Ancestral sequence reconstruction with Maximum Parsimony
Herbst, Lina; Fischer, Mareike
2017-01-01
One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference as well as for ancestral sequence inference is Maximum Parsimony (...
Reconstructing phylogenetic networks using maximum parsimony.
Nakhleh, Luay; Jin, Guohua; Zhao, Fengmei; Mellor-Crummey, John
2005-01-01
Phylogenies - the evolutionary histories of groups of organisms - are one of the most widely used tools throughout the life sciences, as well as objects of research within systematics, evolutionary biology, epidemiology, etc. Almost every tool devised to date to reconstruct phylogenies produces trees; yet it is widely understood and accepted that trees oversimplify the evolutionary histories of many groups of organims, most prominently bacteria (because of horizontal gene transfer) and plants (because of hybrid speciation). Various methods and criteria have been introduced for phylogenetic tree reconstruction. Parsimony is one of the most widely used and studied criteria, and various accurate and efficient heuristics for reconstructing trees based on parsimony have been devised. Jotun Hein suggested a straightforward extension of the parsimony criterion to phylogenetic networks. In this paper we formalize this concept, and provide the first experimental study of the quality of parsimony as a criterion for constructing and evaluating phylogenetic networks. Our results show that, when extended to phylogenetic networks, the parsimony criterion produces promising results. In a great majority of the cases in our experiments, the parsimony criterion accurately predicts the numbers and placements of non-tree events.
Ancestral Sequence Reconstruction with Maximum Parsimony.
Herbst, Lina; Fischer, Mareike
2017-12-01
One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference and for ancestral sequence inference is Maximum Parsimony (MP). In this manuscript, we focus on this method and on ancestral state inference for fully bifurcating trees. In particular, we investigate a conjecture published by Charleston and Steel in 1995 concerning the number of species which need to have a particular state, say a, at a particular site in order for MP to unambiguously return a as an estimate for the state of the last common ancestor. We prove the conjecture for all even numbers of character states, which is the most relevant case in biology. We also show that the conjecture does not hold in general for odd numbers of character states, but also present some positive results for this case.
Direct maximum parsimony phylogeny reconstruction from genotype data
Sridhar, Srinath; Lam, Fumei; Blelloch, Guy E; Ravi, R; Schwartz, Russell
2007-01-01
Abstract Background Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of ge...
Direct maximum parsimony phylogeny reconstruction from genotype data.
Sridhar, Srinath; Lam, Fumei; Blelloch, Guy E; Ravi, R; Schwartz, Russell
2007-12-05
Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes. In this work, we develop the first practical method for computing maximum parsimony phylogenies directly from genotype data. We show that the standard practice of first inferring haplotypes from genotypes and then reconstructing a phylogeny on the haplotypes often substantially overestimates phylogeny size. As an immediate application, our method can be used to determine the minimum number of mutations required to explain a given set of observed genotypes. Phylogeny reconstruction directly from unphased data is computationally feasible for moderate-sized problem instances and can lead to substantially more accurate tree size inferences than the standard practice of treating phasing and phylogeny construction as two separate analysis stages. The difference between the approaches is particularly important for downstream applications that require a lower-bound on the number of mutations that the genetic region has undergone.
Direct maximum parsimony phylogeny reconstruction from genotype data
Directory of Open Access Journals (Sweden)
Ravi R
2007-12-01
Full Text Available Abstract Background Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes. Results In this work, we develop the first practical method for computing maximum parsimony phylogenies directly from genotype data. We show that the standard practice of first inferring haplotypes from genotypes and then reconstructing a phylogeny on the haplotypes often substantially overestimates phylogeny size. As an immediate application, our method can be used to determine the minimum number of mutations required to explain a given set of observed genotypes. Conclusion Phylogeny reconstruction directly from unphased data is computationally feasible for moderate-sized problem instances and can lead to substantially more accurate tree size inferences than the standard practice of treating phasing and phylogeny construction as two separate analysis stages. The difference between the approaches is particularly important for downstream applications that require a lower-bound on the number of mutations that the genetic region has undergone.
FPGA Hardware Acceleration of a Phylogenetic Tree Reconstruction with Maximum Parsimony Algorithm
BLOCK, Henry; MARUYAMA, Tsutomu
2017-01-01
In this paper, we present an FPGA hardware implementation for a phylogenetic tree reconstruction with a maximum parsimony algorithm. We base our approach on a particular stochastic local search algorithm that uses the Progressive Neighborhood and the Indirect Calculation of Tree Lengths method. This method is widely used for the acceleration of the phylogenetic tree reconstruction algorithm in software. In our implementation, we define a tree structure and accelerate the search by parallel an...
Maximum Parsimony on Phylogenetic networks
2012-01-01
Background Phylogenetic networks are generalizations of phylogenetic trees, that are used to model evolutionary events in various contexts. Several different methods and criteria have been introduced for reconstructing phylogenetic trees. Maximum Parsimony is a character-based approach that infers a phylogenetic tree by minimizing the total number of evolutionary steps required to explain a given set of data assigned on the leaves. Exact solutions for optimizing parsimony scores on phylogenetic trees have been introduced in the past. Results In this paper, we define the parsimony score on networks as the sum of the substitution costs along all the edges of the network; and show that certain well-known algorithms that calculate the optimum parsimony score on trees, such as Sankoff and Fitch algorithms extend naturally for networks, barring conflicting assignments at the reticulate vertices. We provide heuristics for finding the optimum parsimony scores on networks. Our algorithms can be applied for any cost matrix that may contain unequal substitution costs of transforming between different characters along different edges of the network. We analyzed this for experimental data on 10 leaves or fewer with at most 2 reticulations and found that for almost all networks, the bounds returned by the heuristics matched with the exhaustively determined optimum parsimony scores. Conclusion The parsimony score we define here does not directly reflect the cost of the best tree in the network that displays the evolution of the character. However, when searching for the most parsimonious network that describes a collection of characters, it becomes necessary to add additional cost considerations to prefer simpler structures, such as trees over networks. The parsimony score on a network that we describe here takes into account the substitution costs along the additional edges incident on each reticulate vertex, in addition to the substitution costs along the other edges which are
Approximate maximum parsimony and ancestral maximum likelihood.
Alon, Noga; Chor, Benny; Pardi, Fabio; Rapoport, Anat
2010-01-01
We explore the maximum parsimony (MP) and ancestral maximum likelihood (AML) criteria in phylogenetic tree reconstruction. Both problems are NP-hard, so we seek approximate solutions. We formulate the two problems as Steiner tree problems under appropriate distances. The gist of our approach is the succinct characterization of Steiner trees for a small number of leaves for the two distances. This enables the use of known Steiner tree approximation algorithms. The approach leads to a 16/9 approximation ratio for AML and asymptotically to a 1.55 approximation ratio for MP.
Improved Maximum Parsimony Models for Phylogenetic Networks.
Van Iersel, Leo; Jones, Mark; Scornavacca, Celine
2018-05-01
Phylogenetic networks are well suited to represent evolutionary histories comprising reticulate evolution. Several methods aiming at reconstructing explicit phylogenetic networks have been developed in the last two decades. In this article, we propose a new definition of maximum parsimony for phylogenetic networks that permits to model biological scenarios that cannot be modeled by the definitions currently present in the literature (namely, the "hardwired" and "softwired" parsimony). Building on this new definition, we provide several algorithmic results that lay the foundations for new parsimony-based methods for phylogenetic network reconstruction.
Maximum parsimony on subsets of taxa.
Fischer, Mareike; Thatte, Bhalchandra D
2009-09-21
In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular, we consider the question whether the maximum parsimony method applied to a subset of taxa can reconstruct the ancestral state of the root more accurately than when applied to all taxa, and we give an example showing that this indeed is possible. A surprising feature of our example is that ignoring a taxon closer to the root improves the reliability of the method. On the other hand, in the case of the two-state symmetric substitution model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that under a molecular clock the probability that the state at a single taxon is a correct guess of the ancestral state is a lower bound on the reconstruction accuracy of Fitch's method applied to all taxa.
A Maximum Parsimony Model to Reconstruct Phylogenetic Network in Honey Bee Evolution
Usha Chouhan; K. R. Pardasani
2007-01-01
Phylogenies ; The evolutionary histories of groups of species are one of the most widely used tools throughout the life sciences, as well as objects of research with in systematic, evolutionary biology. In every phylogenetic analysis reconstruction produces trees. These trees represent the evolutionary histories of many groups of organisms, bacteria due to horizontal gene transfer and plants due to process of hybridization. The process of gene transfer in bacteria and hyb...
PTree: pattern-based, stochastic search for maximum parsimony phylogenies
Gregor, Ivan; Steinbr?ck, Lars; McHardy, Alice C.
2013-01-01
Phylogenetic reconstruction is vital to analyzing the evolutionary relationship of genes within and across populations of different species. Nowadays, with next generation sequencing technologies producing sets comprising thousands of sequences, robust identification of the tree topology, which is optimal according to standard criteria such as maximum parsimony, maximum likelihood or posterior probability, with phylogenetic inference methods is a computationally very demanding task. Here, we ...
2013-01-01
Background Phylogeny estimation from aligned haplotype sequences has attracted more and more attention in the recent years due to its importance in analysis of many fine-scale genetic data. Its application fields range from medical research, to drug discovery, to epidemiology, to population dynamics. The literature on molecular phylogenetics proposes a number of criteria for selecting a phylogeny from among plausible alternatives. Usually, such criteria can be expressed by means of objective functions, and the phylogenies that optimize them are referred to as optimal. One of the most important estimation criteria is the parsimony which states that the optimal phylogeny T∗for a set H of n haplotype sequences over a common set of variable loci is the one that satisfies the following requirements: (i) it has the shortest length and (ii) it is such that, for each pair of distinct haplotypes hi,hj∈H, the sum of the edge weights belonging to the path from hi to hj in T∗ is not smaller than the observed number of changes between hi and hj. Finding the most parsimonious phylogeny for H involves solving an optimization problem, called the Most Parsimonious Phylogeny Estimation Problem (MPPEP), which is NP-hard in many of its versions. Results In this article we investigate a recent version of the MPPEP that arises when input data consist of single nucleotide polymorphism haplotypes extracted from a population of individuals on a common genomic region. Specifically, we explore the prospects for improving on the implicit enumeration strategy of implicit enumeration strategy used in previous work using a novel problem formulation and a series of strengthening valid inequalities and preliminary symmetry breaking constraints to more precisely bound the solution space and accelerate implicit enumeration of possible optimal phylogenies. We present the basic formulation and then introduce a series of provable valid constraints to reduce the solution space. We then prove
The worst case complexity of maximum parsimony.
Carmel, Amir; Musa-Lempel, Noa; Tsur, Dekel; Ziv-Ukelson, Michal
2014-11-01
One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related organisms. We reexamine the classical maximum parsimony (MP) optimization problem for the general (asymmetric) scoring matrix case, where rooted phylogenies are implied, and analyze the worst case bounds of three approaches to MP: The approach of Cavalli-Sforza and Edwards, the approach of Hendy and Penny, and a new agglomerative, "bottom-up" approach we present in this article. We show that the second and third approaches are faster than the first one by a factor of Θ(√n) and Θ(n), respectively, where n is the number of species.
Bootstrap-based Support of HGT Inferred by Maximum Parsimony
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Nakhleh Luay
2010-05-01
Full Text Available Abstract Background Maximum parsimony is one of the most commonly used criteria for reconstructing phylogenetic trees. Recently, Nakhleh and co-workers extended this criterion to enable reconstruction of phylogenetic networks, and demonstrated its application to detecting reticulate evolutionary relationships. However, one of the major problems with this extension has been that it favors more complex evolutionary relationships over simpler ones, thus having the potential for overestimating the amount of reticulation in the data. An ad hoc solution to this problem that has been used entails inspecting the improvement in the parsimony length as more reticulation events are added to the model, and stopping when the improvement is below a certain threshold. Results In this paper, we address this problem in a more systematic way, by proposing a nonparametric bootstrap-based measure of support of inferred reticulation events, and using it to determine the number of those events, as well as their placements. A number of samples is generated from the given sequence alignment, and reticulation events are inferred based on each sample. Finally, the support of each reticulation event is quantified based on the inferences made over all samples. Conclusions We have implemented our method in the NEPAL software tool (available publicly at http://bioinfo.cs.rice.edu/, and studied its performance on both biological and simulated data sets. While our studies show very promising results, they also highlight issues that are inherently challenging when applying the maximum parsimony criterion to detect reticulate evolution.
Bootstrap-based support of HGT inferred by maximum parsimony.
Park, Hyun Jung; Jin, Guohua; Nakhleh, Luay
2010-05-05
Maximum parsimony is one of the most commonly used criteria for reconstructing phylogenetic trees. Recently, Nakhleh and co-workers extended this criterion to enable reconstruction of phylogenetic networks, and demonstrated its application to detecting reticulate evolutionary relationships. However, one of the major problems with this extension has been that it favors more complex evolutionary relationships over simpler ones, thus having the potential for overestimating the amount of reticulation in the data. An ad hoc solution to this problem that has been used entails inspecting the improvement in the parsimony length as more reticulation events are added to the model, and stopping when the improvement is below a certain threshold. In this paper, we address this problem in a more systematic way, by proposing a nonparametric bootstrap-based measure of support of inferred reticulation events, and using it to determine the number of those events, as well as their placements. A number of samples is generated from the given sequence alignment, and reticulation events are inferred based on each sample. Finally, the support of each reticulation event is quantified based on the inferences made over all samples. We have implemented our method in the NEPAL software tool (available publicly at http://bioinfo.cs.rice.edu/), and studied its performance on both biological and simulated data sets. While our studies show very promising results, they also highlight issues that are inherently challenging when applying the maximum parsimony criterion to detect reticulate evolution.
PTree: pattern-based, stochastic search for maximum parsimony phylogenies
Directory of Open Access Journals (Sweden)
Ivan Gregor
2013-06-01
Full Text Available Phylogenetic reconstruction is vital to analyzing the evolutionary relationship of genes within and across populations of different species. Nowadays, with next generation sequencing technologies producing sets comprising thousands of sequences, robust identification of the tree topology, which is optimal according to standard criteria such as maximum parsimony, maximum likelihood or posterior probability, with phylogenetic inference methods is a computationally very demanding task. Here, we describe a stochastic search method for a maximum parsimony tree, implemented in a software package we named PTree. Our method is based on a new pattern-based technique that enables us to infer intermediate sequences efficiently where the incorporation of these sequences in the current tree topology yields a phylogenetic tree with a lower cost. Evaluation across multiple datasets showed that our method is comparable to the algorithms implemented in PAUP* or TNT, which are widely used by the bioinformatics community, in terms of topological accuracy and runtime. We show that our method can process large-scale datasets of 1,000–8,000 sequences. We believe that our novel pattern-based method enriches the current set of tools and methods for phylogenetic tree inference. The software is available under: http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/.
PTree: pattern-based, stochastic search for maximum parsimony phylogenies.
Gregor, Ivan; Steinbrück, Lars; McHardy, Alice C
2013-01-01
Phylogenetic reconstruction is vital to analyzing the evolutionary relationship of genes within and across populations of different species. Nowadays, with next generation sequencing technologies producing sets comprising thousands of sequences, robust identification of the tree topology, which is optimal according to standard criteria such as maximum parsimony, maximum likelihood or posterior probability, with phylogenetic inference methods is a computationally very demanding task. Here, we describe a stochastic search method for a maximum parsimony tree, implemented in a software package we named PTree. Our method is based on a new pattern-based technique that enables us to infer intermediate sequences efficiently where the incorporation of these sequences in the current tree topology yields a phylogenetic tree with a lower cost. Evaluation across multiple datasets showed that our method is comparable to the algorithms implemented in PAUP* or TNT, which are widely used by the bioinformatics community, in terms of topological accuracy and runtime. We show that our method can process large-scale datasets of 1,000-8,000 sequences. We believe that our novel pattern-based method enriches the current set of tools and methods for phylogenetic tree inference. The software is available under: http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/.
On the quirks of maximum parsimony and likelihood on phylogenetic networks.
Bryant, Christopher; Fischer, Mareike; Linz, Simone; Semple, Charles
2017-03-21
Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe evolution accurately. For instance, processes like hybridization or lateral gene transfer that are commonplace in many groups of organisms and result in mosaic patterns of relationships cannot be represented by a single phylogenetic tree. This is why phylogenetic networks, which can display such events, are becoming of more and more interest in phylogenetic research. It is therefore necessary to extend concepts like maximum parsimony from phylogenetic trees to networks. Several suggestions for possible extensions can be found in recent literature, for instance the softwired and the hardwired parsimony concepts. In this paper, we analyze the so-called big parsimony problem under these two concepts, i.e. we investigate maximum parsimonious networks and analyze their properties. In particular, we show that finding a softwired maximum parsimony network is possible in polynomial time. We also show that the set of maximum parsimony networks for the hardwired definition always contains at least one phylogenetic tree. Lastly, we investigate some parallels of parsimony to different likelihood concepts on phylogenetic networks. Copyright © 2017 Elsevier Ltd. All rights reserved.
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.
Maximum parsimony, substitution model, and probability phylogenetic trees.
Weng, J F; Thomas, D A; Mareels, I
2011-01-01
The problem of inferring phylogenies (phylogenetic trees) is one of the main problems in computational biology. There are three main methods for inferring phylogenies-Maximum Parsimony (MP), Distance Matrix (DM) and Maximum Likelihood (ML), of which the MP method is the most well-studied and popular method. In the MP method the optimization criterion is the number of substitutions of the nucleotides computed by the differences in the investigated nucleotide sequences. However, the MP method is often criticized as it only counts the substitutions observable at the current time and all the unobservable substitutions that really occur in the evolutionary history are omitted. In order to take into account the unobservable substitutions, some substitution models have been established and they are now widely used in the DM and ML methods but these substitution models cannot be used within the classical MP method. Recently the authors proposed a probability representation model for phylogenetic trees and the reconstructed trees in this model are called probability phylogenetic trees. One of the advantages of the probability representation model is that it can include a substitution model to infer phylogenetic trees based on the MP principle. In this paper we explain how to use a substitution model in the reconstruction of probability phylogenetic trees and show the advantage of this approach with examples.
MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation.
Hoang, Diep Thi; Vinh, Le Sy; Flouri, Tomáš; Stamatakis, Alexandros; von Haeseler, Arndt; Minh, Bui Quang
2018-02-02
The nonparametric bootstrap is widely used to measure the branch support of phylogenetic trees. However, bootstrapping is computationally expensive and remains a bottleneck in phylogenetic analyses. Recently, an ultrafast bootstrap approximation (UFBoot) approach was proposed for maximum likelihood analyses. However, such an approach is still missing for maximum parsimony. To close this gap we present MPBoot, an adaptation and extension of UFBoot to compute branch supports under the maximum parsimony principle. MPBoot works for both uniform and non-uniform cost matrices. Our analyses on biological DNA and protein showed that under uniform cost matrices, MPBoot runs on average 4.7 (DNA) to 7 times (protein data) (range: 1.2-20.7) faster than the standard parsimony bootstrap implemented in PAUP*; but 1.6 (DNA) to 4.1 times (protein data) slower than the standard bootstrap with a fast search routine in TNT (fast-TNT). However, for non-uniform cost matrices MPBoot is 5 (DNA) to 13 times (protein data) (range:0.3-63.9) faster than fast-TNT. We note that MPBoot achieves better scores more frequently than PAUP* and fast-TNT. However, this effect is less pronounced if an intensive but slower search in TNT is invoked. Moreover, experiments on large-scale simulated data show that while both PAUP* and TNT bootstrap estimates are too conservative, MPBoot bootstrap estimates appear more unbiased. MPBoot provides an efficient alternative to the standard maximum parsimony bootstrap procedure. It shows favorable performance in terms of run time, the capability of finding a maximum parsimony tree, and high bootstrap accuracy on simulated as well as empirical data sets. MPBoot is easy-to-use, open-source and available at http://www.cibiv.at/software/mpboot .
