA barcoding.
Rimantas Rakauskas
2014-03-01
Full Text Available Partial sequences of the mitochondrial COI gene of forty eight European and two Turkish population samples of Myzus cerasi from different winter hosts (Prunus spp. were subjected to phylogenetic analyses. The analysed M. cerasi samples emerged as paraphyletic relative to a Myzus borealis sample used as an out-group, and formed two major clades in neighbor joining, maximum parsimony, maximum likelihood and Bayesian inference trees, corresponding to subspecies living specifically on Prunus avium and P. cerasus. Multivariate discriminant analysis (method of canonical variates was applied to find out if morphological variation of samples correlated with mitochondrial COI and host plant information. Mean scores on the first two canonical variables clustered samples fully in accordance with their COI haplotypes and host plants confirming the existence of two morphologically similar winter host - specific subspecies of M.cerasi in Europe. No single morphological character enabled satisfactory discrimination between apterous viviparous females of the two subspecies. A three-character linear discriminant function enabled 92.37% correct identification of apterous viviparous females of M. cerasi cerasi (n=118 and 93.64% of M. cerasi pruniavium (n=110. A key for the morphological identification of the two subspecies is presented and their taxonomic status is discussed.
Huang, Jie; Yi, Zhenzhen; Miao, Miao; Al-Rasheid, Khaled A. S.; Song, Weibo
2011-03-01
The internal transcribed spacer regions (ITS1 and ITS2) and 5.8S rRNA genes were sequenced in six populations of four Aspidisca species, namely A. leptaspis, A. orthopogon, A. magna and A. aculeata. Phylogenetic trees were constructed by means of Bayesian inference (BI), Maximum Parsimony (MP), Neighbor-Joining (NJ), and Maximum Likelihood (ML) to assess the inter- and intra-species relationships within the genus Aspidisca. All trees show similar topologies with stable supports and indicate that: (1) four well known groups, i.e., Oligotrichia, Stichotrichia, Choreotrichia and Hypotrichia, are distinctly outlined within the class Spirotrichea, and all are monophyletic other than Hypotrichia; (2) members of Aspidisca can be distinguished well, based on the ITS1-5.8S-ITS2 region sequences, and A. leptaspis and A. magna shared a closer relationship than other species; (3) Aspidisca and Euplotes branch early in the subclass Hypotrichia. To compare the phylogenetic relationships based on different genes, SSU rRNA trees were also constructed with nearly the same species inclusion, which revealed different topologies of inter-species, inter-genera and inter-subclasses.
Gutierrez-Jurado, H. A.; Guan, H.; Wang, J.; Wang, H.; Bras, R. L.; Simmons, C. T.
2015-12-01
Quantification of evapotranspiration (ET) and its partition over regions of heterogeneous topography and canopy poses a challenge using traditional approaches. In this study, we report the results of a novel field experiment design guided by the Maximum Entropy Production model of ET (MEP-ET), formulated for estimating evaporation and transpiration from homogeneous soil and canopy. A catchment with complex terrain and patchy vegetation in South Australia was instrumented to measure temperature, humidity and net radiation at soil and canopy surfaces. Performance of the MEP-ET model to quantify transpiration and soil evaporation was evaluated during wet and dry conditions with independently and directly measured transpiration from sapflow and soil evaporation using the Bowen Ratio Energy Balance (BREB). MEP-ET transpiration shows remarkable agreement with that obtained through sapflow measurements during wet conditions, but consistently overestimates the flux during dry periods. However, an additional term introduced to the original MEP-ET model accounting for higher stomatal regulation during dry spells, based on differences between leaf and air vapor pressure deficits and temperatures, significantly improves the model performance. On the other hand, MEP-ET soil evaporation is in good agreement with that from BREB regardless of moisture conditions. The experimental design allows a plot and tree scale quantification of evaporation and transpiration respectively. This study confirms for the first time that the MEP-ET originally developed for homogeneous open bare soil and closed canopy can be used for modeling ET over heterogeneous land surfaces. Furthermore, we show that with the addition of an empirical function simulating the plants ability to regulate transpiration, and based on the same measurements of temperature and humidity, the method can produce reliable estimates of ET during both wet and dry conditions without compromising its parsimony.
Maximum power operation of interacting molecular motors
Golubeva, Natalia; Imparato, Alberto
2013-01-01
We study the mechanical and thermodynamic properties of different traffic models for kinesin which are relevant in biological and experimental contexts. We find that motor-motor interactions play a fundamental role by enhancing the thermodynamic efficiency at maximum power of the motors......, as compared to the non-interacting system, in a wide range of biologically compatible scenarios. We furthermore consider the case where the motor-motor interaction directly affects the internal chemical cycle and investigate the effect on the system dynamics and thermodynamics....
Maximum a posteriori decoder for digital communications
Altes, Richard A. (Inventor)
1997-01-01
A system and method for decoding by identification of the most likely phase coded signal corresponding to received data. The present invention has particular application to communication with signals that experience spurious random phase perturbations. The generalized estimator-correlator uses a maximum a posteriori (MAP) estimator to generate phase estimates for correlation with incoming data samples and for correlation with mean phases indicative of unique hypothesized signals. The result is a MAP likelihood statistic for each hypothesized transmission, wherein the highest value statistic identifies the transmitted signal.
Kernel-based Maximum Entropy Clustering
JIANG Wei; QU Jiao; LI Benxi
2007-01-01
With the development of Support Vector Machine (SVM),the "kernel method" has been studied in a general way.In this paper,we present a novel Kernel-based Maximum Entropy Clustering algorithm (KMEC).By using mercer kernel functions,the proposed algorithm is firstly map the data from their original space to high dimensional space where the data are expected to be more separable,then perform MEC clustering in the feature space.The experimental results show that the proposed method has better performance in the non-hyperspherical and complex data structure.
The sun and heliosphere at solar maximum.
Smith, E J; Marsden, R G; Balogh, A; Gloeckler, G; Geiss, J; McComas, D J; McKibben, R B; MacDowall, R J; Lanzerotti, L J; Krupp, N; Krueger, H; Landgraf, M
2003-11-14
Recent Ulysses observations from the Sun's equator to the poles reveal fundamental properties of the three-dimensional heliosphere at the maximum in solar activity. The heliospheric magnetic field originates from a magnetic dipole oriented nearly perpendicular to, instead of nearly parallel to, the Sun's rotation axis. Magnetic fields, solar wind, and energetic charged particles from low-latitude sources reach all latitudes, including the polar caps. The very fast high-latitude wind and polar coronal holes disappear and reappear together. Solar wind speed continues to be inversely correlated with coronal temperature. The cosmic ray flux is reduced symmetrically at all latitudes.
Conductivity maximum in a charged colloidal suspension
Bastea, S
2009-01-27
Molecular dynamics simulations of a charged colloidal suspension in the salt-free regime show that the system exhibits an electrical conductivity maximum as a function of colloid charge. We attribute this behavior to two main competing effects: colloid effective charge saturation due to counterion 'condensation' and diffusion slowdown due to the relaxation effect. In agreement with previous observations, we also find that the effective transported charge is larger than the one determined by the Stern layer and suggest that it corresponds to the boundary fluid layer at the surface of the colloidal particles.
Maximum entropy signal restoration with linear programming
Mastin, G.A.; Hanson, R.J.
1988-05-01
Dantzig's bounded-variable method is used to express the maximum entropy restoration problem as a linear programming problem. This is done by approximating the nonlinear objective function with piecewise linear segments, then bounding the variables as a function of the number of segments used. The use of a linear programming approach allows equality constraints found in the traditional Lagrange multiplier method to be relaxed. A robust revised simplex algorithm is used to implement the restoration. Experimental results from 128- and 512-point signal restorations are presented.
COMPARISON BETWEEN FORMULAS OF MAXIMUM SHIP SQUAT
PETRU SERGIU SERBAN
2016-06-01
Full Text Available Ship squat is a combined effect of ship’s draft and trim increase due to ship motion in limited navigation conditions. Over time, researchers conducted tests on models and ships to find a mathematical formula that can define squat. Various forms of calculating squat can be found in the literature. Among those most commonly used are of Barrass, Millward, Eryuzlu or ICORELS. This paper presents a comparison between the squat formulas to see the differences between them and which one provides the most satisfactory results. In this respect a cargo ship at different speeds was considered as a model for maximum squat calculations in canal navigation conditions.
Multi-Channel Maximum Likelihood Pitch Estimation
Christensen, Mads Græsbøll
2012-01-01
In this paper, a method for multi-channel pitch estimation is proposed. The method is a maximum likelihood estimator and is based on a parametric model where the signals in the various channels share the same fundamental frequency but can have different amplitudes, phases, and noise characteristics....... This essentially means that the model allows for different conditions in the various channels, like different signal-to-noise ratios, microphone characteristics and reverberation. Moreover, the method does not assume that a certain array structure is used but rather relies on a more general model and is hence...
Maximum entropy PDF projection: A review
Baggenstoss, Paul M.
2017-06-01
We review maximum entropy (MaxEnt) PDF projection, a method with wide potential applications in statistical inference. The method constructs a sampling distribution for a high-dimensional vector x based on knowing the sampling distribution p(z) of a lower-dimensional feature z = T (x). Under mild conditions, the distribution p(x) having highest possible entropy among all distributions consistent with p(z) may be readily found. Furthermore, the MaxEnt p(x) may be sampled, making the approach useful in Monte Carlo methods. We review the theorem and present a case study in model order selection and classification for handwritten character recognition.
CORA: Emission Line Fitting with Maximum Likelihood
Ness, Jan-Uwe; Wichmann, Rainer
2011-12-01
CORA analyzes emission line spectra with low count numbers and fits them to a line using the maximum likelihood technique. CORA uses a rigorous application of Poisson statistics. From the assumption of Poissonian noise, the software derives the probability for a model of the emission line spectrum to represent the measured spectrum. The likelihood function is used as a criterion for optimizing the parameters of the theoretical spectrum and a fixed point equation is derived allowing an efficient way to obtain line fluxes. CORA has been applied to an X-ray spectrum with the Low Energy Transmission Grating Spectrometer (LETGS) on board the Chandra observatory.
Dynamical maximum entropy approach to flocking
Cavagna, Andrea; Giardina, Irene; Ginelli, Francesco; Mora, Thierry; Piovani, Duccio; Tavarone, Raffaele; Walczak, Aleksandra M.
2014-04-01
We derive a new method to infer from data the out-of-equilibrium alignment dynamics of collectively moving animal groups, by considering the maximum entropy model distribution consistent with temporal and spatial correlations of flight direction. When bird neighborhoods evolve rapidly, this dynamical inference correctly learns the parameters of the model, while a static one relying only on the spatial correlations fails. When neighbors change slowly and the detailed balance is satisfied, we recover the static procedure. We demonstrate the validity of the method on simulated data. The approach is applicable to other systems of active matter.
Maximum Temperature Detection System for Integrated Circuits
Frankiewicz, Maciej; Kos, Andrzej
2015-03-01
The paper describes structure and measurement results of the system detecting present maximum temperature on the surface of an integrated circuit. The system consists of the set of proportional to absolute temperature sensors, temperature processing path and a digital part designed in VHDL. Analogue parts of the circuit where designed with full-custom technique. The system is a part of temperature-controlled oscillator circuit - a power management system based on dynamic frequency scaling method. The oscillator cooperates with microprocessor dedicated for thermal experiments. The whole system is implemented in UMC CMOS 0.18 μm (1.8 V) technology.
Zipf's law and maximum sustainable growth
Malevergne, Y; Sornette, D
2010-01-01
Zipf's law states that the number of firms with size greater than S is inversely proportional to S. Most explanations start with Gibrat's rule of proportional growth but require additional constraints. We show that Gibrat's rule, at all firm levels, yields Zipf's law under a balance condition between the effective growth rate of incumbent firms (which includes their possible demise) and the growth rate of investments in entrant firms. Remarkably, Zipf's law is the signature of the long-term optimal allocation of resources that ensures the maximum sustainable growth rate of an economy.
Accurate structural correlations from maximum likelihood superpositions.
Douglas L Theobald
2008-02-01
Full Text Available The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method ("PCA plots" for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology.
Maximum entropy production and the fluctuation theorem
Dewar, R C [Unite EPHYSE, INRA Centre de Bordeaux-Aquitaine, BP 81, 33883 Villenave d' Ornon Cedex (France)
2005-05-27
Recently the author used an information theoretical formulation of non-equilibrium statistical mechanics (MaxEnt) to derive the fluctuation theorem (FT) concerning the probability of second law violating phase-space paths. A less rigorous argument leading to the variational principle of maximum entropy production (MEP) was also given. Here a more rigorous and general mathematical derivation of MEP from MaxEnt is presented, and the relationship between MEP and the FT is thereby clarified. Specifically, it is shown that the FT allows a general orthogonality property of maximum information entropy to be extended to entropy production itself, from which MEP then follows. The new derivation highlights MEP and the FT as generic properties of MaxEnt probability distributions involving anti-symmetric constraints, independently of any physical interpretation. Physically, MEP applies to the entropy production of those macroscopic fluxes that are free to vary under the imposed constraints, and corresponds to selection of the most probable macroscopic flux configuration. In special cases MaxEnt also leads to various upper bound transport principles. The relationship between MaxEnt and previous theories of irreversible processes due to Onsager, Prigogine and Ziegler is also clarified in the light of these results. (letter to the editor)
Thermodynamic hardness and the maximum hardness principle
Franco-Pérez, Marco; Gázquez, José L.; Ayers, Paul W.; Vela, Alberto
2017-08-01
An alternative definition of hardness (called the thermodynamic hardness) within the grand canonical ensemble formalism is proposed in terms of the partial derivative of the electronic chemical potential with respect to the thermodynamic chemical potential of the reservoir, keeping the temperature and the external potential constant. This temperature dependent definition may be interpreted as a measure of the propensity of a system to go through a charge transfer process when it interacts with other species, and thus it keeps the philosophy of the original definition. When the derivative is expressed in terms of the three-state ensemble model, in the regime of low temperatures and up to temperatures of chemical interest, one finds that for zero fractional charge, the thermodynamic hardness is proportional to T-1(I -A ) , where I is the first ionization potential, A is the electron affinity, and T is the temperature. However, the thermodynamic hardness is nearly zero when the fractional charge is different from zero. Thus, through the present definition, one avoids the presence of the Dirac delta function. We show that the chemical hardness defined in this way provides meaningful and discernible information about the hardness properties of a chemical species exhibiting integer or a fractional average number of electrons, and this analysis allowed us to establish a link between the maximum possible value of the hardness here defined, with the minimum softness principle, showing that both principles are related to minimum fractional charge and maximum stability conditions.
Maximum Likelihood Analysis in the PEN Experiment
Lehman, Martin
2013-10-01
The experimental determination of the π+ -->e+ ν (γ) decay branching ratio currently provides the most accurate test of lepton universality. The PEN experiment at PSI, Switzerland, aims to improve the present world average experimental precision of 3 . 3 ×10-3 to 5 ×10-4 using a stopped beam approach. During runs in 2008-10, PEN has acquired over 2 ×107 πe 2 events. The experiment includes active beam detectors (degrader, mini TPC, target), central MWPC tracking with plastic scintillator hodoscopes, and a spherical pure CsI electromagnetic shower calorimeter. The final branching ratio will be calculated using a maximum likelihood analysis. This analysis assigns each event a probability for 5 processes (π+ -->e+ ν , π+ -->μ+ ν , decay-in-flight, pile-up, and hadronic events) using Monte Carlo verified probability distribution functions of our observables (energies, times, etc). A progress report on the PEN maximum likelihood analysis will be presented. Work supported by NSF grant PHY-0970013.
Lake Basin Fetch and Maximum Length/Width
Minnesota Department of Natural Resources — Linear features representing the Fetch, Maximum Length and Maximum Width of a lake basin. Fetch, maximum length and average width are calcuated from the lake polygon...
Maximum entropy principle and texture formation
Arminjon, M; Arminjon, Mayeul; Imbault, Didier
2006-01-01
The macro-to-micro transition in a heterogeneous material is envisaged as the selection of a probability distribution by the Principle of Maximum Entropy (MAXENT). The material is made of constituents, e.g. given crystal orientations. Each constituent is itself made of a large number of elementary constituents. The relevant probability is the volume fraction of the elementary constituents that belong to a given constituent and undergo a given stimulus. Assuming only obvious constraints in MAXENT means describing a maximally disordered material. This is proved to have the same average stimulus in each constituent. By adding a constraint in MAXENT, a new model, potentially interesting e.g. for texture prediction, is obtained.
MLDS: Maximum Likelihood Difference Scaling in R
Kenneth Knoblauch
2008-01-01
Full Text Available The MLDS package in the R programming language can be used to estimate perceptual scales based on the results of psychophysical experiments using the method of difference scaling. In a difference scaling experiment, observers compare two supra-threshold differences (a,b and (c,d on each trial. The approach is based on a stochastic model of how the observer decides which perceptual difference (or interval (a,b or (c,d is greater, and the parameters of the model are estimated using a maximum likelihood criterion. We also propose a method to test the model by evaluating the self-consistency of the estimated scale. The package includes an example in which an observer judges the differences in correlation between scatterplots. The example may be readily adapted to estimate perceptual scales for arbitrary physical continua.
Maximum Profit Configurations of Commercial Engines
Yiran Chen
2011-06-01
Full Text Available An investigation of commercial engines with finite capacity low- and high-price economic subsystems and a generalized commodity transfer law [n ∝ Δ (P m] in commodity flow processes, in which effects of the price elasticities of supply and demand are introduced, is presented in this paper. Optimal cycle configurations of commercial engines for maximum profit are obtained by applying optimal control theory. In some special cases, the eventual state—market equilibrium—is solely determined by the initial conditions and the inherent characteristics of two subsystems; while the different ways of transfer affect the model in respects of the specific forms of the paths of prices and the instantaneous commodity flow, i.e., the optimal configuration.
Maximum Segment Sum, Monadically (distilled tutorial
Jeremy Gibbons
2011-09-01
Full Text Available The maximum segment sum problem is to compute, given a list of integers, the largest of the sums of the contiguous segments of that list. This problem specification maps directly onto a cubic-time algorithm; however, there is a very elegant linear-time solution too. The problem is a classic exercise in the mathematics of program construction, illustrating important principles such as calculational development, pointfree reasoning, algebraic structure, and datatype-genericity. Here, we take a sideways look at the datatype-generic version of the problem in terms of monadic functional programming, instead of the traditional relational approach; the presentation is tutorial in style, and leavened with exercises for the reader.
Maximum Information and Quantum Prediction Algorithms
McElwaine, J N
1997-01-01
This paper describes an algorithm for selecting a consistent set within the consistent histories approach to quantum mechanics and investigates its properties. The algorithm uses a maximum information principle to select from among the consistent sets formed by projections defined by the Schmidt decomposition. The algorithm unconditionally predicts the possible events in closed quantum systems and ascribes probabilities to these events. A simple spin model is described and a complete classification of all exactly consistent sets of histories formed from Schmidt projections in the model is proved. This result is used to show that for this example the algorithm selects a physically realistic set. Other tentative suggestions in the literature for set selection algorithms using ideas from information theory are discussed.
Maximum process problems in optimal control theory
Goran Peskir
2005-01-01
Full Text Available Given a standard Brownian motion (Btt≥0 and the equation of motion dXt=vtdt+2dBt, we set St=max0≤s≤tXs and consider the optimal control problem supvE(Sτ−Cτ, where c>0 and the supremum is taken over all admissible controls v satisfying vt∈[μ0,μ1] for all t up to τ=inf{t>0|Xt∉(ℓ0,ℓ1} with μ0g∗(St, where s↦g∗(s is a switching curve that is determined explicitly (as the unique solution to a nonlinear differential equation. The solution found demonstrates that the problem formulations based on a maximum functional can be successfully included in optimal control theory (calculus of variations in addition to the classic problem formulations due to Lagrange, Mayer, and Bolza.
Maximum Spectral Luminous Efficacy of White Light
Murphy, T W
2013-01-01
As lighting efficiency improves, it is useful to understand the theoretical limits to luminous efficacy for light that we perceive as white. Independent of the efficiency with which photons are generated, there exists a spectrally-imposed limit to the luminous efficacy of any source of photons. We find that, depending on the acceptable bandpass and---to a lesser extent---the color temperature of the light, the ideal white light source achieves a spectral luminous efficacy of 250--370 lm/W. This is consistent with previous calculations, but here we explore the maximum luminous efficacy as a function of photopic sensitivity threshold, color temperature, and color rendering index; deriving peak performance as a function of all three parameters. We also present example experimental spectra from a variety of light sources, quantifying the intrinsic efficacy of their spectral distributions.
Maximum entropy model for business cycle synchronization
Xi, Ning; Muneepeerakul, Rachata; Azaele, Sandro; Wang, Yougui
2014-11-01
The global economy is a complex dynamical system, whose cyclical fluctuations can mainly be characterized by simultaneous recessions or expansions of major economies. Thus, the researches on the synchronization phenomenon are key to understanding and controlling the dynamics of the global economy. Based on a pairwise maximum entropy model, we analyze the business cycle synchronization of the G7 economic system. We obtain a pairwise-interaction network, which exhibits certain clustering structure and accounts for 45% of the entire structure of the interactions within the G7 system. We also find that the pairwise interactions become increasingly inadequate in capturing the synchronization as the size of economic system grows. Thus, higher-order interactions must be taken into account when investigating behaviors of large economic systems.
Quantum gravity momentum representation and maximum energy
Moffat, J. W.
2016-11-01
We use the idea of the symmetry between the spacetime coordinates xμ and the energy-momentum pμ in quantum theory to construct a momentum space quantum gravity geometry with a metric sμν and a curvature tensor Pλ μνρ. For a closed maximally symmetric momentum space with a constant 3-curvature, the volume of the p-space admits a cutoff with an invariant maximum momentum a. A Wheeler-DeWitt-type wave equation is obtained in the momentum space representation. The vacuum energy density and the self-energy of a charged particle are shown to be finite, and modifications of the electromagnetic radiation density and the entropy density of a system of particles occur for high frequencies.
Video segmentation using Maximum Entropy Model
QIN Li-juan; ZHUANG Yue-ting; PAN Yun-he; WU Fei
2005-01-01
Detecting objects of interest from a video sequence is a fundamental and critical task in automated visual surveillance.Most current approaches only focus on discriminating moving objects by background subtraction whether or not the objects of interest can be moving or stationary. In this paper, we propose layers segmentation to detect both moving and stationary target objects from surveillance video. We extend the Maximum Entropy (ME) statistical model to segment layers with features, which are collected by constructing a codebook with a set of codewords for each pixel. We also indicate how the training models are used for the discrimination of target objects in surveillance video. Our experimental results are presented in terms of the success rate and the segmenting precision.
Evaluation of pliers' grip spans in the maximum gripping task and sub-maximum cutting task.
Kim, Dae-Min; Kong, Yong-Ku
2016-12-01
A total of 25 males participated to investigate the effects of the grip spans of pliers on the total grip force, individual finger forces and muscle activities in the maximum gripping task and wire-cutting tasks. In the maximum gripping task, results showed that the 50-mm grip span had significantly higher total grip strength than the other grip spans. In the cutting task, the 50-mm grip span also showed significantly higher grip strength than the 65-mm and 80-mm grip spans, whereas the muscle activities showed a higher value at 80-mm grip span. The ratios of cutting force to maximum grip strength were also investigated. Ratios of 30.3%, 31.3% and 41.3% were obtained by grip spans of 50-mm, 65-mm, and 80-mm, respectively. Thus, the 50-mm grip span for pliers might be recommended to provide maximum exertion in gripping tasks, as well as lower maximum-cutting force ratios in the cutting tasks.
Cosmic shear measurement with maximum likelihood and maximum a posteriori inference
Hall, Alex
2016-01-01
We investigate the problem of noise bias in maximum likelihood and maximum a posteriori estimators for cosmic shear. We derive the leading and next-to-leading order biases and compute them in the context of galaxy ellipticity measurements, extending previous work on maximum likelihood inference for weak lensing. We show that a large part of the bias on these point estimators can be removed using information already contained in the likelihood when a galaxy model is specified, without the need for external calibration. We test these bias-corrected estimators on simulated galaxy images similar to those expected from planned space-based weak lensing surveys, with very promising results. We find that the introduction of an intrinsic shape prior mitigates noise bias, such that the maximum a posteriori estimate can be made less biased than the maximum likelihood estimate. Second-order terms offer a check on the convergence of the estimators, but are largely sub-dominant. We show how biases propagate to shear estima...
Wang, J.; Parolari, A.; Huang, S. Y.
2014-12-01
The objective of this study is to formulate and test plant water stress parameterizations for the recently proposed maximum entropy production (MEP) model of evapotranspiration (ET) over vegetated surfaces. . The MEP model of ET is a parsimonious alternative to existing land surface parameterizations of surface energy fluxes from net radiation, temperature, humidity, and a small number of parameters. The MEP model was previously tested for vegetated surfaces under well-watered and dry, dormant conditions, when the surface energy balance is relatively insensitive to plant physiological activity. Under water stressed conditions, however, the plant water stress response strongly affects the surface energy balance. This effect occurs through plant physiological adjustments that reduce ET to maintain leaf turgor pressure as soil moisture is depleted during drought. To improve MEP model of ET predictions under water stress conditions, the model was modified to incorporate this plant-mediated feedback between soil moisture and ET. We compare MEP model predictions to observations under a range of field conditions, including bare soil, grassland, and forest. The results indicate a water stress function that combines the soil water potential in the surface soil layer with the atmospheric humidity successfully reproduces observed ET decreases during drought. In addition to its utility as a modeling tool, the calibrated water stress functions also provide a means to infer ecosystem influence on the land surface state. Challenges associated with sampling model input data (i.e., net radiation, surface temperature, and surface humidity) are also discussed.
无
2008-01-01
The variation of the exon 2 of the major histo-compatibility complex (MHC) class Ⅱ gene DRB locus in three feline species were examined on clouded leopard (Neofelis nebulosa), leopard (Panthera pardus) and Amur tiger (Panthera tigris altaica). A pair of degenerated primers was used to amplify DRB locus covering almost the whole exon 2. Exon 2 encodes the β1 domain which is the most vari-able fragments of the MHC class Ⅱ molecule. Single-strand conformational polymorphism (SSCP) analysis was applied to detect different MHC class Ⅱ DRB haplotypes. Fifteen recombinant plasmids for each individual were screened out, isolated, purified and sequenced finally. Totally eight distinct haplotypes of exon 2 were obtained in four individuals. With-in 237 bp nucleotide sequences from four samples, 30 vari-able positions were found, and 21 putative peptide-binding positions were disclosed in 79 amino acid residues. The ratio of nonsynonymous substitutions (dN) was much higher than that of synonymous substitutions (dS), which indicated that balancing selection probably maintain the variation ofexon 2. MEGA neighbor joining (N J) and PAUP maximum parsimo-ny (MP) methods were used to reconstruct phylogenetic trees among species, respectively. Results displayed a more close relationship between leopard and tiger; however, clouded leopard has a comparatively distant relationship form the other two.
Zhu, Qianglong; Gao, Peng; Liu, Shi; Amanullah, Sikandar; Luan, Feishi
2016-12-01
A variety of melons are cultivated worldwide, and their specific biological properties make them an attractive model for molecular studies. This study aimed to investigate the single nucleotide polymorphisms (SNPs) from the mitochondrial, chloroplast, and nuclear genomes of seven melon accessions (Cucumis melo L.) to identify the phylogenetic relationships among melon cultivars with the Illumina HiSeq 2000 platform and bioinformatical analyses. The data showed that there were a total of 658 mitochondrial SNPs (207-295 in each), while there were 0-60 chloroplast SNPs among these seven melon cultivars, compared to the reference genome. Bioinformatical analysis showed that the mitochondrial tree topology was unable to separate the melon features, whereas the maximum parsimony/neighbor joining (MP/NJ) tree of the chloroplast SNPs could define melon features such as seed length, width, thickness, 100-seed weight, and type. SNPs of the nuclear genome were better than the mitochondrial and chloroplast SNPs in the identification of melon features. The data demonstrated the usefulness of mitochondrial, chloroplast, and nuclear SNPs in identification of phylogenetic associations among these seven melon cultivars.
无
2007-01-01
The ribosomal DNA internal transcribed spacer (ITS) region is a useful genomic region for understanding evolutionary and genetic relationships. In the current study, the molecular phylogenetic analysis of Pectinidae (Mollusca: Bivalvia) was performed using the nucleotide sequences of the nuclear ITS region in nine species of this family. The sequences were obtained from the scallop species Argopecten irradians, Mizuhopecten yessoensis, Amusium pleuronectes and Mimachlamys nobilis, and compared with the published sequences of Aequipecten opercularis, Chlamys farreri, C. distorta, M. varia, Pecten maximus, and an outgroup species Perna viridis. The molecular phylogenetic tree was constructed by the neighbor-joining and maximum parsimony methods. Phylogenetic analysis based on ITS1, ITS2, or their combination always yielded trees of similar topology. The results support the morphological classifications of bivalve and are nearly consistent with classification of two subfamilies (Chlamydinae and Pectininae) formulated by Waller. However, A. irradians, together with A. opercularis made up of genera Amusium, evidences that they may belong to the subfamily Pectinidae. The data are incompatible with the conclusion of Waller who placed them in Chlamydinae by morphological characteristics. These results provide new insights into the evolutionary relationships among scallop species and contribute to the improvement of existing classification systems.
LI Xueyan; YANG Shuang; XIE Meng; LIANG Xingcai
2006-01-01
We sequenced partial mitochondrial 16S ribosomal DNA (16S rDNA) of 18 firefly species from Southwest of China.Combined with homologous sequences previously reported, phylogenetic trees including Japanese, Korean and Chinese species were reconstructed by neighbor-joining, maximum parsimony and Bayesian methods. All reconstructions agree on most nodes of the trees. Monophyly of Lampyridae is not supported because Rhagophthalmus ohbai in Rhagophthalmidae is included within it. Lamprigera, a genus placed unreliably in Lampyrinae, shows a close relationship to Amydetinae. Monophyly of Luciolinae is not supported because Pristolycus sagulatus (Lampyrinae) is included within it. In the Luciolinae, monophyly of Curtos and Hotaria is well established, respectively, but both morphological and molecular data continue to indicate that Luciola is not monophyletic and its subdivision is indeed necessary. Within the Lampyrinae, both Pyrocoelia and Diaphanes are not monophyletic, but monophyly of Pyrocoelia + Diaphanes is well supported. Phylogeny of Diaphanes is discussed for the first time. Generic placement of a newly discovered species (Diaphanes pectinealis Li et Liang)sharing some characters of Pyrocoelia and Diaphanes challenges the delimitation of these two similar genera. With references to the firefly mating systems, we suggest that more emphases should be placed on those sexually selected characters such as antennal structure in taxonomy of Lampyridae.
Asian origin for Polystichum (Dryopteridaceae)based on rbcL sequences
LI Chunxiang; LU Shugang; YANG Qun
2004-01-01
Chloroplast rbcL sequences of 60 species of Polystichum sensu lato (s.l.), including 23 new sequences from southwest China, were used to assess the phylogenetic relationships within the genus. On the basis of estimated evolution rate of rbcL gene and the genetic distance data that passed relative-rate tests, we further estimated the divergence times between some clades of the genus. The phylogenetic relationships were inferred using the neighbor-joining and maximum-parsimony methods, both methods producing trees with completely congruent topology. These trees reveal that all species of Polystichum s.l. in this study (including Cyrtomium and Cyrtomidictyum) form a monophyletic group.The basal split in Polystichum s.l. separates a clade with all Asian members from a clade containing other species from all over the world. The phylogenetic and divergence time estimation results lead us to suggest that Polystichum s.l.originated in Asia in the late Late Cretacous (≈76 Ma) and migrated into other places in the world in early Eocene (≈46 Ma).
Taxonomic relationships among Phenacomys voles as inferred by cytochrome b
Bellinger, M.R.; Haig, S.M.; Forsman, E.D.; Mullins, T.D.
2005-01-01
Taxonomic relationships among red tree voles (Phenacomys longicaudus longicaudus, P. l. silvicola), the Sonoma tree vole (P. pomo), the white-footed vole (P. albipes), and the heather vole (P. intermedius) were examined using 664 base pairs of the mitochondrial cytochrome b gene. Results indicate specific differences among red tree voles, Sonoma tree voles, white-footed voles, and heather voles, but no clear difference between the 2 Oregon subspecies of red tree voles (P. l. longicaudus and P. l. silvicola). Our data further indicated a close relationship between tree voles and albipes, validating inclusion of albipes in the subgenus Arborimus. These 3 congeners shared a closer relationship to P. intermedius than to other arvicolids. A moderate association between porno and albipes was indicated by maximum parsimony and neighbor-joining phylogenetic analyses. Molecular clock estimates suggest a Pleistocene radiation of the Arborimus clade, which is concordant with pulses of diversification observed in other murid rodents. The generic rank of Arborimus is subject to interpretation of data.
Lah, Ernieenor Faraliana Che; Yaakop, Salmah; Ahamad, Mariana; George, Ernna; Nor, Shukor Md
2014-09-01
Identification of a local species of tick, Ixodes granulatus from the family Ixodidae is essential because it has potential to be vector for spotted fever group (SFG) rickettsia and tick thypus. The aim of this study is to portray the relationships among several populations of I. granulatus collected from different species of animal hosts and localities in Peninsular Malaysia. Polymerase Chain Reaction was conducted by amplifying mitochondrial DNA marker, namely cytochrome oxidase subunit I (COI) sequences from 15 individual ticks that attached to five different hosts caught from three different localities. Confirmation of the species identity was accomplished using BLAST program. Neighbor-joining (NJ) and Maximum Parsimony (MP) tree based on COI sequences were constructed by using PAUP 4.0b10 to identify the relationship among species. The result of this study showed a high genetic heterogeneity between I. granulatus and other species of the same genus (7.2-23.7%). Furthermore, a low intraspecific variation was observed among the species of I. granulatus collected from different localities (0-3.7%). This study produced the first establishment of molecular marker for clarifying genetic species variation and diversity of local I. granulatus tick which contribute to the control of tick-borne infections.
Identification of astigmatid mites using ITS2 and COI regions.
Yang, Bin; Cai, Junlong; Cheng, Xunjia
2011-02-01
Identification of astigmatid mites based on their morphological characteristics is difficult because of the similarity of their organs, especially in immature mites. The ribosomal second internal transcribed spacer (ITS2) and the mitochondrial cytochrome oxidase subunit I (COI) regions are highly conserved in the eukaryotes and are usually used as barcodes. The ITS2 and COI regions of six species of astigmatid mites (Aleuroglyphus ovatus, Blomia tropicalis, Dermatophagoides farinae, Dermatophagoides pteronyssinus, Euroglyphus maynei, Tyrophagus putrescentiae) were obtained by polymerase chain reaction and sequenced. The lengths of the ITS2 sequences varied from 316 to 488 bp, while the COI regions were 377 or 378 bp long. Considering the ITS2 genes, the intraspecific genetic distance was in the range of 0.00-0.077844, whereas the interspecific genetic distance was 0.202426-0.912959. The values were 0.000-0.029748 and 0.138403-0.279304 for intra- and interspecific genetic distances when COI genes were used. The phylogenetic trees inferred from the ITS2 and the COI regions, by using maximum parsimony and neighbor-joining methods, were identical to those based on their morphological classification. Thus, the ITS2 and COI regions can be applied as barcodes to identify different species of astigmatid mites.
PHYRN: a robust method for phylogenetic analysis of highly divergent sequences.
Gaurav Bhardwaj
Full Text Available Both multiple sequence alignment and phylogenetic analysis are problematic in the "twilight zone" of sequence similarity (≤ 25% amino acid identity. Herein we explore the accuracy of phylogenetic inference at extreme sequence divergence using a variety of simulated data sets. We evaluate four leading multiple sequence alignment (MSA methods (MAFFT, T-COFFEE, CLUSTAL, and MUSCLE and six commonly used programs of tree estimation (Distance-based: Neighbor-Joining; Character-based: PhyML, RAxML, GARLI, Maximum Parsimony, and Bayesian against a novel MSA-independent method (PHYRN described here. Strikingly, at "midnight zone" genetic distances (~7% pairwise identity and 4.0 gaps per position, PHYRN returns high-resolution phylogenies that outperform traditional approaches. We reason this is due to PHRYN's capability to amplify informative positions, even at the most extreme levels of sequence divergence. We also assess the applicability of the PHYRN algorithm for inferring deep evolutionary relationships in the divergent DANGER protein superfamily, for which PHYRN infers a more robust tree compared to MSA-based approaches. Taken together, these results demonstrate that PHYRN represents a powerful mechanism for mapping uncharted frontiers in highly divergent protein sequence data sets.
Mitochondrial cytochrome b sequence variations and phylogeny of the East Asian bagrid catfishes
无
2002-01-01
The mitochondrial DNA cytochrome b gene was sequenced from 8 bagrid catfishes in China. Aligned with cytochrome b sequences from 9 bagrid catfishes in Japan, Korea and Russia retrieved from GenBank, and selected Silurus meridionalis, Liobagrus anguillicauda, Liobagrus reini and Phenacogrammus interruptus as outgroups, we constructed a matrix of 21 DNA sequences. The Kimura's two-parameter distances were calculated and molecular phylogenetic trees were constructed by using the maximum parsimony (MP) and neighbor-joining (NJ) methods. The results show that (i) there exist 3-bp deletions of mitochondrial cytochrome b gene compared with cypriniforms and characiforms; (ii) the molecular phylogenetic tree suggests that bagrid catfishes form a monophyletic group, and the genus Mystus is the earliest divergent in the East Asian bagrid catfishes, as well as the genus Pseudobagrus is a monophyletic group but the genus Pelteobagrus and Leiocassis are complicated; and (iii) the evolution rate of the East Asian bagrids mitochondrial cytochrome b gene is about 0.18%～0.30% sequence divergence per million years.
[Molecular phylogeny of the gayal inferred from the analysis of cytochrome b gene entire sequences].
Li, Shi-Ping; Chang, Hong; Ma, Guo-Long; Chen, Hong-Yu; Ji, De-Jun; Geng, Rong-Qing
2008-01-01
The gayal (Bos frontalis) is a very rare, semi-wild and semi-domestic bovine species. There still exist remarkable divergences on the gayal's origin and phylogenetic status. The cytochrome b (Cyt b) gene entire sequences (1,140 bp) of 11 gayals were sequenced and analyzed. Combined with other bovine Cyt b entire sequences cited in GenBank, the phylogenetic trees of genus Bos were reconstructed by neighbor-joining (NJ) and maximum parsimony (MP) methods with Bubalus bubalis as outgroup. Sequence analysis showed that, among 1,140 sites of Cyt b gene entire sequences of 11 gayals, 95 variable sites (8.33% of all sites) and 6 haplotypes were found, showing abundant genetic diversity in mitochondrial Cyt b gene of the gayals. Both NJ and MP trees demonstrated that the gayals in this study were markedly divided into three embranchments: one embranchment clustering with Bos taurus, another clustering with Bos indicus, and the third clustering with Bos gaurus. The result of phylogenetic analysis suggested that the gayal might be the domesticated form of the gaur (Bos gaurus), and a great proportion of the gayal bloodline was invaded by other bovine species.
Phylogenetic relationships of 18 passerines based on Adenylate Kinase Intron 5 sequences
GUO Hui-yan; YU Hui-xin; BAI Su-ying; MA Yu-kun
2008-01-01
The 18 species of bird studied originally are known to belong to muscicapids, robins and sylviids of passerines, but some disputations are always present in their classification systems. In this experiment, phylogenetic relationships of 18 species of passerines were studied using Adenylate Kinase Intron 5 (AK5) sequences and DNA techniques. Through sequences analysis in comparison with each other, phylogenetic tree figures of 18 species of passerines were constructed using Neighbor-Joining (NJ) and Maximum-Parsimony (MP) methods . The results showed that sylviids should be listed as an independent family, while robins and flycatchers should be listed into Muscicapidae. Since the phylogenetic relationships between long-tailed tits and old world warblers are closer than that between long-tailed tits and parids, the long-tailed tits should be independent of paridae and be categorized into aegithalidae. Muscicapidae and Paridae are known to be two monophylitic families, but Sylviidae is not a monophyletic group. AK5 sequences had better efficacy in resolving close relationships of interspecies among intrageneric groups.
Zhong-Xing Wu; Nan-Qin Gan; Li-Rong Song
2007-01-01
Twenty strains of Microcystis Kütz were isolated from different freshwater bodies in China to analyze the diversity,geographical distribution and toxin profiles. Based on whole-cell polymerase chain reaction of cpcBA-IGS nucleotide sequence, the derived neighbor-joining (NJ) and maximum parsimony (MP) trees indicate that these strains of Microcystis can be divided into four clusters. The strains from south, middle and north region of China formed distinct lineages, suggesting high diversity and a geographical distribution from south to north locations. Moreover,the results being indicating high variable genotypes of the strains of the Microcystis strains from the same lake show that there is high diversity of Microcystis within a water bloom population. Comparing the results of the present study with those reported for compared with 43 strains of Microcystis from other locations, also reveals Chinese strains have high similarity with those from regions in the North Hemispherical. This suggests that the Microcystis strains in the world might have a geographical distribution. Analysis of 30 strains using the primers MCF/TER and TOX2P/TOX2M showed that there was no correlation between the gene of cpcBA-IGS and the presence of mcy. Toxic strains were founded to be predominant in different water bodies throughout China.
Molecular characterization of Leishmania species isolated from cutaneous leishmaniasis in Yemen.
Mohammed A K Mahdy
Full Text Available BACKGROUND: Cutaneous leishmaniasis (CL is a neglected tropical disease endemic in the tropics and subtropics with a global yearly incidence of 1.5 million. Although CL is the most common form of leishmaniasis, which is responsible for 60% of DALYs lost due to tropical-cluster diseases prevalent in Yemen, available information is very limited. METHODOLOGY/PRINCIPAL FINDINGS: This study was conducted to determine the molecular characterization of Leishmania species isolated from human cutaneous lesions in Yemen. Dermal scrapes were collected and examined for Leishmania amastigotes using the Giemsa staining technique. Amplification of the ribosomal internal transcribed spacer 1(ITS-1 gene was carried out using nested PCR and subsequent sequencing. The sequences from Leishmania isolates were subjected to phylogenetic analysis using the neighbor-joining and maximum parsimony methods. The trees identified Leishmania tropica from 16 isolates which were represented by two sequence types. CONCLUSIONS/SIGNIFICANCE: The predominance of the anthroponotic species (i.e. L. tropica indicates the probability of anthroponotic transmission of cutaneous leishmaniasis in Yemen. These findings will help public health authorities to build an effective control strategy taking into consideration person-to-person transmission as the main dynamic of transmission of CL.
Precise identification of different stages of a tick,Ixodes granulatus Supino,1897(Acari:Ixodidae)
Ernieenor Faraliana Che Lah; Salmah Yaakop; Mariana Ahamad; Ernna George; Shukor Md Nor
2016-01-01
Objective: To identify different stages of Ixodes granulatus(I. granulatus) based on morphological characters prior to molecular identification which is significant for confirming and identifying the nymphal stages of I. granulatus.Methods: A total of 14 individuals of adult, engorged and nymphal ticks collected from three different localities were examined morphologically using taxonomic keys, followed by PCR using cytochrome oxidase subunit I(COI). Clustering analysis based on COI sequences was carried out by constructing neighbor-joining and maximum parsimony tree to clarify the genetic variation and diversity of local I. granulatus.Results: Based on external morphological characterizations, nine individuals(64.3%)were successfully identified as I. granulatus, while five individuals were recognized only as Ixodes sp. due to lack of morphological characters visible and development during that stage. Molecular analysis of local I. granulatus using COI gene revealed 93%–94% sequence homology from available sequence in Gen Bank and was in concordance with the morphological identification. Furthermore, a low intraspecific variation was observed among the species of I. granulatus collected from different localities(0%–3.7%).Conclusions: These findings demonstrated for the first time the establishment of COI gene for identifying I. granulatus nymphal tick which is of paramount importance to the control of potential tick-borne infections in Malaysia. Moreover, this study provides evidence that a combination of morphology and molecular data was corroborated as an accurate tool for tick identification.
Ernieenor Faraliana Che Lah; Salmah Yaakop; Mariana Ahamad; Ernna George; Shukor Md Nor
2016-01-01
Objective: To identify different stages of Ixodes granulatus (I. granulatus) based on morphological characters prior to molecular identification which is significant for con-firming and identifying the nymphal stages of I. granulatus. Methods: A total of 14 individuals of adult, engorged and nymphal ticks collected from three different localities were examined morphologically using taxonomic keys, followed by PCR using cytochrome oxidase subunit I (COI). Clustering analysis based on COI sequences was carried out by constructing neighbor-joining and maximum parsimony tree to clarify the genetic variation and diversity of local I. granulatus. Results: Based on external morphological characterizations, nine individuals (64.3%) were successfully identified as I. granulatus, while five individuals were recognized only as Ixodes sp. due to lack of morphological characters visible and development during that stage. Molecular analysis of local I. granulatus using COI gene revealed 93%–94%sequence homology from available sequence in GenBank and was in concordance with the morphological identification. Furthermore, a low intraspecific variation was observed among the species of I. granulatus collected from different localities (0%–3.7%). Conclusions: These findings demonstrated for the first time the establishment of COI gene for identifying I. granulatus nymphal tick which is of paramount importance to the control of potential tick-borne infections in Malaysia. Moreover, this study provides evidence that a combination of morphology and molecular data was corroborated as an accurate tool for tick identification.
[DNA barcoding of COI gene in some medicinal animals of Lacertilia].