Efficient parsimony-based methods for phylogenetic network reconstruction.
Jin, Guohua; Nakhleh, Luay; Snir, Sagi; Tuller, Tamir
2007-01-15
Phylogenies--the evolutionary histories of groups of organisms-play a major role in representing relationships among biological entities. Although many biological processes can be effectively modeled as tree-like relationships, others, such as hybrid speciation and horizontal gene transfer (HGT), result in networks, rather than trees, of relationships. Hybrid speciation is a significant evolutionary mechanism in plants, fish and other groups of species. HGT plays a major role in bacterial genome diversification and is a significant mechanism by which bacteria develop resistance to antibiotics. Maximum parsimony is one of the most commonly used criteria for phylogenetic tree inference. Roughly speaking, inference based on this criterion seeks the tree that minimizes the amount of evolution. In 1990, Jotun Hein proposed using this criterion for inferring the evolution of sequences subject to recombination. Preliminary results on small synthetic datasets. Nakhleh et al. (2005) demonstrated the criterion's application to phylogenetic network reconstruction in general and HGT detection in particular. However, the naive algorithms used by the authors are inapplicable to large datasets due to their demanding computational requirements. Further, no rigorous theoretical analysis of computing the criterion was given, nor was it tested on biological data. In the present work we prove that the problem of scoring the parsimony of a phylogenetic network is NP-hard and provide an improved fixed parameter tractable algorithm for it. Further, we devise efficient heuristics for parsimony-based reconstruction of phylogenetic networks. We test our methods on both synthetic and biological data (rbcL gene in bacteria) and obtain very promising results.
Time-Dependent-Asymmetric-Linear-Parsimonious Ancestral State Reconstruction.
Didier, Gilles
2017-10-01
The time-dependent-asymmetric-linear parsimony is an ancestral state reconstruction method which extends the standard linear parsimony (a.k.a. Wagner parsimony) approach by taking into account both branch lengths and asymmetric evolutionary costs for reconstructing quantitative characters (asymmetric costs amount to assuming an evolutionary trend toward the direction with the lowest cost). A formal study of the influence of the asymmetry parameter shows that the time-dependent-asymmetric-linear parsimony infers states which are all taken among the known states, except for some degenerate cases corresponding to special values of the asymmetry parameter. This remarkable property holds in particular for the Wagner parsimony. This study leads to a polynomial algorithm which determines, and provides a compact representation of, the parametric reconstruction of a phylogenetic tree, that is for all the unknown nodes, the set of all the possible reconstructed states associated with the asymmetry parameters leading to them. The time-dependent-asymmetric-linear parsimony is finally illustrated with the parametric reconstruction of the body size of cetaceans.
On the Quirks of Maximum Parsimony and Likelihood on Phylogenetic Networks
Bryant, Christopher; Fischer, Mareike; Linz, Simone; Semple, Charles
2015-01-01
Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe evolution accurately. For instance, processes like hybridization or lateral gene transfer that are commonplace in many groups of organisms and result in mosaic patterns of relationships cannot be represented by a single phylogenetic tree. This is why phylogene...
Khan, Haseeb A.; Arif, Ibrahim A.; Bahkali, Ali H.; Al Farhan, Ahmad H.; Al Homaidan, Ali A.
2008-01-01
This investigation was aimed to compare the inference of antelope phylogenies resulting from the 16S rRNA, cytochrome-b (cyt-b) and d-loop segments of mitochondrial DNA using three different computational models including Bayesian (BA), maximum parsimony (MP) and unweighted pair group method with arithmetic mean (UPGMA). The respective nucleotide sequences of three Oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) and an out-group (Addax nasomaculatus) were aligned and subjected to B...
Inferring phylogenetic networks by the maximum parsimony criterion: a case study.
Jin, Guohua; Nakhleh, Luay; Snir, Sagi; Tuller, Tamir
2007-01-01
Horizontal gene transfer (HGT) may result in genes whose evolutionary histories disagree with each other, as well as with the species tree. In this case, reconciling the species and gene trees results in a network of relationships, known as the "phylogenetic network" of the set of species. A phylogenetic network that incorporates HGT consists of an underlying species tree that captures vertical inheritance and a set of edges which model the "horizontal" transfer of genetic material. In a series of papers, Nakhleh and colleagues have recently formulated a maximum parsimony (MP) criterion for phylogenetic networks, provided an array of computationally efficient algorithms and heuristics for computing it, and demonstrated its plausibility on simulated data. In this article, we study the performance and robustness of this criterion on biological data. Our findings indicate that MP is very promising when its application is extended to the domain of phylogenetic network reconstruction and HGT detection. In all cases we investigated, the MP criterion detected the correct number of HGT events required to map the evolutionary history of a gene data set onto the species phylogeny. Furthermore, our results indicate that the criterion is robust with respect to both incomplete taxon sampling and the use of different site substitution matrices. Finally, our results show that the MP criterion is very promising in detecting HGT in chimeric genes, whose evolutionary histories are a mix of vertical and horizontal evolution. Besides the performance analysis of MP, our findings offer new insights into the evolution of 4 biological data sets and new possible explanations of HGT scenarios in their evolutionary history.
Tamura, Koichiro; Peterson, Daniel; Peterson, Nicholas; Stecher, Glen; Nei, Masatoshi; Kumar, Sudhir
2011-01-01
Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net. PMID:21546353
Pedersen, Niklas; Holyoak, David T; Newton, Angela E
2007-06-01
The Bryaceae are a large cosmopolitan moss family including genera of significant morphological and taxonomic complexity. Phylogenetic relationships within the Bryaceae were reconstructed based on DNA sequence data from all three genomic compartments. In addition, maximum parsimony and Bayesian inference were employed to reconstruct ancestral character states of 38 morphological plus four habitat characters and eight insertion/deletion events. The recovered phylogenetic patterns are generally in accord with previous phylogenies based on chloroplast DNA sequence data and three major clades are identified. The first clade comprises Bryum bornholmense, B. rubens, B. caespiticium, and Plagiobryum. This corroborates the hypothesis suggested by previous studies that several Bryum species are more closely related to Plagiobryum than to the core Bryum species. The second clade includes Acidodontium, Anomobryum, and Haplodontium, while the third clade contains the core Bryum species plus Imbribryum. Within the latter clade, B. subapiculatum and B. tenuisetum form the sister clade to Imbribryum. Reconstructions of ancestral character states under maximum parsimony and Bayesian inference suggest fourteen morphological synapomorphies for the ingroup and synapomorphies are detected for most clades within the ingroup. Maximum parsimony and Bayesian reconstructions of ancestral character states are mostly congruent although Bayesian inference shows that the posterior probability of ancestral character states may decrease dramatically when node support is taken into account. Bayesian inference also indicates that reconstructions may be ambiguous at internal nodes for highly polymorphic characters.
On the Accuracy of Ancestral Sequence Reconstruction for Ultrametric Trees with Parsimony.
Herbst, Lina; Fischer, Mareike
2018-04-01
We examine a mathematical question concerning the reconstruction accuracy of the Fitch algorithm for reconstructing the ancestral sequence of the most recent common ancestor given a phylogenetic tree and sequence data for all taxa under consideration. In particular, for the symmetric four-state substitution model which is also known as Jukes-Cantor model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that for any ultrametric phylogenetic tree and a symmetric model, the Fitch parsimony method using all terminal taxa is more accurate, or at least as accurate, for ancestral state reconstruction than using any particular terminal taxon or any particular pair of taxa. This conjecture had so far only been answered for two-state data by Fischer and Thatte. Here, we focus on answering the biologically more relevant case with four states, which corresponds to ancestral sequence reconstruction from DNA or RNA data.
Khan, Haseeb A; Arif, Ibrahim A; Bahkali, Ali H; Al Farhan, Ahmad H; Al Homaidan, Ali A
2008-10-06
This investigation was aimed to compare the inference of antelope phylogenies resulting from the 16S rRNA, cytochrome-b (cyt-b) and d-loop segments of mitochondrial DNA using three different computational models including Bayesian (BA), maximum parsimony (MP) and unweighted pair group method with arithmetic mean (UPGMA). The respective nucleotide sequences of three Oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) and an out-group (Addax nasomaculatus) were aligned and subjected to BA, MP and UPGMA models for comparing the topologies of respective phylogenetic trees. The 16S rRNA region possessed the highest frequency of conserved sequences (97.65%) followed by cyt-b (94.22%) and d-loop (87.29%). There were few transitions (2.35%) and none transversions in 16S rRNA as compared to cyt-b (5.61% transitions and 0.17% transversions) and d-loop (11.57% transitions and 1.14% transversions) while comparing the four taxa. All the three mitochondrial segments clearly differentiated the genus Addax from Oryx using the BA or UPGMA models. The topologies of all the gamma-corrected Bayesian trees were identical irrespective of the marker type. The UPGMA trees resulting from 16S rRNA and d-loop sequences were also identical (Oryx dammah grouped with Oryx leucoryx) to Bayesian trees except that the UPGMA tree based on cyt-b showed a slightly different phylogeny (Oryx dammah grouped with Oryx gazella) with a low bootstrap support. However, the MP model failed to differentiate the genus Addax from Oryx. These findings demonstrate the efficiency and robustness of BA and UPGMA methods for phylogenetic analysis of antelopes using mitochondrial markers.
Last Glacial Maximum Salinity Reconstruction
Homola, K.; Spivack, A. J.
2016-12-01
It has been previously demonstrated that salinity can be reconstructed from sediment porewater. The goal of our study is to reconstruct high precision salinity during the Last Glacial Maximum (LGM). Salinity is usually determined at high precision via conductivity, which requires a larger volume of water than can be extracted from a sediment core, or via chloride titration, which yields lower than ideal precision. It has been demonstrated for water column samples that high precision density measurements can be used to determine salinity at the precision of a conductivity measurement using the equation of state of seawater. However, water column seawater has a relatively constant composition, in contrast to porewater, where variations from standard seawater composition occur. These deviations, which affect the equation of state, must be corrected for through precise measurements of each ion's concentration and knowledge of apparent partial molar density in seawater. We have developed a density-based method for determining porewater salinity that requires only 5 mL of sample, achieving density precisions of 10-6 g/mL. We have applied this method to porewater samples extracted from long cores collected along a N-S transect across the western North Atlantic (R/V Knorr cruise KN223). Density was determined to a precision of 2.3x10-6 g/mL, which translates to salinity uncertainty of 0.002 gms/kg if the effect of differences in composition is well constrained. Concentrations of anions (Cl-, and SO4-2) and cations (Na+, Mg+, Ca+2, and K+) were measured. To correct salinities at the precision required to unravel LGM Meridional Overturning Circulation, our ion precisions must be better than 0.1% for SO4-/Cl- and Mg+/Na+, and 0.4% for Ca+/Na+, and K+/Na+. Alkalinity, pH and Dissolved Inorganic Carbon of the porewater were determined to precisions better than 4% when ratioed to Cl-, and used to calculate HCO3-, and CO3-2. Apparent partial molar densities in seawater were
Maximum Likelihood Reconstruction for Magnetic Resonance Fingerprinting.
Zhao, Bo; Setsompop, Kawin; Ye, Huihui; Cauley, Stephen F; Wald, Lawrence L
2016-08-01
This paper introduces a statistical estimation framework for magnetic resonance (MR) fingerprinting, a recently proposed quantitative imaging paradigm. Within this framework, we present a maximum likelihood (ML) formalism to estimate multiple MR tissue parameter maps directly from highly undersampled, noisy k-space data. A novel algorithm, based on variable splitting, the alternating direction method of multipliers, and the variable projection method, is developed to solve the resulting optimization problem. Representative results from both simulations and in vivo experiments demonstrate that the proposed approach yields significantly improved accuracy in parameter estimation, compared to the conventional MR fingerprinting reconstruction. Moreover, the proposed framework provides new theoretical insights into the conventional approach. We show analytically that the conventional approach is an approximation to the ML reconstruction; more precisely, it is exactly equivalent to the first iteration of the proposed algorithm for the ML reconstruction, provided that a gridding reconstruction is used as an initialization.
Maximum entropy method in momentum density reconstruction
International Nuclear Information System (INIS)
Dobrzynski, L.; Holas, A.
1997-01-01
The Maximum Entropy Method (MEM) is applied to the reconstruction of the 3-dimensional electron momentum density distributions observed through the set of Compton profiles measured along various crystallographic directions. It is shown that the reconstruction of electron momentum density may be reliably carried out with the aid of simple iterative algorithm suggested originally by Collins. A number of distributions has been simulated in order to check the performance of MEM. It is shown that MEM can be recommended as a model-free approach. (author). 13 refs, 1 fig
Automatic maximum entropy spectral reconstruction in NMR
International Nuclear Information System (INIS)
Mobli, Mehdi; Maciejewski, Mark W.; Gryk, Michael R.; Hoch, Jeffrey C.
2007-01-01
Developments in superconducting magnets, cryogenic probes, isotope labeling strategies, and sophisticated pulse sequences together have enabled the application, in principle, of high-resolution NMR spectroscopy to biomolecular systems approaching 1 megadalton. In practice, however, conventional approaches to NMR that utilize the fast Fourier transform, which require data collected at uniform time intervals, result in prohibitively lengthy data collection times in order to achieve the full resolution afforded by high field magnets. A variety of approaches that involve nonuniform sampling have been proposed, each utilizing a non-Fourier method of spectrum analysis. A very general non-Fourier method that is capable of utilizing data collected using any of the proposed nonuniform sampling strategies is maximum entropy reconstruction. A limiting factor in the adoption of maximum entropy reconstruction in NMR has been the need to specify non-intuitive parameters. Here we describe a fully automated system for maximum entropy reconstruction that requires no user-specified parameters. A web-accessible script generator provides the user interface to the system
A practical exact maximum compatibility algorithm for reconstruction of recent evolutionary history.
Cherry, Joshua L
2017-02-23
Maximum compatibility is a method of phylogenetic reconstruction that is seldom applied to molecular sequences. It may be ideal for certain applications, such as reconstructing phylogenies of closely-related bacteria on the basis of whole-genome sequencing. Here I present an algorithm that rapidly computes phylogenies according to a compatibility criterion. Although based on solutions to the maximum clique problem, this algorithm deals properly with ambiguities in the data. The algorithm is applied to bacterial data sets containing up to nearly 2000 genomes with several thousand variable nucleotide sites. Run times are several seconds or less. Computational experiments show that maximum compatibility is less sensitive than maximum parsimony to the inclusion of nucleotide data that, though derived from actual sequence reads, has been identified as likely to be misleading. Maximum compatibility is a useful tool for certain phylogenetic problems, such as inferring the relationships among closely-related bacteria from whole-genome sequence data. The algorithm presented here rapidly solves fairly large problems of this type, and provides robustness against misleading characters than can pollute large-scale sequencing data.
A unifying model of genome evolution under parsimony.
Paten, Benedict; Zerbino, Daniel R; Hickey, Glenn; Haussler, David
2014-06-19
Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation. We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double cut and join (DCJ) rearrangements in the presence of duplications. The problem of constructing parsimonious history graphs thus subsumes related maximum parsimony problems in the fields of phylogenetic reconstruction and genome rearrangement. We show that tractable functions can be used to define upper and lower bounds on the minimum number of substitutions and DCJ rearrangements needed to explain any history graph. These bounds become tight for a special type of unambiguous history graph called an ancestral variation graph (AVG), which constrains in its combinatorial structure the number of operations required. We finally demonstrate that for a given history graph G, a finite set of AVGs describe all parsimonious interpretations of G, and this set can be explored with a few sampling moves. This theoretical study describes a model in which the inference of genome rearrangements and phylogeny can be unified under parsimony.
Simultaneous maximum a posteriori longitudinal PET image reconstruction
Ellis, Sam; Reader, Andrew J.
2017-09-01
Positron emission tomography (PET) is frequently used to monitor functional changes that occur over extended time scales, for example in longitudinal oncology PET protocols that include routine clinical follow-up scans to assess the efficacy of a course of treatment. In these contexts PET datasets are currently reconstructed into images using single-dataset reconstruction methods. Inspired by recently proposed joint PET-MR reconstruction methods, we propose to reconstruct longitudinal datasets simultaneously by using a joint penalty term in order to exploit the high degree of similarity between longitudinal images. We achieved this by penalising voxel-wise differences between pairs of longitudinal PET images in a one-step-late maximum a posteriori (MAP) fashion, resulting in the MAP simultaneous longitudinal reconstruction (SLR) method. The proposed method reduced reconstruction errors and visually improved images relative to standard maximum likelihood expectation-maximisation (ML-EM) in simulated 2D longitudinal brain tumour scans. In reconstructions of split real 3D data with inserted simulated tumours, noise across images reconstructed with MAP-SLR was reduced to levels equivalent to doubling the number of detected counts when using ML-EM. Furthermore, quantification of tumour activities was largely preserved over a variety of longitudinal tumour changes, including changes in size and activity, with larger changes inducing larger biases relative to standard ML-EM reconstructions. Similar improvements were observed for a range of counts levels, demonstrating the robustness of the method when used with a single penalty strength. The results suggest that longitudinal regularisation is a simple but effective method of improving reconstructed PET images without using resolution degrading priors.
Peyronie's Reconstruction for Maximum Length and Girth Gain: Geometrical Principles
Directory of Open Access Journals (Sweden)
Paulo H. Egydio
2008-01-01
Full Text Available Peyronie's disease has been associated with penile shortening and some degree of erectile dysfunction. Surgical reconstruction should be based on giving a functional penis, that is, rectifying the penis with rigidity enough to make the sexual intercourse. The procedure should be discussed preoperatively in terms of length and girth reconstruction in order to improve patient satisfaction. The tunical reconstruction for maximum penile length and girth restoration should be based on the maximum length of the dissected neurovascular bundle possible and the application of geometrical principles to define the precise site and size of tunical incision and grafting procedure. As penile rectification and rigidity are required to achieve complete functional restoration of the penis and 20 to 54% of patients experience associated erectile dysfunction, penile straightening alone may not be enough to provide complete functional restoration. Therefore, phosphodiesterase inhibitors, self-injection, or penile prosthesis may need to be added in some cases.
A short proof that phylogenetic tree reconstruction by maximum likelihood is hard.
Roch, Sebastien
2006-01-01
Maximum likelihood is one of the most widely used techniques to infer evolutionary histories. Although it is thought to be intractable, a proof of its hardness has been lacking. Here, we give a short proof that computing the maximum likelihood tree is NP-hard by exploiting a connection between likelihood and parsimony observed by Tuffley and Steel.
A Short Proof that Phylogenetic Tree Reconstruction by Maximum Likelihood is Hard
Roch, S.
2005-01-01
Maximum likelihood is one of the most widely used techniques to infer evolutionary histories. Although it is thought to be intractable, a proof of its hardness has been lacking. Here, we give a short proof that computing the maximum likelihood tree is NP-hard by exploiting a connection between likelihood and parsimony observed by Tuffley and Steel.
LensEnt2: Maximum-entropy weak lens reconstruction
Marshall, P. J.; Hobson, M. P.; Gull, S. F.; Bridle, S. L.