Li, Xiao-Ling; Zhang, Yue-Yun; Xu, Yong-Li; Zhao, Cheng-Jian; Gu, Ying-Le; Li, Li
2013-04-01
To identify some medicinal animals of Lacertilia, in total 59 individuals belonging to 12 species 7 genera 3 families, we used the universal barcoding primers to sequence these species, compared with other homologous sequences (564 bp) obtaining from the GenBank and finally constructed phylogenetic trees using Neighbor-joining, Maximum parsimony and Bayesian inference, respectively. As a result, the mean content of G + C (46.5%) was lower than that of A + T (53.5%). As calculated by Kimera-2-parameter model, the whole individuals mean distance for interspecies and intraspecies was 35. 5% and 1.7%, respectively. The mean distance for interspecies was 21 times as much as that for intraspecies. The mean distance for intraspecies of Gekko swinhonis, Hemidactylus frenatus and G. gecko was greater than 2%, respectively. Further analyses suggested that geographical groups of the three species might be of different subSpecies, even species. Of course, incorporating morphological characters and other unlinked genetic markers in future studies will offer further insights into the divergence. On the basis of phylogenetic trees constructed by COI, our results indicated that the taxonomy of the category (family, genus, and species) by DNA barcoding is consistent with morphological characters. Therefore, DNA barcoding is a useful tool for both identification and phylogeny of medicinal animals of Lacertilia, particularly for nonprofessor identifying authentication of Chinese crude drugs of these species.
Brazilian Flavivirus phylogeny based on NS5.
Baleotti, Flúvia Graciela; Moreli, Marcos Lázaro; Figueiredo, Luiz Tadeu Moraes
2003-04-01
In this work, a comprehensive phylogenetic study based on 600 base pair nucleotide and on putative 200 amino acid sequences of NS5 was carried out in order to establish genetic relationships among 15 strains of 10 Brazilian flaviviruses: Bussuquara, Cacipacore, dengue type 1, 2 and 4, Iguape, Ilheus, Rocio, Saint Louis encephalitis (SLE), and yellow fever. Phylogenetic trees were created by neighbor-joining and maximum parsimony methods. These trees showed Brazilian flaviviruses grouped into three main branches: yellow fever branch, dengue branch subdivided in types 1, 2 and 4 branches, and Japanese encephalitis virus (JEV) complex branch including SLE virus strains, Cacipacore, Iguape, Rocio, Ilheus and Bussuquara. Viruses transmitted by Aedes mosquitoes, such as dengue and urban yellow fever, that are also the only Flavivirus causing hemorrhagic fevers in Brazil, were grouped in the same cluster. Encephalitis associated viruses, transmitted by Culex mosquitoes such as JEV complex branch including SLE virus strains, Cacipacore, Iguape, Rocio, Ilheus and Bussuquara were also grouped in the same clade.
20 CFR 211.14 - Maximum creditable compensation.
2010-04-01
... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Maximum creditable compensation. 211.14... CREDITABLE RAILROAD COMPENSATION § 211.14 Maximum creditable compensation. Maximum creditable compensation... Employment Accounts shall notify each employer of the amount of maximum creditable compensation applicable...
49 CFR 230.24 - Maximum allowable stress.
2010-10-01
... 49 Transportation 4 2010-10-01 2010-10-01 false Maximum allowable stress. 230.24 Section 230.24... Allowable Stress § 230.24 Maximum allowable stress. (a) Maximum allowable stress value. The maximum allowable stress value on any component of a steam locomotive boiler shall not exceed 1/4 of the ultimate...
Theoretical Estimate of Maximum Possible Nuclear Explosion
Bethe, H. A.
1950-01-31
The maximum nuclear accident which could occur in a Na-cooled, Be moderated, Pu and power producing reactor is estimated theoretically. (T.R.H.) 2O82 Results of nuclear calculations for a variety of compositions of fast, heterogeneous, sodium-cooled, U-235-fueled, plutonium- and power-producing reactors are reported. Core compositions typical of plate-, pin-, or wire-type fuel elements and with uranium as metal, alloy, and oxide were considered. These compositions included atom ratios in the following range: U-23B to U-235 from 2 to 8; sodium to U-235 from 1.5 to 12; iron to U-235 from 5 to 18; and vanadium to U-235 from 11 to 33. Calculations were performed to determine the effect of lead and iron reflectors between the core and blanket. Both natural and depleted uranium were evaluated as the blanket fertile material. Reactors were compared on a basis of conversion ratio, specific power, and the product of both. The calculated results are in general agreement with the experimental results from fast reactor assemblies. An analysis of the effect of new cross-section values as they became available is included. (auth)
Proposed principles of maximum local entropy production.
Ross, John; Corlan, Alexandru D; Müller, Stefan C
2012-07-12
Articles have appeared that rely on the application of some form of "maximum local entropy production principle" (MEPP). This is usually an optimization principle that is supposed to compensate for the lack of structural information and measurements about complex systems, even systems as complex and as little characterized as the whole biosphere or the atmosphere of the Earth or even of less known bodies in the solar system. We select a number of claims from a few well-known papers that advocate this principle and we show that they are in error with the help of simple examples of well-known chemical and physical systems. These erroneous interpretations can be attributed to ignoring well-established and verified theoretical results such as (1) entropy does not necessarily increase in nonisolated systems, such as "local" subsystems; (2) macroscopic systems, as described by classical physics, are in general intrinsically deterministic-there are no "choices" in their evolution to be selected by using supplementary principles; (3) macroscopic deterministic systems are predictable to the extent to which their state and structure is sufficiently well-known; usually they are not sufficiently known, and probabilistic methods need to be employed for their prediction; and (4) there is no causal relationship between the thermodynamic constraints and the kinetics of reaction systems. In conclusion, any predictions based on MEPP-like principles should not be considered scientifically founded.
Maximum entropy production and plant optimization theories.
Dewar, Roderick C
2010-05-12
Plant ecologists have proposed a variety of optimization theories to explain the adaptive behaviour and evolution of plants from the perspective of natural selection ('survival of the fittest'). Optimization theories identify some objective function--such as shoot or canopy photosynthesis, or growth rate--which is maximized with respect to one or more plant functional traits. However, the link between these objective functions and individual plant fitness is seldom quantified and there remains some uncertainty about the most appropriate choice of objective function to use. Here, plants are viewed from an alternative thermodynamic perspective, as members of a wider class of non-equilibrium systems for which maximum entropy production (MEP) has been proposed as a common theoretical principle. I show how MEP unifies different plant optimization theories that have been proposed previously on the basis of ad hoc measures of individual fitness--the different objective functions of these theories emerge as examples of entropy production on different spatio-temporal scales. The proposed statistical explanation of MEP, that states of MEP are by far the most probable ones, suggests a new and extended paradigm for biological evolution--'survival of the likeliest'--which applies from biomacromolecules to ecosystems, not just to individuals.
Maximum likelihood continuity mapping for fraud detection
Hogden, J.
1997-05-01
The author describes a novel time-series analysis technique called maximum likelihood continuity mapping (MALCOM), and focuses on one application of MALCOM: detecting fraud in medical insurance claims. Given a training data set composed of typical sequences, MALCOM creates a stochastic model of sequence generation, called a continuity map (CM). A CM maximizes the probability of sequences in the training set given the model constraints, CMs can be used to estimate the likelihood of sequences not found in the training set, enabling anomaly detection and sequence prediction--important aspects of data mining. Since MALCOM can be used on sequences of categorical data (e.g., sequences of words) as well as real valued data, MALCOM is also a potential replacement for database search tools such as N-gram analysis. In a recent experiment, MALCOM was used to evaluate the likelihood of patient medical histories, where ``medical history`` is used to mean the sequence of medical procedures performed on a patient. Physicians whose patients had anomalous medical histories (according to MALCOM) were evaluated for fraud by an independent agency. Of the small sample (12 physicians) that has been evaluated, 92% have been determined fraudulent or abusive. Despite the small sample, these results are encouraging.
Maximum life spiral bevel reduction design
Savage, M.; Prasanna, M. G.; Coe, H. H.
1992-07-01
Optimization is applied to the design of a spiral bevel gear reduction for maximum life at a given size. A modified feasible directions search algorithm permits a wide variety of inequality constraints and exact design requirements to be met with low sensitivity to initial values. Gear tooth bending strength and minimum contact ratio under load are included in the active constraints. The optimal design of the spiral bevel gear reduction includes the selection of bearing and shaft proportions in addition to gear mesh parameters. System life is maximized subject to a fixed back-cone distance of the spiral bevel gear set for a specified speed ratio, shaft angle, input torque, and power. Significant parameters in the design are: the spiral angle, the pressure angle, the numbers of teeth on the pinion and gear, and the location and size of the four support bearings. Interpolated polynomials expand the discrete bearing properties and proportions into continuous variables for gradient optimization. After finding the continuous optimum, a designer can analyze near optimal designs for comparison and selection. Design examples show the influence of the bearing lives on the gear parameters in the optimal configurations. For a fixed back-cone distance, optimal designs with larger shaft angles have larger service lives.
CORA - emission line fitting with Maximum Likelihood
Ness, J.-U.; Wichmann, R.
2002-07-01
The advent of pipeline-processed data both from space- and ground-based observatories often disposes of the need of full-fledged data reduction software with its associated steep learning curve. In many cases, a simple tool doing just one task, and doing it right, is all one wishes. In this spirit we introduce CORA, a line fitting tool based on the maximum likelihood technique, which has been developed for the analysis of emission line spectra with low count numbers and has successfully been used in several publications. CORA uses a rigorous application of Poisson statistics. From the assumption of Poissonian noise we derive the probability for a model of the emission line spectrum to represent the measured spectrum. The likelihood function is used as a criterion for optimizing the parameters of the theoretical spectrum and a fixed point equation is derived allowing an efficient way to obtain line fluxes. As an example we demonstrate the functionality of the program with an X-ray spectrum of Capella obtained with the Low Energy Transmission Grating Spectrometer (LETGS) on board the Chandra observatory and choose the analysis of the Ne IX triplet around 13.5 Å.
Finding maximum JPEG image block code size
Lakhani, Gopal
2012-07-01
We present a study of JPEG baseline coding. It aims to determine the minimum storage needed to buffer the JPEG Huffman code bits of 8-bit image blocks. Since DC is coded separately, and the encoder represents each AC coefficient by a pair of run-length/AC coefficient level, the net problem is to perform an efficient search for the optimal run-level pair sequence. We formulate it as a two-dimensional, nonlinear, integer programming problem and solve it using a branch-and-bound based search method. We derive two types of constraints to prune the search space. The first one is given as an upper-bound for the sum of squares of AC coefficients of a block, and it is used to discard sequences that cannot represent valid DCT blocks. The second type constraints are based on some interesting properties of the Huffman code table, and these are used to prune sequences that cannot be part of optimal solutions. Our main result is that if the default JPEG compression setting is used, space of minimum of 346 bits and maximum of 433 bits is sufficient to buffer the AC code bits of 8-bit image blocks. Our implementation also pruned the search space extremely well; the first constraint reduced the initial search space of 4 nodes down to less than 2 nodes, and the second set of constraints reduced it further by 97.8%.
Maximum likelihood estimates of pairwise rearrangement distances.
Serdoz, Stuart; Egri-Nagy, Attila; Sumner, Jeremy; Holland, Barbara R; Jarvis, Peter D; Tanaka, Mark M; Francis, Andrew R
2017-06-21
Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. Distances can be estimated using a range of different evolutionary models, from single nucleotide polymorphisms to large-scale genome rearrangements. Corresponding corrections for genome rearrangement distances fall into 3 categories: Empirical computational studies, Bayesian/MCMC approaches, and combinatorial approaches. Here, we introduce a maximum likelihood estimator for the inversion distance between a pair of genomes, using a group-theoretic approach to modelling inversions introduced recently. This MLE functions as a corrected distance: in particular, we show that because of the way sequences of inversions interact with each other, it is quite possible for minimal distance and MLE distance to differently order the distances of two genomes from a third. The second aspect tackles the problem of accounting for the symmetries of circular arrangements. While, generally, a frame of reference is locked, and all computation made accordingly, this work incorporates the action of the dihedral group so that distance estimates are free from any a priori frame of reference. The philosophy of accounting for symmetries can be applied to any existing correction method, for which examples are offered. Copyright © 2017 Elsevier Ltd. All rights reserved.
Boedeker, Peter
2017-01-01
Hierarchical linear modeling (HLM) is a useful tool when analyzing data collected from groups. There are many decisions to be made when constructing and estimating a model in HLM including which estimation technique to use. Three of the estimation techniques available when analyzing data with HLM are maximum likelihood, restricted maximum…
Maximum likelihood molecular clock comb: analytic solutions.
Chor, Benny; Khetan, Amit; Snir, Sagi
2006-04-01
Maximum likelihood (ML) is increasingly used as an optimality criterion for selecting evolutionary trees, but finding the global optimum is a hard computational task. Because no general analytic solution is known, numeric techniques such as hill climbing or expectation maximization (EM), are used in order to find optimal parameters for a given tree. So far, analytic solutions were derived only for the simplest model--three taxa, two state characters, under a molecular clock. Four taxa rooted trees have two topologies--the fork (two subtrees with two leaves each) and the comb (one subtree with three leaves, the other with a single leaf). In a previous work, we devised a closed form analytic solution for the ML molecular clock fork. In this work, we extend the state of the art in the area of analytic solutions ML trees to the family of all four taxa trees under the molecular clock assumption. The change from the fork topology to the comb incurs a major increase in the complexity of the underlying algebraic system and requires novel techniques and approaches. We combine the ultrametric properties of molecular clock trees with the Hadamard conjugation to derive a number of topology dependent identities. Employing these identities, we substantially simplify the system of polynomial equations. We finally use tools from algebraic geometry (e.g., Gröbner bases, ideal saturation, resultants) and employ symbolic algebra software to obtain analytic solutions for the comb. We show that in contrast to the fork, the comb has no closed form solutions (expressed by radicals in the input data). In general, four taxa trees can have multiple ML points. In contrast, we can now prove that under the molecular clock assumption, the comb has a unique (local and global) ML point. (Such uniqueness was previously shown for the fork.).
Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent; Anisimova, Maria; Hordijk, Wim; Gascuel, Olivier
2010-05-01
PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
The Prediction of Maximum Amplitudes of Solar Cycles and the Maximum Amplitude of Solar Cycle 24
无
2002-01-01
We present a brief review of predictions of solar cycle maximum ampli-tude with a lead time of 2 years or more. It is pointed out that a precise predictionof the maximum amplitude with such a lead-time is still an open question despiteprogress made since the 1960s. A method of prediction using statistical character-istics of solar cycles is developed: the solar cycles are divided into two groups, ahigh rising velocity (HRV) group and a low rising velocity (LRV) group, dependingon the rising velocity in the ascending phase for a given duration of the ascendingphase. The amplitude of Solar Cycle 24 can be predicted after the start of thecycle using the formula derived in this paper. Now, about 5 years before the startof the cycle, we can make a preliminary prediction of 83.2-119.4 for its maximumamplitude.
Pattern formation, logistics, and maximum path probability
Kirkaldy, J. S.
1985-05-01
The concept of pattern formation, which to current researchers is a synonym for self-organization, carries the connotation of deductive logic together with the process of spontaneous inference. Defining a pattern as an equivalence relation on a set of thermodynamic objects, we establish that a large class of irreversible pattern-forming systems, evolving along idealized quasisteady paths, approaches the stable steady state as a mapping upon the formal deductive imperatives of a propositional function calculus. In the preamble the classical reversible thermodynamics of composite systems is analyzed as an externally manipulated system of space partitioning and classification based on ideal enclosures and diaphragms. The diaphragms have discrete classification capabilities which are designated in relation to conserved quantities by descriptors such as impervious, diathermal, and adiabatic. Differentiability in the continuum thermodynamic calculus is invoked as equivalent to analyticity and consistency in the underlying class or sentential calculus. The seat of inference, however, rests with the thermodynamicist. In the transition to an irreversible pattern-forming system the defined nature of the composite reservoirs remains, but a given diaphragm is replaced by a pattern-forming system which by its nature is a spontaneously evolving volume partitioner and classifier of invariants. The seat of volition or inference for the classification system is thus transferred from the experimenter or theoretician to the diaphragm, and with it the full deductive facility. The equivalence relations or partitions associated with the emerging patterns may thus be associated with theorems of the natural pattern-forming calculus. The entropy function, together with its derivatives, is the vehicle which relates the logistics of reservoirs and diaphragms to the analog logistics of the continuum. Maximum path probability or second-order differentiability of the entropy in isolation are
Cardiorespiratory Fitness of Inmates of a Maximum Security Prison ...
USER
Maximum Security Prison; and also to determine the effects of age, gender, and period of incarceration on CRF. A total of 247 apparently healthy inmates of Maiduguri Maximum Security ... with different types of cardiovascular and metabolic.
Maximum likelihood polynomial regression for robust speech recognition
LU Yong; WU Zhenyang
2011-01-01
The linear hypothesis is the main disadvantage of maximum likelihood linear re- gression （MLLR）. This paper applies the polynomial regression method to model adaptation and establishes a nonlinear model adaptation algorithm using maximum likelihood polyno
M. Mihelich
2014-11-01
Full Text Available We derive rigorous results on the link between the principle of maximum entropy production and the principle of maximum Kolmogorov–Sinai entropy using a Markov model of the passive scalar diffusion called the Zero Range Process. We show analytically that both the entropy production and the Kolmogorov–Sinai entropy seen as functions of f admit a unique maximum denoted fmaxEP and fmaxKS. The behavior of these two maxima is explored as a function of the system disequilibrium and the system resolution N. The main result of this article is that fmaxEP and fmaxKS have the same Taylor expansion at first order in the deviation of equilibrium. We find that fmaxEP hardly depends on N whereas fmaxKS depends strongly on N. In particular, for a fixed difference of potential between the reservoirs, fmaxEP(N tends towards a non-zero value, while fmaxKS(N tends to 0 when N goes to infinity. For values of N typical of that adopted by Paltridge and climatologists (N ≈ 10 ~ 100, we show that fmaxEP and fmaxKS coincide even far from equilibrium. Finally, we show that one can find an optimal resolution N* such that fmaxEP and fmaxKS coincide, at least up to a second order parameter proportional to the non-equilibrium fluxes imposed to the boundaries. We find that the optimal resolution N* depends on the non equilibrium fluxes, so that deeper convection should be represented on finer grids. This result points to the inadequacy of using a single grid for representing convection in climate and weather models. Moreover, the application of this principle to passive scalar transport parametrization is therefore expected to provide both the value of the optimal flux, and of the optimal number of degrees of freedom (resolution to describe the system.
Vijaykumar, Archana; Saini, Ajay; Jawali, Narendra
2010-01-01
Molecular phylogeny among species belonging to subgenus Vigna (genus Vigna) was inferred based on internal transcribed spacer (ITS) sequences of 18S-5.8S-26S ribosomal RNA gene unit. Analysis showed a total of 356 polymorphic sites of which approximately 80% were parsimony informative. Phylogenetic reconstruction by neighbor joining and maximum parsimony methods placed the 57 Vigna accessions (belonging to 15 species) into 5 major clades. Five species viz. Vigna heterophylla, Vigna pubigera, Vigna parkeri, Vigna laurentii, and Vigna gracilis whose position in the subgenus was previously not known were placed in the section Vigna. A single accession (Vigna unguiculata ssp. tenuis, NI 1637) harbored 2 intragenomic ITS variants, indicative of 2 different types of ribosomal DNA (rDNA) repeat units. ITS variant type-I was close to ITS from V. unguiculata ssp. pubescens, whereas type-II was close to V. unguiculata ssp. tenuis. Transcript analysis clearly demonstrates that in accession NI 1637, rDNA repeat units with only type-II ITS variants are transcriptionally active. Evidence from sequence analysis (of 5.8S, ITS1, and ITS2) and secondary structure analysis (of ITS1 and ITS2) indicates that the type-I ITS variant probably does not belong to the pseudogenic rDNA repeat units. The results from phylogenetic and transcript analysis suggest that the rDNA units with the type-I ITS may have introgressed as a result of hybridization (between ssp. tenuis and ssp. pubescens); however, it has been epigenetically silenced. The results also demonstrate differential evolution of ITS sequence among wild and cultivated forms of V. unguiculata.
20 CFR 617.14 - Maximum amount of TRA.
2010-04-01
... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Maximum amount of TRA. 617.14 Section 617.14... FOR WORKERS UNDER THE TRADE ACT OF 1974 Trade Readjustment Allowances (TRA) § 617.14 Maximum amount of TRA. (a) General rule. Except as provided under paragraph (b) of this section, the maximum amount of...
40 CFR 94.107 - Determination of maximum test speed.
2010-07-01
... specified in 40 CFR 1065.510. These data points form the lug curve. It is not necessary to generate the... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Determination of maximum test speed... Determination of maximum test speed. (a) Overview. This section specifies how to determine maximum test...
14 CFR 25.1505 - Maximum operating limit speed.
2010-01-01
... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Maximum operating limit speed. 25.1505... Operating Limitations § 25.1505 Maximum operating limit speed. The maximum operating limit speed (V MO/M MO airspeed or Mach Number, whichever is critical at a particular altitude) is a speed that may not...
Maximum Performance Tests in Children with Developmental Spastic Dysarthria.
Wit, J.; And Others
1993-01-01
Three Maximum Performance Tasks (Maximum Sound Prolongation, Fundamental Frequency Range, and Maximum Repetition Rate) were administered to 11 children (ages 6-11) with spastic dysarthria resulting from cerebral palsy and 11 controls. Despite intrasubject and intersubject variability in normal and pathological speakers, the tasks were found to be…
Maximum physical capacity testing in cancer patients undergoing chemotherapy
Knutsen, L.; Quist, M; Midtgaard, J
2006-01-01
BACKGROUND: Over the past few years there has been a growing interest in the field of physical exercise in rehabilitation of cancer patients, leading to requirements for objective maximum physical capacity measurement (maximum oxygen uptake (VO(2max)) and one-repetition maximum (1RM)) to determine...
Berry, Vincent; Nicolas, François
2006-01-01
Given a set of evolutionary trees on a same set of taxa, the maximum agreement subtree problem (MAST), respectively, maximum compatible tree problem (MCT), consists of finding a largest subset of taxa such that all input trees restricted to these taxa are isomorphic, respectively compatible. These problems have several applications in phylogenetics such as the computation of a consensus of phylogenies obtained from different data sets, the identification of species subjected to horizontal gene transfers and, more recently, the inference of supertrees, e.g., Trees Of Life. We provide two linear time algorithms to check the isomorphism, respectively, compatibility, of a set of trees or otherwise identify a conflict between the trees with respect to the relative location of a small subset of taxa. Then, we use these algorithms as subroutines to solve MAST and MCT on rooted or unrooted trees of unbounded degree. More precisely, we give exact fixed-parameter tractable algorithms, whose running time is uniformly polynomial when the number of taxa on which the trees disagree is bounded. The improves on a known result for MAST and proves fixed-parameter tractability for MCT.
Present and Last Glacial Maximum climates as states of maximum entropy production
Herbert, Corentin; Kageyama, Masa; Dubrulle, Berengere
2011-01-01
The Earth, like other planets with a relatively thick atmosphere, is not locally in radiative equilibrium and the transport of energy by the geophysical fluids (atmosphere and ocean) plays a fundamental role in determining its climate. Using simple energy-balance models, it was suggested a few decades ago that the meridional energy fluxes might follow a thermodynamic Maximum Entropy Production (MEP) principle. In the present study, we assess the MEP hypothesis in the framework of a minimal climate model based solely on a robust radiative scheme and the MEP principle, with no extra assumptions. Specifically, we show that by choosing an adequate radiative exchange formulation, the Net Exchange Formulation, a rigorous derivation of all the physical parameters can be performed. The MEP principle is also extended to surface energy fluxes, in addition to meridional energy fluxes. The climate model presented here is extremely fast, needs very little empirical data and does not rely on ad hoc parameterizations. We in...
A Note on k-Limited Maximum Base
Yang Ruishun; Yang Xiaowei
2006-01-01
The problem of k-limited maximum base was specified into two special problems of k-limited maximum base; that is, let subset D of the problem of k-limited maximum base be an independent set and a circuit of the matroid, respectively. It was proved that under this circumstance the collections of k-limited base satisfy base axioms. Then a new matroid was determined, and the problem of k-limited maximum base was transformed to the problem of maximum base of this new matroid. Aiming at the problem, two algorithms, which in essence are greedy algorithms based on former matroid, were presented for the two special problems of k-limited maximum base. They were proved to be reasonable and more efficient than the algorithm presented by Ma Zhongfan in view of the complexity of algorithm.
Almog, Assaf; Garlaschelli, Diego
2014-09-01
The dynamics of complex systems, from financial markets to the brain, can be monitored in terms of multiple time series of activity of the constituent units, such as stocks or neurons, respectively. While the main focus of time series analysis is on the magnitude of temporal increments, a significant piece of information is encoded into the binary projection (i.e. the sign) of such increments. In this paper we provide further evidence of this by showing strong nonlinear relations between binary and non-binary properties of financial time series. These relations are a novel quantification of the fact that extreme price increments occur more often when most stocks move in the same direction. We then introduce an information-theoretic approach to the analysis of the binary signature of single and multiple time series. Through the definition of maximum-entropy ensembles of binary matrices and their mapping to spin models in statistical physics, we quantify the information encoded into the simplest binary properties of real time series and identify the most informative property given a set of measurements. Our formalism is able to accurately replicate, and mathematically characterize, the observed binary/non-binary relations. We also obtain a phase diagram allowing us to identify, based only on the instantaneous aggregate return of a set of multiple time series, a regime where the so-called ‘market mode’ has an optimal interpretation in terms of collective (endogenous) effects, a regime where it is parsimoniously explained by pure noise, and a regime where it can be regarded as a combination of endogenous and exogenous factors. Our approach allows us to connect spin models, simple stochastic processes, and ensembles of time series inferred from partial information.
An Interval Maximum Entropy Method for Quadratic Programming Problem
RUI Wen-juan; CAO De-xin; SONG Xie-wu
2005-01-01
With the idea of maximum entropy function and penalty function methods, we transform the quadratic programming problem into an unconstrained differentiable optimization problem, discuss the interval extension of the maximum entropy function, provide the region deletion test rules and design an interval maximum entropy algorithm for quadratic programming problem. The convergence of the method is proved and numerical results are presented. Both theoretical and numerical results show that the method is reliable and efficient.
Hutchinson, Thomas H. [Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3DH (United Kingdom)], E-mail: thom1@pml.ac.uk; Boegi, Christian [BASF SE, Product Safety, GUP/PA, Z470, 67056 Ludwigshafen (Germany); Winter, Matthew J. [AstraZeneca Safety, Health and Environment, Brixham Environmental Laboratory, Devon TQ5 8BA (United Kingdom); Owens, J. Willie [The Procter and Gamble Company, Central Product Safety, 11810 East Miami River Road, Cincinnati, OH 45252 (United States)
2009-02-19
There is increasing recognition of the need to identify specific sublethal effects of chemicals, such as reproductive toxicity, and specific modes of actions of the chemicals, such as interference with the endocrine system. To achieve these aims requires criteria which provide a basis to interpret study findings so as to separate these specific toxicities and modes of action from not only acute lethality per se but also from severe inanition and malaise that non-specifically compromise reproductive capacity and the response of endocrine endpoints. Mammalian toxicologists have recognized that very high dose levels are sometimes required to elicit both specific adverse effects and present the potential of non-specific 'systemic toxicity'. Mammalian toxicologists have developed the concept of a maximum tolerated dose (MTD) beyond which a specific toxicity or action cannot be attributed to a test substance due to the compromised state of the organism. Ecotoxicologists are now confronted by a similar challenge and must develop an analogous concept of a MTD and the respective criteria. As examples of this conundrum, we note recent developments in efforts to validate protocols for fish reproductive toxicity and endocrine screens (e.g. some chemicals originally selected as 'negatives' elicited decreases in fecundity or changes in endpoints intended to be biomarkers for endocrine modes of action). Unless analogous criteria can be developed, the potentially confounding effects of systemic toxicity may then undermine the reliable assessment of specific reproductive effects or biomarkers such as vitellogenin or spiggin. The same issue confronts other areas of aquatic toxicology (e.g., genotoxicity) and the use of aquatic animals for preclinical assessments of drugs (e.g., use of zebrafish for drug safety assessment). We propose that there are benefits to adopting the concept of an MTD for toxicology and pharmacology studies using fish and other aquatic
Integer Programming Model for Maximum Clique in Graph
YUAN Xi-bo; YANG You; ZENG Xin-hai
2005-01-01
The maximum clique or maximum independent set of graph is a classical problem in graph theory. Combined with Boolean algebra and integer programming, two integer programming models for maximum clique problem,which improve the old results were designed in this paper. Then, the programming model for maximum independent set is a corollary of the main results. These two models can be easily applied to computer algorithm and software, and suitable for graphs of any scale. Finally the models are presented as Lingo algorithms, verified and compared by several examples.
Counterexamples to convergence theorem of maximum-entropy clustering algorithm
于剑; 石洪波; 黄厚宽; 孙喜晨; 程乾生
2003-01-01
In this paper, we surveyed the development of maximum-entropy clustering algorithm, pointed out that the maximum-entropy clustering algorithm is not new in essence, and constructed two examples to show that the iterative sequence given by the maximum-entropy clustering algorithm may not converge to a local minimum of its objective function, but a saddle point. Based on these results, our paper shows that the convergence theorem of maximum-entropy clustering algorithm put forward by Kenneth Rose et al. does not hold in general cases.
Combining Experiments and Simulations Using the Maximum Entropy Principle
Boomsma, Wouter; Ferkinghoff-Borg, Jesper; Lindorff-Larsen, Kresten
2014-01-01
are not in quantitative agreement with experimental data. The principle of maximum entropy is a general procedure for constructing probability distributions in the light of new data, making it a natural tool in cases when an initial model provides results that are at odds with experiments. The number of maximum entropy...
49 CFR 174.86 - Maximum allowable operating speed.
2010-10-01
... 49 Transportation 2 2010-10-01 2010-10-01 false Maximum allowable operating speed. 174.86 Section... operating speed. (a) For molten metals and molten glass shipped in packagings other than those prescribed in § 173.247 of this subchapter, the maximum allowable operating speed may not exceed 24 km/hour (15...
Parametric optimization of thermoelectric elements footprint for maximum power generation
Rezania, A.; Rosendahl, Lasse; Yin, Hao
2014-01-01
The development studies in thermoelectric generator (TEG) systems are mostly disconnected to parametric optimization of the module components. In this study, optimum footprint ratio of n- and p-type thermoelectric (TE) elements is explored to achieve maximum power generation, maximum cost-perform...
30 CFR 56.19066 - Maximum riders in a conveyance.
2010-07-01
... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Maximum riders in a conveyance. 56.19066 Section 56.19066 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND... Hoisting Hoisting Procedures § 56.19066 Maximum riders in a conveyance. In shafts inclined over 45...
30 CFR 57.19066 - Maximum riders in a conveyance.
2010-07-01
... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Maximum riders in a conveyance. 57.19066 Section 57.19066 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND... Hoisting Hoisting Procedures § 57.19066 Maximum riders in a conveyance. In shafts inclined over 45...
Maximum Atmospheric Entry Angle for Specified Retrofire Impulse
T. N. Srivastava
1969-07-01
Full Text Available Maximum atmospheric entry angles for vehicles initially moving in elliptic orbits are investigated and it is shown that tangential retrofire impulse at the apogee results in the maximum entry angle. Equivalence of maximizing the entry angle and minimizing the retrofire impulse is also established.
5 CFR 838.711 - Maximum former spouse survivor annuity.
2010-01-01
... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Maximum former spouse survivor annuity... Orders Awarding Former Spouse Survivor Annuities Limitations on Survivor Annuities § 838.711 Maximum former spouse survivor annuity. (a) Under CSRS, payments under a court order may not exceed the...
46 CFR 151.45-6 - Maximum amount of cargo.
2010-10-01
... 46 Shipping 5 2010-10-01 2010-10-01 false Maximum amount of cargo. 151.45-6 Section 151.45-6 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) CERTAIN BULK DANGEROUS CARGOES BARGES CARRYING BULK LIQUID HAZARDOUS MATERIAL CARGOES Operations § 151.45-6 Maximum amount of cargo. (a)...
20 CFR 226.52 - Total annuity subject to maximum.
2010-04-01
... rate effective on the date the supplemental annuity begins, before any reduction for a private pension... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Total annuity subject to maximum. 226.52... COMPUTING EMPLOYEE, SPOUSE, AND DIVORCED SPOUSE ANNUITIES Railroad Retirement Family Maximum § 226.52...
49 CFR 195.406 - Maximum operating pressure.
2010-10-01
... 49 Transportation 3 2010-10-01 2010-10-01 false Maximum operating pressure. 195.406 Section 195... HAZARDOUS LIQUIDS BY PIPELINE Operation and Maintenance § 195.406 Maximum operating pressure. (a) Except for surge pressures and other variations from normal operations, no operator may operate a pipeline at a...
Maximum-entropy clustering algorithm and its global convergence analysis
无
2001-01-01
Constructing a batch of differentiable entropy functions touniformly approximate an objective function by means of the maximum-entropy principle, a new clustering algorithm, called maximum-entropy clustering algorithm, is proposed based on optimization theory. This algorithm is a soft generalization of the hard C-means algorithm and possesses global convergence. Its relations with other clustering algorithms are discussed.
Distribution of maximum loss of fractional Brownian motion with drift
Çağlar, Mine; Vardar-Acar, Ceren
2013-01-01
In this paper, we find bounds on the distribution of the maximum loss of fractional Brownian motion with H >= 1/2 and derive estimates on its tail probability. Asymptotically, the tail of the distribution of maximum loss over [0, t] behaves like the tail of the marginal distribution at time t.
48 CFR 436.575 - Maximum workweek-construction schedule.
2010-10-01
...-construction schedule. 436.575 Section 436.575 Federal Acquisition Regulations System DEPARTMENT OF AGRICULTURE... Maximum workweek-construction schedule. The contracting officer shall insert the clause at 452.236-75, Maximum Workweek-Construction Schedule, if the clause at FAR 52.236-15 is used and the contractor's...
30 CFR 57.5039 - Maximum permissible concentration.
2010-07-01
... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Maximum permissible concentration. 57.5039... Maximum permissible concentration. Except as provided by standard § 57.5005, persons shall not be exposed to air containing concentrations of radon daughters exceeding 1.0 WL in active workings. ...
5 CFR 550.105 - Biweekly maximum earnings limitation.
2010-01-01
... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Biweekly maximum earnings limitation. 550.105 Section 550.105 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Premium Pay Maximum Earnings Limitations § 550.105 Biweekly...
5 CFR 550.106 - Annual maximum earnings limitation.
2010-01-01
... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Annual maximum earnings limitation. 550.106 Section 550.106 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY ADMINISTRATION (GENERAL) Premium Pay Maximum Earnings Limitations § 550.106 Annual...
32 CFR 842.35 - Depreciation and maximum allowances.
2010-07-01
... 32 National Defense 6 2010-07-01 2010-07-01 false Depreciation and maximum allowances. 842.35... LITIGATION ADMINISTRATIVE CLAIMS Personnel Claims (31 U.S.C. 3701, 3721) § 842.35 Depreciation and maximum allowances. The military services have jointly established the “Allowance List-Depreciation Guide”...
秦峰; 付文博; 周善义
2011-01-01
对凤蝶科6属25种的COI基因和20种Cytb基因的部分序列进行测定和分析,探讨它们之间的系统发育关系;以茶小卷叶蛾 Adoxophyes honmai为外群,用邻接法(neighbor-joining,NJ)、最大简约法(maximum parsimony,MP)和贝叶斯法(Bayesian inference,BI)重建了凤蝶科6属的分子系统树.结果表明:COI基因部分序列长度为661bp,其中保守位点417个,可变位点244个,简约信息位点191个;A+T的平均含量为70.3%,明显高于C+G的平均含量29.6%.Cytb基因部分序列长度为433bp,其中保守位点239个,可变位点194个,简约信息位点135个;A+T的平均含量为74.2%,明显高于C+G的平均含量25.7%.分子系统树表明,凤蝶属Papilio、斑凤蝶属Chilasa、尾凤蝶属Bhutanitis、珠风蝶属Pachliopta和喙凤蝶属Teinopalpus为单系性,与传统形态分类结果相一致.但青凤蝶属Graphium单系性不够明确,需要进一步探讨.研究结果为我国凤蝶科分子系统学研究积累了资料.%Partial sequences of CO I genes of 25 species and Cyt b genes of 20 species in six genera of Papilionoidea were sequenced and analyzed for exploring their phylogenetic relationships. Adoxophyes honmai was used as outgroup to reconstruct the phylogenetic trees of six genera with neighbor-joining ( NJ),maximum parsimony (MP) and Bayesian inference (BI) methods. The results indicated that CO I genes are 661 bp in length by alignment, including 417 conserved, 244 variable and 191 parsimonious-informative sites, and the average percentage of A + T is 70.3％, much higher than that of C + G (29.6％). The Cytb genes are 433 bp in length by alignment, including 239 conserved, 194 variable and 135 parsimoniousinformative sites; and the average percentage of A + T is 74. 2％, much higher than that of C + G (25.7％). The molecular phylogenetic trees showed that the genera Papilio, Chilasa, Bhutanitis,Pachliopta and Teinopalpus are all monophyletic clades and separated from each other in the
Maximum Principles for Discrete and Semidiscrete Reaction-Diffusion Equation
Petr Stehlík
2015-01-01
Full Text Available We study reaction-diffusion equations with a general reaction function f on one-dimensional lattices with continuous or discrete time ux′ (or Δtux=k(ux-1-2ux+ux+1+f(ux, x∈Z. We prove weak and strong maximum and minimum principles for corresponding initial-boundary value problems. Whereas the maximum principles in the semidiscrete case (continuous time exhibit similar features to those of fully continuous reaction-diffusion model, in the discrete case the weak maximum principle holds for a smaller class of functions and the strong maximum principle is valid in a weaker sense. We describe in detail how the validity of maximum principles depends on the nonlinearity and the time step. We illustrate our results on the Nagumo equation with the bistable nonlinearity.
Experimental study on prediction model for maximum rebound ratio
LEI Wei-dong; TENG Jun; A.HEFNY; ZHAO Jian; GUAN Jiong
2007-01-01
The proposed prediction model for estimating the maximum rebound ratio was applied to a field explosion test, Mandai test in Singapore.The estimated possible maximum Deak particle velocities(PPVs)were compared with the field records.Three of the four available field-recorded PPVs lie exactly below the estimated possible maximum values as expected.while the fourth available field-recorded PPV lies close to and a bit higher than the estimated maximum possible PPV The comparison results show that the predicted PPVs from the proposed prediction model for the maximum rebound ratio match the field.recorded PPVs better than those from two empirical formulae.The very good agreement between the estimated and field-recorded values validates the proposed prediction model for estimating PPV in a rock mass with a set of ipints due to application of a two dimensional compressional wave at the boundary of a tunnel or a borehole.
Parsimony Principles for Software Components and Metalanguages
Veldhuizen, Todd L
2007-01-01
Software is a communication system. The usual topic of communication is program behavior, as encoded by programs. Domain-specific libraries are codebooks, domain-specific languages are coding schemes, and so forth. To turn metaphor into method, we adapt toolsfrom information theory--the study of efficient communication--to probe the efficiency with which languages and libraries let us communicate programs. In previous work we developed an information-theoretic analysis of software reuse in problem domains. This new paper uses information theory to analyze tradeoffs in the design of components, generators, and metalanguages. We seek answers to two questions: (1) How can we judge whether a component is over- or under-generalized? Drawing on minimum description length principles, we propose that the best component yields the most succinct representation of the use cases. (2) If we view a programming language as an assemblage of metalanguages, each providing a complementary style of abstraction, how can these met...
Most parsimonious haplotype allele sharing determination
Xu Jiaofen
2009-04-01
Full Text Available Abstract Background The "common disease – common variant" hypothesis and genome-wide association studies have achieved numerous successes in the last three years, particularly in genetic mapping in human diseases. Nevertheless, the power of the association study methods are still low, in particular on quantitative traits, and the description of the full allelic spectrum is deemed still far from reach. Given increasing density of single nucleotide polymorphisms available and suggested by the block-like structure of the human genome, a popular and prosperous strategy is to use haplotypes to try to capture the correlation structure of SNPs in regions of little recombination. The key to the success of this strategy is thus the ability to unambiguously determine the haplotype allele sharing status among the members. The association studies based on haplotype sharing status would have significantly reduced degrees of freedom and be able to capture the combined effects of tightly linked causal variants. Results For pedigree genotype datasets of medium density of SNPs, we present two methods for haplotype allele sharing status determination among the pedigree members. Extensive simulation study showed that both methods performed nearly perfectly on breakpoint discovery, mutation haplotype allele discovery, and shared chromosomal region discovery. Conclusion For pedigree genotype datasets, the haplotype allele sharing status among the members can be deterministically, efficiently, and accurately determined, even for very small pedigrees. Given their excellent performance, the presented haplotype allele sharing status determination programs can be useful in many downstream applications including haplotype based association studies.
Parsimonious Linear Fingerprinting for Time Series
2010-09-01
like to detect such groups of harmonics. Fig. 1(d) gives a quick preview of the visualization and effectiveness of the proposed PLiF method: For the...coefficients of each individual frequency. As we find harmonic frequency sets in music , in real time- series like motions, we will expect to usually find
Incoming editorial: bigger, purple, pragmatic, and parsimony.
Hilsenroth, Mark J
2011-03-01
It is with great excitement and enthusiasm that I write to you regarding several updates, new initiatives and changes with our journal. As you may have already noticed, this includes the change to a larger format, and a return to the color purple that helped define this journal from the early 1980s through the turn of the century, as well as to the original title "Psychotherapy." The change in format will allow us to benefit from the standard American Psychological Association (APA) journal design and layout, leading to more efficient processing and arrangement within their electronic journal system. I have found this first year as the Incoming Editor of Psychotherapy to be as challenging, rewarding, and intellectually stimulating as I imagined it would be, and I remain quite excited and enthusiastic about the work ahead. (PsycINFO Database Record (c) 2011 APA, all rights reserved).
2010-07-01
... as specified in 40 CFR 1065.610. This is the maximum in-use engine speed used for calculating the NOX... procedures of 40 CFR part 1065, based on the manufacturer's design and production specifications for the..., power density, and maximum in-use engine speed. 1042.140 Section 1042.140 Protection of...
Salem, Abeer M; Adham, Fatma K; Picard, Christine J
2015-05-01
Minimum postmortem interval estimations of a corpse using blow fly larvae in medicolegal investigations require correct identification and the application of appropriate developmental data of the identified fly species. Species identification of forensically relevant blow flies could be very difficult and time consuming when specimens are damaged or in the event of morphologically indistinguishable immature stages, which are most common at crime scenes. In response to this, an alternative, accurate determination of species may depend on sequencing and molecular techniques for identification. Chrysomyinae specimens (n = 158) belonging to three forensically important species [Chrysomya albiceps (Wiedemann), Chrysomya megacephala (F.), and Chrysomya marginalis (Wiedemann)] (Diptera: Calliphoridae) were collected from four locations in Egypt (Giza, Dayrout, Minya, and North Sinai) and sequenced across the mitochondrial cytochrome oxidase subunit I (COI) gene. Phylogenetic analyses using neighbor-joining, maximum likelihood and maximum parsimony methods resulted in the same topological structure and confirmed DNA based identification of all specimens. Interspecific divergence between pairs of species was 5.3% (C. marginalis-C. megacephala), 7% (C. albiceps-C. megacephala), and 8% (C. albiceps-C. marginalis). These divergences are sufficient to confirm the utility of cytochrome oxidase subunit I gene in the molecular identification of these flies in Egypt. Importantly, the maximum intraspecific divergence among individuals within a species was <1% and the least nucleotide divergence between species used for phylogenetic analysis was 3.6%. This study highlights the need for thorough and diverse sampling to capture all of the possible genetic diversity if DNA barcoding is to be used for molecular identification.
Stone, Wesley W.; Gilliom, Robert J.; Crawford, Charles G.
2008-01-01
Regression models were developed for predicting annual maximum and selected annual maximum moving-average concentrations of atrazine in streams using the Watershed Regressions for Pesticides (WARP) methodology developed by the National Water-Quality Assessment Program (NAWQA) of the U.S. Geological Survey (USGS). The current effort builds on the original WARP models, which were based on the annual mean and selected percentiles of the annual frequency distribution of atrazine concentrations. Estimates of annual maximum and annual maximum moving-average concentrations for selected durations are needed to characterize the levels of atrazine and other pesticides for comparison to specific water-quality benchmarks for evaluation of potential concerns regarding human health or aquatic life. Separate regression models were derived for the annual maximum and annual maximum 21-day, 60-day, and 90-day moving-average concentrations. Development of the regression models used the same explanatory variables, transformations, model development data, model validation data, and regression methods as those used in the original development of WARP. The models accounted for 72 to 75 percent of the variability in the concentration statistics among the 112 sampling sites used for model development. Predicted concentration statistics from the four models were within a factor of 10 of the observed concentration statistics for most of the model development and validation sites. Overall, performance of the models for the development and validation sites supports the application of the WARP models for predicting annual maximum and selected annual maximum moving-average atrazine concentration in streams and provides a framework to interpret the predictions in terms of uncertainty. For streams with inadequate direct measurements of atrazine concentrations, the WARP model predictions for the annual maximum and the annual maximum moving-average atrazine concentrations can be used to characterize
Maximum Likelihood Estimation of the Identification Parameters and Its Correction
无
2002-01-01
By taking the subsequence out of the input-output sequence of a system polluted by white noise, anindependent observation sequence and its probability density are obtained and then a maximum likelihood estimation of theidentification parameters is given. In order to decrease the asymptotic error, a corrector of maximum likelihood (CML)estimation with its recursive algorithm is given. It has been proved that the corrector has smaller asymptotic error thanthe least square methods. A simulation example shows that the corrector of maximum likelihood estimation is of higherapproximating precision to the true parameters than the least square methods.