2013-08-01
LensEnt2 is a maximum entropy reconstructor of weak lensing mass maps. The method takes each galaxy shape as an independent estimator of the reduced shear field and incorporates an intrinsic smoothness, determined by Bayesian methods, into the reconstruction. The uncertainties from both the intrinsic distribution of galaxy shapes and galaxy shape estimation are carried through to the final mass reconstruction, and the mass within arbitrarily shaped apertures are calculated with corresponding uncertainties. The input is a galaxy ellipticity catalog with each measured galaxy shape treated as a noisy tracer of the reduced shear field, which is inferred on a fine pixel grid assuming positivity, and smoothness on scales of w arcsec where w is an input parameter. The ICF width w can be chosen by computing the evidence for it.
Preliminary attempt on maximum likelihood tomosynthesis reconstruction of DEI data
International Nuclear Information System (INIS)
Wang Zhentian; Huang Zhifeng; Zhang Li; Kang Kejun; Chen Zhiqiang; Zhu Peiping
2009-01-01
Tomosynthesis is a three-dimension reconstruction method that can remove the effect of superimposition with limited angle projections. It is especially promising in mammography where radiation dose is concerned. In this paper, we propose a maximum likelihood tomosynthesis reconstruction algorithm (ML-TS) on the apparent absorption data of diffraction enhanced imaging (DEI). The motivation of this contribution is to develop a tomosynthesis algorithm in low-dose or noisy circumstances and make DEI get closer to clinic application. The theoretical statistical models of DEI data in physics are analyzed and the proposed algorithm is validated with the experimental data at the Beijing Synchrotron Radiation Facility (BSRF). The results of ML-TS have better contrast compared with the well known 'shift-and-add' algorithm and FBP algorithm. (authors)
A maximum entropy reconstruction technique for tomographic particle image velocimetry
International Nuclear Information System (INIS)
Bilsky, A V; Lozhkin, V A; Markovich, D M; Tokarev, M P
2013-01-01
This paper studies a novel approach for reducing tomographic PIV computational complexity. The proposed approach is an algebraic reconstruction technique, termed MENT (maximum entropy). This technique computes the three-dimensional light intensity distribution several times faster than SMART, using at least ten times less memory. Additionally, the reconstruction quality remains nearly the same as with SMART. This paper presents the theoretical computation performance comparison for MENT, SMART and MART, followed by validation using synthetic particle images. Both the theoretical assessment and validation of synthetic images demonstrate significant computational time reduction. The data processing accuracy of MENT was compared to that of SMART in a slot jet experiment. A comparison of the average velocity profiles shows a high level of agreement between the results obtained with MENT and those obtained with SMART. (paper)
Energy Technology Data Exchange (ETDEWEB)
Papoular, R
1997-07-01
The Fourier Transform is of central importance to Crystallography since it allows the visualization in real space of tridimensional scattering densities pertaining to physical systems from diffraction data (powder or single-crystal diffraction, using x-rays, neutrons, electrons or else). In turn, this visualization makes it possible to model and parametrize these systems, the crystal structures of which are eventually refined by Least-Squares techniques (e.g., the Rietveld method in the case of Powder Diffraction). The Maximum Entropy Method (sometimes called MEM or MaxEnt) is a general imaging technique, related to solving ill-conditioned inverse problems. It is ideally suited for tackling undetermined systems of linear questions (for which the number of variables is much larger than the number of equations). It is already being applied successfully in Astronomy, Radioastronomy and Medical Imaging. The advantages of using MAXIMUM Entropy over conventional Fourier and `difference Fourier` syntheses stem from the following facts: MaxEnt takes the experimental error bars into account; MaxEnt incorporate Prior Knowledge (e.g., the positivity of the scattering density in some instances); MaxEnt allows density reconstructions from incompletely phased data, as well as from overlapping Bragg reflections; MaxEnt substantially reduces truncation errors to which conventional experimental Fourier reconstructions are usually prone. The principles of Maximum Entropy imaging as applied to Crystallography are first presented. The method is then illustrated by a detailed example specific to Neutron Diffraction: the search for proton in solids. (author). 17 refs.
Superfast maximum-likelihood reconstruction for quantum tomography
Shang, Jiangwei; Zhang, Zhengyun; Ng, Hui Khoon
2017-06-01
Conventional methods for computing maximum-likelihood estimators (MLE) often converge slowly in practical situations, leading to a search for simplifying methods that rely on additional assumptions for their validity. In this work, we provide a fast and reliable algorithm for maximum-likelihood reconstruction that avoids this slow convergence. Our method utilizes the state-of-the-art convex optimization scheme, an accelerated projected-gradient method, that allows one to accommodate the quantum nature of the problem in a different way than in the standard methods. We demonstrate the power of our approach by comparing its performance with other algorithms for n -qubit state tomography. In particular, an eight-qubit situation that purportedly took weeks of computation time in 2005 can now be completed in under a minute for a single set of data, with far higher accuracy than previously possible. This refutes the common claim that MLE reconstruction is slow and reduces the need for alternative methods that often come with difficult-to-verify assumptions. In fact, recent methods assuming Gaussian statistics or relying on compressed sensing ideas are demonstrably inapplicable for the situation under consideration here. Our algorithm can be applied to general optimization problems over the quantum state space; the philosophy of projected gradients can further be utilized for optimization contexts with general constraints.
Preconditioned alternating projection algorithms for maximum a posteriori ECT reconstruction
International Nuclear Information System (INIS)
Krol, Andrzej; Li, Si; Shen, Lixin; Xu, Yuesheng
2012-01-01
We propose a preconditioned alternating projection algorithm (PAPA) for solving the maximum a posteriori (MAP) emission computed tomography (ECT) reconstruction problem. Specifically, we formulate the reconstruction problem as a constrained convex optimization problem with the total variation (TV) regularization. We then characterize the solution of the constrained convex optimization problem and show that it satisfies a system of fixed-point equations defined in terms of two proximity operators raised from the convex functions that define the TV-norm and the constraint involved in the problem. The characterization (of the solution) via the proximity operators that define two projection operators naturally leads to an alternating projection algorithm for finding the solution. For efficient numerical computation, we introduce to the alternating projection algorithm a preconditioning matrix (the EM-preconditioner) for the dense system matrix involved in the optimization problem. We prove theoretically convergence of the PAPA. In numerical experiments, performance of our algorithms, with an appropriately selected preconditioning matrix, is compared with performance of the conventional MAP expectation-maximization (MAP-EM) algorithm with TV regularizer (EM-TV) and that of the recently developed nested EM-TV algorithm for ECT reconstruction. Based on the numerical experiments performed in this work, we observe that the alternating projection algorithm with the EM-preconditioner outperforms significantly the EM-TV in all aspects including the convergence speed, the noise in the reconstructed images and the image quality. It also outperforms the nested EM-TV in the convergence speed while providing comparable image quality. (paper)
Dirichlet Process Parsimonious Mixtures for clustering
Chamroukhi, Faicel; Bartcus, Marius; Glotin, Hervé
2015-01-01
The parsimonious Gaussian mixture models, which exploit an eigenvalue decomposition of the group covariance matrices of the Gaussian mixture, have shown their success in particular in cluster analysis. Their estimation is in general performed by maximum likelihood estimation and has also been considered from a parametric Bayesian prospective. We propose new Dirichlet Process Parsimonious mixtures (DPPM) which represent a Bayesian nonparametric formulation of these parsimonious Gaussian mixtur...
Maximum entropy reconstruction of spin densities involving non uniform prior
International Nuclear Information System (INIS)
Schweizer, J.; Ressouche, E.; Papoular, R.J.; Zheludev, A.I.
1997-01-01
Diffraction experiments give microscopic information on structures in crystals. A method which uses the concept of maximum of entropy (MaxEnt), appears to be a formidable improvement in the treatment of diffraction data. This method is based on a bayesian approach: among all the maps compatible with the experimental data, it selects that one which has the highest prior (intrinsic) probability. Considering that all the points of the map are equally probable, this probability (flat prior) is expressed via the Boltzman entropy of the distribution. This method has been used for the reconstruction of charge densities from X-ray data, for maps of nuclear densities from unpolarized neutron data as well as for distributions of spin density. The density maps obtained by this method, as compared to those resulting from the usual inverse Fourier transformation, are tremendously improved. In particular, any substantial deviation from the background is really contained in the data, as it costs entropy compared to a map that would ignore such features. However, in most of the cases, before the measurements are performed, some knowledge exists about the distribution which is investigated. It can range from the simple information of the type of scattering electrons to an elaborate theoretical model. In these cases, the uniform prior which considers all the different pixels as equally likely, is too weak a requirement and has to be replaced. In a rigorous bayesian analysis, Skilling has shown that prior knowledge can be encoded into the Maximum Entropy formalism through a model m(rvec r), via a new definition for the entropy given in this paper. In the absence of any data, the maximum of the entropy functional is reached for ρ(rvec r) = m(rvec r). Any substantial departure from the model, observed in the final map, is really contained in the data as, with the new definition, it costs entropy. This paper presents illustrations of model testing
On the Five-Moment Hamburger Maximum Entropy Reconstruction
Summy, D. P.; Pullin, D. I.
2018-05-01
We consider the Maximum Entropy Reconstruction (MER) as a solution to the five-moment truncated Hamburger moment problem in one dimension. In the case of five monomial moment constraints, the probability density function (PDF) of the MER takes the form of the exponential of a quartic polynomial. This implies a possible bimodal structure in regions of moment space. An analytical model is developed for the MER PDF applicable near a known singular line in a centered, two-component, third- and fourth-order moment (μ _3 , μ _4 ) space, consistent with the general problem of five moments. The model consists of the superposition of a perturbed, centered Gaussian PDF and a small-amplitude packet of PDF-density, called the outlying moment packet (OMP), sitting far from the mean. Asymptotic solutions are obtained which predict the shape of the perturbed Gaussian and both the amplitude and position on the real line of the OMP. The asymptotic solutions show that the presence of the OMP gives rise to an MER solution that is singular along a line in (μ _3 , μ _4 ) space emanating from, but not including, the point representing a standard normal distribution, or thermodynamic equilibrium. We use this analysis of the OMP to develop a numerical regularization of the MER, creating a procedure we call the Hybrid MER (HMER). Compared with the MER, the HMER is a significant improvement in terms of robustness and efficiency while preserving accuracy in its prediction of other important distribution features, such as higher order moments.
Maximum likelihood pedigree reconstruction using integer linear programming.
Cussens, James; Bartlett, Mark; Jones, Elinor M; Sheehan, Nuala A
2013-01-01
Large population biobanks of unrelated individuals have been highly successful in detecting common genetic variants affecting diseases of public health concern. However, they lack the statistical power to detect more modest gene-gene and gene-environment interaction effects or the effects of rare variants for which related individuals are ideally required. In reality, most large population studies will undoubtedly contain sets of undeclared relatives, or pedigrees. Although a crude measure of relatedness might sometimes suffice, having a good estimate of the true pedigree would be much more informative if this could be obtained efficiently. Relatives are more likely to share longer haplotypes around disease susceptibility loci and are hence biologically more informative for rare variants than unrelated cases and controls. Distant relatives are arguably more useful for detecting variants with small effects because they are less likely to share masking environmental effects. Moreover, the identification of relatives enables appropriate adjustments of statistical analyses that typically assume unrelatedness. We propose to exploit an integer linear programming optimisation approach to pedigree learning, which is adapted to find valid pedigrees by imposing appropriate constraints. Our method is not restricted to small pedigrees and is guaranteed to return a maximum likelihood pedigree. With additional constraints, we can also search for multiple high-probability pedigrees and thus account for the inherent uncertainty in any particular pedigree reconstruction. The true pedigree is found very quickly by comparison with other methods when all individuals are observed. Extensions to more complex problems seem feasible. © 2012 Wiley Periodicals, Inc.
Phylogenetic analysis using parsimony and likelihood methods.
Yang, Z
1996-02-01
The assumptions underlying the maximum-parsimony (MP) method of phylogenetic tree reconstruction were intuitively examined by studying the way the method works. Computer simulations were performed to corroborate the intuitive examination. Parsimony appears to involve very stringent assumptions concerning the process of sequence evolution, such as constancy of substitution rates between nucleotides, constancy of rates across nucleotide sites, and equal branch lengths in the tree. For practical data analysis, the requirement of equal branch lengths means similar substitution rates among lineages (the existence of an approximate molecular clock), relatively long interior branches, and also few species in the data. However, a small amount of evolution is neither a necessary nor a sufficient requirement of the method. The difficulties involved in the application of current statistical estimation theory to tree reconstruction were discussed, and it was suggested that the approach proposed by Felsenstein (1981, J. Mol. Evol. 17: 368-376) for topology estimation, as well as its many variations and extensions, differs fundamentally from the maximum likelihood estimation of a conventional statistical parameter. Evidence was presented showing that the Felsenstein approach does not share the asymptotic efficiency of the maximum likelihood estimator of a statistical parameter. Computer simulations were performed to study the probability that MP recovers the true tree under a hierarchy of models of nucleotide substitution; its performance relative to the likelihood method was especially noted. The results appeared to support the intuitive examination of the assumptions underlying MP. When a simple model of nucleotide substitution was assumed to generate data, the probability that MP recovers the true topology could be as high as, or even higher than, that for the likelihood method. When the assumed model became more complex and realistic, e.g., when substitution rates were
Meij, E.; Weerkamp, W.; Balog, K.; de Rijke, M.; Myang, S.-H.; Oard, D.W.; Sebastiani, F.; Chua, T.-S.; Leong, M.-K.
2008-01-01
We describe a method for applying parsimonious language models to re-estimate the term probabilities assigned by relevance models. We apply our method to six topic sets from test collections in five different genres. Our parsimonious relevance models (i) improve retrieval effectiveness in terms of
A practical exact maximum compatibility algorithm for reconstruction of recent evolutionary history
Cherry, Joshua L.
2017-01-01
Background Maximum compatibility is a method of phylogenetic reconstruction that is seldom applied to molecular sequences. It may be ideal for certain applications, such as reconstructing phylogenies of closely-related bacteria on the basis of whole-genome sequencing. Results Here I present an algorithm that rapidly computes phylogenies according to a compatibility criterion. Although based on solutions to the maximum clique problem, this algorithm deals properly with ambiguities in the data....
Parsimonious Surface Wave Interferometry
Li, Jing
2017-10-24
To decrease the recording time of a 2D seismic survey from a few days to one hour or less, we present a parsimonious surface-wave interferometry method. Interferometry allows for the creation of a large number of virtual shot gathers from just two reciprocal shot gathers by crosscoherence of trace pairs, where the virtual surface waves can be inverted for the S-wave velocity model by wave-equation dispersion inversion (WD). Synthetic and field data tests suggest that parsimonious wave-equation dispersion inversion (PWD) gives S-velocity tomograms that are comparable to those obtained from a full survey with a shot at each receiver. The limitation of PWD is that the virtual data lose some information so that the resolution of the S-velocity tomogram can be modestly lower than that of the S-velocity tomogram inverted from a conventional survey.
Parsimonious Surface Wave Interferometry
Li, Jing; Hanafy, Sherif; Schuster, Gerard T.
2017-01-01
To decrease the recording time of a 2D seismic survey from a few days to one hour or less, we present a parsimonious surface-wave interferometry method. Interferometry allows for the creation of a large number of virtual shot gathers from just two reciprocal shot gathers by crosscoherence of trace pairs, where the virtual surface waves can be inverted for the S-wave velocity model by wave-equation dispersion inversion (WD). Synthetic and field data tests suggest that parsimonious wave-equation dispersion inversion (PWD) gives S-velocity tomograms that are comparable to those obtained from a full survey with a shot at each receiver. The limitation of PWD is that the virtual data lose some information so that the resolution of the S-velocity tomogram can be modestly lower than that of the S-velocity tomogram inverted from a conventional survey.
Penalized maximum likelihood reconstruction for x-ray differential phase-contrast tomography
International Nuclear Information System (INIS)
Brendel, Bernhard; Teuffenbach, Maximilian von; Noël, Peter B.; Pfeiffer, Franz; Koehler, Thomas
2016-01-01
Purpose: The purpose of this work is to propose a cost function with regularization to iteratively reconstruct attenuation, phase, and scatter images simultaneously from differential phase contrast (DPC) acquisitions, without the need of phase retrieval, and examine its properties. Furthermore this reconstruction method is applied to an acquisition pattern that is suitable for a DPC tomographic system with continuously rotating gantry (sliding window acquisition), overcoming the severe smearing in noniterative reconstruction. Methods: We derive a penalized maximum likelihood reconstruction algorithm to directly reconstruct attenuation, phase, and scatter image from the measured detector values of a DPC acquisition. The proposed penalty comprises, for each of the three images, an independent smoothing prior. Image quality of the proposed reconstruction is compared to images generated with FBP and iterative reconstruction after phase retrieval. Furthermore, the influence between the priors is analyzed. Finally, the proposed reconstruction algorithm is applied to experimental sliding window data acquired at a synchrotron and results are compared to reconstructions based on phase retrieval. Results: The results show that the proposed algorithm significantly increases image quality in comparison to reconstructions based on phase retrieval. No significant mutual influence between the proposed independent priors could be observed. Further it could be illustrated that the iterative reconstruction of a sliding window acquisition results in images with substantially reduced smearing artifacts. Conclusions: Although the proposed cost function is inherently nonconvex, it can be used to reconstruct images with less aliasing artifacts and less streak artifacts than reconstruction methods based on phase retrieval. Furthermore, the proposed method can be used to reconstruct images of sliding window acquisitions with negligible smearing artifacts
International Nuclear Information System (INIS)
Bastiens, K.; Lemahieu, I.
1994-01-01
The application of a maximum entropy reconstruction algorithm to PET images requires a lot of computing resources. A parallel implementation could seriously reduce the execution time. However, programming a parallel application is still a non trivial task, needing specialized people. In this paper a programming environment based on a visual programming language is used for a parallel implementation of the reconstruction algorithm. This programming environment allows less experienced programmers to use the performance of multiprocessor systems. (authors)
Energy Technology Data Exchange (ETDEWEB)
Bastiens, K; Lemahieu, I [University of Ghent - ELIS Department, St. Pietersnieuwstraat 41, B-9000 Ghent (Belgium)
1994-12-31
The application of a maximum entropy reconstruction algorithm to PET images requires a lot of computing resources. A parallel implementation could seriously reduce the execution time. However, programming a parallel application is still a non trivial task, needing specialized people. In this paper a programming environment based on a visual programming language is used for a parallel implementation of the reconstruction algorithm. This programming environment allows less experienced programmers to use the performance of multiprocessor systems. (authors). 8 refs, 3 figs, 1 tab.
Comparison of tomography reconstruction by maximum entropy and filtered retro projection
International Nuclear Information System (INIS)
Abdala, F.J.P.; Simpson, D.M.; Roberty, N.C.
1992-01-01
The tomographic reconstruction with few projections is studied, comparing the maximum entropy method with filtered retro projection. Simulations with and without the presence of noise and also with the presence of an object of high density inside of the skull are showed. (C.G.C.)
Parsimonious refraction interferometry
Hanafy, Sherif
2016-09-06
We present parsimonious refraction interferometry where a densely populated refraction data set can be obtained from just two shot gathers. The assumptions are that the first arrivals are comprised of head waves and direct waves, and a pair of reciprocal shot gathers is recorded over the line of interest. The refraction traveltimes from these reciprocal shot gathers can be picked and decomposed into O(N2) refraction traveltimes generated by N virtual sources, where N is the number of geophones in the 2D survey. This enormous increase in the number of virtual traveltime picks and associated rays, compared to the 2N traveltimes from the two reciprocal shot gathers, allows for increased model resolution and better condition numbers in the normal equations. Also, a reciprocal survey is far less time consuming than a standard refraction survey with a dense distribution of sources.