Maximum frequency of the decametric radiation from Jupiter
Barrow, C. H.; Alexander, J. K.
1980-01-01
The upper frequency limits of Jupiter's decametric radio emission are found to be essentially the same when observed from the earth or, with considerably higher sensitivity, from the Voyager spacecraft close to Jupiter. This suggests that the maximum frequency is a real cut-off corresponding to a maximum gyrofrequency of about 38-40 MHz at Jupiter. It no longer appears to be necessary to specify different cut-off frequencies for the Io and non-Io emission as the maximum frequencies are roughly the same in each case.
The Application of Maximum Principle in Supply Chain Cost Optimization
Zhou Ling; Wang Jun
2013-01-01
In this paper, using the maximum principle for analyzing dynamic cost, we propose a new two-stage supply chain model of the manufacturing-assembly mode for high-tech perishable products supply chain...
Maximum Principle for Nonlinear Cooperative Elliptic Systems on IR N
LEADI Liamidi; MARCOS Aboubacar
2011-01-01
We investigate in this work necessary and sufficient conditions for having a Maximum Principle for a cooperative elliptic system on the whole (IR)N.Moreover,we prove the existence of solutions by an approximation method for the considered system.
Maximum Likelihood Factor Structure of the Family Environment Scale.
Fowler, Patrick C.
1981-01-01
Presents the maximum likelihood factor structure of the Family Environment Scale. The first bipolar dimension, "cohesion v conflict," measures relationship-centered concerns, while the second unipolar dimension is an index of "organizational and control" activities. (Author)
Multiresolution maximum intensity volume rendering by morphological adjunction pyramids
Roerdink, Jos B.T.M.
We describe a multiresolution extension to maximum intensity projection (MIP) volume rendering, allowing progressive refinement and perfect reconstruction. The method makes use of morphological adjunction pyramids. The pyramidal analysis and synthesis operators are composed of morphological 3-D
Multiresolution Maximum Intensity Volume Rendering by Morphological Adjunction Pyramids
Roerdink, Jos B.T.M.
2001-01-01
We describe a multiresolution extension to maximum intensity projection (MIP) volume rendering, allowing progressive refinement and perfect reconstruction. The method makes use of morphological adjunction pyramids. The pyramidal analysis and synthesis operators are composed of morphological 3-D
Changes in context and perception of maximum reaching height.
Wagman, Jeffrey B; Day, Brian M
2014-01-01
Successfully performing a given behavior requires flexibility in both perception and behavior. In particular, doing so requires perceiving whether that behavior is possible across the variety of contexts in which it might be performed. Three experiments investigated how (changes in) context (ie point of observation and intended reaching task) influenced perception of maximum reaching height. The results of experiment 1 showed that perceived maximum reaching height more closely reflected actual reaching ability when perceivers occupied a point of observation that was compatible with that required for the reaching task. The results of experiments 2 and 3 showed that practice perceiving maximum reaching height from a given point of observation improved perception of maximum reaching height from a different point of observation, regardless of whether such practice occurred at a compatible or incompatible point of observation. In general, such findings show bounded flexibility in perception of affordances and are thus consistent with a description of perceptual systems as smart perceptual devices.
Water Quality Assessment and Total Maximum Daily Loads Information (ATTAINS)
U.S. Environmental Protection Agency — The Water Quality Assessment TMDL Tracking And Implementation System (ATTAINS) stores and tracks state water quality assessment decisions, Total Maximum Daily Loads...
Combining Experiments and Simulations Using the Maximum Entropy Principle
Boomsma, Wouter; Ferkinghoff-Borg, Jesper; Lindorff-Larsen, Kresten
2014-01-01
are not in quantitative agreement with experimental data. The principle of maximum entropy is a general procedure for constructing probability distributions in the light of new data, making it a natural tool in cases when an initial model provides results that are at odds with experiments. The number of maximum entropy...... in the context of a simple example, after which we proceed with a real-world application in the field of molecular simulations, where the maximum entropy procedure has recently provided new insight. Given the limited accuracy of force fields, macromolecular simulations sometimes produce results....... Three very recent papers have explored this problem using the maximum entropy approach, providing both new theoretical and practical insights to the problem. We highlight each of these contributions in turn and conclude with a discussion on remaining challenges....
On the sufficiency of the linear maximum principle
Vidal, Rene Victor Valqui
1987-01-01
Presents a family of linear maximum principles for the discrete-time optimal control problem, derived from the saddle-point theorem of mathematical programming. Some simple examples illustrate the applicability of the main theoretical results...
Maximum Photovoltaic Penetration Levels on Typical Distribution Feeders: Preprint
Hoke, A.; Butler, R.; Hambrick, J.; Kroposki, B.
2012-07-01
This paper presents simulation results for a taxonomy of typical distribution feeders with various levels of photovoltaic (PV) penetration. For each of the 16 feeders simulated, the maximum PV penetration that did not result in steady-state voltage or current violation is presented for several PV location scenarios: clustered near the feeder source, clustered near the midpoint of the feeder, clustered near the end of the feeder, randomly located, and evenly distributed. In addition, the maximum level of PV is presented for single, large PV systems at each location. Maximum PV penetration was determined by requiring that feeder voltages stay within ANSI Range A and that feeder currents stay within the ranges determined by overcurrent protection devices. Simulations were run in GridLAB-D using hourly time steps over a year with randomized load profiles based on utility data and typical meteorological year weather data. For 86% of the cases simulated, maximum PV penetration was at least 30% of peak load.
16 CFR 1505.8 - Maximum acceptable material temperatures.
2010-01-01
... Association, 155 East 44th Street, New York, NY 10017. Material Degrees C. Degrees F. Capacitors (1) (1) Class... capacitor has no marked temperature limit, the maximum acceptable temperature will be assumed to be 65...
Environmental Monitoring, Water Quality - Total Maximum Daily Load (TMDL)
NSGIC GIS Inventory (aka Ramona) — The Clean Water Act Section 303(d) establishes the Total Maximum Daily Load (TMDL) program. The purpose of the TMDL program is to identify sources of pollution and...
PREDICTION OF MAXIMUM DRY DENSITY OF LOCAL GRANULAR ...
methods. A test on a soil of relatively high solid density revealed that the developed relation looses ... where, Pd max is the laboratory maximum dry ... Addis-Jinima Road Rehabilitation. ..... data sets that differ considerably in the magnitude.
Environmental Monitoring, Water Quality - Total Maximum Daily Load (TMDL)
NSGIC Education | GIS Inventory — The Clean Water Act Section 303(d) establishes the Total Maximum Daily Load (TMDL) program. The purpose of the TMDL program is to identify sources of pollution and...
Solar Panel Maximum Power Point Tracker for Power Utilities
Sandeep Banik,
2014-01-01
Full Text Available ―Solar Panel Maximum Power Point Tracker For power utilities‖ As the name implied, it is a photovoltaic system that uses the photovoltaic array as a source of electrical power supply and since every photovoltaic (PV array has an optimum operating point, called the maximum power point, which varies depending on the insolation level and array voltage. A maximum power point tracker (MPPT is needed to operate the PV array at its maximum power point. The objective of this thesis project is to build a photovoltaic (PV array Of 121.6V DC Voltage(6 cell each 20V, 100watt And convert the DC voltage to Single phase 120v,50Hz AC voltage by switch mode power converter‘s and inverter‘s.
A Family of Maximum SNR Filters for Noise Reduction
Huang, Gongping; Benesty, Jacob; Long, Tao;
2014-01-01
This paper is devoted to the study and analysis of the maximum signal-to-noise ratio (SNR) filters for noise reduction both in the time and short-time Fourier transform (STFT) domains with one single microphone and multiple microphones. In the time domain, we show that the maximum SNR filters can...... significantly increase the SNR but at the expense of tremendous speech distortion. As a consequence, the speech quality improvement, measured by the perceptual evaluation of speech quality (PESQ) algorithm, is marginal if any, regardless of the number of microphones used. In the STFT domain, the maximum SNR....... This demonstrates that the maximum SNR filters, particularly the multichannel ones, in the STFT domain may be of great practical value....
Maximum likelihood estimation of finite mixture model for economic data
Phoong, Seuk-Yen; Ismail, Mohd Tahir
2014-06-01
Finite mixture model is a mixture model with finite-dimension. This models are provides a natural representation of heterogeneity in a finite number of latent classes. In addition, finite mixture models also known as latent class models or unsupervised learning models. Recently, maximum likelihood estimation fitted finite mixture models has greatly drawn statistician's attention. The main reason is because maximum likelihood estimation is a powerful statistical method which provides consistent findings as the sample sizes increases to infinity. Thus, the application of maximum likelihood estimation is used to fit finite mixture model in the present paper in order to explore the relationship between nonlinear economic data. In this paper, a two-component normal mixture model is fitted by maximum likelihood estimation in order to investigate the relationship among stock market price and rubber price for sampled countries. Results described that there is a negative effect among rubber price and stock market price for Malaysia, Thailand, Philippines and Indonesia.
On the maximum sufficient range of interstellar vessels
Cartin, Daniel
2011-01-01
This paper considers the likely maximum range of space vessels providing the basis of a mature interstellar transportation network. Using the principle of sufficiency, it is argued that this range will be less than three parsecs for the average interstellar vessel. This maximum range provides access from the Solar System to a large majority of nearby stellar systems, with total travel distances within the network not excessively greater than actual physical distance.
Efficiency at Maximum Power of Interacting Molecular Machines
Golubeva, Natalia; Imparato, Alberto
2012-01-01
We investigate the efficiency of systems of molecular motors operating at maximum power. We consider two models of kinesin motors on a microtubule: for both the simplified and the detailed model, we find that the many-body exclusion effect enhances the efficiency at maximum power of the many- motor...... system, with respect to the single motor case. Remarkably, we find that this effect occurs in a limited region of the system parameters, compatible with the biologically relevant range....
Filtering Additive Measurement Noise with Maximum Entropy in the Mean
Gzyl, Henryk
2007-01-01
The purpose of this note is to show how the method of maximum entropy in the mean (MEM) may be used to improve parametric estimation when the measurements are corrupted by large level of noise. The method is developed in the context on a concrete example: that of estimation of the parameter in an exponential distribution. We compare the performance of our method with the bayesian and maximum likelihood approaches.
The maximum entropy production principle: two basic questions.
Martyushev, Leonid M
2010-05-12
The overwhelming majority of maximum entropy production applications to ecological and environmental systems are based on thermodynamics and statistical physics. Here, we discuss briefly maximum entropy production principle and raises two questions: (i) can this principle be used as the basis for non-equilibrium thermodynamics and statistical mechanics and (ii) is it possible to 'prove' the principle? We adduce one more proof which is most concise today.
A tropospheric ozone maximum over the equatorial Southern Indian Ocean
L. Zhang
2012-05-01
Full Text Available We examine the distribution of tropical tropospheric ozone (O_{3} from the Microwave Limb Sounder (MLS and the Tropospheric Emission Spectrometer (TES by using a global three-dimensional model of tropospheric chemistry (GEOS-Chem. MLS and TES observations of tropospheric O_{3} during 2005 to 2009 reveal a distinct, persistent O_{3} maximum, both in mixing ratio and tropospheric column, in May over the Equatorial Southern Indian Ocean (ESIO. The maximum is most pronounced in 2006 and 2008 and less evident in the other three years. This feature is also consistent with the total column O_{3} observations from the Ozone Mapping Instrument (OMI and the Atmospheric Infrared Sounder (AIRS. Model results reproduce the observed May O_{3} maximum and the associated interannual variability. The origin of the maximum reflects a complex interplay of chemical and dynamic factors. The O_{3} maximum is dominated by the O_{3} production driven by lightning nitrogen oxides (NO_{x} emissions, which accounts for 62% of the tropospheric column O_{3} in May 2006. We find the contribution from biomass burning, soil, anthropogenic and biogenic sources to the O_{3} maximum are rather small. The O_{3} productions in the lightning outflow from Central Africa and South America both peak in May and are directly responsible for the O_{3} maximum over the western ESIO. The lightning outflow from Equatorial Asia dominates over the eastern ESIO. The interannual variability of the O_{3} maximum is driven largely by the anomalous anti-cyclones over the southern Indian Ocean in May 2006 and 2008. The lightning outflow from Central Africa and South America is effectively entrained by the anti-cyclones followed by northward transport to the ESIO.
On the sufficiency of the linear maximum principle
Vidal, Rene Victor Valqui
1987-01-01
Presents a family of linear maximum principles for the discrete-time optimal control problem, derived from the saddle-point theorem of mathematical programming. Some simple examples illustrate the applicability of the main theoretical results......Presents a family of linear maximum principles for the discrete-time optimal control problem, derived from the saddle-point theorem of mathematical programming. Some simple examples illustrate the applicability of the main theoretical results...
Semidefinite Programming for Approximate Maximum Likelihood Sinusoidal Parameter Estimation
2009-01-01
We study the convex optimization approach for parameter estimation of several sinusoidal models, namely, single complex/real tone, multiple complex sinusoids, and single two-dimensional complex tone, in the presence of additive Gaussian noise. The major difficulty for optimally determining the parameters is that the corresponding maximum likelihood (ML) estimators involve finding the global minimum or maximum of multimodal cost functions because the frequencies are nonlinear in the observed s...
Hybrid TOA/AOA Approximate Maximum Likelihood Mobile Localization
Mohamed Zhaounia; Mohamed Adnan Landolsi; Ridha Bouallegue
2010-01-01
This letter deals with a hybrid time-of-arrival/angle-of-arrival (TOA/AOA) approximate maximum likelihood (AML) wireless location algorithm. Thanks to the use of both TOA/AOA measurements, the proposed technique can rely on two base stations (BS) only and achieves better performance compared to the original approximate maximum likelihood (AML) method. The use of two BSs is an important advantage in wireless cellular communication systems because it avoids hearability problems and reduces netw...
[Study on the maximum entropy principle and population genetic equilibrium].
Zhang, Hong-Li; Zhang, Hong-Yan
2006-03-01
A general mathematic model of population genetic equilibrium about one locus was constructed based on the maximum entropy principle by WANG Xiao-Long et al. They proved that the maximum solve of the model was just the frequency distribution that a population reached Hardy-Weinberg genetic equilibrium. It can suggest that a population reached Hardy-Weinberg genetic equilibrium when the genotype entropy of the population reached the maximal possible value, and that the frequency distribution of the maximum entropy was equivalent to the distribution of Hardy-Weinberg equilibrium law about one locus. They further assumed that the frequency distribution of the maximum entropy was equivalent to all genetic equilibrium distributions. This is incorrect, however. The frequency distribution of the maximum entropy was only equivalent to the distribution of Hardy-Weinberg equilibrium with respect to one locus or several limited loci. The case with regard to limited loci was proved in this paper. Finally we also discussed an example where the maximum entropy principle was not the equivalent of other genetic equilibria.
Kuracina Richard
2015-06-01
Full Text Available The article deals with the measurement of maximum explosion pressure and the maximum rate of exposure pressure rise of wood dust cloud. The measurements were carried out according to STN EN 14034-1+A1:2011 Determination of explosion characteristics of dust clouds. Part 1: Determination of the maximum explosion pressure pmax of dust clouds and the maximum rate of explosion pressure rise according to STN EN 14034-2+A1:2012 Determination of explosion characteristics of dust clouds - Part 2: Determination of the maximum rate of explosion pressure rise (dp/dtmax of dust clouds. The wood dust cloud in the chamber is achieved mechanically. The testing of explosions of wood dust clouds showed that the maximum value of the pressure was reached at the concentrations of 450 g / m3 and its value is 7.95 bar. The fastest increase of pressure was observed at the concentrations of 450 g / m3 and its value was 68 bar / s.
Individual Module Maximum Power Point Tracking for Thermoelectric Generator Systems
Vadstrup, Casper; Schaltz, Erik; Chen, Min
2013-07-01
In a thermoelectric generator (TEG) system the DC/DC converter is under the control of a maximum power point tracker which ensures that the TEG system outputs the maximum possible power to the load. However, if the conditions, e.g., temperature, health, etc., of the TEG modules are different, each TEG module will not produce its maximum power. If each TEG module is controlled individually, each TEG module can be operated at its maximum power point and the TEG system output power will therefore be higher. In this work a power converter based on noninverting buck-boost converters capable of handling four TEG modules is presented. It is shown that, when each module in the TEG system is operated under individual maximum power point tracking, the system output power for this specific application can be increased by up to 8.4% relative to the situation when the modules are connected in series and 16.7% relative to the situation when the modules are connected in parallel.
Size dependence of efficiency at maximum power of heat engine
Izumida, Y.
2013-10-01
We perform a molecular dynamics computer simulation of a heat engine model to study how the engine size difference affects its performance. Upon tactically increasing the size of the model anisotropically, we determine that there exists an optimum size at which the model attains the maximum power for the shortest working period. This optimum size locates between the ballistic heat transport region and the diffusive heat transport one. We also study the size dependence of the efficiency at the maximum power. Interestingly, we find that the efficiency at the maximum power around the optimum size attains a value that has been proposed as a universal upper bound, and it even begins to exceed the bound as the size further increases. We explain this behavior of the efficiency at maximum power by using a linear response theory for the heat engine operating under a finite working period, which naturally extends the low-dissipation Carnot cycle model [M. Esposito, R. Kawai, K. Lindenberg, C. Van den Broeck, Phys. Rev. Lett. 105, 150603 (2010)]. The theory also shows that the efficiency at the maximum power under an extreme condition may reach the Carnot efficiency in principle.© EDP Sciences Società Italiana di Fisica Springer-Verlag 2013.
How long do centenarians survive? Life expectancy and maximum lifespan.
Modig, K; Andersson, T; Vaupel, J; Rau, R; Ahlbom, A
2017-08-01
The purpose of this study was to explore the pattern of mortality above the age of 100 years. In particular, we aimed to examine whether Scandinavian data support the theory that mortality reaches a plateau at particularly old ages. Whether the maximum length of life increases with time was also investigated. The analyses were based on individual level data on all Swedish and Danish centenarians born from 1870 to 1901; in total 3006 men and 10 963 women were included. Birth cohort-specific probabilities of dying were calculated. Exact ages were used for calculations of maximum length of life. Whether maximum age changed over time was analysed taking into account increases in cohort size. The results confirm that there has not been any improvement in mortality amongst centenarians in the past 30 years and that the current rise in life expectancy is driven by reductions in mortality below the age of 100 years. The death risks seem to reach a plateau of around 50% at the age 103 years for men and 107 years for women. Despite the rising life expectancy, the maximum age does not appear to increase, in particular after accounting for the increasing number of individuals of advanced age. Mortality amongst centenarians is not changing despite improvements at younger ages. An extension of the maximum lifespan and a sizeable extension of life expectancy both require reductions in mortality above the age of 100 years. © 2017 The Association for the Publication of the Journal of Internal Medicine.
Predicting species' maximum dispersal distances from simple plant traits.
Tamme, Riin; Götzenberger, Lars; Zobel, Martin; Bullock, James M; Hooftman, Danny A P; Kaasik, Ants; Pärtel, Meelis
2014-02-01
Many studies have shown plant species' dispersal distances to be strongly related to life-history traits, but how well different traits can predict dispersal distances is not yet known. We used cross-validation techniques and a global data set (576 plant species) to measure the predictive power of simple plant traits to estimate species' maximum dispersal distances. Including dispersal syndrome (wind, animal, ant, ballistic, and no special syndrome), growth form (tree, shrub, herb), seed mass, seed release height, and terminal velocity in different combinations as explanatory variables we constructed models to explain variation in measured maximum dispersal distances and evaluated their power to predict maximum dispersal distances. Predictions are more accurate, but also limited to a particular set of species, if data on more specific traits, such as terminal velocity, are available. The best model (R2 = 0.60) included dispersal syndrome, growth form, and terminal velocity as fixed effects. Reasonable predictions of maximum dispersal distance (R2 = 0.53) are also possible when using only the simplest and most commonly measured traits; dispersal syndrome and growth form together with species taxonomy data. We provide a function (dispeRsal) to be run in the software package R. This enables researchers to estimate maximum dispersal distances with confidence intervals for plant species using measured traits as predictors. Easily obtainable trait data, such as dispersal syndrome (inferred from seed morphology) and growth form, enable predictions to be made for a large number of species.
Prediction of three dimensional maximum isometric neck strength.
Fice, Jason B; Siegmund, Gunter P; Blouin, Jean-Sébastien
2014-09-01
We measured maximum isometric neck strength under combinations of flexion/extension, lateral bending and axial rotation to determine whether neck strength in three dimensions (3D) can be predicted from principal axes strength. This would allow biomechanical modelers to validate their neck models across many directions using only principal axis strength data. Maximum isometric neck moments were measured in 9 male volunteers (29±9 years) for 17 directions. The 3D moments were normalized by the principal axis moments, and compared to unity for all directions tested. Finally, each subject's maximum principal axis moments were used to predict their resultant moment in the off-axis directions. Maximum moments were 30±6 N m in flexion, 32±9 N m in lateral bending, 51±11 N m in extension, and 13±5 N m in axial rotation. The normalized 3D moments were not significantly different from unity (95% confidence interval contained one), except for three directions that combined ipsilateral axial rotation and lateral bending; in these directions the normalized moments exceeded one. Predicted resultant moments compared well to the actual measured values (r2=0.88). Despite exceeding unity, the normalized moments were consistent across subjects to allow prediction of maximum 3D neck strength using principal axes neck strength.
Ribeiro, Tatiana Corrêa; Weiblen, Carla; de Azevedo, Maria Isabel; de Avila Botton, Sônia; Robe, Lizandra Jaqueline; Pereira, Daniela Isabel Brayer; Monteiro, Danieli Urach; Lorensetti, Douglas Miotto; Santurio, Janio Morais
2017-03-01
Pythium insidiosum is an important oomycete due to its ability to infect humans and animals. It causes pythiosis, a disease of difficult treatment that occurs more frequently in humans in Thailand and in horses in Brazil. Since cell-wall components are frequently related to host shifts, we decided here to use sequences from the exo-1,3-β-glucanase gene (exo1), which encodes an immunodominant protein putatively involved in cell wall remodeling, to investigate the microevolutionary relationships of Brazilian and Thai isolates of P. insidiosum. After neutrality ratification, the phylogenetic analyses performed through Maximum parsimony (MP), Neighbor-joining (NJ), Maximum likelihood (ML), and Bayesian analysis (BA) strongly supported Thai isolates being paraphyletic in relation to those from Brazil. The structure recovered by these analyses, as well as by Spatial Analysis of Molecular Variance (SAMOVA), suggests the subdivision of P. insidiosum into three clades or population groups, which are able to explain almost 81% of the variation encountered for exo1. Moreover, the two identified Thai clades were almost as strongly differentiated between each other, as they were from the Brazilian clade, suggesting an ancient Asian subdivision. The derived positioning in the phylogenetic tree, linked to the lower diversity values and the recent expansion signs detected for the Brazilian clade, further support this clade as derived in relation to the Asian populations. Thus, although some patterns presented here are compatible with those recovered with different molecular markers, exo1 was revealed to be a good marker for studying evolution in Pythium, providing robust and strongly supported results with regard to the patterns of origin and diversification of P. insidiosum. Copyright © 2016 Elsevier B.V. All rights reserved.