Parsimonious refraction interferometry
Hanafy, Sherif; Schuster, Gerard T.
2016-01-01
We present parsimonious refraction interferometry where a densely populated refraction data set can be obtained from just two shot gathers. The assumptions are that the first arrivals are comprised of head waves and direct waves, and a pair of reciprocal shot gathers is recorded over the line of interest. The refraction traveltimes from these reciprocal shot gathers can be picked and decomposed into O(N2) refraction traveltimes generated by N virtual sources, where N is the number of geophones in the 2D survey. This enormous increase in the number of virtual traveltime picks and associated rays, compared to the 2N traveltimes from the two reciprocal shot gathers, allows for increased model resolution and better condition numbers in the normal equations. Also, a reciprocal survey is far less time consuming than a standard refraction survey with a dense distribution of sources.
B-Spline potential function for maximum a-posteriori image reconstruction in fluorescence microscopy
Directory of Open Access Journals (Sweden)
Shilpa Dilipkumar
2015-03-01
Full Text Available An iterative image reconstruction technique employing B-Spline potential function in a Bayesian framework is proposed for fluorescence microscopy images. B-splines are piecewise polynomials with smooth transition, compact support and are the shortest polynomial splines. Incorporation of the B-spline potential function in the maximum-a-posteriori reconstruction technique resulted in improved contrast, enhanced resolution and substantial background reduction. The proposed technique is validated on simulated data as well as on the images acquired from fluorescence microscopes (widefield, confocal laser scanning fluorescence and super-resolution 4Pi microscopy. A comparative study of the proposed technique with the state-of-art maximum likelihood (ML and maximum-a-posteriori (MAP with quadratic potential function shows its superiority over the others. B-Spline MAP technique can find applications in several imaging modalities of fluorescence microscopy like selective plane illumination microscopy, localization microscopy and STED.
A maximum-likelihood reconstruction algorithm for tomographic gamma-ray nondestructive assay
International Nuclear Information System (INIS)
Prettyman, T.H.; Estep, R.J.; Cole, R.A.; Sheppard, G.A.
1994-01-01
A new tomographic reconstruction algorithm for nondestructive assay with high resolution gamma-ray spectroscopy (HRGS) is presented. The reconstruction problem is formulated using a maximum-likelihood approach in which the statistical structure of both the gross and continuum measurements used to determine the full-energy response in HRGS is precisely modeled. An accelerated expectation-maximization algorithm is used to determine the optimal solution. The algorithm is applied to safeguards and environmental assays of large samples (for example, 55-gal. drums) in which high continuum levels caused by Compton scattering are routinely encountered. Details of the implementation of the algorithm and a comparative study of the algorithm's performance are presented
Chen, Yihang; Xiao, Chijie; Yang, Xiaoyi; Wang, Tianbo; Xu, Tianchao; Yu, Yi; Xu, Min; Wang, Long; Lin, Chen; Wang, Xiaogang
2017-10-01
The Laser-driven Ion beam trace probe (LITP) is a new diagnostic method for measuring poloidal magnetic field (Bp) and radial electric field (Er) in tokamaks. LITP injects a laser-driven ion beam into the tokamak, and Bp and Er profiles can be reconstructed using tomography methods. A reconstruction code has been developed to validate the LITP theory, and both 2D reconstruction of Bp and simultaneous reconstruction of Bp and Er have been attained. To reconstruct from experimental data with noise, Maximum Entropy and Gaussian-Bayesian tomography methods were applied and improved according to the characteristics of the LITP problem. With these improved methods, a reconstruction error level below 15% has been attained with a data noise level of 10%. These methods will be further tested and applied in the following LITP experiments. Supported by the ITER-CHINA program 2015GB120001, CHINA MOST under 2012YQ030142 and National Natural Science Foundation Abstract of China under 11575014 and 11375053.
Maximum a posteriori reconstruction of the Patlak parametric image from sinograms in dynamic PET
International Nuclear Information System (INIS)
Wang Guobao; Fu Lin; Qi Jinyi
2008-01-01
Parametric imaging using the Patlak graphical method has been widely used to analyze dynamic PET data. Conventionally a Patlak parametric image is generated by reconstructing a sequence of dynamic images first and then performing Patlak graphical analysis on the time-activity curves pixel-by-pixel. However, because it is rather difficult to model the noise distribution in reconstructed images, the spatially variant noise correlation is simply ignored in the Patlak analysis, which leads to sub-optimal results. In this paper we present a Bayesian method for reconstructing Patlak parametric images directly from raw sinogram data by incorporating the Patlak plot model into the image reconstruction procedure. A preconditioned conjugate gradient algorithm is used to find the maximum a posteriori solution. The proposed direct method is statistically more efficient than the conventional indirect approach because the Poisson noise distribution in PET data can be accurately modeled in the direct reconstruction. The computation cost of the direct method is similar to reconstruction time of two dynamic frames. Therefore, when more than two dynamic frames are used in the Patlak analysis, the direct method is faster than the conventional indirect approach. We conduct computer simulations to validate the proposed direct method. Comparisons with the conventional indirect approach show that the proposed method results in a more accurate estimate of the parametric image. The proposed method has been applied to dynamic fully 3D PET data from a microPET scanner
Ellis, Sam; Reader, Andrew J
2018-04-26
Many clinical contexts require the acquisition of multiple positron emission tomography (PET) scans of a single subject, for example to observe and quantify changes in functional behaviour in tumours after treatment in oncology. Typically, the datasets from each of these scans are reconstructed individually, without exploiting the similarities between them. We have recently shown that sharing information between longitudinal PET datasets by penalising voxel-wise differences during image reconstruction can improve reconstructed images by reducing background noise and increasing the contrast-to-noise ratio of high activity lesions. Here we present two additional novel longitudinal difference-image priors and evaluate their performance using 2D simulation studies and a 3D real dataset case study. We have previously proposed a simultaneous difference-image-based penalised maximum likelihood (PML) longitudinal image reconstruction method that encourages sparse difference images (DS-PML), and in this work we propose two further novel prior terms. The priors are designed to encourage longitudinal images with corresponding differences which have i) low entropy (DE-PML), and ii) high sparsity in their spatial gradients (DTV-PML). These two new priors and the originally proposed longitudinal prior were applied to 2D simulated treatment response [ 18 F]fluorodeoxyglucose (FDG) brain tumour datasets and compared to standard maximum likelihood expectation-maximisation (MLEM) reconstructions. These 2D simulation studies explored the effects of penalty strengths, tumour behaviour, and inter-scan coupling on reconstructed images. Finally, a real two-scan longitudinal data series acquired from a head and neck cancer patient was reconstructed with the proposed methods and the results compared to standard reconstruction methods. Using any of the three priors with an appropriate penalty strength produced images with noise levels equivalent to those seen when using standard
Reconstruction of the electron momentum density distribution by the maximum entropy method
International Nuclear Information System (INIS)
Dobrzynski, L.
1996-01-01
The application of the Maximum Entropy Algorithm to the analysis of the Compton profiles is discussed. It is shown that the reconstruction of electron momentum density may be reliably carried out. However, there are a number of technical problems which have to be overcome in order to produce trustworthy results. In particular one needs the experimental Compton profiles measured for many directions, and to have efficient computational resources. The use of various cross-checks is recommended. (orig.)
Reconstruction of North American drainage basins and river discharge since the Last Glacial Maximum
Directory of Open Access Journals (Sweden)
A. D. Wickert
2016-11-01
Full Text Available Over the last glacial cycle, ice sheets and the resultant glacial isostatic adjustment (GIA rearranged river systems. As these riverine threads that tied the ice sheets to the sea were stretched, severed, and restructured, they also shrank and swelled with the pulse of meltwater inputs and time-varying drainage basin areas, and sometimes delivered enough meltwater to the oceans in the right places to influence global climate. Here I present a general method to compute past river flow paths, drainage basin geometries, and river discharges, by combining models of past ice sheets, glacial isostatic adjustment, and climate. The result is a time series of synthetic paleohydrographs and drainage basin maps from the Last Glacial Maximum to present for nine major drainage basins – the Mississippi, Rio Grande, Colorado, Columbia, Mackenzie, Hudson Bay, Saint Lawrence, Hudson, and Susquehanna/Chesapeake Bay. These are based on five published reconstructions of the North American ice sheets. I compare these maps with drainage reconstructions and discharge histories based on a review of observational evidence, including river deposits and terraces, isotopic records, mineral provenance markers, glacial moraine histories, and evidence of ice stream and tunnel valley flow directions. The sharp boundaries of the reconstructed past drainage basins complement the flexurally smoothed GIA signal that is more often used to validate ice-sheet reconstructions, and provide a complementary framework to reduce nonuniqueness in model reconstructions of the North American ice-sheet complex.
Goolsby, Eric W
2017-04-01
Ancestral state reconstruction is a method used to study the evolutionary trajectories of quantitative characters on phylogenies. Although efficient methods for univariate ancestral state reconstruction under a Brownian motion model have been described for at least 25 years, to date no generalization has been described to allow more complex evolutionary models, such as multivariate trait evolution, non-Brownian models, missing data, and within-species variation. Furthermore, even for simple univariate Brownian motion models, most phylogenetic comparative R packages compute ancestral states via inefficient tree rerooting and full tree traversals at each tree node, making ancestral state reconstruction extremely time-consuming for large phylogenies. Here, a computationally efficient method for fast maximum likelihood ancestral state reconstruction of continuous characters is described. The algorithm has linear complexity relative to the number of species and outperforms the fastest existing R implementations by several orders of magnitude. The described algorithm is capable of performing ancestral state reconstruction on a 1,000,000-species phylogeny in fewer than 2 s using a standard laptop, whereas the next fastest R implementation would take several days to complete. The method is generalizable to more complex evolutionary models, such as phylogenetic regression, within-species variation, non-Brownian evolutionary models, and multivariate trait evolution. Because this method enables fast repeated computations on phylogenies of virtually any size, implementation of the described algorithm can drastically alleviate the computational burden of many otherwise prohibitively time-consuming tasks requiring reconstruction of ancestral states, such as phylogenetic imputation of missing data, bootstrapping procedures, Expectation-Maximization algorithms, and Bayesian estimation. The described ancestral state reconstruction algorithm is implemented in the Rphylopars
Maximum-entropy networks pattern detection, network reconstruction and graph combinatorics
Squartini, Tiziano
2017-01-01
This book is an introduction to maximum-entropy models of random graphs with given topological properties and their applications. Its original contribution is the reformulation of many seemingly different problems in the study of both real networks and graph theory within the unified framework of maximum entropy. Particular emphasis is put on the detection of structural patterns in real networks, on the reconstruction of the properties of networks from partial information, and on the enumeration and sampling of graphs with given properties. After a first introductory chapter explaining the motivation, focus, aim and message of the book, chapter 2 introduces the formal construction of maximum-entropy ensembles of graphs with local topological constraints. Chapter 3 focuses on the problem of pattern detection in real networks and provides a powerful way to disentangle nontrivial higher-order structural features from those that can be traced back to simpler local constraints. Chapter 4 focuses on the problem o...
Parsimonious Refraction Interferometry and Tomography
Hanafy, Sherif; Schuster, Gerard T.
2017-01-01
We present parsimonious refraction interferometry and tomography where a densely populated refraction data set can be obtained from two reciprocal and several infill shot gathers. The assumptions are that the refraction arrivals are head waves
Dynamical reconstruction of the global ocean state during the Last Glacial Maximum
Kurahashi-Nakamura, Takasumi; Paul, André; Losch, Martin
2017-04-01
The global ocean state for the modern age and for the Last Glacial Maximum (LGM) was dynamically reconstructed with a sophisticated data assimilation technique. A substantial amount of data including global seawater temperature, salinity (only for the modern estimate), and the isotopic composition of oxygen and carbon (only in the Atlantic for the LGM) were integrated into an ocean general circulation model with the help of the adjoint method, thereby the model was optimized to reconstruct plausible continuous fields of tracers, overturning circulation and water mass distribution. The adjoint-based LGM state estimation of this study represents the state of the art in terms of the length of forward model runs, the number of observations assimilated, and the model domain. Compared to the modern state, the reconstructed continuous sea-surface temperature field for the LGM shows a global-mean cooling of 2.2 K, and the reconstructed LGM ocean has a more vigorous Atlantic meridional overturning circulation, shallower North Atlantic Deep Water (NADW) equivalent, stronger stratification, and more saline deep water.
Maximum entropy based reconstruction of soft X ray emissivity profiles in W7-AS
International Nuclear Information System (INIS)
Ertl, K.; Linden, W. von der; Dose, V.; Weller, A.
1996-01-01
The reconstruction of 2-D emissivity profiles from soft X ray tomography measurements constitutes a highly underdetermined and ill-posed inversion problem, because of the restricted viewing access, the number of chords and the increased noise level in most plasma devices. An unbiased and consistent probabilistic approach within the framework of Bayesian inference is provided by the maximum entropy method, which is independent of model assumptions, but allows any prior knowledge available to be incorporated. The formalism is applied to the reconstruction of emissivity profiles in an NBI heated plasma discharge to determine the dependence of the Shafranov shift on β, the reduction of which was a particular objective in designing the advanced W7-AS stellarator. (author). 40 refs, 7 figs
A new global reconstruction of temperature changes at the Last Glacial Maximum
Directory of Open Access Journals (Sweden)
J. D. Annan
2013-02-01
Full Text Available Some recent compilations of proxy data both on land and ocean (MARGO Project Members, 2009; Bartlein et al., 2011; Shakun et al., 2012, have provided a new opportunity for an improved assessment of the overall climatic state of the Last Glacial Maximum. In this paper, we combine these proxy data with the ensemble of structurally diverse state of the art climate models which participated in the PMIP2 project (Braconnot et al., 2007 to generate a spatially complete reconstruction of surface air (and sea surface temperatures. We test a variety of approaches, and show that multiple linear regression performs well for this application. Our reconstruction is significantly different to and more accurate than previous approaches and we obtain an estimated global mean cooling of 4.0 ± 0.8 °C (95% CI.
Bentley, Michael J.; Ó Cofaigh, Colm; Anderson, John B.; Conway, Howard; Davies, Bethan; Graham, Alastair G. C.; Hillenbrand, Claus-Dieter; Hodgson, Dominic A.; Jamieson, Stewart S. R.; Larter, Robert D.; Mackintosh, Andrew; Smith, James A.; Verleyen, Elie; Ackert, Robert P.; Bart, Philip J.; Berg, Sonja; Brunstein, Daniel; Canals, Miquel; Colhoun, Eric A.; Crosta, Xavier; Dickens, William A.; Domack, Eugene; Dowdeswell, Julian A.; Dunbar, Robert; Ehrmann, Werner; Evans, Jeffrey; Favier, Vincent; Fink, David; Fogwill, Christopher J.; Glasser, Neil F.; Gohl, Karsten; Golledge, Nicholas R.; Goodwin, Ian; Gore, Damian B.; Greenwood, Sarah L.; Hall, Brenda L.; Hall, Kevin; Hedding, David W.; Hein, Andrew S.; Hocking, Emma P.; Jakobsson, Martin; Johnson, Joanne S.; Jomelli, Vincent; Jones, R. Selwyn; Klages, Johann P.; Kristoffersen, Yngve; Kuhn, Gerhard; Leventer, Amy; Licht, Kathy; Lilly, Katherine; Lindow, Julia; Livingstone, Stephen J.; Massé, Guillaume; McGlone, Matt S.; McKay, Robert M.; Melles, Martin; Miura, Hideki; Mulvaney, Robert; Nel, Werner; Nitsche, Frank O.; O'Brien, Philip E.; Post, Alexandra L.; Roberts, Stephen J.; Saunders, Krystyna M.; Selkirk, Patricia M.; Simms, Alexander R.; Spiegel, Cornelia; Stolldorf, Travis D.; Sugden, David E.; van der Putten, Nathalie; van Ommen, Tas; Verfaillie, Deborah; Vyverman, Wim; Wagner, Bernd; White, Duanne A.; Witus, Alexandra E.; Zwartz, Dan
2014-09-01
A robust understanding of Antarctic Ice Sheet deglacial history since the Last Glacial Maximum is important in order to constrain ice sheet and glacial-isostatic adjustment models, and to explore the forcing mechanisms responsible for ice sheet retreat. Such understanding can be derived from a broad range of geological and glaciological datasets and recent decades have seen an upsurge in such data gathering around the continent and Sub-Antarctic islands. Here, we report a new synthesis of those datasets, based on an accompanying series of reviews of the geological data, organised by sector. We present a series of timeslice maps for 20 ka, 15 ka, 10 ka and 5 ka, including grounding line position and ice sheet thickness changes, along with a clear assessment of levels of confidence. The reconstruction shows that the Antarctic Ice sheet did not everywhere reach the continental shelf edge at its maximum, that initial retreat was asynchronous, and that the spatial pattern of deglaciation was highly variable, particularly on the inner shelf. The deglacial reconstruction is consistent with a moderate overall excess ice volume and with a relatively small Antarctic contribution to meltwater pulse 1a. We discuss key areas of uncertainty both around the continent and by time interval, and we highlight potential priorities for future work. The synthesis is intended to be a resource for the modelling and glacial geological community.
Wobbling and LSF-based maximum likelihood expectation maximization reconstruction for wobbling PET
International Nuclear Information System (INIS)
Kim, Hang-Keun; Son, Young-Don; Kwon, Dae-Hyuk; Joo, Yohan; Cho, Zang-Hee
2016-01-01
Positron emission tomography (PET) is a widely used imaging modality; however, the PET spatial resolution is not yet satisfactory for precise anatomical localization of molecular activities. Detector size is the most important factor because it determines the intrinsic resolution, which is approximately half of the detector size and determines the ultimate PET resolution. Detector size, however, cannot be made too small because both the decreased detection efficiency and the increased septal penetration effect degrade the image quality. A wobbling and line spread function (LSF)-based maximum likelihood expectation maximization (WL-MLEM) algorithm, which combined the MLEM iterative reconstruction algorithm with wobbled sampling and LSF-based deconvolution using the system matrix, was proposed for improving the spatial resolution of PET without reducing the scintillator or detector size. The new algorithm was evaluated using a simulation, and its performance was compared with that of the existing algorithms, such as conventional MLEM and LSF-based MLEM. Simulations demonstrated that the WL-MLEM algorithm yielded higher spatial resolution and image quality than the existing algorithms. The WL-MLEM algorithm with wobbling PET yielded substantially improved resolution compared with conventional algorithms with stationary PET. The algorithm can be easily extended to other iterative reconstruction algorithms, such as maximum a priori (MAP) and ordered subset expectation maximization (OSEM). The WL-MLEM algorithm with wobbling PET may offer improvements in both sensitivity and resolution, the two most sought-after features in PET design. - Highlights: • This paper proposed WL-MLEM algorithm for PET and demonstrated its performance. • WL-MLEM algorithm effectively combined wobbling and line spread function based MLEM. • WL-MLEM provided improvements in the spatial resolution and the PET image quality. • WL-MLEM can be easily extended to the other iterative
Bayesian hierarchical models for regional climate reconstructions of the last glacial maximum
Weitzel, Nils; Hense, Andreas; Ohlwein, Christian
2017-04-01
Spatio-temporal reconstructions of past climate are important for the understanding of the long term behavior of the climate system and the sensitivity to forcing changes. Unfortunately, they are subject to large uncertainties, have to deal with a complex proxy-climate structure, and a physically reasonable interpolation between the sparse proxy observations is difficult. Bayesian Hierarchical Models (BHMs) are a class of statistical models that is well suited for spatio-temporal reconstructions of past climate because they permit the inclusion of multiple sources of information (e.g. records from different proxy types, uncertain age information, output from climate simulations) and quantify uncertainties in a statistically rigorous way. BHMs in paleoclimatology typically consist of three stages which are modeled individually and are combined using Bayesian inference techniques. The data stage models the proxy-climate relation (often named transfer function), the process stage models the spatio-temporal distribution of the climate variables of interest, and the prior stage consists of prior distributions of the model parameters. For our BHMs, we translate well-known proxy-climate transfer functions for pollen to a Bayesian framework. In addition, we can include Gaussian distributed local climate information from preprocessed proxy records. The process stage combines physically reasonable spatial structures from prior distributions with proxy records which leads to a multivariate posterior probability distribution for the reconstructed climate variables. The prior distributions that constrain the possible spatial structure of the climate variables are calculated from climate simulation output. We present results from pseudoproxy tests as well as new regional reconstructions of temperatures for the last glacial maximum (LGM, ˜ 21,000 years BP). These reconstructions combine proxy data syntheses with information from climate simulations for the LGM that were
Yang, Li; Wang, Guobao; Qi, Jinyi
2016-04-01
Detecting cancerous lesions is a major clinical application of emission tomography. In a previous work, we studied penalized maximum-likelihood (PML) image reconstruction for lesion detection in static PET. Here we extend our theoretical analysis of static PET reconstruction to dynamic PET. We study both the conventional indirect reconstruction and direct reconstruction for Patlak parametric image estimation. In indirect reconstruction, Patlak parametric images are generated by first reconstructing a sequence of dynamic PET images, and then performing Patlak analysis on the time activity curves (TACs) pixel-by-pixel. In direct reconstruction, Patlak parametric images are estimated directly from raw sinogram data by incorporating the Patlak model into the image reconstruction procedure. PML reconstruction is used in both the indirect and direct reconstruction methods. We use a channelized Hotelling observer (CHO) to assess lesion detectability in Patlak parametric images. Simplified expressions for evaluating the lesion detectability have been derived and applied to the selection of the regularization parameter value to maximize detection performance. The proposed method is validated using computer-based Monte Carlo simulations. Good agreements between the theoretical predictions and the Monte Carlo results are observed. Both theoretical predictions and Monte Carlo simulation results show the benefit of the indirect and direct methods under optimized regularization parameters in dynamic PET reconstruction for lesion detection, when compared with the conventional static PET reconstruction.
Implementation of non-linear filters for iterative penalized maximum likelihood image reconstruction
International Nuclear Information System (INIS)
Liang, Z.; Gilland, D.; Jaszczak, R.; Coleman, R.
1990-01-01
In this paper, the authors report on the implementation of six edge-preserving, noise-smoothing, non-linear filters applied in image space for iterative penalized maximum-likelihood (ML) SPECT image reconstruction. The non-linear smoothing filters implemented were the median filter, the E 6 filter, the sigma filter, the edge-line filter, the gradient-inverse filter, and the 3-point edge filter with gradient-inverse filter, and the 3-point edge filter with gradient-inverse weight. A 3 x 3 window was used for all these filters. The best image obtained, by viewing the profiles through the image in terms of noise-smoothing, edge-sharpening, and contrast, was the one smoothed with the 3-point edge filter. The computation time for the smoothing was less than 1% of one iteration, and the memory space for the smoothing was negligible. These images were compared with the results obtained using Bayesian analysis
International Nuclear Information System (INIS)
Stsepankou, D; Arns, A; Hesser, J; Ng, S K; Zygmanski, P
2012-01-01
The objective of this paper is to evaluate an iterative maximum likelihood (ML) cone–beam computed tomography (CBCT) reconstruction with total variation (TV) regularization with respect to the robustness of the algorithm due to data inconsistencies. Three different and (for clinical application) typical classes of errors are considered for simulated phantom and measured projection data: quantum noise, defect detector pixels and projection matrix errors. To quantify those errors we apply error measures like mean square error, signal-to-noise ratio, contrast-to-noise ratio and streak indicator. These measures are derived from linear signal theory and generalized and applied for nonlinear signal reconstruction. For quality check, we focus on resolution and CT-number linearity based on a Catphan phantom. All comparisons are made versus the clinical standard, the filtered backprojection algorithm (FBP). In our results, we confirm and substantially extend previous results on iterative reconstruction such as massive undersampling of the number of projections. Errors of projection matrix parameters of up to 1° projection angle deviations are still in the tolerance level. Single defect pixels exhibit ring artifacts for each method. However using defect pixel compensation, allows up to 40% of defect pixels for passing the standard clinical quality check. Further, the iterative algorithm is extraordinarily robust in the low photon regime (down to 0.05 mAs) when compared to FPB, allowing for extremely low-dose image acquisitions, a substantial issue when considering daily CBCT imaging for position correction in radiotherapy. We conclude that the ML method studied herein is robust under clinical quality assurance conditions. Consequently, low-dose regime imaging, especially for daily patient localization in radiation therapy is possible without change of the current hardware of the imaging system. (paper)
Linsen, Sabine S; Oikonomou, Annina; Martini, Markus; Teschke, Marcus
2018-05-01
The purpose was to analyze mandibular kinematics and maximum voluntary bite force in patients following segmental resection of the mandible without and with reconstruction (autologous bone, alloplastic total temporomandibular joint replacement (TMJ TJR)). Subjects operated from April 2002 to August 2014 were enrolled in the study. Condylar (CRoM) and incisal (InRoM) range of motion and deflection during opening, condylar retrusion, incisal lateral excursion, mandibular rotation angle during opening, and maximum voluntary bite force were determined on the non-affected site and compared between groups. Influence of co-factors (defect size, soft tissue deficit, neck dissection, radiotherapy, occlusal contact zones (OCZ), and time) was determined. Twelve non-reconstructed and 26 reconstructed patients (13 autologous, 13 TMJ TJR) were included in the study. InRoM opening and bite force were significantly higher (P ≤ .024), and both condylar and incisal deflection during opening significantly lower (P ≤ .027) in reconstructed patients compared with non-reconstructed. Differences between the autologous and the TMJ TJR group were statistically not significant. Co-factors defect size, soft tissue deficit, and neck dissection had the greatest impact on kinematics and number of OCZs on bite force. Reconstructed patients (both autologous and TMJ TJR) have better overall function than non-reconstructed patients. Reconstruction of segmental mandibular resection has positive effects on mandibular function. TMJ TJR seems to be a suitable technique for the reconstruction of mandibular defects including the TMJ complex.
Miller, J.; Dekens, P. S.; Weber, M. E.; Spiess, V.; France-Lanord, C.
2015-12-01
The International Ocean Discovery Program (IODP) Expedition 354 drilled 7 sites in the Bay of Bengal, providing a unique opportunity to improve our understanding of the link between glacial cycles, tropical oceanographic changes, and monsoon strength. Deep-sea sediment cores of the Bengal Fan fluctuate between sand, hemipelagic and terrestrial sediment layers. All but one of the sites (U1454) contain a layer of calcareous clay in the uppermost part of the core that is late Pleistocene in age. During Expedition 354 site U1452C was sampled at high resolution (every 2cm) by a broad group of collaborators with the goal of reconstructing monsoon strength and oceanographic conditions using a variety of proxies. The top 480 cm of site U1452C (8ºN, 87ºE, 3671m water depth) contains primarily nannofossil rich calcareous clay. The relatively high abundance of foraminifera will allow us to generate a high resolution record of sea surface temperature (SST) and sea surface salinity (SSS) using standard foraminifera proxies. We will present oxygen isotopes (δ18O) and Mg/Ca data of mixed layer planktonic foraminifera from the top 70cm of the core, representing the Holocene to the last glacial maximum. δ18O of planktonic foraminifera records global ice volume and local SST and SSS, while Mg/Ca of foraminifera is a proxy for SST. The paired Mg/Ca and δ18O measurements on the same samples of foraminifera, together with published estimates with global ocean δ18O, can be used to reconstruct both SST and local δ18O of seawater, which is a function of the evaporation/precipitation balance. In future work, the local SSS and SST during the LGM will be paired with terrestrial and other oceanic proxies to increase our understanding of how global climate is connected to monsoon strength.
Parsimonious Language Models for Information Retrieval
Hiemstra, Djoerd; Robertson, Stephen; Zaragoza, Hugo
We systematically investigate a new approach to estimating the parameters of language models for information retrieval, called parsimonious language models. Parsimonious language models explicitly address the relation between levels of language models that are typically used for smoothing. As such,
Implementation of linear filters for iterative penalized maximum likelihood SPECT reconstruction
International Nuclear Information System (INIS)
Liang, Z.
1991-01-01
This paper reports on six low-pass linear filters applied in frequency space implemented for iterative penalized maximum-likelihood (ML) SPECT image reconstruction. The filters implemented were the Shepp-Logan filter, the Butterworth filer, the Gaussian filter, the Hann filter, the Parzen filer, and the Lagrange filter. The low-pass filtering was applied in frequency space to projection data for the initial estimate and to the difference of projection data and reprojected data for higher order approximations. The projection data were acquired experimentally from a chest phantom consisting of non-uniform attenuating media. All the filters could effectively remove the noise and edge artifacts associated with ML approach if the frequency cutoff was properly chosen. The improved performance of the Parzen and Lagrange filters relative to the others was observed. The best image, by viewing its profiles in terms of noise-smoothing, edge-sharpening, and contrast, was the one obtained with the Parzen filter. However, the Lagrange filter has the potential to consider the characteristics of detector response function
International Nuclear Information System (INIS)
Kubo, S.; Narihara, K.; Tomita, Y.; Hasegawa, M.; Tsuzuki, T.; Mohri, A.
1988-01-01
A multichannel HCN laser interferometer system has been developed to investigate the plasma electron confinement properties in SPAC VII device. Maximum entropy method is applied to reconstruct the electron density profile from measured line integrated data. Particle diffusion coefficient in the peripheral region of the REB ring core spherator was obtained from the evolution of the density profile. (author)
The Red Sea during the Last Glacial Maximum: implications for sea level reconstructions
Gildor, H.; Biton, E.; Peltier, W. R.
2006-12-01
The Red Sea (RS) is a semi-enclosed basin connected to the Indian Ocean via a narrow and shallow strait, and surrounded by arid areas which exhibits high sensitivity to atmospheric changes and sea level reduction. We have used the MIT GCM to investigate the changes in the hydrography and circulation in the RS in response to reduced sea level, variability in the Indian monsoons, and changes in atmospheric temperature and humidity that occurred during the Last Glacial Maximum (LGM). The model results show high sensitivity to sea level reduction especially in the salinity field (increasing with the reduction in sea level) together with a mild atmospheric impact. Sea level reduction decreases the stratification, increases subsurface temperatures, and alters the circulation pattern at the Strait of Bab el Mandab, which experiences a transition from submaximal flow to maximal flow. The reduction in sea level at LGM alters the location of deep water formation which shifts to an open sea convective site in the northern part of the RS compared to present day situation in which deep water is formed from the Gulf of Suez outflow. Our main result based on both the GCM and on a simple hydraulic control model which takes into account mixing process at the Strait of Bab El Mandeb, is that sea level was reduced by only ~100 m in the Bab El Mandeb region during the LGM, i.e. the water depth at the Hanish sill (the shallowest part in the Strait Bab el Mandab) was around 34 m. This result agrees with the recent reconstruction of the LGM low stand of the sea in this region based upon the ICE-5G (VM2) model of Peltier (2004).
2010-07-01
... Administrator, and shall provide a summary in a compatible electronic format for inclusion in the MACT data base... paragraph (d) of this section. (2) In each instance where a constructed or reconstructed major source would...) In each instance where the owner or operator contends that a constructed or reconstructed major...
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.
Reconstruction algorithm in compressed sensing based on maximum a posteriori estimation
International Nuclear Information System (INIS)
Takeda, Koujin; Kabashima, Yoshiyuki
2013-01-01
We propose a systematic method for constructing a sparse data reconstruction algorithm in compressed sensing at a relatively low computational cost for general observation matrix. It is known that the cost of ℓ 1 -norm minimization using a standard linear programming algorithm is O(N 3 ). We show that this cost can be reduced to O(N 2 ) by applying the approach of posterior maximization. Furthermore, in principle, the algorithm from our approach is expected to achieve the widest successful reconstruction region, which is evaluated from theoretical argument. We also discuss the relation between the belief propagation-based reconstruction algorithm introduced in preceding works and our approach
International Nuclear Information System (INIS)
Hyde, Derek E.; Habets, Damiaan F.; Fox, Allan J.; Gulka, Irene; Kalapos, Paul; Lee, Don H.; Pelz, David M.; Holdsworth, David W.
2007-01-01
Digital subtraction angiography is being supplanted by three-dimensional imaging techniques in many clinical applications, leading to extensive use of maximum intensity projection (MIP) images to depict volumetric vascular data. The MIP algorithm produces intensity profiles that are different than conventional angiograms, and can also increase the vessel-to-tissue contrast-to-noise ratio. We evaluated the effect of the MIP algorithm in a clinical application where quantitative vessel measurement is important: internal carotid artery stenosis grading. Three-dimensional computed rotational angiography (CRA) was performed on 26 consecutive symptomatic patients to verify an internal carotid artery stenosis originally found using duplex ultrasound. These volumes of data were visualized using two different postprocessing projection techniques: MIP and digitally reconstructed radiographic (DRR) projection. A DRR is a radiographic image simulating a conventional digitally subtracted angiogram, but it is derived computationally from the same CRA dataset as the MIP. By visualizing a single volume with two different projection techniques, the postprocessing effect of the MIP algorithm is isolated. Vessel measurements were made, according to the NASCET guidelines, and percentage stenosis grades were calculated. The paired t-test was used to determine if the measurement difference between the two techniques was statistically significant. The CRA technique provided an isotropic voxel spacing of 0.38 mm. The MIPs and DRRs had a mean signal-difference-to-noise-ratio of 30:1 and 26:1, respectively. Vessel measurements from MIPs were, on average, 0.17 mm larger than those from DRRs (P<0.0001). The NASCET-type stenosis grades tended to be underestimated on average by 2.4% with the MIP algorithm, although this was not statistically significant (P=0.09). The mean interobserver variability (standard deviation) of both the MIP and DRR images was 0.35 mm. It was concluded that the MIP
Regional compensation for statistical maximum likelihood reconstruction error of PET image pixels
International Nuclear Information System (INIS)
Forma, J; Ruotsalainen, U; Niemi, J A
2013-01-01
In positron emission tomography (PET), there is an increasing interest in studying not only the regional mean tracer concentration, but its variation arising from local differences in physiology, the tissue heterogeneity. However, in reconstructed images this physiological variation is shadowed by a large reconstruction error, which is caused by noisy data and the inversion of tomographic problem. We present a new procedure which can quantify the error variation in regional reconstructed values for given PET measurement, and reveal the remaining tissue heterogeneity. The error quantification is made by creating and reconstructing the noise realizations of virtual sinograms, which are statistically similar with the measured sinogram. Tests with physical phantom data show that the characterization of error variation and the true heterogeneity are possible, despite the existing model error when real measurement is considered. (paper)
International Nuclear Information System (INIS)
Jang, Yun Hee; Cho, Bum Sang; Kang, Min Ho; Kang, Woo Young; Lee, Jisun; Kim, Yook; Lee, Soo Hyun; Lee, Soo Jung; Lee, Jin Yong
2016-01-01
The purpose of this study was to determine a suitable position in which the measured length on ultrasound is close to the true renal length obtained through a multiplanar reconstructed MR image. A total of 33 individuals (males: 15, females: 18) without any underlying renal disease were included in the present study. Renal length was measured as the longest axis at the level of the renal hilum in three positions-supine, lateral decubitus, and prone, respectively. With a 3.0 T MR scanner, 3D eTHRIVE was acquired. Subsequently, the maximum longitudinal length of both the kidneys was measured through multiplanar reconstructed MR images. Paired t-test was used to compare the renal length obtained from ultrasonographic measurement with the length obtained through multiplanar reconstructed MR images. Our study demonstrated significant difference between sonographic renal length in three positions and renal length through MRI (p < 0.001). However, the longest longitudinal length of right kidney among the measured three values by ultrasound was statistically similar to the renal length measured by reconstructed MR image. Among them, the lateral decubitus position showed the strongest correlation with true renal length (right: 0.887; left: 0.849). We recommend measurement of the maximum renal longitudinal length in all possible positions on ultrasonography. If not allowed, the best measurement is on the lateral decubitus showing the strongest correlation coefficient with true renal length
Energy Technology Data Exchange (ETDEWEB)
Jang, Yun Hee; Cho, Bum Sang; Kang, Min Ho; Kang, Woo Young; Lee, Jisun; Kim, Yook; Lee, Soo Hyun; Lee, Soo Jung [Dept. of Radiology, Chungbuk National University Hospital, Cheongju (Korea, Republic of); Lee, Jin Yong [Public Health Medical Service, Seoul National University Boramae Medical Center, Seoul (Korea, Republic of)
2016-07-15
The purpose of this study was to determine a suitable position in which the measured length on ultrasound is close to the true renal length obtained through a multiplanar reconstructed MR image. A total of 33 individuals (males: 15, females: 18) without any underlying renal disease were included in the present study. Renal length was measured as the longest axis at the level of the renal hilum in three positions-supine, lateral decubitus, and prone, respectively. With a 3.0 T MR scanner, 3D eTHRIVE was acquired. Subsequently, the maximum longitudinal length of both the kidneys was measured through multiplanar reconstructed MR images. Paired t-test was used to compare the renal length obtained from ultrasonographic measurement with the length obtained through multiplanar reconstructed MR images. Our study demonstrated significant difference between sonographic renal length in three positions and renal length through MRI (p < 0.001). However, the longest longitudinal length of right kidney among the measured three values by ultrasound was statistically similar to the renal length measured by reconstructed MR image. Among them, the lateral decubitus position showed the strongest correlation with true renal length (right: 0.887; left: 0.849). We recommend measurement of the maximum renal longitudinal length in all possible positions on ultrasonography. If not allowed, the best measurement is on the lateral decubitus showing the strongest correlation coefficient with true renal length.
Assessing the accuracy of ancestral protein reconstruction methods.
Directory of Open Access Journals (Sweden)
Paul D Williams
2006-06-01
Full Text Available The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess the accuracy of ancestral protein reconstruction methods, we performed computational population evolution simulations featuring near-neutral evolution under purifying selection, speciation, and divergence using an off-lattice protein model where fitness depends on the ability to be stable in a specified target structure. We were thus able to compare the thermodynamic properties of the true ancestral sequences with the properties of "ancestral sequences" inferred by maximum parsimony, maximum likelihood, and Bayesian methods. Surprisingly, we found that methods such as maximum parsimony and maximum likelihood that reconstruct a "best guess" amino acid at each position overestimate thermostability, while a Bayesian method that sometimes chooses less-probable residues from the posterior probability distribution does not. Maximum likelihood and maximum parsimony apparently tend to eliminate variants at a position that are slightly detrimental to structural stability simply because such detrimental variants are less frequent. Other properties of ancestral proteins might be similarly overestimated. This suggests that ancestral reconstruction studies require greater care to come to credible conclusions regarding functional evolution. Inferred functional patterns that mimic reconstruction bias should be reevaluated.