Leebens-Mack, Jim; Raubeson, Linda A.; Cui, Liying; Kuehl,Jennifer V.; Fourcade, Matthew H.; Chumley, Timothy W.; Boore, JeffreyL.; Jansen, Robert K.; dePamphilis, Claude W.
2005-05-27
While there has been strong support for Amborella and Nymphaeales (water lilies) as branching from basal-most nodes in the angiosperm phylogeny, this hypothesis has recently been challenged by phylogenetic analyses of 61 protein-coding genes extracted from the chloroplast genome sequences of Amborella, Nymphaea and 12 other available land plant chloroplast genomes. These character-rich analyses placed the monocots, represented by three grasses (Poaceae), as sister to all other extant angiosperm lineages. We have extracted protein-coding regions from draft sequences for six additional chloroplast genomes to test whether this surprising result could be an artifact of long-branch attraction due to limited taxon sampling. The added taxa include three monocots (Acorus, Yucca and Typha), a water lily (Nuphar), a ranunculid(Ranunculus), and a gymnosperm (Ginkgo). Phylogenetic analyses of the expanded DNA and protein datasets together with microstructural characters (indels) provided unambiguous support for Amborella and the Nymphaeales as branching from the basal-most nodes in the angiospermphylogeny. However, their relative positions proved to be dependent on method of analysis, with parsimony favoring Amborella as sister to all other angiosperms, and maximum likelihood and neighbor-joining methods favoring an Amborella + Nympheales clade as sister. The maximum likelihood phylogeny supported the later hypothesis, but the likelihood for the former hypothesis was not significantly different. Parametric bootstrap analysis, single gene phylogenies, estimated divergence dates and conflicting in del characters all help to illuminate the nature of the conflict in resolution of the most basal nodes in the angiospermphylogeny. Molecular dating analyses provided median age estimates of 161 mya for the most recent common ancestor of all extant angiosperms and 145 mya for the most recent common ancestor of monocots, magnoliids andeudicots. Whereas long sequences reduce variance in
Hidden genetic diversity in the green alga Spirogyra (Zygnematophyceae, Streptophyta
Chen Charlotte
2012-06-01
Full Text Available Abstract Background The unbranched filamentous green alga Spirogyra (Streptophyta, Zygnemataceae is easily recognizable based on its vegetative morphology, which shows one to several spiral chloroplasts. This simple structure falsely points to a low genetic diversity: Spirogyra is commonly excluded from phylogenetic analyses because the genus is known as a long-branch taxon caused by a high evolutionary rate. Results We focused on this genetic diversity and sequenced 130 Spirogyra small subunit nuclear ribosomal DNA (SSU rDNA strands of different origin. The resulting SSU rDNA sequences were used for phylogenetic analyses using complex evolutionary models (posterior probability, maximum likelihood, neighbor joining, and maximum parsimony methods. The sequences were between 1672 and 1779 nucleotides long. Sequence comparisons revealed 53 individual clones, but our results still support monophyly of the genus. Our data set did not contain a single slow-evolving taxon that would have been placed on a shorter branch compared to the remaining sequences. Out of 130 accessions analyzed, 72 showed a secondary loss of the 1506 group I intron, which formed a long-branched group within the genus. The phylogenetic relationship to the genus Spirotaenia was not resolved satisfactorily. The genetic distance within the genus Spirogyra exceeded the distances measured within any other genus of the remaining Zygnemataceae included in this study. Conclusion Overall, we define eight distinct clades of Spirogyra, one of them including the genus Sirogonium. A large number of non-homoplasious synapomorphies (NHS; 114 NHS in total was found for Spirogyra (41 NHS and for each clade (totaling 73 NHS. This emphasizes the high genetic diversity of this genus and the distance to the remaining Zygnematophyceae.
Karanovic, Ivana; Orduña-Martínez, Lorena; Ardisson, Pedro-Luis
2015-03-01
Previous studies have suggested incongruence between current systematics and molecular phylogenies of Sarsielloidea, with a possible polyphyly of the family Philomedidae. Here, we provide molecular phylogenetic analyses based on 18S rDNA and 28S rDNA. The former includes five new sequences and 12 from the GenBank, and the latter two new and six sequences from the GenBank. We use three methods, maximum likelihood, maximum parsimony, and neighbor joining, and all reconstructed phylogenies support previously suggested polyphyly, indicating a closer relationship of the subfamily Pseudophilomedinae with one subfamily of Sarsiellidae than with the nominotypical subfamily of Philomedidae. Morphological characters that may be key indicators of the phylogenetic relationships between three Sarsielloidea families are discussed. We also describe the 21st representative of the Pseudophilomedinae genus, Harbansus Kornicker, (Smith Contrib Zool 260:75, 1978), Harbansus ningalooi n. sp., from the Ningaloo Reef, Western Australia. This is the first Harbansus reported from the Australian west coast and the second from the Australian coral reef systems. It differs from all other congeners by peculiar claw-like processes on the posterior infold. Most Harbansus species have relatively restricted distributions, except Harbansus paucichelatus (Kornicker, in Inst Mar Sci 5:195-300, 1958), which has also been postulated to represent a species complex. We present a detailed morphological redescription of this species, based on the freshly collected material from the Yucatan Peninsula, as well as four mitochondrial COI sequences. These become the first COI sequences of the entire superfamily Sarsielloidea available on the GenBank. To facilitate future identification, we include a key to species of Harbansus.
Molecular characterization of trichomonads isolated from animal hosts in the Philippines.
Dimasuay, Kris Genelyn B; Rivera, Windell L
2013-09-23
Trichomonads are amitochondrial anaerobic flagellated protists that are either parasites or commensals, generally living in the digestive or genitourinary tract of humans and animals. It has been reported that these protozoa can migrate to other sites in their target host, can adapt to new hosts, and are capable of zoonotic transmission. In this study, 59 trichomonad isolates from different animal hosts in the Philippines were identified and characterized. Primer sets were designed and were successful in amplifying the 18S rRNA gene sequences of the isolates. Phylogenetic trees were constructed using neighbor-joining (NJ), maximum parsimony (MP), maximum-likelihood (ML) and Bayesian inference (BI) analyses. Results showed that BLAST analysis of the isolates corresponded to the clustering of the isolates together with reference sequences in the constructed ML tree. Cattle and pig isolates were most likely Tetratrichomonas buttreyi, which were observed to be commensal in both animals. All duck and rooster isolates were similar with Tetratrichomonas gallinarum. All dog isolates together with single isolates from boa, goat, and owl were identical to Pentatrichomonas hominis. Occurrence of P. hominis in Boa constrictor imperator (boa) and Otus megalotis (Philippine scops owl) suggested the adaptation of the trichomonad to new hosts. Reptile hosts were observed to harbor Trichomitus batrachorum or Hypotrichomonas acosta. Three reptile isolates (Igu2, Igu4, and Liz7) suggest novel species belonging to Class Hypotrichomonadea. Furthermore, iguanas were infected with T. batrachorum or H. acosta. Trichomonads in animal hosts are commensal and the mode of transmission is via fecal-oral route. They are capable of adaptation to new hosts and therefore, zoonotic transmission is possible as well as pathogenesis in host. Thus, trichomonads can pose threats to the health of humans and animals. Copyright © 2013 Elsevier B.V. All rights reserved.
Negrisolo, Enrico; Kuhl, Heiner; Forcato, Claudio; Vitulo, Nicola; Reinhardt, Richard; Patarnello, Tomaso; Bargelloni, Luca
2010-12-01
Comparative genomics holds the promise to magnify the information obtained from individual genome sequencing projects, revealing common features conserved across genomes and identifying lineage-specific characteristics. To implement such a comparative approach, a robust phylogenetic framework is required to accurately reconstruct evolution at the genome level. Among vertebrate taxa, teleosts represent the second best characterized group, with high-quality draft genome sequences for five model species (Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes, and Tetraodon nigroviridis), and several others are in the finishing lane. However, the relationships among the acanthomorph teleost model fishes remain an unresolved taxonomic issue. Here, a genomic region spanning over 1.2 million base pairs was sequenced in the teleost fish Dicentrarchus labrax. Together with genomic data available for the above fish models, the new sequence was used to identify unique orthologous genomic regions shared across all target taxa. Different strategies were applied to produce robust multiple gene and genomic alignments spanning from 11,802 to 186,474 amino acid/nucleotide positions. Ten data sets were analyzed according to Bayesian inference, maximum likelihood, maximum parsimony, and neighbor joining methods. Extensive analyses were performed to explore the influence of several factors (e.g., alignment methodology, substitution model, data set partitions, and long-branch attraction) on the tree topology. Although a general consensus was observed for a closer relationship between G. aculeatus (Gasterosteidae) and Di. labrax (Moronidae) with the atherinomorph O. latipes (Beloniformes) sister taxon of this clade, with the tetraodontiform group Ta. rubripes and Te. nigroviridis (Tetraodontiformes) representing a more distantly related taxon among acanthomorph model fish species, conflicting results were obtained between data sets and methods, especially with respect
Azevedo, M I; Botton, S A; Pereira, D I B; Robe, L J; Jesus, F P K; Mahl, C D; Costa, M M; Alves, S H; Santurio, J M
2012-09-14
Pythium insidiosum is an aquatic oomycete that is the causative agent of pythiosis. Advances in molecular methods have enabled increased accuracy in the diagnosis of pythiosis, and in studies of the phylogenetic relationships of this oomycete. To evaluate the phylogenetic relationships among isolates of P. insidiosum from different regions of Brazil, and also regarding to other American and Thai isolates, in this study a total of thirty isolates of P. insidiosum from different regions of Brazil was used and had their ITS1, 5.8S rRNA and ITS2 rDNA (ITS) region and the partial sequence of cytochrome oxidase II (COX II) gene sequenced and analyzed. The outgroup consisted of six isolates of other Pythium species and one of Lagenidium giganteum. Phylogenetic analyses of ITS and COX II genes were conducted, both individually and in combination, using four different methods: Maximum parsimony (MP); Neighbor-joining (NJ); Maximum likelihood (ML); and Bayesian analysis (BA). Our data supported P. insidiosum as monophyletic in relation to the other Pythium species, and COX II showed that P. insidiosum appears to be subdivided into three major polytomous groups, whose arrangement provides the Thai isolates as paraphyletic in relation to the Brazilian ones. The molecular analyses performed in this study suggest an evolutionary proximity among all American isolates, including the Brazilian and the Central and North America isolates, which were grouped together in a single entirely polytomous clade. The COX II network results presented signals of a recent expansion for the American isolates, probably originated from an Asian invasion source. Here, COX II showed higher levels bias, although it was the source of higher levels of phylogenetic information when compared to ITS. Nevertheless, the two markers chosen for this study proved to be entirely congruent, at least with respect to phylogenetic relationships between different isolates of P. insidiosum. Copyright © 2012 Elsevier
Claudia Helena Tagliaro
2005-03-01
Full Text Available The systematics of the subfamily Callitrichinae (Platyrrhini, Primates, a group of small monkeys from South America and Panama, remains an area of considerable discussion despite many investigations, there being continuing controversy over subgeneric taxonomic classifications based on morphological characters. The purpose of our research was to help elucidate the phylogenetic relationships within the monkey genus Saguinus (Callitrichinae using a molecular approach to discover whether or not the two different sections containing hairy-faced and bare-faced species are monophyletic, whether Saguinus midas midas and Saguinus bicolor are more closely related than are S. midas midas and Saguinus midas niger, and if Saguinus fuscicollis melanoleucus and Saguinus fuscicollis weddelli really are different species. We sequenced the 957 bp ND1 mitochondrial gene of 21 Saguinus monkeys (belonging to six species and nine morphotypes and one Cebus monkey (the outgroup and constructed phylogenetic trees using maximum parsimony, neighbor joining, and maximum likelihood methods. The phylogenetic trees obtained divided the genus Saguinus into two groups, one containing the small-bodied species S. fuscicollis and the other, the large-bodied species S. mystax, S. leucopus, S. oedipus, S. midas, S. bicolor. The most derived taxa, S. midas and S. bicolor, grouped together, while S. fuscicollis melanoleucus and S. f. weddelli showed divergence values that did not support the division of these morphotypes into subspecies. On the other hand, S. midas individuals showed divergence compatible with the existence of three subspecies, two of them with the same morphotype as the subspecies S. midas niger. The results of our study suggest that there is at least one Saguinus subspecies that has not yet been described and that the conservation status of Saguinus species and subspecies should be carefully revised using modern molecular approaches.
Cheng, Xue-Fang; Zhang, Le-Ping; Yu, Dan-Na; Storey, Kenneth B; Zhang, Jia-Yong
2016-07-15
Three complete mitochondrial genomes of Blaberidae (Insecta: Blattodea) (Gromphadorhina portentosa, Panchlora nivea, Blaptica dubia) and one complete mt genome of Blattidae (Insecta: Blattodea) (Shelfordella lateralis) were sequenced to further understand the characteristics of cockroach mitogenomes and reconstruct the phylogenetic relationship of Blattodea. The gene order and orientation of these four cockroach genomes were similar to known cockroach mt genomes, and contained 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. The mt genomes of Blattodea exhibited a characteristics of a high A+T composition (70.7%-74.3%) and dominant usage of the TAA stop codon. The AT content of the whole mt genome, PCGs and total tRNAs in G. portentosa was the lowest in known cockroaches. The presence of a 71-bp intergenic spacer region between trnQ and trnM was a unique feature in B. dubia, but absent in other cockroaches, which can be explained by the duplication/random loss model. Based on the nucleotide and amino acid datasets of the 13 PCGs genes, neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and bayesian inference (BI) analyses were used to rebuild the phylogenetic relationship of cockroaches. All phylogenetic analyses consistently placed Isoptera as the sister cluster to Cryptocercidae of Blattodea. Ectobiidae and Blaberidae (Blaberoidea) formed a sister clade to Blattidae. Corydiidae is a sister clade of all the remaining cockroach species with a high value in NJ and MP analyses of nucleotide and amino acid datasets, and ML and BI analyses of the amino acid dataset.
Molecular evolution of connective tissue growth factor in Cyprinidae (Teleostei: Cypriniformes)
Xianghui Kong; Xuzhen Wang; Xiaoni Gan; Junbing Li; Shunping He
2008-01-01
Connective tissue growth factor (CTGF) plays an important role in regulation ofcell growth, differentiation, apoptosis and individual development in animals. The study of sequences variation and molecular evolution of CTGF gene across various species of the cyprinid could be helpful for understanding of speciation and gene divergence in this kind of fish. In this study, 19 novel sequences of CTGF gene were obtained from the representative species of the family Cyprinidae using PCR amplification, cloning and sequencing. Phylogenetic relationships of Cyprinidae were reconstructed by neighbor-joining (N J), maximum parsimony (MP), maximum likelihood (ML) and Bayesian method. Oryzias latipes from the family Cyprinodontidae was assigned to be the outgroup taxon. Leuciscini and Barbini were clustered into the monophyletic lineages, respectively, with the high nodal supports. The estimation of the ratio of non-synonymous to synonymous substitution (dN/dS) for the various branches indicated that there stood the different evolution rates between the Leuciscini and the Barbini. With the ratio of dN/dS of the Leuciscini being lower than that of the Barbini, species within the Barbini were demonstrated to be subjected to the relatively less selection pressure and under the relaxable evolution background. A 6 bp indel (insertion/deletion) was found at the 5' end of CTGF gene of Cyprinidae, and this 6 bp deletion only appeared in the Leuciscini, which is a typical characteristic of the Leuciscini and provides evidence for the monophylogeny of the Leuciscini. For the amino acid sequences of CTGF protein, the most variations and indels were distributed in the signal region and IGFBP region of this protein, implying that these variations were correlated with the regulation of the CTGF gene expression and protein activity.
Pyron, R Alexander; Hendry, Catriona R; Chou, Vincent M; Lemmon, Emily M; Lemmon, Alan R; Burbrink, Frank T
2014-12-01
Next-generation genomic sequencing promises to quickly and cheaply resolve remaining contentious nodes in the Tree of Life, and facilitates species-tree estimation while taking into account stochastic genealogical discordance among loci. Recent methods for estimating species trees bypass full likelihood-based estimates of the multi-species coalescent, and approximate the true species-tree using simpler summary metrics. These methods converge on the true species-tree with sufficient genomic sampling, even in the anomaly zone. However, no studies have yet evaluated their efficacy on a large-scale phylogenomic dataset, and compared them to previous concatenation strategies. Here, we generate such a dataset for Caenophidian snakes, a group with >2500 species that contains several rapid radiations that were poorly resolved with fewer loci. We generate sequence data for 333 single-copy nuclear loci with ∼100% coverage (∼0% missing data) for 31 major lineages. We estimate phylogenies using neighbor joining, maximum parsimony, maximum likelihood, and three summary species-tree approaches (NJst, STAR, and MP-EST). All methods yield similar resolution and support for most nodes. However, not all methods support monophyly of Caenophidia, with Acrochordidae placed as the sister taxon to Pythonidae in some analyses. Thus, phylogenomic species-tree estimation may occasionally disagree with well-supported relationships from concatenated analyses of small numbers of nuclear or mitochondrial genes, a consideration for future studies. In contrast for at least two diverse, rapid radiations (Lamprophiidae and Colubridae), phylogenomic data and species-tree inference do little to improve resolution and support. Thus, certain nodes may lack strong signal, and larger datasets and more sophisticated analyses may still fail to resolve them.
范振鑫; 王璐萱; 张修月; 刘少英
2010-01-01
大耳姬鼠Apodemus latronum的分类地位,尤其它和龙姬鼠A.draco的关系,还存在着争议.用PCR扩增了采集自5个不同地点的大耳姬鼠的线粒体细胞色素b(cyt b)基因,并和GenBank已有的3条大耳姬鼠cyt b序列一起分析其碱基组成和变异情况.采用邻接法(Neighbor-joining,NJ)、最大简约法(Maximum parsimony,MP)、最大似然法(Maximum likelihood,ML)和贝叶斯法(Bayesian inference,BI)构建了大耳姬鼠和龙姬鼠的系统发育树.4种方法构建的系统发育树拓扑结构一致,大耳姬鼠和龙姬鼠均各自形成单系,龙姬鼠先与台湾森鼠A.semotus聚在一起,再与大耳姬鼠形成姐妹群.此外,大耳姬鼠和龙姬鼠两者间的K2P平均遗传距离达到0.14.因此,认为大耳姬鼠是一个独立的种,而不是龙姬鼠的一个亚种.
Abebe, Eyualem; Ferebee, Briana; Taylor, Tarreyca; Mundo-Ocampo, Manuel; Mekete, Tesfamariam; De Ley, Paul
2013-01-01
Two new species, Neotobrilus nicsmolae n. sp. and Chronogaster carolinensis n. sp. are described from a small, acidic, temperate, natural lake in North Carolina. N. nicsmolae n. sp. comes close to three members of the genus reported from North America, N. filipjevi, N. longus, and N. hopei. However, N. nicsmolae is unique with in the genus in having a combination of characters: size smaller than 1,700 μm, shorter outer labial and cephalic setae, tail shorter than 250 μm, last ventromedian supplement close (about 5 μm) to cloacal opening, spicule length of 61 to 85 μm, flagelloid sperm, and possession of subterminal setae. Assessment of relationships among clades within the Triplonchida using DNA sequences of the D2D3 expansion segment of the LSU rDNA showed that the family Trichodoridae and the genus Tripyla were recovered as monophyletic. The genus Tobrilus was recovered as monophyletic in the neighbor-joining and maximum likelihood trees, but that was not so in the maximum-parsimony tree. The separation among genera of the Trichodoridae, i.e., Trichodorus and Paratrichodorus, was not clear-cut in all phylograms. Chronogaster carolinensis n. sp. in having one ventral mucro with no spine and vacuolated lateral glandular bodies comes close to C. typica and C. ethiopica but differs from all hitherto known species in a combination of characteristics: in having long cephalic setae, long stoma, crystalloid bodies, vacuolated lateral glandular bodies, and a tail terminus with blunt ventral mucro, and its lack of lateral line. PMID:23589662
Phylogenetic relationships among Lemuridae (Primates): evidence from mtDNA.
Pastorini, Jennifer; Forstner, Michael R J; Martin, Robert D
2002-10-01
The family Lemuridae includes four genera: Eulemur, Hapalemur, Lemur,Varecia. Taxonomy and phylogenetic relationships between L. catta, Eulemur and Hapalemur, and of Varecia to these other lemurids, continue to be hotly debated. Nodal relationships among the five Eulemur species also remain contentious. A mitochondrial DNA sequence dataset from the ND 3, ND 4 L, ND 4 genes and five tRNAs (Gly, Arg, His, Ser, Leu) was generated to try to clarify phylogenetic relationships w ithin the Lemuridae. Samples (n=39) from all ten lemurid species were collected and analysed. Three Daubentonia madagascariensis were included as outgroup taxa. The approximately 2400 bp sequences were analysed using maximum parsimony, neighbor-joining and maximum likelihood methods. The results support monophyly of Eulemur, a basal divergence of Varecia, and a sister-group relationship for Lemur/Hapalemur. Based on tree topology, bootstrap values, and pairwise distance comparisons, we conclude thatVarecia and Eulemur both represent distinct genera separate from L. catta. H. griseus andH. aureus form a clade with strong support, but the sequence data do not permit robust resolution of the trichotomy involving H. simus, H. aureus/H. griseus and L. catta. Within Eulemur there is strong support for a clade containing E. fulvus, E. mongoz and E. rubriventer. However, analyses failed to clearly resolve relationships among those three species or with the more distantly related E. coronatus and E. macaco. Our sequencing data support the current subspecific status of E.m. macaco and E.m. flavifrons, and that of V.v. variegata and V.v. rubra. However, tree topology and relatively large genetic distances among individual V.v. variegata indicate that there may be more phylogenetic structure within this taxon than is indicated by current taxonomy.
Predicting Maximum Sunspot Number in Solar Cycle 24
Nipa J Bhatt; Rajmal Jain; Malini Aggarwal
2009-03-01
A few prediction methods have been developed based on the precursor technique which is found to be successful for forecasting the solar activity. Considering the geomagnetic activity aa indices during the descending phase of the preceding solar cycle as the precursor, we predict the maximum amplitude of annual mean sunspot number in cycle 24 to be 111 ± 21. This suggests that the maximum amplitude of the upcoming cycle 24 will be less than cycles 21–22. Further, we have estimated the annual mean geomagnetic activity aa index for the solar maximum year in cycle 24 to be 20.6 ± 4.7 and the average of the annual mean sunspot number during the descending phase of cycle 24 is estimated to be 48 ± 16.8.