Assessing the accuracy of ancestral protein reconstruction methods.
Williams, Paul D; Pollock, David D; Blackburne, Benjamin P; Goldstein, Richard A
2006-06-23
The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess the accuracy of ancestral protein reconstruction methods, we performed computational population evolution simulations featuring near-neutral evolution under purifying selection, speciation, and divergence using an off-lattice protein model where fitness depends on the ability to be stable in a specified target structure. We were thus able to compare the thermodynamic properties of the true ancestral sequences with the properties of "ancestral sequences" inferred by maximum parsimony, maximum likelihood, and Bayesian methods. Surprisingly, we found that methods such as maximum parsimony and maximum likelihood that reconstruct a "best guess" amino acid at each position overestimate thermostability, while a Bayesian method that sometimes chooses less-probable residues from the posterior probability distribution does not. Maximum likelihood and maximum parsimony apparently tend to eliminate variants at a position that are slightly detrimental to structural stability simply because such detrimental variants are less frequent. Other properties of ancestral proteins might be similarly overestimated. This suggests that ancestral reconstruction studies require greater care to come to credible conclusions regarding functional evolution. Inferred functional patterns that mimic reconstruction bias should be reevaluated.
International Nuclear Information System (INIS)
Llacer, J.; Veklerov, E.
1987-05-01
We review our recent work characterizing the image reconstruction properties of the MLE algorithm. We studied its convergence properties and confirmed the onset of image deterioration, which is a function of the number of counts in the source. By modulating the weight given to projection tubes with high numbers of counts with respect to those with low numbers of counts in the reconstruction process, we have confirmed that image deterioration is due to an attempt by the algorithm to match projection data tubes with high numbers of counts too closely to the iterative image projections. We developed a stopping rule for the algorithm that tests the hypothesis that a reconstructed image could have given the initial projection data in a manner consistent with the underlying assumption of Poisson distributed variables. The rule was applied to two mathematically generated phantoms with success and to a third phantom with exact (no statistical fluctuations) projection data. We conclude that the behavior of the target functions whose extrema are sought in iterative schemes is more important in the early stages of the reconstruction than in the later stages, when the extrema are being approached but with the Poisson nature of the measurement. 11 refs., 14 figs
Papaconstadopoulos, P; Levesque, I R; Maglieri, R; Seuntjens, J
2016-02-07
Direct determination of the source intensity distribution of clinical linear accelerators is still a challenging problem for small field beam modeling. Current techniques most often involve special equipment and are difficult to implement in the clinic. In this work we present a maximum-likelihood expectation-maximization (MLEM) approach to the source reconstruction problem utilizing small fields and a simple experimental set-up. The MLEM algorithm iteratively ray-traces photons from the source plane to the exit plane and extracts corrections based on photon fluence profile measurements. The photon fluence profiles were determined by dose profile film measurements in air using a high density thin foil as build-up material and an appropriate point spread function (PSF). The effect of other beam parameters and scatter sources was minimized by using the smallest field size ([Formula: see text] cm(2)). The source occlusion effect was reproduced by estimating the position of the collimating jaws during this process. The method was first benchmarked against simulations for a range of typical accelerator source sizes. The sources were reconstructed with an accuracy better than 0.12 mm in the full width at half maximum (FWHM) to the respective electron sources incident on the target. The estimated jaw positions agreed within 0.2 mm with the expected values. The reconstruction technique was also tested against measurements on a Varian Novalis Tx linear accelerator and compared to a previously commissioned Monte Carlo model. The reconstructed FWHM of the source agreed within 0.03 mm and 0.11 mm to the commissioned electron source in the crossplane and inplane orientations respectively. The impact of the jaw positioning, experimental and PSF uncertainties on the reconstructed source distribution was evaluated with the former presenting the dominant effect.
Seeking parsimony in hydrology and water resources technology
Koutsoyiannis, D.
2009-04-01
systems to single numbers (a probability or an expected value), and statistics provides the empirical basis of summarizing data, making inference from them, and supporting decision making in water resource management. Unfortunately, the current state of the art in probability, statistics and their union, often called stochastics, is not fully satisfactory for the needs of modelling of hydrological and water resource systems. A first problem is that stochastic modelling has traditionally relied on classical statistics, which is based on the independent "coin-tossing" prototype, rather than on the study of real-world systems whose behaviour is very different from the classical prototype. A second problem is that the stochastic models (particularly the multivariate ones) are often not parsimonious themselves. Therefore, substantial advancement of stochastics is necessary in a new paradigm of parsimonious hydrological modelling. These ideas are illustrated using several examples, namely: (a) hydrological modelling of a karst system in Bosnia and Herzegovina using three different approaches ranging from parsimonious to detailed "physically-based"; (b) parsimonious modelling of a peculiar modified catchment in Greece; (c) a stochastic approach that can replace parameter-excessive ARMA-type models with a generalized algorithm that produces any shape of autocorrelation function (consistent with the accuracy provided by the data) using a couple of parameters; (d) a multivariate stochastic approach which replaces a huge number of parameters estimated from data with coefficients estimated by the principle of maximum entropy; and (e) a parsimonious approach for decision making in multi-reservoir systems using a handful of parameters instead of thousands of decision variables.
A framelet-based iterative maximum-likelihood reconstruction algorithm for spectral CT
Wang, Yingmei; Wang, Ge; Mao, Shuwei; Cong, Wenxiang; Ji, Zhilong; Cai, Jian-Feng; Ye, Yangbo
2016-11-01
Standard computed tomography (CT) cannot reproduce spectral information of an object. Hardware solutions include dual-energy CT which scans the object twice in different x-ray energy levels, and energy-discriminative detectors which can separate lower and higher energy levels from a single x-ray scan. In this paper, we propose a software solution and give an iterative algorithm that reconstructs an image with spectral information from just one scan with a standard energy-integrating detector. The spectral information obtained can be used to produce color CT images, spectral curves of the attenuation coefficient μ (r,E) at points inside the object, and photoelectric images, which are all valuable imaging tools in cancerous diagnosis. Our software solution requires no change on hardware of a CT machine. With the Shepp-Logan phantom, we have found that although the photoelectric and Compton components were not perfectly reconstructed, their composite effect was very accurately reconstructed as compared to the ground truth and the dual-energy CT counterpart. This means that our proposed method has an intrinsic benefit in beam hardening correction and metal artifact reduction. The algorithm is based on a nonlinear polychromatic acquisition model for x-ray CT. The key technique is a sparse representation of iterations in a framelet system. Convergence of the algorithm is studied. This is believed to be the first application of framelet imaging tools to a nonlinear inverse problem.
Wang, Qi; Wang, Huaxiang; Cui, Ziqiang; Yang, Chengyi
2012-11-01
Electrical impedance tomography (EIT) calculates the internal conductivity distribution within a body using electrical contact measurements. The image reconstruction for EIT is an inverse problem, which is both non-linear and ill-posed. The traditional regularization method cannot avoid introducing negative values in the solution. The negativity of the solution produces artifacts in reconstructed images in presence of noise. A statistical method, namely, the expectation maximization (EM) method, is used to solve the inverse problem for EIT in this paper. The mathematical model of EIT is transformed to the non-negatively constrained likelihood minimization problem. The solution is obtained by the gradient projection-reduced Newton (GPRN) iteration method. This paper also discusses the strategies of choosing parameters. Simulation and experimental results indicate that the reconstructed images with higher quality can be obtained by the EM method, compared with the traditional Tikhonov and conjugate gradient (CG) methods, even with non-negative processing. Copyright © 2012 ISA. Published by Elsevier Ltd. All rights reserved.
International Nuclear Information System (INIS)
Llacer, J.; Veklerov, E.; Nolan, D.; Grafton, S.T.; Mazziotta, J.C.; Hawkins, R.A.; Hoh, C.K.; Hoffman, E.J.
1990-10-01
This paper will report on the progress to date in carrying out Receiver Operating Characteristics (ROC) studies comparing Maximum Likelihood Estimator (MLE) and Filtered Backprojection (FBP) reconstructions of normal and abnormal human brain PET data in a clinical setting. A previous statistical study of reconstructions of the Hoffman brain phantom with real data indicated that the pixel-to-pixel standard deviation in feasible MLE images is approximately proportional to the square root of the number of counts in a region, as opposed to a standard deviation which is high and largely independent of the number of counts in FBP. A preliminary ROC study carried out with 10 non-medical observers performing a relatively simple detectability task indicates that, for the majority of observers, lower standard deviation translates itself into a statistically significant detectability advantage in MLE reconstructions. The initial results of ongoing tests with four experienced neurologists/nuclear medicine physicians are presented. Normal cases of 18 F -- fluorodeoxyglucose (FDG) cerebral metabolism studies and abnormal cases in which a variety of lesions have been introduced into normal data sets have been evaluated. We report on the results of reading the reconstructions of 90 data sets, each corresponding to a single brain slice. It has become apparent that the design of the study based on reading single brain slices is too insensitive and we propose a variation based on reading three consecutive slices at a time, rating only the center slice. 9 refs., 2 figs., 1 tab
O'Reilly, Joseph E; Puttick, Mark N; Parry, Luke; Tanner, Alastair R; Tarver, James E; Fleming, James; Pisani, Davide; Donoghue, Philip C J
2016-04-01
Different analytical methods can yield competing interpretations of evolutionary history and, currently, there is no definitive method for phylogenetic reconstruction using morphological data. Parsimony has been the primary method for analysing morphological data, but there has been a resurgence of interest in the likelihood-based Mk-model. Here, we test the performance of the Bayesian implementation of the Mk-model relative to both equal and implied-weight implementations of parsimony. Using simulated morphological data, we demonstrate that the Mk-model outperforms equal-weights parsimony in terms of topological accuracy, and implied-weights performs the most poorly. However, the Mk-model produces phylogenies that have less resolution than parsimony methods. This difference in the accuracy and precision of parsimony and Bayesian approaches to topology estimation needs to be considered when selecting a method for phylogeny reconstruction. © 2016 The Authors.
REGEN: Ancestral Genome Reconstruction for Bacteria
Directory of Open Access Journals (Sweden)
João C. Setubal
2012-07-01
Full Text Available Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each branch of the phylogenetic tree, REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related, which will usually be the case for bacteria within the same taxonomic order. We evaluated REGEN using simulated genomes and genomes in the Rhizobiales order.
REGEN: Ancestral Genome Reconstruction for Bacteria.
Yang, Kuan; Heath, Lenwood S; Setubal, João C
2012-07-18
Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each branch of the phylogenetic tree, REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related, which will usually be the case for bacteria within the same taxonomic order. We evaluated REGEN using simulated genomes and genomes in the Rhizobiales order.
International Nuclear Information System (INIS)
Davis, Sergio
2013-01-01
In this work we develop a method for inferring the underlying configurational density of states of a molecular system by combining information from several microcanonical molecular dynamics or Monte Carlo simulations at different energies. This method is based on Jaynes' Maximum Entropy formalism (MaxEnt) for Bayesian statistical inference under known expectation values. We present results of its application to measure thermodynamic entropy and free energy differences in embedded-atom models of metals.
Maximum likelihood reconstruction in fully 3D PET via the SAGE algorithm
International Nuclear Information System (INIS)
Ollinger, J.M.; Goggin, A.S.
1996-01-01
The SAGE and ordered subsets algorithms have been proposed as fast methods to compute penalized maximum likelihood estimates in PET. We have implemented both for use in fully 3D PET and completed a preliminary evaluation. The technique used to compute the transition matrix is fully described. The evaluation suggests that the ordered subsets algorithm converges much faster than SAGE, but that it stops short of the optimal solution
Maximum likelihood reconstruction for pinhole SPECT with a displaced center-of-rotation
International Nuclear Information System (INIS)
Li, J.; Jaszczak, R.J.; Coleman, R.E.
1995-01-01
In this paper, the authors describe the implementation of a maximum likelihood (ML), algorithm using expectation maximization (EM) for pin-hole SPECT with a displaced center-of-rotation. A ray-tracing technique is used in implementing the ML-EM algorithm. The proposed ML-EM algorithm is able to correct the center of rotation displacement which can be characterized by two orthogonal components. The algorithm is tested using experimentally acquired data, and the results demonstrate that the pinhole ML-EM algorithm is able to correct artifacts associated with the center-of-rotation displacement
Polk, J.; van Beynen, P.; DeLong, K. L.; Asmerom, Y.; Polyak, V. J.
2017-12-01
Teleconnections between the tropical-subtropical regions of the Americas since the Last Glacial Maximum (LGM), particularly the Mid- to Late-Holocene, and high-resolution proxy records refining climate variability over this period continue to receive increasing attention. Here, we present a high-resolution, precisely dated speleothem record spanning multiple periods of time since the LGM ( 30 ka) for the Florida peninsula. The data indicate that the amount effect plays a significant role in determining the isotopic signal of the speleothem calcite. Collectively, the records indicate distinct differences in climate in the region between the LGM, Mid-Holocene, and Late Holocene, including a progressive shift in ocean composition and precipitation isotopic values through the period, suggesting Florida's sensitivity to regional and global climatic shifts. Comparisons between speleothem δ18O values and Gulf of Mexico marine records reveal a strong connection between the Gulf region and the terrestrial subtropical climate in the Late Holocene, while the North Atlantic's influence is clear in the earlier portions of the record. Warmer sea surface temperatures correspond to enhanced evaporation, leading to more intense atmospheric convection in Florida, and thereby modulating the isotopic composition of rainfall above the cave. These regional signals in climate extend from the subtropics to the tropics, with a clear covariance between the speleothem signal and other proxy records from around the region, as well as global agreement during the LGM period with other records. These latter connections appear to be driven by changes in the mean position of the Intertropical Convergence Zone and time series analysis of the δ18O values reveals significant multidecadal periodicities in the record, which are evidenced by agreement with the AMV and other multidecadal influences (NAO and PDO) likely having varying influence throughout the period of record. The climate variability
L.U.St: a tool for approximated maximum likelihood supertree reconstruction.
Akanni, Wasiu A; Creevey, Christopher J; Wilkinson, Mark; Pisani, Davide
2014-06-12
Supertrees combine disparate, partially overlapping trees to generate a synthesis that provides a high level perspective that cannot be attained from the inspection of individual phylogenies. Supertrees can be seen as meta-analytical tools that can be used to make inferences based on results of previous scientific studies. Their meta-analytical application has increased in popularity since it was realised that the power of statistical tests for the study of evolutionary trends critically depends on the use of taxon-dense phylogenies. Further to that, supertrees have found applications in phylogenomics where they are used to combine gene trees and recover species phylogenies based on genome-scale data sets. Here, we present the L.U.St package, a python tool for approximate maximum likelihood supertree inference and illustrate its application using a genomic data set for the placental mammals. L.U.St allows the calculation of the approximate likelihood of a supertree, given a set of input trees, performs heuristic searches to look for the supertree of highest likelihood, and performs statistical tests of two or more supertrees. To this end, L.U.St implements a winning sites test allowing ranking of a collection of a-priori selected hypotheses, given as a collection of input supertree topologies. It also outputs a file of input-tree-wise likelihood scores that can be used as input to CONSEL for calculation of standard tests of two trees (e.g. Kishino-Hasegawa, Shimidoara-Hasegawa and Approximately Unbiased tests). This is the first fully parametric implementation of a supertree method, it has clearly understood properties, and provides several advantages over currently available supertree approaches. It is easy to implement and works on any platform that has python installed. bitBucket page - https://afro-juju@bitbucket.org/afro-juju/l.u.st.git. Davide.Pisani@bristol.ac.uk.
Parsimonious Wavelet Kernel Extreme Learning Machine
Directory of Open Access Journals (Sweden)
Wang Qin
2015-11-01
Full Text Available In this study, a parsimonious scheme for wavelet kernel extreme learning machine (named PWKELM was introduced by combining wavelet theory and a parsimonious algorithm into kernel extreme learning machine (KELM. In the wavelet analysis, bases that were localized in time and frequency to represent various signals effectively were used. Wavelet kernel extreme learning machine (WELM maximized its capability to capture the essential features in “frequency-rich” signals. The proposed parsimonious algorithm also incorporated significant wavelet kernel functions via iteration in virtue of Householder matrix, thus producing a sparse solution that eased the computational burden and improved numerical stability. The experimental results achieved from the synthetic dataset and a gas furnace instance demonstrated that the proposed PWKELM is efficient and feasible in terms of improving generalization accuracy and real time performance.
Méthodes avancées pour la résolution du problème de maximum parcimonie
Vazquez Ortiz , Karla Esmeralda
2016-01-01
Phylogenetic reconstruction is considered a central underpinning of diverse fields like ecology, molecular biology and physiology where genealogical relationships of species or gene sequences represented as trees can provide the most meaningful insights into biology. Maximum Parsimony (MP) is an important approach to solve the phylogenetic reconstruction based on an optimality criterion under which the tree that minimizes the total number of genetic transformations is preferred. In this thesi...
Tremblay, Marissa; Spagnolo, Matteo; Ribolini, Adriano; Shuster, David
2016-04-01
The Gesso Valley, located in the southwestern-most, Maritime portion of the European Alps, contains an exceptionally well-preserved record of glacial advances during the late Pleistocene and Holocene. Detailed geomorphic mapping, geochronology of glacial deposits, and glacier reconstructions indicate that glaciers in this Mediterranean region responded to millennial scale climate variability differently than glaciers in the interior of the European Alps. This suggests that the Mediterranean Sea somehow modulated the climate of this region. However, since glaciers respond to changes in temperature and precipitation, both variables were potentially influenced by proximity to the Sea. To disentangle the competing effects of temperature and precipitation changes on glacier size, we are constraining past temperature variations in the Gesso Valley since the Last Glacial Maximum (LGM) using cosmogenic noble gas paleothermometry. The cosmogenic noble gases 3He and 21Ne experience diffusive loss from common minerals like quartz and feldspars at Earth surface temperatures. Cosmogenic noble gas paleothermometry utilizes this open-system behavior to quantitatively constrain thermal histories of rocks during exposure to cosmic ray particles at the Earth's surface. We will present measurements of cosmogenic 3He in quartz sampled from moraines in the Gesso Valley with LGM, Bühl stadial, and Younger Dryas ages. With these 3He measurements and experimental data quantifying the diffusion kinetics of 3He in quartz, we will provide a preliminary temperature reconstruction for the Gesso Valley since the LGM. Future work on samples from younger moraines in the valley system will be used to fill in details of the more recent temperature history.
International Nuclear Information System (INIS)
Veklerov, E.; Llacer, J.; Hoffman, E.J.
1987-10-01
In order to study properties of the Maximum Likelihood Estimator (MLE) algorithm for image reconstruction in Positron Emission Tomographyy (PET), the algorithm is applied to data obtained by the ECAT-III tomograph from a brain phantom. The procedure for subtracting accidental coincidences from the data stream generated by this physical phantom is such that he resultant data are not Poisson distributed. This makes the present investigation different from other investigations based on computer-simulated phantoms. It is shown that the MLE algorithm is robust enough to yield comparatively good images, especially when the phantom is in the periphery of the field of view, even though the underlying assumption of the algorithm is violated. Two transition matrices are utilized. The first uses geometric considerations only. The second is derived by a Monte Carlo simulation which takes into account Compton scattering in the detectors, positron range, etc. in the detectors. It is demonstrated that the images obtained from the Monte Carlo matrix are superior in some specific ways. A stopping rule derived earlier and allowing the user to stop the iterative process before the images begin to deteriorate is tested. Since the rule is based on the Poisson assumption, it does not work well with the presently available data, although it is successful wit computer-simulated Poisson data
A large version of the small parsimony problem
DEFF Research Database (Denmark)
Fredslund, Jakob; Hein, Jotun; Scharling, Tejs
2003-01-01
the most parsimonious assignment of nucleotides. The gaps of the alignment are represented in a so-called gap graph, and through theoretically sound preprocessing the graph is reduced to pave the way for a running time which in all but the most pathological examples is far better than the exponential worst......Given a multiple alignment over $k$ sequences, an evolutionary tree relating the sequences, and a subadditive gap penalty function (e.g. an affine function), we reconstruct the internal nodes of the tree optimally: we find the optimal explanation in terms of indels of the observed gaps and find...... case time. E.g. for a tree with nine leaves and a random alignment of length 10.000 with 60% gaps, the running time is on average around 45 seconds. For a real alignment of length 9868 of nine HIV-1 sequences, the running time is less than one second....