Construction and enumeration of Boolean functions with maximum algebraic immunity
ZHANG WenYing; WU ChuanKun; LIU XiangZhong
2009-01-01
Algebraic immunity is a new cryptographic criterion proposed against algebraic attacks. In order to resist algebraic attacks, Boolean functions used in many stream ciphers should possess high algebraic immunity. This paper presents two main results to find balanced Boolean functions with maximum algebraic immunity. Through swapping the values of two bits, and then generalizing the result to swap some pairs of bits of the symmetric Boolean function constructed by Dalai, a new class of Boolean functions with maximum algebraic immunity are constructed. Enumeration of such functions is also given. For a given function p(x) with deg(p(x)) < [n/2], we give a method to construct functions in the form p(x)+q(x) which achieve the maximum algebraic immunity, where every term with nonzero coefficient in the ANF of q(x) has degree no less than [n/2].
Propane spectral resolution enhancement by the maximum entropy method
Bonavito, N. L.; Stewart, K. P.; Hurley, E. J.; Yeh, K. C.; Inguva, R.
1990-01-01
The Burg algorithm for maximum entropy power spectral density estimation is applied to a time series of data obtained from a Michelson interferometer and compared with a standard FFT estimate for resolution capability. The propane transmittance spectrum was estimated by use of the FFT with a 2 to the 18th data sample interferogram, giving a maximum unapodized resolution of 0.06/cm. This estimate was then interpolated by zero filling an additional 2 to the 18th points, and the final resolution was taken to be 0.06/cm. Comparison of the maximum entropy method (MEM) estimate with the FFT was made over a 45/cm region of the spectrum for several increasing record lengths of interferogram data beginning at 2 to the 10th. It is found that over this region the MEM estimate with 2 to the 16th data samples is in close agreement with the FFT estimate using 2 to the 18th samples.
Mass mortality of the vermetid gastropod Ceraesignum maximum
Brown, A. L.; Frazer, T. K.; Shima, J. S.; Osenberg, C. W.
2016-09-01
Ceraesignum maximum (G.B. Sowerby I, 1825), formerly Dendropoma maximum, was subject to a sudden, massive die-off in the Society Islands, French Polynesia, in 2015. On Mo'orea, where we have detailed documentation of the die-off, these gastropods were previously found in densities up to 165 m-2. In July 2015, we surveyed shallow back reefs of Mo'orea before, during and after the die-off, documenting their swift decline. All censused populations incurred 100% mortality. Additional surveys and observations from Mo'orea, Tahiti, Bora Bora, and Huahine (but not Taha'a) suggested a similar, and approximately simultaneous, die-off. The cause(s) of this cataclysmic mass mortality are currently unknown. Given the previously documented negative effects of C. maximum on corals, we expect the die-off will have cascading effects on the reef community.
The optimal polarizations for achieving maximum contrast in radar images
Swartz, A. A.; Yueh, H. A.; Kong, J. A.; Novak, L. M.; Shin, R. T.
1988-01-01
There is considerable interest in determining the optimal polarizations that maximize contrast between two scattering classes in polarimetric radar images. A systematic approach is presented for obtaining the optimal polarimetric matched filter, i.e., that filter which produces maximum contrast between two scattering classes. The maximization procedure involves solving an eigenvalue problem where the eigenvector corresponding to the maximum contrast ratio is an optimal polarimetric matched filter. To exhibit the physical significance of this filter, it is transformed into its associated transmitting and receiving polarization states, written in terms of horizontal and vertical vector components. For the special case where the transmitting polarization is fixed, the receiving polarization which maximizes the contrast ratio is also obtained. Polarimetric filtering is then applies to synthetic aperture radar images obtained from the Jet Propulsion Laboratory. It is shown, both numerically and through the use of radar imagery, that maximum image contrast can be realized when data is processed with the optimal polarimeter matched filter.
Penalized maximum likelihood estimation and variable selection in geostatistics
Chu, Tingjin; Wang, Haonan; 10.1214/11-AOS919
2012-01-01
We consider the problem of selecting covariates in spatial linear models with Gaussian process errors. Penalized maximum likelihood estimation (PMLE) that enables simultaneous variable selection and parameter estimation is developed and, for ease of computation, PMLE is approximated by one-step sparse estimation (OSE). To further improve computational efficiency, particularly with large sample sizes, we propose penalized maximum covariance-tapered likelihood estimation (PMLE$_{\\mathrm{T}}$) and its one-step sparse estimation (OSE$_{\\mathrm{T}}$). General forms of penalty functions with an emphasis on smoothly clipped absolute deviation are used for penalized maximum likelihood. Theoretical properties of PMLE and OSE, as well as their approximations PMLE$_{\\mathrm{T}}$ and OSE$_{\\mathrm{T}}$ using covariance tapering, are derived, including consistency, sparsity, asymptotic normality and the oracle properties. For covariance tapering, a by-product of our theoretical results is consistency and asymptotic normal...
Influence of maximum decking charge on intensity of blasting vibration
无
2006-01-01
Based on the character of short-time non-stationary random signal, the relationship between the maximum decking charge and energy distribution of blasting vibration signals was investigated by means of the wavelet packet method. Firstly, the characteristics of wavelet transform and wavelet packet analysis were described. Secondly, the blasting vibration signals were analyzed by wavelet packet based on software MATLAB, and the change of energy distribution curve at different frequency bands were obtained. Finally, the law of energy distribution of blasting vibration signals changing with the maximum decking charge was analyzed. The results show that with the increase of decking charge, the ratio of the energy of high frequency to total energy decreases, the dominant frequency bands of blasting vibration signals tend towards low frequency and blasting vibration does not depend on the maximum decking charge.
The subsequence weight distribution of summed maximum length digital sequences
Weathers, G. D.; Graf, E. R.; Wallace, G. R.
1974-01-01
An attempt is made to develop mathematical formulas to provide the basis for the design of pseudorandom signals intended for applications requiring accurate knowledge of the statistics of the signals. The analysis approach involves calculating the first five central moments of the weight distribution of subsequences of hybrid-sum sequences. The hybrid-sum sequence is formed from the modulo-two sum of k maximum length sequences and is an extension of the sum sequences formed from two maximum length sequences that Gilson (1966) evaluated. The weight distribution of the subsequences serves as an approximation to the filtering process. The basic reason for the analysis of hybrid-sum sequences is to establish a large group of sequences with good statistical properties. It is shown that this can be accomplished much more efficiently using the hybrid-sum approach rather than forming the group strictly from maximum length sequences.
Maximum power point tracking for optimizing energy harvesting process
Akbari, S.; Thang, P. C.; Veselov, D. S.
2016-10-01
There has been a growing interest in using energy harvesting techniques for powering wireless sensor networks. The reason for utilizing this technology can be explained by the sensors limited amount of operation time which results from the finite capacity of batteries and the need for having a stable power supply in some applications. Energy can be harvested from the sun, wind, vibration, heat, etc. It is reasonable to develop multisource energy harvesting platforms for increasing the amount of harvesting energy and to mitigate the issue concerning the intermittent nature of ambient sources. In the context of solar energy harvesting, it is possible to develop algorithms for finding the optimal operation point of solar panels at which maximum power is generated. These algorithms are known as maximum power point tracking techniques. In this article, we review the concept of maximum power point tracking and provide an overview of the research conducted in this area for wireless sensor networks applications.
Proscriptive Bayesian Programming and Maximum Entropy: a Preliminary Study
Koike, Carla Cavalcante
2008-11-01
Some problems found in robotics systems, as avoiding obstacles, can be better described using proscriptive commands, where only prohibited actions are indicated in contrast to prescriptive situations, which demands that a specific command be specified. An interesting question arises regarding the possibility to learn automatically if proscriptive commands are suitable and which parametric function could be better applied. Lately, a great variety of problems in robotics domain are object of researches using probabilistic methods, including the use of Maximum Entropy in automatic learning for robot control systems. This works presents a preliminary study on automatic learning of proscriptive robot control using maximum entropy and using Bayesian Programming. It is verified whether Maximum entropy and related methods can favour proscriptive commands in an obstacle avoidance task executed by a mobile robot.
Multitime maximum principle approach of minimal submanifolds and harmonic maps
Udriste, Constantin
2011-01-01
Some optimization problems coming from the Differential Geometry, as for example, the minimal submanifolds problem and the harmonic maps problem are solved here via interior solutions of appropriate multitime optimal control problems. Section 1 underlines some science domains where appear multitime optimal control problems. Section 2 (Section 3) recalls the multitime maximum principle for optimal control problems with multiple (curvilinear) integral cost functionals and $m$-flow type constraint evolution. Section 4 shows that there exists a multitime maximum principle approach of multitime variational calculus. Section 5 (Section 6) proves that the minimal submanifolds (harmonic maps) are optimal solutions of multitime evolution PDEs in an appropriate multitime optimal control problem. Section 7 uses the multitime maximum principle to show that of all solids having a given surface area, the sphere is the one having the greatest volume. Section 8 studies the minimal area of a multitime linear flow as optimal c...
A Maximum Entropy Estimator for the Aggregate Hierarchical Logit Model
Pedro Donoso
2011-08-01
Full Text Available A new approach for estimating the aggregate hierarchical logit model is presented. Though usually derived from random utility theory assuming correlated stochastic errors, the model can also be derived as a solution to a maximum entropy problem. Under the latter approach, the Lagrange multipliers of the optimization problem can be understood as parameter estimators of the model. Based on theoretical analysis and Monte Carlo simulations of a transportation demand model, it is demonstrated that the maximum entropy estimators have statistical properties that are superior to classical maximum likelihood estimators, particularly for small or medium-size samples. The simulations also generated reduced bias in the estimates of the subjective value of time and consumer surplus.
Approximate maximum-entropy moment closures for gas dynamics
McDonald, James G.
2016-11-01
Accurate prediction of flows that exist between the traditional continuum regime and the free-molecular regime have proven difficult to obtain. Current methods are either inaccurate in this regime or prohibitively expensive for practical problems. Moment closures have long held the promise of providing new, affordable, accurate methods in this regime. The maximum-entropy hierarchy of closures seems to offer particularly attractive physical and mathematical properties. Unfortunately, several difficulties render the practical implementation of maximum-entropy closures very difficult. This work examines the use of simple approximations to these maximum-entropy closures and shows that physical accuracy that is vastly improved over continuum methods can be obtained without a significant increase in computational cost. Initially the technique is demonstrated for a simple one-dimensional gas. It is then extended to the full three-dimensional setting. The resulting moment equations are used for the numerical solution of shock-wave profiles with promising results.
Semidefinite Programming for Approximate Maximum Likelihood Sinusoidal Parameter Estimation
Kenneth W. K. Lui
2009-01-01
Full Text Available We study the convex optimization approach for parameter estimation of several sinusoidal models, namely, single complex/real tone, multiple complex sinusoids, and single two-dimensional complex tone, in the presence of additive Gaussian noise. The major difficulty for optimally determining the parameters is that the corresponding maximum likelihood (ML estimators involve finding the global minimum or maximum of multimodal cost functions because the frequencies are nonlinear in the observed signals. By relaxing the nonconvex ML formulations using semidefinite programs, high-fidelity approximate solutions are obtained in a globally optimum fashion. Computer simulations are included to contrast the estimation performance of the proposed semi-definite relaxation methods with the iterative quadratic maximum likelihood technique as well as Cramér-Rao lower bound.
Remarks on the strong maximum principle for nonlocal operators
Jerome Coville
2008-05-01
Full Text Available In this note, we study the existence of a strong maximum principle for the nonlocal operator $$ mathcal{M}[u](x :=int_{G}J(gu(x*g^{-1}dmu(g - u(x, $$ where $G$ is a topological group acting continuously on a Hausdorff space $X$ and $u in C(X$. First we investigate the general situation and derive a pre-maximum principle. Then we restrict our analysis to the case of homogeneous spaces (i.e., $ X=G /H$. For such Hausdorff spaces, depending on the topology, we give a condition on $J$ such that a strong maximum principle holds for $mathcal{M}$. We also revisit the classical case of the convolution operator (i.e. $G=(mathbb{R}^n,+, X=mathbb{R}^n, dmu =dy$.
Resource-constrained maximum network throughput on space networks
Yanling Xing; Ning Ge; Youzheng Wang
2015-01-01
This paper investigates the maximum network through-put for resource-constrained space networks based on the delay and disruption-tolerant networking (DTN) architecture. Specifical y, this paper proposes a methodology for calculating the maximum network throughput of multiple transmission tasks under storage and delay constraints over a space network. A mixed-integer linear programming (MILP) is formulated to solve this problem. Simula-tions results show that the proposed methodology can successful y calculate the optimal throughput of a space network under storage and delay constraints, as wel as a clear, monotonic relationship between end-to-end delay and the maximum network throughput under storage constraints. At the same time, the optimization re-sults shine light on the routing and transport protocol design in space communication, which can be used to obtain the optimal network throughput.
Semidefinite Programming for Approximate Maximum Likelihood Sinusoidal Parameter Estimation
Lui, Kenneth W. K.; So, H. C.
2009-12-01
We study the convex optimization approach for parameter estimation of several sinusoidal models, namely, single complex/real tone, multiple complex sinusoids, and single two-dimensional complex tone, in the presence of additive Gaussian noise. The major difficulty for optimally determining the parameters is that the corresponding maximum likelihood (ML) estimators involve finding the global minimum or maximum of multimodal cost functions because the frequencies are nonlinear in the observed signals. By relaxing the nonconvex ML formulations using semidefinite programs, high-fidelity approximate solutions are obtained in a globally optimum fashion. Computer simulations are included to contrast the estimation performance of the proposed semi-definite relaxation methods with the iterative quadratic maximum likelihood technique as well as Cramér-Rao lower bound.
Quality, precision and accuracy of the maximum No. 40 anemometer
Obermeir, J. [Otech Engineering, Davis, CA (United States); Blittersdorf, D. [NRG Systems Inc., Hinesburg, VT (United States)
1996-12-31
This paper synthesizes available calibration data for the Maximum No. 40 anemometer. Despite its long history in the wind industry, controversy surrounds the choice of transfer function for this anemometer. Many users are unaware that recent changes in default transfer functions in data loggers are producing output wind speed differences as large as 7.6%. Comparison of two calibration methods used for large samples of Maximum No. 40 anemometers shows a consistent difference of 4.6% in output speeds. This difference is significantly larger than estimated uncertainty levels. Testing, initially performed to investigate related issues, reveals that Gill and Maximum cup anemometers change their calibration transfer functions significantly when calibrated in the open atmosphere compared with calibration in a laminar wind tunnel. This indicates that atmospheric turbulence changes the calibration transfer function of cup anemometers. These results call into question the suitability of standard wind tunnel calibration testing for cup anemometers. 6 refs., 10 figs., 4 tabs.
The evolution of maximum body size of terrestrial mammals.
Smith, Felisa A; Boyer, Alison G; Brown, James H; Costa, Daniel P; Dayan, Tamar; Ernest, S K Morgan; Evans, Alistair R; Fortelius, Mikael; Gittleman, John L; Hamilton, Marcus J; Harding, Larisa E; Lintulaakso, Kari; Lyons, S Kathleen; McCain, Christy; Okie, Jordan G; Saarinen, Juha J; Sibly, Richard M; Stephens, Patrick R; Theodor, Jessica; Uhen, Mark D
2010-11-26
The extinction of dinosaurs at the Cretaceous/Paleogene (K/Pg) boundary was the seminal event that opened the door for the subsequent diversification of terrestrial mammals. Our compilation of maximum body size at the ordinal level by sub-epoch shows a near-exponential increase after the K/Pg. On each continent, the maximum size of mammals leveled off after 40 million years ago and thereafter remained approximately constant. There was remarkable congruence in the rate, trajectory, and upper limit across continents, orders, and trophic guilds, despite differences in geological and climatic history, turnover of lineages, and ecological variation. Our analysis suggests that although the primary driver for the evolution of giant mammals was diversification to fill ecological niches, environmental temperature and land area may have ultimately constrained the maximum size achieved.
The maximum force in a column under constant speed compression
Kuzkin, Vitaly A
2015-01-01
Dynamic buckling of an elastic column under compression at constant speed is investigated assuming the first-mode buckling. Two cases are considered: (i) an imperfect column (Hoff's statement), and (ii) a perfect column having an initial lateral deflection. The range of parameters, where the maximum load supported by a column exceeds Euler static force is determined. In this range, the maximum load is represented as a function of the compression rate, slenderness ratio, and imperfection/initial deflection. Considering the results we answer the following question: "How slowly the column should be compressed in order to measure static load-bearing capacity?" This question is important for the proper setup of laboratory experiments and computer simulations of buckling. Additionally, it is shown that the behavior of a perfect column having an initial deflection differ significantlys form the behavior of an imperfect column. In particular, the dependence of the maximum force on the compression rate is non-monotoni...
Maximum-Entropy Inference with a Programmable Annealer
Chancellor, Nicholas; Vinci, Walter; Aeppli, Gabriel; Warburton, Paul A
2015-01-01
Optimisation problems in science and engineering typically involve finding the ground state (i.e. the minimum energy configuration) of a cost function with respect to many variables. If the variables are corrupted by noise then this approach maximises the likelihood that the solution found is correct. An alternative approach is to make use of prior statistical information about the noise in conjunction with Bayes's theorem. The maximum entropy solution to the problem then takes the form of a Boltzmann distribution over the ground and excited states of the cost function. Here we use a programmable Josephson junction array for the information decoding problem which we simulate as a random Ising model in a field. We show experimentally that maximum entropy decoding at finite temperature can in certain cases give competitive and even slightly better bit-error-rates than the maximum likelihood approach at zero temperature, confirming that useful information can be extracted from the excited states of the annealing...
Estimating the maximum potential revenue for grid connected electricity storage :
Byrne, Raymond Harry; Silva Monroy, Cesar Augusto.
2012-12-01
The valuation of an electricity storage device is based on the expected future cash flow generated by the device. Two potential sources of income for an electricity storage system are energy arbitrage and participation in the frequency regulation market. Energy arbitrage refers to purchasing (stor- ing) energy when electricity prices are low, and selling (discharging) energy when electricity prices are high. Frequency regulation is an ancillary service geared towards maintaining system frequency, and is typically procured by the independent system operator in some type of market. This paper outlines the calculations required to estimate the maximum potential revenue from participating in these two activities. First, a mathematical model is presented for the state of charge as a function of the storage device parameters and the quantities of electricity purchased/sold as well as the quantities o ered into the regulation market. Using this mathematical model, we present a linear programming optimization approach to calculating the maximum potential revenue from an elec- tricity storage device. The calculation of the maximum potential revenue is critical in developing an upper bound on the value of storage, as a benchmark for evaluating potential trading strate- gies, and a tool for capital nance risk assessment. Then, we use historical California Independent System Operator (CAISO) data from 2010-2011 to evaluate the maximum potential revenue from the Tehachapi wind energy storage project, an American Recovery and Reinvestment Act of 2009 (ARRA) energy storage demonstration project. We investigate the maximum potential revenue from two di erent scenarios: arbitrage only and arbitrage combined with the regulation market. Our analysis shows that participation in the regulation market produces four times the revenue compared to arbitrage in the CAISO market using 2010 and 2011 data. Then we evaluate several trading strategies to illustrate how they compare to the
Spatio-temporal observations of tertiary ozone maximum
V. F. Sofieva
2009-03-01
Full Text Available We present spatio-temporal distributions of tertiary ozone maximum (TOM, based on GOMOS (Global Ozone Monitoring by Occultation of Stars ozone measurements in 2002–2006. The tertiary ozone maximum is typically observed in the high-latitude winter mesosphere at altitude ~72 km. Although the explanation for this phenomenon has been found recently – low concentrations of odd-hydrogen cause the subsequent decrease in odd-oxygen losses – models have had significant deviations from existing observations until recently. Good coverage of polar night regions by GOMOS data has allowed for the first time obtaining spatial and temporal observational distributions of night-time ozone mixing ratio in the mesosphere.
The distributions obtained from GOMOS data have specific features, which are variable from year to year. In particular, due to a long lifetime of ozone in polar night conditions, the downward transport of polar air by the meridional circulation is clearly observed in the tertiary ozone maximum time series. Although the maximum tertiary ozone mixing ratio is achieved close to the polar night terminator (as predicted by the theory, TOM can be observed also at very high latitudes, not only in the beginning and at the end, but also in the middle of winter. We have compared the observational spatio-temporal distributions of tertiary ozone maximum with that obtained using WACCM (Whole Atmosphere Community Climate Model and found that the specific features are reproduced satisfactorily by the model.
Since ozone in the mesosphere is very sensitive to HO_{x} concentrations, energetic particle precipitation can significantly modify the shape of the ozone profiles. In particular, GOMOS observations have shown that the tertiary ozone maximum was temporarily destroyed during the January 2005 and December 2006 solar proton events as a result of the HO_{x} enhancement from the increased ionization.
Beat the Deviations in Estimating Maximum Power of Thermoelectric Modules
Gao, Junling; Chen, Min
2013-01-01
Under a certain temperature difference, the maximum power of a thermoelectric module can be estimated by the open-circuit voltage and the short-circuit current. In practical measurement, there exist two switch modes, either from open to short or from short to open, but the two modes can give...... different estimations on the maximum power. Using TEG-127-2.8-3.5-250 and TEG-127-1.4-1.6-250 as two examples, the difference is about 10%, leading to some deviations with the temperature change. This paper analyzes such differences by means of a nonlinear numerical model of thermoelectricity, and finds out...
Microcanonical origin of the maximum entropy principle for open systems.
Lee, Julian; Pressé, Steve
2012-10-01
There are two distinct approaches for deriving the canonical ensemble. The canonical ensemble either follows as a special limit of the microcanonical ensemble or alternatively follows from the maximum entropy principle. We show the equivalence of these two approaches by applying the maximum entropy formulation to a closed universe consisting of an open system plus bath. We show that the target function for deriving the canonical distribution emerges as a natural consequence of partial maximization of the entropy over the bath degrees of freedom alone. By extending this mathematical formalism to dynamical paths rather than equilibrium ensembles, the result provides an alternative justification for the principle of path entropy maximization as well.
Information Entropy Production of Spatio-Temporal Maximum Entropy Distributions
Cofre, Rodrigo
2015-01-01
Spiking activity from populations of neurons display causal interactions and memory effects. Therefore, they are expected to show some degree of irreversibility in time. Motivated by the spike train statistics, in this paper we build a framework to quantify the degree of irreversibility of any maximum entropy distribution. Our approach is based on the transfer matrix technique, which enables us to find an homogeneous irreducible Markov chain that shares the same maximum entropy measure. We provide relevant examples in the context of spike train statistics
Semiparametric maximum likelihood for nonlinear regression with measurement errors.
Suh, Eun-Young; Schafer, Daniel W
2002-06-01
This article demonstrates semiparametric maximum likelihood estimation of a nonlinear growth model for fish lengths using imprecisely measured ages. Data on the species corvina reina, found in the Gulf of Nicoya, Costa Rica, consist of lengths and imprecise ages for 168 fish and precise ages for a subset of 16 fish. The statistical problem may therefore be classified as nonlinear errors-in-variables regression with internal validation data. Inferential techniques are based on ideas extracted from several previous works on semiparametric maximum likelihood for errors-in-variables problems. The illustration of the example clarifies practical aspects of the associated computational, inferential, and data analytic techniques.
Maximum length scale in density based topology optimization
Lazarov, Boyan Stefanov; Wang, Fengwen
2017-01-01
The focus of this work is on two new techniques for imposing maximum length scale in topology optimization. Restrictions on the maximum length scale provide designers with full control over the optimized structure and open possibilities to tailor the optimized design for broader range...... of manufacturing processes by fulfilling the associated technological constraints. One of the proposed methods is based on combination of several filters and builds on top of the classical density filtering which can be viewed as a low pass filter applied to the design parametrization. The main idea...
On the Effect of Mortgages of Maximum Amount
YangZongping
2005-01-01
Since the enactment of the PRC Guarantee Law, mortgages of maximum amount has won wide application in a variety of business occupations and particularly in banking. Compared with the rich content of the 21clause statute on mortgages of maximum amount in Japan's Civil Law, the Chinese law has only four principled clauses. Its lack of operability plus its legislative gaps and defects has a severe impact on the positive effectiveness of the law. The core issue is the question of effectiveness. Because the principles stipulated in the Law run counter to the diversity of its actual practices,
A Maximum Entropy Method for a Robust Portfolio Problem
Yingying Xu
2014-06-01
Full Text Available We propose a continuous maximum entropy method to investigate the robustoptimal portfolio selection problem for the market with transaction costs and dividends.This robust model aims to maximize the worst-case portfolio return in the case that allof asset returns lie within some prescribed intervals. A numerical optimal solution tothe problem is obtained by using a continuous maximum entropy method. Furthermore,some numerical experiments indicate that the robust model in this paper can result in betterportfolio performance than a classical mean-variance model.
On the maximum grain size entrained by photoevaporative winds
Hutchison, Mark A; Maddison, Sarah T
2016-01-01
We model the behaviour of dust grains entrained by photoevaporation-driven winds from protoplanetary discs assuming a non-rotating, plane-parallel disc. We obtain an analytic expression for the maximum entrainable grain size in extreme-UV radiation-driven winds, which we demonstrate to be proportional to the mass loss rate of the disc. When compared with our hydrodynamic simulations, the model reproduces almost all of the wind properties for the gas and dust. In typical turbulent discs, the entrained grain sizes in the wind are smaller than the theoretical maximum everywhere but the inner disc due to dust settling.
Modified maximum likelihood registration based on information fusion
Yongqing Qi; Zhongliang Jing; Shiqiang Hu
2007-01-01
The bias estimation of passive sensors is considered based on information fusion in multi-platform multisensor tracking system. The unobservable problem of bearing-only tracking in blind spot is analyzed. A modified maximum likelihood method, which uses the redundant information of multi-sensor system to calculate the target position, is investigated to estimate the biases. Monte Carlo simulation results show that the modified method eliminates the effect of unobservable problem in the blind spot and can estimate the biases more rapidly and accurately than maximum likelihood method. It is statistically efficient since the standard deviation of bias estimation errors meets the theoretical lower bounds.
Maximum-entropy distributions of correlated variables with prespecified marginals.
Larralde, Hernán
2012-12-01
The problem of determining the joint probability distributions for correlated random variables with prespecified marginals is considered. When the joint distribution satisfying all the required conditions is not unique, the "most unbiased" choice corresponds to the distribution of maximum entropy. The calculation of the maximum-entropy distribution requires the solution of rather complicated nonlinear coupled integral equations, exact solutions to which are obtained for the case of Gaussian marginals; otherwise, the solution can be expressed as a perturbation around the product of the marginals if the marginal moments exist.
A discussion on maximum entropy production and information theory
Bruers, Stijn [Instituut voor Theoretische Fysica, Celestijnenlaan 200D, Katholieke Universiteit Leuven, B-3001 Leuven (Belgium)
2007-07-06
We will discuss the maximum entropy production (MaxEP) principle based on Jaynes' information theoretical arguments, as was done by Dewar (2003 J. Phys. A: Math. Gen. 36 631-41, 2005 J. Phys. A: Math. Gen. 38 371-81). With the help of a simple mathematical model of a non-equilibrium system, we will show how to derive minimum and maximum entropy production. Furthermore, the model will help us to clarify some confusing points and to see differences between some MaxEP studies in the literature.
Generalized Relativistic Wave Equations with Intrinsic Maximum Momentum
Ching, Chee Leong
2013-01-01
We examine the nonperturbative effect of maximum momentum on the relativistic wave equations. In momentum representation, we obtain the exact eigen-energies and wavefunctions of one-dimensional Klein-Gordon and Dirac equation with linear confining potentials, and the Dirac oscillator. Bound state solutions are only possible when the strength of scalar potential are stronger than vector potential. The energy spectrum of the systems studied are bounded from above, whereby classical characteristics are observed in the uncertainties of position and momentum operators. Also, there is a truncation in the maximum number of bound states that is allowed. Some of these quantum-gravitational features may have future applications.
Generalized relativistic wave equations with intrinsic maximum momentum
Ching, Chee Leong; Ng, Wei Khim
2014-05-01
We examine the nonperturbative effect of maximum momentum on the relativistic wave equations. In momentum representation, we obtain the exact eigen-energies and wave functions of one-dimensional Klein-Gordon and Dirac equation with linear confining potentials, and the Dirac oscillator. Bound state solutions are only possible when the strength of scalar potential is stronger than vector potential. The energy spectrum of the systems studied is bounded from above, whereby classical characteristics are observed in the uncertainties of position and momentum operators. Also, there is a truncation in the maximum number of bound states that is allowed. Some of these quantum-gravitational features may have future applications.
Parameter estimation in X-ray astronomy using maximum likelihood
Wachter, K.; Leach, R.; Kellogg, E.
1979-01-01
Methods of estimation of parameter values and confidence regions by maximum likelihood and Fisher efficient scores starting from Poisson probabilities are developed for the nonlinear spectral functions commonly encountered in X-ray astronomy. It is argued that these methods offer significant advantages over the commonly used alternatives called minimum chi-squared because they rely on less pervasive statistical approximations and so may be expected to remain valid for data of poorer quality. Extensive numerical simulations of the maximum likelihood method are reported which verify that the best-fit parameter value and confidence region calculations are correct over a wide range of input spectra.
A maximum in the strength of nanocrystalline copper
Schiøtz, Jakob; Jacobsen, Karsten Wedel
2003-01-01
We used molecular dynamics simulations with system sizes up to 100 million atoms to simulate plastic deformation of nanocrystalline copper. By varying the grain size between 5 and 50 nanometers, we show that the flow stress and thus the strength exhibit a maximum at a grain size of 10 to 15...... nanometers. This maximum is because of a shift in the microscopic deformation mechanism from dislocation-mediated plasticity in the coarse-grained material to grain boundary sliding in the nanocrystalline region. The simulations allow us to observe the mechanisms behind the grain-size dependence...
Efficiency of autonomous soft nanomachines at maximum power.
Seifert, Udo
2011-01-14
We consider nanosized artificial or biological machines working in steady state enforced by imposing nonequilibrium concentrations of solutes or by applying external forces, torques, or electric fields. For unicyclic and strongly coupled multicyclic machines, efficiency at maximum power is not bounded by the linear response value 1/2. For strong driving, it can even approach the thermodynamic limit 1. Quite generally, such machines fall into three different classes characterized, respectively, as "strong and efficient," "strong and inefficient," and "balanced." For weakly coupled multicyclic machines, efficiency at maximum power has lost any universality even in the linear response regime.
A Brooks type theorem for the maximum local edge connectivity
Stiebitz, Michael; Toft, Bjarne
2017-01-01
For a graph $G$, let $\\cn(G)$ and $\\la(G)$ denote the chromatic number of $G$ and the maximum local edge connectivity of $G$, respectively. A result of Dirac \\cite{Dirac53} implies that every graph $G$ satisfies $\\cn(G)\\leq \\la(G)+1$. In this paper we characterize the graphs $G$ for which $\\cn(G)...
Prediction of Maximum Oxygen Consumption from Walking, Jogging, or Running.
Larsen, Gary E.; George, James D.; Alexander, Jeffrey L.; Fellingham, Gilbert W.; Aldana, Steve G.; Parcell, Allen C.
2002-01-01
Developed a cardiorespiratory endurance test that retained the inherent advantages of submaximal testing while eliminating reliance on heart rate measurement in predicting maximum oxygen uptake (VO2max). College students completed three exercise tests. The 1.5-mile endurance test predicted VO2max from submaximal exercise without requiring heart…
On the maximum backscattering cross section of passive linear arrays
Solymar, L.; Appel-Hansen, Jørgen
1974-01-01
The maximum backscattering cross section of an equispaced linear array connected to a reactive network and consisting of isotropic radiators is calculated forn = 2, 3, and 4 elements as a function of the incident angle and of the distance between the elements. On the basis of the results obtained...
Scientific substantination of maximum allowable concentration of fluopicolide in water
Pelo I.М.
2014-03-01
Full Text Available In order to substantiate fluopicolide maximum allowable concentration in the water of water reservoirs the research was carried out. Methods of study: laboratory hygienic experiment using organoleptic and sanitary-chemical, sanitary-toxicological, sanitary-microbiological and mathematical methods. The results of fluopicolide influence on organoleptic properties of water, sanitary regimen of reservoirs for household purposes were given and its subthreshold concentration in water by sanitary and toxicological hazard index was calculated. The threshold concentration of the substance by the main hazard criteria was established, the maximum allowable concentration in water was substantiated. The studies led to the following conclusions: fluopicolide threshold concentration in water by organoleptic hazard index (limiting criterion – the smell – 0.15 mg/dm3, general sanitary hazard index (limiting criteria – impact on the number of saprophytic microflora, biochemical oxygen demand and nitrification – 0.015 mg/dm3, the maximum noneffective concentration – 0.14 mg/dm3, the maximum allowable concentration - 0.015 mg/dm3.
Effects of bruxism on the maximum bite force
Todić Jelena T.
2017-01-01
Full Text Available Background/Aim. Bruxism is a parafunctional activity of the masticatory system, which is characterized by clenching or grinding of teeth. The purpose of this study was to determine whether the presence of bruxism has impact on maximum bite force, with particular reference to the potential impact of gender on bite force values. Methods. This study included two groups of subjects: without and with bruxism. The presence of bruxism in the subjects was registered using a specific clinical questionnaire on bruxism and physical examination. The subjects from both groups were submitted to the procedure of measuring the maximum bite pressure and occlusal contact area using a single-sheet pressure-sensitive films (Fuji Prescale MS and HS Film. Maximal bite force was obtained by multiplying maximal bite pressure and occlusal contact area values. Results. The average values of maximal bite force were significantly higher in the subjects with bruxism compared to those without bruxism (p 0.01. Maximal bite force was significantly higher in the males compared to the females in all segments of the research. Conclusion. The presence of bruxism influences the increase in the maximum bite force as shown in this study. Gender is a significant determinant of bite force. Registration of maximum bite force can be used in diagnosing and analysing pathophysiological events during bruxism.
A Unified Maximum Likelihood Approach to Document Retrieval.
Bodoff, David; Enache, Daniel; Kambil, Ajit; Simon, Gary; Yukhimets, Alex
2001-01-01
Addresses the query- versus document-oriented dichotomy in information retrieval. Introduces a maximum likelihood approach to utilizing feedback data that can be used to construct a concrete object function that estimates both document and query parameters in accordance with all available feedback data. (AEF)
Sequential and Parallel Algorithms for Finding a Maximum Convex Polygon
Fischer, Paul
1997-01-01
such a polygon which is maximal with respect to area can be found in time O(n³ log n). With the same running time one can also find such a polygon which contains a maximum number of positive points. If, in addition, the number of vertices of the polygon is restricted to be at most M, then the running time...
Prediction of Maximum Oxygen Consumption from Walking, Jogging, or Running.
Larsen, Gary E.; George, James D.; Alexander, Jeffrey L.; Fellingham, Gilbert W.; Aldana, Steve G.; Parcell, Allen C.
2002-01-01
Developed a cardiorespiratory endurance test that retained the inherent advantages of submaximal testing while eliminating reliance on heart rate measurement in predicting maximum oxygen uptake (VO2max). College students completed three exercise tests. The 1.5-mile endurance test predicted VO2max from submaximal exercise without requiring heart…
34 CFR 682.204 - Maximum loan amounts.
2010-07-01
... 34 Education 3 2010-07-01 2010-07-01 false Maximum loan amounts. 682.204 Section 682.204 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF POSTSECONDARY EDUCATION, DEPARTMENT OF EDUCATION FEDERAL FAMILY EDUCATION LOAN (FFEL) PROGRAM General Provisions § 682.204...
Triadic conceptual structure of the maximum entropy approach to evolution.
Herrmann-Pillath, Carsten; Salthe, Stanley N
2011-03-01
Many problems in evolutionary theory are cast in dyadic terms, such as the polar oppositions of organism and environment. We argue that a triadic conceptual structure offers an alternative perspective under which the information generating role of evolution as a physical process can be analyzed, and propose a new diagrammatic approach. Peirce's natural philosophy was deeply influenced by his reception of both Darwin's theory and thermodynamics. Thus, we elaborate on a new synthesis which puts together his theory of signs and modern Maximum Entropy approaches to evolution in a process discourse. Following recent contributions to the naturalization of Peircean semiosis, pointing towards 'physiosemiosis' or 'pansemiosis', we show that triadic structures involve the conjunction of three different kinds of causality, efficient, formal and final. In this, we accommodate the state-centered thermodynamic framework to a process approach. We apply this on Ulanowicz's analysis of autocatalytic cycles as primordial patterns of life. This paves the way for a semiotic view of thermodynamics which is built on the idea that Peircean interpretants are systems of physical inference devices evolving under natural selection. In this view, the principles of Maximum Entropy, Maximum Power, and Maximum Entropy Production work together to drive the emergence of information carrying structures, which at the same time maximize information capacity as well as the gradients of energy flows, such that ultimately, contrary to Schrödinger's seminal contribution, the evolutionary process is seen to be a physical expression of the Second Law.
Maximum-entropy probability distributions under Lp-norm constraints
Dolinar, S.
1991-01-01
Continuous probability density functions and discrete probability mass functions are tabulated which maximize the differential entropy or absolute entropy, respectively, among all probability distributions with a given L sub p norm (i.e., a given pth absolute moment when p is a finite integer) and unconstrained or constrained value set. Expressions for the maximum entropy are evaluated as functions of the L sub p norm. The most interesting results are obtained and plotted for unconstrained (real valued) continuous random variables and for integer valued discrete random variables. The maximum entropy expressions are obtained in closed form for unconstrained continuous random variables, and in this case there is a simple straight line relationship between the maximum differential entropy and the logarithm of the L sub p norm. Corresponding expressions for arbitrary discrete and constrained continuous random variables are given parametrically; closed form expressions are available only for special cases. However, simpler alternative bounds on the maximum entropy of integer valued discrete random variables are obtained by applying the differential entropy results to continuous random variables which approximate the integer valued random variables in a natural manner. All the results are presented in an integrated framework that includes continuous and discrete random variables, constraints on the permissible value set, and all possible values of p. Understanding such as this is useful in evaluating the performance of data compression schemes.
Exploiting the Maximum Entropy Principle to Increase Retrieval Effectiveness.
Cooper, William S.
1983-01-01
Presents information retrieval design approach in which queries of computer-based system consist of sets of terms, either unweighted or weighted with subjective term precision estimates, and retrieval outputs ranked by probability of usefulness estimated by "maximum entropy principle." Boolean and weighted request systems are discussed.…
The constraint rule of the maximum entropy principle
Uffink, J.
2001-01-01
The principle of maximum entropy is a method for assigning values to probability distributions on the basis of partial information. In usual formulations of this and related methods of inference one assumes that this partial information takes the form of a constraint on allowed probability distribut
On the maximum entropy principle in non-extensive thermostatistics
Naudts, Jan
2004-01-01
It is possible to derive the maximum entropy principle from thermodynamic stability requirements. Using as a starting point the equilibrium probability distribution, currently used in non-extensive thermostatistics, it turns out that the relevant entropy function is Renyi's alpha-entropy, and not Tsallis' entropy.
MAXIMUM-LIKELIHOOD-ESTIMATION OF THE ENTROPY OF AN ATTRACTOR
SCHOUTEN, JC; TAKENS, F; VANDENBLEEK, CM
1994-01-01
In this paper, a maximum-likelihood estimate of the (Kolmogorov) entropy of an attractor is proposed that can be obtained directly from a time series. Also, the relative standard deviation of the entropy estimate is derived; it is dependent on the entropy and on the number of samples used in the est
Maximum-Entropy Inference with a Programmable Annealer.
Chancellor, Nicholas; Szoke, Szilard; Vinci, Walter; Aeppli, Gabriel; Warburton, Paul A
2016-03-03
Optimisation problems typically involve finding the ground state (i.e. the minimum energy configuration) of a cost function with respect to many variables. If the variables are corrupted by noise then this maximises the likelihood that the solution is correct. The maximum entropy solution on the other hand takes the form of a Boltzmann distribution over the ground and excited states of the cost function to correct for noise. Here we use a programmable annealer for the information decoding problem which we simulate as a random Ising model in a field. We show experimentally that finite temperature maximum entropy decoding can give slightly better bit-error-rates than the maximum likelihood approach, confirming that useful information can be extracted from the excited states of the annealer. Furthermore we introduce a bit-by-bit analytical method which is agnostic to the specific application and use it to show that the annealer samples from a highly Boltzmann-like distribution. Machines of this kind are therefore candidates for use in a variety of machine learning applications which exploit maximum entropy inference, including language processing and image recognition.
40 CFR 35.145 - Maximum federal share.
2010-07-01
... STATE AND LOCAL ASSISTANCE Environmental Program Grants Air Pollution Control (section 105) § 35.145 Maximum federal share. (a) The Regional Administrator may provide air pollution control agencies, as... programs for the prevention and control of air pollution or implementing national primary and...
Maximum Safety Regenerative Power Tracking for DC Traction Power Systems
Guifu Du
2017-02-01
Full Text Available Direct current (DC traction power systems are widely used in metro transport systems, with running rails usually being used as return conductors. When traction current flows through the running rails, a potential voltage known as “rail potential” is generated between the rails and ground. Currently, abnormal rises of rail potential exist in many railway lines during the operation of railway systems. Excessively high rail potentials pose a threat to human life and to devices connected to the rails. In this paper, the effect of regenerative power distribution on rail potential is analyzed. Maximum safety regenerative power tracking is proposed for the control of maximum absolute rail potential and energy consumption during the operation of DC traction power systems. The dwell time of multiple trains at each station and the trigger voltage of the regenerative energy absorbing device (READ are optimized based on an improved particle swarm optimization (PSO algorithm to manage the distribution of regenerative power. In this way, the maximum absolute rail potential and energy consumption of DC traction power systems can be reduced. The operation data of Guangzhou Metro Line 2 are used in the simulations, and the results show that the scheme can reduce the maximum absolute rail potential and energy consumption effectively and guarantee the safety in energy saving of DC traction power systems.
A MAXIMUM ENTROPY METHOD FOR CONSTRAINED SEMI-INFINITEPROGRAMMING PROBLEMS
ZHOU Guanglu; WANG Changyu; SHI Zhenjun; SUN Qingying
1999-01-01
This paper presents a new method, called the maximum entropy method,for solving semi-infinite programming problems, in which thesemi-infinite programming problem is approximated by one with a singleconstraint. The convergence properties for this method are discussed.Numerical examples are given to show the high effciency of thealgorithm.
Closed form maximum likelihood estimator of conditional random fields
Zhu, Zhemin; Hiemstra, Djoerd; Apers, Peter M.G.; Wombacher, Andreas
2013-01-01
Training Conditional Random Fields (CRFs) can be very slow for big data. In this paper, we present a new training method for CRFs called {\\em Empirical Training} which is motivated by the concept of co-occurrence rate. We show that the standard training (unregularized) can have many maximum likeliho
Heteroscedastic one-factor models and marginal maximum likelihood estimation
Hessen, D.J.; Dolan, C.V.
2009-01-01
In the present paper, a general class of heteroscedastic one-factor models is considered. In these models, the residual variances of the observed scores are explicitly modelled as parametric functions of the one-dimensional factor score. A marginal maximum likelihood procedure for parameter estimati
Estruturas silicosas na gramínea Panicum maximum
Pedro Fontana Junior
1957-05-01
Full Text Available The silica structure of the grass Panicum maximum were studied by electron and phase contrast microscopy. Several interesting kinds of silica formation (spiklets were found. The most ineresting structures ressembels the "Schaumstruktur" found by HELMCKE in diatoms. Another interesting structure was described in the "silica cells" and a detailed study of the mophology of some different kinds of spiklets was made.
Bias Correction for Alternating Iterative Maximum Likelihood Estimators
Gang YU; Wei GAO; Ningzhong SHI
2013-01-01
In this paper,we give a definition of the alternating iterative maximum likelihood estimator (AIMLE) which is a biased estimator.Furthermore we adjust the AIMLE to result in asymptotically unbiased and consistent estimators by using a bootstrap iterative bias correction method as in Kuk (1995).Two examples and simulation results reported illustrate the performance of the bias correction for AIMLE.
21 CFR 801.415 - Maximum acceptable level of ozone.
2010-04-01
... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Maximum acceptable level of ozone. 801.415 Section... level of ozone. (a) Ozone is a toxic gas with no known useful medical application in specific, adjunctive, or preventive therapy. In order for ozone to be effective as a germicide, it must be present in...
The maximum number of minimal codewords in long codes
Alahmadi, A.; Aldred, R.E.L.; dela Cruz, R.;
2013-01-01
Upper bounds on the maximum number of minimal codewords in a binary code follow from the theory of matroids. Random coding provides lower bounds. In this paper, we compare these bounds with analogous bounds for the cycle code of graphs. This problem (in the graphic case) was considered in 1981...
A Monte Carlo Evaluation of Maximum Likelihood Multidimensional Scaling Methods
Bijmolt, T.H.A.; Wedel, M.
1996-01-01
We compare three alternative Maximum Likelihood Multidimensional Scaling methods for pairwise dissimilarity ratings, namely MULTISCALE, MAXSCAL, and PROSCAL in a Monte Carlo study.The three MLMDS methods recover the true con gurations very well.The recovery of the true dimensionality depends on the
Quantum-dot Carnot engine at maximum power.
Esposito, Massimiliano; Kawai, Ryoichi; Lindenberg, Katja; Van den Broeck, Christian
2010-04-01
We evaluate the efficiency at maximum power of a quantum-dot Carnot heat engine. The universal values of the coefficients at the linear and quadratic order in the temperature gradient are reproduced. Curzon-Ahlborn efficiency is recovered in the limit of weak dissipation.