Reconstruction of ancestral RNA sequences under multiple structural constraints
Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldisp?hl, J?r?me
2016-01-01
Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given...
Li, Mingqi; Huang, Lei; Yin, Zhi-Yong; Shao, Xuemei
2017-11-01
This study presents a 304-year mean July-October maximum temperature reconstruction for the southeastern Tibetan Plateau based on both tree-ring width and maximum latewood density data. The reconstruction explained 58% of the variance in July-October maximum temperature during the calibration period (1958-2005). On the decadal scale, we identified two prominent cold periods during AD 1801-1833 and 1961-2003 and two prominent warm periods during AD 1730-1800 and 1928-1960, which are consistent with other reconstructions from the nearby region. Based on the reconstructed temperature series and volcanic eruption chronology, we found that most extreme cold years were in good agreement with major volcanic eruptions, such as 1816 after the Tambora eruption in 1815. Also, clusters of volcanic eruptions probably made the 1810s the coldest decade in the past 300 years. Our results indicated that fingerprints of major volcanic eruptions can be found in the reconstructed temperature records, while the responses of regional climate to these eruption events varied in space and time in the southeastern Tibetan Plateau.
Lin, Yu; Hu, Fei; Tang, Jijun; Moret, Bernard M E
2013-01-01
The rapid accumulation of whole-genome data has renewed interest in the study of the evolution of genomic architecture, under such events as rearrangements, duplications, losses. Comparative genomics, evolutionary biology, and cancer research all require tools to elucidate the mechanisms, history, and consequences of those evolutionary events, while phylogenetics could use whole-genome data to enhance its picture of the Tree of Life. Current approaches in the area of phylogenetic analysis are limited to very small collections of closely related genomes using low-resolution data (typically a few hundred syntenic blocks); moreover, these approaches typically do not include duplication and loss events. We describe a maximum likelihood (ML) approach for phylogenetic analysis that takes into account genome rearrangements as well as duplications, insertions, and losses. Our approach can handle high-resolution genomes (with 40,000 or more markers) and can use in the same analysis genomes with very different numbers of markers. Because our approach uses a standard ML reconstruction program (RAxML), it scales up to large trees. We present the results of extensive testing on both simulated and real data showing that our approach returns very accurate results very quickly. In particular, we analyze a dataset of 68 high-resolution eukaryotic genomes, with from 3,000 to 42,000 genes, from the eGOB database; the analysis, including bootstrapping, takes just 3 hours on a desktop system and returns a tree in agreement with all well supported branches, while also suggesting resolutions for some disputed placements.
Principle of Parsimony, Fake Science, and Scales
Yeh, T. C. J.; Wan, L.; Wang, X. S.
2017-12-01
Considering difficulties in predicting exact motions of water molecules, and the scale of our interests (bulk behaviors of many molecules), Fick's law (diffusion concept) has been created to predict solute diffusion process in space and time. G.I. Taylor (1921) demonstrated that random motion of the molecules reach the Fickian regime in less a second if our sampling scale is large enough to reach ergodic condition. Fick's law is widely accepted for describing molecular diffusion as such. This fits the definition of the parsimony principle at the scale of our concern. Similarly, advection-dispersion or convection-dispersion equation (ADE or CDE) has been found quite satisfactory for analysis of concentration breakthroughs of solute transport in uniformly packed soil columns. This is attributed to the solute is often released over the entire cross-section of the column, which has sampled many pore-scale heterogeneities and met the ergodicity assumption. Further, the uniformly packed column contains a large number of stationary pore-size heterogeneity. The solute thus reaches the Fickian regime after traveling a short distance along the column. Moreover, breakthrough curves are concentrations integrated over the column cross-section (the scale of our interest), and they meet the ergodicity assumption embedded in the ADE and CDE. To the contrary, scales of heterogeneity in most groundwater pollution problems evolve as contaminants travel. They are much larger than the scale of our observations and our interests so that the ergodic and the Fickian conditions are difficult. Upscaling the Fick's law for solution dispersion, and deriving universal rules of the dispersion to the field- or basin-scale pollution migrations are merely misuse of the parsimony principle and lead to a fake science ( i.e., the development of theories for predicting processes that can not be observed.) The appropriate principle of parsimony for these situations dictates mapping of large
Bashalkhanov, S I; Konstantinov, Iu M; Verbitskiĭ, D S; Kobzev, V F
2003-10-01
To reconstruct the systematic relationships of larch Larix sukaczewii, we used the chloroplast trnK intron sequences of L. decidua, L. sukaczewii, L. sibirica, L. czekanovskii, and L. gmelinii. Analysis of phylogenetic trees constructed using the maximum parsimony and maximum likelihood methods showed a clear divergence of the trnK intron sequences between L. sukaczewii and L. sibirica. This divergence reaches intraspecific level, which supports a previously published hypothesis on the taxonomic isolation of L. sukaczewii.
Directory of Open Access Journals (Sweden)
Yunfeng Shan
2008-01-01
Full Text Available Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced as well as plants that have the fossil-supported true phylogenetic trees available. In this study, we generated single gene trees of seven yeast species as well as single gene trees of nine baculovirus species using all the orthologous genes among the species compared. Homologous genes among seven known plants were used for validation of the ﬁnding. Four algorithms—maximum parsimony (MP, minimum evolution (ME, maximum likelihood (ML, and neighbor-joining (NJ—were used. Trees were reconstructed before and after weighting the DNA and protein sequence lengths among genes. Rarely a gene can always generate the “true tree” by all the four algorithms. However, the most frequent gene tree, termed “maximum gene-support tree” (MGS tree, or WMGS tree for the weighted one, in yeasts, baculoviruses, or plants was consistently found to be the “true tree” among the species. The results provide insights into the overall degree of divergence of orthologous genes of the genomes analyzed and suggest the following: 1 The true tree relationship among the species studied is still maintained by the largest group of orthologous genes; 2 There are usually more orthologous genes with higher similarities between genetically closer species than between genetically more distant ones; and 3 The maximum gene-support tree reﬂects the phylogenetic relationship among species in comparison.
Cases in which ancestral maximum likelihood will be confusingly misleading.
Handelman, Tomer; Chor, Benny
2017-05-07
Ancestral maximum likelihood (AML) is a phylogenetic tree reconstruction criteria that "lies between" maximum parsimony (MP) and maximum likelihood (ML). ML has long been known to be statistically consistent. On the other hand, Felsenstein (1978) showed that MP is statistically inconsistent, and even positively misleading: There are cases where the parsimony criteria, applied to data generated according to one tree topology, will be optimized on a different tree topology. The question of weather AML is statistically consistent or not has been open for a long time. Mossel et al. (2009) have shown that AML can "shrink" short tree edges, resulting in a star tree with no internal resolution, which yields a better AML score than the original (resolved) model. This result implies that AML is statistically inconsistent, but not that it is positively misleading, because the star tree is compatible with any other topology. We show that AML is confusingly misleading: For some simple, four taxa (resolved) tree, the ancestral likelihood optimization criteria is maximized on an incorrect (resolved) tree topology, as well as on a star tree (both with specific edge lengths), while the tree with the original, correct topology, has strictly lower ancestral likelihood. Interestingly, the two short edges in the incorrect, resolved tree topology are of length zero, and are not adjacent, so this resolved tree is in fact a simple path. While for MP, the underlying phenomenon can be described as long edge attraction, it turns out that here we have long edge repulsion. Copyright © 2017. Published by Elsevier Ltd.
International Nuclear Information System (INIS)
Chen, Z.Q.; Wang, S.J.
1999-01-01
A newly developed maximum entropy method, which was realized by the computer program MELT introduced by Shukla et al., was used to analyze positron lifetime spectra measured in semiconductors. Several simulation studies were done to test the performance of this algorithm. Reliable reconstruction of positron lifetime distributions can be extracted at relatively lower counts, which shows the applicability and superiority of this method. Two positron lifetime spectra measured in ion-implanted p-InP(Zn) at 140 and 280 K, respectively were analyzed by this program. The lifetime distribution differed greatly for the two temperatures, giving direct evidence of the existence of shallow positron traps at low temperature
Parsimonious Ways to Use Vision for Navigation
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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
DEFF Research Database (Denmark)
Bisgaard, Søren; Kulahci, Murat
2009-01-01
Some of the issues involved in selecting adequate models for time series data are discussed using an example concerning the number of users of an Internet server. The process of selecting an appropriate model is subjective and requires experience and judgment. The authors believe an important...... consideration in model selection should be parameter parsimony. They favor the use of parsimonious mixed ARMA models, noting that research has shown that a model building strategy that considers only autoregressive representations will lead to non-parsimonious models and to loss of forecasting accuracy....
A comparison of ancestral state reconstruction methods for quantitative characters.
Royer-Carenzi, Manuela; Didier, Gilles
2016-09-07
Choosing an ancestral state reconstruction method among the alternatives available for quantitative characters may be puzzling. We present here a comparison of seven of them, namely the maximum likelihood, restricted maximum likelihood, generalized least squares under Brownian, Brownian-with-trend and Ornstein-Uhlenbeck models, phylogenetic independent contrasts and squared parsimony methods. A review of the relations between these methods shows that the maximum likelihood, the restricted maximum likelihood and the generalized least squares under Brownian model infer the same ancestral states and can only be distinguished by the distributions accounting for the reconstruction uncertainty which they provide. The respective accuracy of the methods is assessed over character evolution simulated under a Brownian motion with (and without) directional or stabilizing selection. We give the general form of ancestral state distributions conditioned on leaf states under the simulation models. Ancestral distributions are used first, to give a theoretical lower bound of the expected reconstruction error, and second, to develop an original evaluation scheme which is more efficient than comparing the reconstructed and the simulated states. Our simulations show that: (i) the distributions of the reconstruction uncertainty provided by the methods generally make sense (some more than others); (ii) it is essential to detect the presence of an evolutionary trend and to choose a reconstruction method accordingly; (iii) all the methods show good performances on characters under stabilizing selection; (iv) without trend or stabilizing selection, the maximum likelihood method is generally the most accurate. Copyright © 2016 Elsevier Ltd. All rights reserved.
Krishnan, Neeraja M; Seligmann, Hervé; Stewart, Caro-Beth; De Koning, A P Jason; Pollock, David D
2004-10-01
Reconstruction of ancestral DNA and amino acid sequences is an important means of inferring information about past evolutionary events. Such reconstructions suggest changes in molecular function and evolutionary processes over the course of evolution and are used to infer adaptation and convergence. Maximum likelihood (ML) is generally thought to provide relatively accurate reconstructed sequences compared to parsimony, but both methods lead to the inference of multiple directional changes in nucleotide frequencies in primate mitochondrial DNA (mtDNA). To better understand this surprising result, as well as to better understand how parsimony and ML differ, we constructed a series of computationally simple "conditional pathway" methods that differed in the number of substitutions allowed per site along each branch, and we also evaluated the entire Bayesian posterior frequency distribution of reconstructed ancestral states. We analyzed primate mitochondrial cytochrome b (Cyt-b) and cytochrome oxidase subunit I (COI) genes and found that ML reconstructs ancestral frequencies that are often more different from tip sequences than are parsimony reconstructions. In contrast, frequency reconstructions based on the posterior ensemble more closely resemble extant nucleotide frequencies. Simulations indicate that these differences in ancestral sequence inference are probably due to deterministic bias caused by high uncertainty in the optimization-based ancestral reconstruction methods (parsimony, ML, Bayesian maximum a posteriori). In contrast, ancestral nucleotide frequencies based on an average of the Bayesian set of credible ancestral sequences are much less biased. The methods involving simpler conditional pathway calculations have slightly reduced likelihood values compared to full likelihood calculations, but they can provide fairly unbiased nucleotide reconstructions and may be useful in more complex phylogenetic analyses than considered here due to their speed and
A simplified parsimonious higher order multivariate Markov chain model
Wang, Chao; Yang, Chuan-sheng
2017-09-01
In this paper, a simplified parsimonious higher-order multivariate Markov chain model (SPHOMMCM) is presented. Moreover, parameter estimation method of TPHOMMCM is give. Numerical experiments shows the effectiveness of TPHOMMCM.
A tridiagonal parsimonious higher order multivariate Markov chain model
Wang, Chao; Yang, Chuan-sheng
2017-09-01
In this paper, we present a tridiagonal parsimonious higher-order multivariate Markov chain model (TPHOMMCM). Moreover, estimation method of the parameters in TPHOMMCM is give. Numerical experiments illustrate the effectiveness of TPHOMMCM.
Choosing the best ancestral character state reconstruction method.
Royer-Carenzi, Manuela; Pontarotti, Pierre; Didier, Gilles
2013-03-01
Despite its intrinsic difficulty, ancestral character state reconstruction is an essential tool for testing evolutionary hypothesis. Two major classes of approaches to this question can be distinguished: parsimony- or likelihood-based approaches. We focus here on the second class of methods, more specifically on approaches based on continuous-time Markov modeling of character evolution. Among them, we consider the most-likely-ancestor reconstruction, the posterior-probability reconstruction, the likelihood-ratio method, and the Bayesian approach. We discuss and compare the above-mentioned methods over several phylogenetic trees, adding the maximum-parsimony method performance in the comparison. Under the assumption that the character evolves according a continuous-time Markov process, we compute and compare the expectations of success of each method for a broad range of model parameter values. Moreover, we show how the knowledge of the evolution model parameters allows to compute upper bounds of reconstruction performances, which are provided as references. The results of all these reconstruction methods are quite close one to another, and the expectations of success are not so far from their theoretical upper bounds. But the performance ranking heavily depends on the topology of the studied tree, on the ancestral node that is to be inferred and on the parameter values. Consequently, we propose a protocol providing for each parameter value the best method in terms of expectation of success, with regard to the phylogenetic tree and the ancestral node to infer. Copyright © 2012 Elsevier Inc. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Otto-Bliesner, Bette L.; Brady, E.C. [National Center for Atmospheric Research, Climate and Global Dynamics Division, Boulder, CO (United States); Schneider, Ralph; Weinelt, M. [Christian-Albrechts Universitaet, Institut fuer Geowissenschaften, Kiel (Germany); Kucera, M. [Eberhard-Karls Universitaet Tuebingen, Institut fuer Geowissenschaften, Tuebingen (Germany); Abe-Ouchi, A. [The University of Tokyo, Center for Climate System Research, Kashiwa (Japan); Bard, E. [CEREGE, College de France, CNRS, Universite Aix-Marseille, Aix-en-Provence (France); Braconnot, P.; Kageyama, M.; Marti, O.; Waelbroeck, C. [Unite mixte CEA-CNRS-UVSQ, Laboratoire des Sciences du Climat et de l' Environnement, Gif-sur-Yvette Cedex (France); Crucifix, M. [Universite Catholique de Louvain, Institut d' Astronomie et de Geophysique Georges Lemaitre, Louvain-la-Neuve (Belgium); Hewitt, C.D. [Met Office Hadley Centre, Exeter (United Kingdom); Paul, A. [Bremen University, Department of Geosciences, Bremen (Germany); Rosell-Mele, A. [Universitat Autonoma de Barcelona, ICREA and Institut de Ciencia i Tecnologia Ambientals, Barcelona (Spain); Weber, S.L. [Royal Netherlands Meteorological Institute (KNMI), De Bilt (Netherlands); Yu, Y. [Chinese Academy of Sciences, LASG, Institute of Atmospheric Physics, Beijing (China)
2009-05-15
Results from multiple model simulations are used to understand the tropical sea surface temperature (SST) response to the reduced greenhouse gas concentrations and large continental ice sheets of the last glacial maximum (LGM). We present LGM simulations from the Paleoclimate Modelling Intercomparison Project, Phase 2 (PMIP2) and compare these simulations to proxy data collated and harmonized within the Multiproxy Approach for the Reconstruction of the Glacial Ocean Surface Project (MARGO). Five atmosphere-ocean coupled climate models (AOGCMs) and one coupled model of intermediate complexity have PMIP2 ocean results available for LGM. The models give a range of tropical (defined for this paper as 15 S-15 N) SST cooling of 1.0-2.4 C, comparable to the MARGO estimate of annual cooling of 1.7{+-}1 C. The models simulate greater SST cooling in the tropical Atlantic than tropical Pacific, but interbasin and intrabasin variations of cooling are much smaller than those found in the MARGO reconstruction. The simulated tropical coolings are relatively insensitive to season, a feature also present in the MARGO transferred-based estimates calculated from planktonic foraminiferal assemblages for the Indian and Pacific Oceans. These assemblages indicate seasonality in cooling in the Atlantic basin, with greater cooling in northern summer than northern winter, not captured by the model simulations. Biases in the simulations of the tropical upwelling and thermocline found in the preindustrial control simulations remain for the LGM simulations and are partly responsible for the more homogeneous spatial and temporal LGM tropical cooling simulated by the models. The PMIP2 LGM simulations give estimates for the climate sensitivity parameter of 0.67 -0.83 C per Wm{sup -2}, which translates to equilibrium climate sensitivity for doubling of atmospheric CO{sub 2} of 2.6-3.1 C. (orig.)
Ruiz Fernández, Jesús; Oliva, Marc; Fernández Menéndez, Susana del Carmen; García Hernández, Cristina; Menéndez Duarte, Rosa Ana; Pellitero Ondicol, Ramón; Pérez Alberti, Augusto; Schimmelpfennig, Irene
2017-04-01
CRONOANTAR brings together researchers from Spain, Portugal, France and United Kingdom with the objective of spatially and temporally reconstruct the deglaciation process at the two largest islands in the South Shetlands Archipelago (Maritime Antarctica), since the Global Last Glacial Maximum. Glacier retreat in polar areas has major implications at a local, regional and even planetary scale. Global average sea level rise is the most obvious and socio-economically relevant, but there are others such as the arrival of new fauna to deglaciated areas, plant colonisation or permafrost formation and degradation. This project will study the ice-free areas in Byers and Hurd peninsulas (Livingston Island) and Fildes and Potter peninsulas (King George Island). Ice-cap glacier retreat chronology will be revealed by the use of cosmogenic isotopes (mainly 36Cl) on glacially originated sedimentary and erosive records. Cosmogenic dating will be complemented by other dating methods (C14 and OSL), which will permit the validation of these methods in regions with cold-based glaciers. Given the geomorphological evidences and the obtained ages, a deglaciation calendar will be proposed and we will use a GIS methodology to reconstruct the glacier extent and the ice thickness. The results emerging from this project will allow to assess whether the high glacier retreat rates observed during the last decades were registered in the past, or if they are conversely the consequence (and evidence) of the Global Change in Antarctica. Acknowledgements This work has been funded by the Spanish Ministry of Economy, Industry and Competitiveness (Reference: CTM2016-77878-P).
Parsimonious Charge Deconvolution for Native Mass Spectrometry
2018-01-01
Charge deconvolution infers the mass from mass over charge (m/z) measurements in electrospray ionization mass spectra. When applied over a wide input m/z or broad target mass range, charge-deconvolution algorithms can produce artifacts, such as false masses at one-half or one-third of the correct mass. Indeed, a maximum entropy term in the objective function of MaxEnt, the most commonly used charge deconvolution algorithm, favors a deconvolved spectrum with many peaks over one with fewer peaks. Here we describe a new “parsimonious” charge deconvolution algorithm that produces fewer artifacts. The algorithm is especially well-suited to high-resolution native mass spectrometry of intact glycoproteins and protein complexes. Deconvolution of native mass spectra poses special challenges due to salt and small molecule adducts, multimers, wide mass ranges, and fewer and lower charge states. We demonstrate the performance of the new deconvolution algorithm on a range of samples. On the heavily glycosylated plasma properdin glycoprotein, the new algorithm could deconvolve monomer and dimer simultaneously and, when focused on the m/z range of the monomer, gave accurate and interpretable masses for glycoforms that had previously been analyzed manually using m/z peaks rather than deconvolved masses. On therapeutic antibodies, the new algorithm facilitated the analysis of extensions, truncations, and Fab glycosylation. The algorithm facilitates the use of native mass spectrometry for the qualitative and quantitative analysis of protein and protein assemblies. PMID:29376659
Barclay, R. S.; Wing, S. L.
2013-12-01
The Paleocene-Eocene Thermal Maximum (PETM) was a geologically brief interval of intense global warming 56 million years ago. It is arguably the best geological analog for a worst-case scenario of anthropogenic carbon emissions. The PETM is marked by a ~4-6‰ negative carbon isotope excursion (CIE) and extensive marine carbonate dissolution, which together are powerful evidence for a massive addition of carbon to the oceans and atmosphere. In spite of broad agreement that the PETM reflects a large carbon cycle perturbation, atmospheric concentrations of CO2 (pCO2) during the event are not well constrained. The goal of this study is to produce a high resolution reconstruction of pCO2 using stomatal frequency proxies (both stomatal index and stomatal density) before, during, and after the PETM. These proxies rely upon a genetically controlled mechanism whereby plants decrease the proportion of gas-exchange pores (stomata) in response to increased pCO2. Terrestrial sections in the Bighorn Basin, Wyoming, contain macrofossil plants with cuticle immediately bracketing the PETM, as well as dispersed plant cuticle from within the body of the CIE. These fossils allow for the first stomatal-based reconstruction of pCO2 near the Paleocene-Eocene boundary; we also use them to determine the relative timing of pCO2 change in relation to the CIE that defines the PETM. Preliminary results come from macrofossil specimens of Ginkgo adiantoides, collected from an ~200ka interval prior to the onset of the CIE (~230-30ka before), and just after the 'recovery interval' of the CIE. Stomatal index values decreased by 37% within an ~70ka time interval at least 100ka prior to the onset of the CIE. The decrease in stomatal index is interpreted as a significant increase in pCO2, and has a magnitude equivalent to the entire range of stomatal index adjustment observed in modern Ginkgo biloba during the anthropogenic CO2 rise during the last 150 years. The inferred CO2 increase prior to the
Reconstruction of ancestral RNA sequences under multiple structural constraints
Directory of Open Access Journals (Sweden)
Olivier Tremblay-Savard
2016-11-01
Full Text Available Abstract Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. Results We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Conclusions Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .
Reconstruction of ancestral RNA sequences under multiple structural constraints.
Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldispühl, Jérôme
2016-11-11
Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .
Live phylogeny with polytomies: Finding the most compact parsimonious trees.
Papamichail, D; Huang, A; Kennedy, E; Ott, J-L; Miller, A; Papamichail, G
2017-08-01
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral evolution and transmission, paleontology, linguistics, and phylogenetic stemmatics, often require phylogeny inference that involves placing input species on ancestral tree nodes (live phylogeny), and polytomies. These requirements, despite their prevalence, lead to computationally harder algorithmic solutions and have been sparsely examined in the literature to date. In this article we prove some unique properties of most parsimonious live phylogenetic trees with polytomies, and their mapping to traditional binary phylogenetic trees. We show that our problem reduces to finding the most compact parsimonious tree for n species, and describe a novel efficient algorithm to find such trees without resorting to exhaustive enumeration of all possible tree topologies. Copyright © 2017 Elsevier Ltd. All rights reserved.
McCann, Jamie; Schneeweiss, Gerald M; Stuessy, Tod F; Villaseñor, Jose L; Weiss-Schneeweiss, Hanna
2016-01-01
Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction.
Directory of Open Access Journals (Sweden)
Jamie McCann
Full Text Available Chromosome number change (polyploidy and dysploidy plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods, branch length model (phylograms versus chronograms and phylogenetic uncertainty (topological and branch length uncertainty on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively with no prevailing direction.
Energy Technology Data Exchange (ETDEWEB)
Wu, Haibin [Chinese Academy of Sciences, SKLLQ, Institute of Earth Environment, Xi' an (China); CEREGE, UMR 6635, CNRS/Universite Paul Cezanne, CEREGE BP 80, Europole Mediterraneen de l' Arbois, Aix-en-Provence Cedex 4 (France); Guiot, Joel; Brewer, Simon [CEREGE, UMR 6635, CNRS/Universite Paul Cezanne, CEREGE BP 80, Europole Mediterraneen de l' Arbois, Aix-en-Provence Cedex 4 (France); Guo, Zhengtang [Chinese Academy of Sciences, SKLLQ, Institute of Earth Environment, Xi' an (China); Chinese Academy of Sciences, Institute of Geology and Geophysics, P.O. Box 9825, Beijing (China)
2007-08-15
In order to improve the reliability of climate reconstruction, especially the climatologies outside the modern observed climate space, an improved inverse vegetation model using a recent version of BIOME4 has been designed to quantitatively reconstruct past climates, based on pollen biome scores from the BIOME6000 project. The method has been validated with surface pollen spectra from Eurasia and Africa, and applied to palaeoclimate reconstruction. At 6 cal ka BP (calendar years), the climate was generally wetter than today in southern Europe and northern Africa, especially in the summer. Winter temperatures were higher (1-5 C) than present in southern Scandinavia, northeastern Europe, and southern Africa, but cooler in southern Eurasia and in tropical Africa, especially in Mediterranean regions. Summer temperatures were generally higher than today in most of Eurasia and Africa, with a significant warming from {proportional_to}3 to 5 C over northwestern and southern Europe, southern Africa, and eastern Africa. In contrast, summers were 1-3 C cooler than present in the Mediterranean lowlands and in a band from the eastern Black Sea to Siberia. At 21 cal ka BP, a marked hydrological change can be seen in the tropical zone, where annual precipitation was {proportional_to}200-1,000 mm/year lower than today in equatorial East Africa compared to the present. A robust inverse relationship is shown between precipitation change and elevation in Africa. This relationship indicates that precipitation likely had an important role in controlling equilibrium-line altitudes (ELA) changes in the tropics during the LGM period. In Eurasia, hydrological decreases follow a longitudinal gradient from Europe to Siberia. Winter temperatures were {proportional_to}10-17 C lower than today in Eurasia with a more significant decrease in northern regions. In Africa, winter temperature was {proportional_to}10-15 C lower than present in the south, while it was only reduced by {proportional_to}0
Quality Assurance Based on Descriptive and Parsimonious Appearance Models
DEFF Research Database (Denmark)
Nielsen, Jannik Boll; Eiríksson, Eyþór Rúnar; Kristensen, Rasmus Lyngby
2015-01-01
In this positional paper, we discuss the potential benefits of using appearance models in additive manufacturing, metal casting, wind turbine blade production, and 3D content acquisition. Current state of the art in acquisition and rendering of appearance cannot easily be used for quality assurance...... in these areas. The common denominator is the need for descriptive and parsimonious appearance models. By ‘parsimonious’ we mean with few parameters so that a model is useful both for fast acquisition, robust fitting, and fast rendering of appearance. The word ‘descriptive’ refers to the fact that a model should...
Nelles, A.; Buitink, S.; Corstanje, A.; Enriquez, J. E.; Falcke, H.; Hörandel, J. R.; Rachen, J. P.; Rossetto, L.; Schellart, P.; Scholten, O.; ter Veen, S.; Thoudam, S.; Trinh, Gia
2015-01-01
The pattern of the radio emission of air showers is finely sampled with the Low-Frequency ARray (LOFAR). A set of 382 measured air showers is used to test a fast, analytic parameterization of the distribution of pulse powers. Using this parameterization we are able to reconstruct the shower axis and
A Parsimonious Bootstrap Method to Model Natural Inflow Energy Series
Directory of Open Access Journals (Sweden)
Fernando Luiz Cyrino Oliveira
2014-01-01
Full Text Available The Brazilian energy generation and transmission system is quite peculiar in its dimension and characteristics. As such, it can be considered unique in the world. It is a high dimension hydrothermal system with huge participation of hydro plants. Such strong dependency on hydrological regimes implies uncertainties related to the energetic planning, requiring adequate modeling of the hydrological time series. This is carried out via stochastic simulations of monthly inflow series using the family of Periodic Autoregressive models, PAR(p, one for each period (month of the year. In this paper it is shown the problems in fitting these models by the current system, particularly the identification of the autoregressive order “p” and the corresponding parameter estimation. It is followed by a proposal of a new approach to set both the model order and the parameters estimation of the PAR(p models, using a nonparametric computational technique, known as Bootstrap. This technique allows the estimation of reliable confidence intervals for the model parameters. The obtained results using the Parsimonious Bootstrap Method of Moments (PBMOM produced not only more parsimonious model orders but also adherent stochastic scenarios and, in the long range, lead to a better use of water resources in the energy operation planning.
High-Performance Phylogeny Reconstruction
Energy Technology Data Exchange (ETDEWEB)
Tiffani L. Williams
2004-11-10
Under the Alfred P. Sloan Fellowship in Computational Biology, I have been afforded the opportunity to study phylogenetics--one of the most important and exciting disciplines in computational biology. A phylogeny depicts an evolutionary relationship among a set of organisms (or taxa). Typically, a phylogeny is represented by a binary tree, where modern organisms are placed at the leaves and ancestral organisms occupy internal nodes, with the edges of the tree denoting evolutionary relationships. The task of phylogenetics is to infer this tree from observations upon present-day organisms. Reconstructing phylogenies is a major component of modern research programs in many areas of biology and medicine, but it is enormously expensive. The most commonly used techniques attempt to solve NP-hard problems such as maximum likelihood and maximum parsimony, typically by bounded searches through an exponentially-sized tree-space. For example, there are over 13 billion possible trees for 13 organisms. Phylogenetic heuristics that quickly analyze large amounts of data accurately will revolutionize the biological field. This final report highlights my activities in phylogenetics during the two-year postdoctoral period at the University of New Mexico under Prof. Bernard Moret. Specifically, this report reports my scientific, community and professional activities as an Alfred P. Sloan Postdoctoral Fellow in Computational Biology.
A Practical pedestrian approach to parsimonious regression with inaccurate inputs
Directory of Open Access Journals (Sweden)
Seppo Karrila
2014-04-01
Full Text Available A measurement result often dictates an interval containing the correct value. Interval data is also created by roundoff, truncation, and binning. We focus on such common interval uncertainty in data. Inaccuracy in model inputs is typically ignored on model fitting. We provide a practical approach for regression with inaccurate data: the mathematics is easy, and the linear programming formulations simple to use even in a spreadsheet. This self-contained elementary presentation introduces interval linear systems and requires only basic knowledge of algebra. Feature selection is automatic; but can be controlled to find only a few most relevant inputs; and joint feature selection is enabled for multiple modeled outputs. With more features than cases, a novel connection to compressed sensing emerges: robustness against interval errors-in-variables implies model parsimony, and the input inaccuracies determine the regularization term. A small numerical example highlights counterintuitive results and a dramatic difference to total least squares.
Things fall apart: biological species form unconnected parsimony networks.
Hart, Michael W; Sunday, Jennifer
2007-10-22
The generality of operational species definitions is limited by problematic definitions of between-species divergence. A recent phylogenetic species concept based on a simple objective measure of statistically significant genetic differentiation uses between-species application of statistical parsimony networks that are typically used for population genetic analysis within species. Here we review recent phylogeographic studies and reanalyse several mtDNA barcoding studies using this method. We found that (i) alignments of DNA sequences typically fall apart into a separate subnetwork for each Linnean species (but with a higher rate of true positives for mtDNA data) and (ii) DNA sequences from single species typically stick together in a single haplotype network. Departures from these patterns are usually consistent with hybridization or cryptic species diversity.
A parsimonious dynamic model for river water quality assessment.
Mannina, Giorgio; Viviani, Gaspare
2010-01-01
Water quality modelling is of crucial importance for the assessment of physical, chemical, and biological changes in water bodies. Mathematical approaches to water modelling have become more prevalent over recent years. Different model types ranging from detailed physical models to simplified conceptual models are available. Actually, a possible middle ground between detailed and simplified models may be parsimonious models that represent the simplest approach that fits the application. The appropriate modelling approach depends on the research goal as well as on data available for correct model application. When there is inadequate data, it is mandatory to focus on a simple river water quality model rather than detailed ones. The study presents a parsimonious river water quality model to evaluate the propagation of pollutants in natural rivers. The model is made up of two sub-models: a quantity one and a quality one. The model employs a river schematisation that considers different stretches according to the geometric characteristics and to the gradient of the river bed. Each stretch is represented with a conceptual model of a series of linear channels and reservoirs. The channels determine the delay in the pollution wave and the reservoirs cause its dispersion. To assess the river water quality, the model employs four state variables: DO, BOD, NH(4), and NO. The model was applied to the Savena River (Italy), which is the focus of a European-financed project in which quantity and quality data were gathered. A sensitivity analysis of the model output to the model input or parameters was done based on the Generalised Likelihood Uncertainty Estimation methodology. The results demonstrate the suitability of such a model as a tool for river water quality management.
Bias in phylogenetic reconstruction of vertebrate rhodopsin sequences.
Chang, B S; Campbell, D L
2000-08-01
Two spurious nodes were found in phylogenetic analyses of vertebrate rhodopsin sequences in comparison with well-established vertebrate relationships. These spurious reconstructions were well supported in bootstrap analyses and occurred independently of the method of phylogenetic analysis used (parsimony, distance, or likelihood). Use of this data set of vertebrate rhodopsin sequences allowed us to exploit established vertebrate relationships, as well as the considerable amount known about the molecular evolution of this gene, in order to identify important factors contributing to the spurious reconstructions. Simulation studies using parametric bootstrapping indicate that it is unlikely that the spurious nodes in the parsimony analyses are due to long branches or other topological effects. Rather, they appear to be due to base compositional bias at third positions, codon bias, and convergent evolution at nucleotide positions encoding the hydrophobic residues isoleucine, leucine, and valine. LogDet distance methods, as well as maximum-likelihood methods which allow for nonstationary changes in base composition, reduce but do not entirely eliminate support for the spurious resolutions. Inclusion of five additional rhodopsin sequences in the phylogenetic analyses largely corrected one of the spurious reconstructions while leaving the other unaffected. The additional sequences not only were more proximal to the corrected node, but were also found to have intermediate levels of base composition and codon bias as compared with neighboring sequences on the tree. This study shows that the spurious reconstructions can be corrected either by excluding third positions, as well as those encoding the amino acids Ile, Val, and Leu (which may not be ideal, as these sites can contain useful phylogenetic signal for other parts of the tree), or by the addition of sequences that reduce problems associated with convergent evolution.
DeVore, Matthew S.; Gull, Stephen F.; Johnson, Carey K.
2013-08-01
We analyzed single molecule FRET burst measurements using Bayesian nested sampling. The MultiNest algorithm produces accurate FRET efficiency distributions from single-molecule data. FRET efficiency distributions recovered by MultiNest and classic maximum entropy are compared for simulated data and for calmodulin labeled at residues 44 and 117. MultiNest compares favorably with maximum entropy analysis for simulated data, judged by the Bayesian evidence. FRET efficiency distributions recovered for calmodulin labeled with two different FRET dye pairs depended on the dye pair and changed upon Ca2+ binding. We also looked at the FRET efficiency distributions of calmodulin bound to the calcium/calmodulin dependent protein kinase II (CaMKII) binding domain. For both dye pairs, the FRET efficiency distribution collapsed to a single peak in the case of calmodulin bound to the CaMKII peptide. These measurements strongly suggest that consideration of dye-protein interactions is crucial in forming an accurate picture of protein conformations from FRET data.
Devore, Matthew S; Gull, Stephen F; Johnson, Carey K
2013-08-30
We analyze single molecule FRET burst measurements using Bayesian nested sampling. The MultiNest algorithm produces accurate FRET efficiency distributions from single-molecule data. FRET efficiency distributions recovered by MultiNest and classic maximum entropy are compared for simulated data and for calmodulin labeled at residues 44 and 117. MultiNest compares favorably with maximum entropy analysis for simulated data, judged by the Bayesian evidence. FRET efficiency distributions recovered for calmodulin labeled with two different FRET dye pairs depended on the dye pair and changed upon Ca 2+ binding. We also looked at the FRET efficiency distributions of calmodulin bound to the calcium/calmodulin dependent protein kinase II (CaMKII) binding domain. For both dye pairs, the FRET efficiency distribution collapsed to a single peak in the case of calmodulin bound to the CaMKII peptide. These measurements strongly suggest that consideration of dye-protein interactions is crucial in forming an accurate picture of protein conformations from FRET data.
Directory of Open Access Journals (Sweden)
R. Schneider
2013-11-01
δ13Catm level in the Penultimate (~ 140 000 yr BP and Last Glacial Maximum (~ 22 000 yr BP, which can be explained by either (i changes in the isotopic composition or (ii intensity of the carbon input fluxes to the combined ocean/atmosphere carbon reservoir or (iii by long-term peat buildup. Our isotopic data suggest that the carbon cycle evolution along Termination II and the subsequent interglacial was controlled by essentially the same processes as during the last 24 000 yr, but with different phasing and magnitudes. Furthermore, a 5000 yr lag in the CO2 decline relative to EDC temperatures is confirmed during the glacial inception at the end of MIS5.5 (120 000 yr BP. Based on our isotopic data this lag can be explained by terrestrial carbon release and carbonate compensation.
A new mathematical modeling for pure parsimony haplotyping problem.
Feizabadi, R; Bagherian, M; Vaziri, H R; Salahi, M
2016-11-01
Pure parsimony haplotyping (PPH) problem is important in bioinformatics because rational haplotyping inference plays important roles in analysis of genetic data, mapping complex genetic diseases such as Alzheimer's disease, heart disorders and etc. Haplotypes and genotypes are m-length sequences. Although several integer programing models have already been presented for PPH problem, its NP-hardness characteristic resulted in ineffectiveness of those models facing the real instances especially instances with many heterozygous sites. In this paper, we assign a corresponding number to each haplotype and genotype and based on those numbers, we set a mixed integer programing model. Using numbers, instead of sequences, would lead to less complexity of the new model in comparison with previous models in a way that there are neither constraints nor variables corresponding to heterozygous nucleotide sites in it. Experimental results approve the efficiency of the new model in producing better solution in comparison to two state-of-the art haplotyping approaches. Copyright © 2016 Elsevier Inc. All rights reserved.
Pengintegrasian Model Leadership Menuju Model yang Lebih Komprhensip dan Parsimoni
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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.
Staines-Urías, Francisca; Seidenkrantz, Marit-Solveig; Fischel, Andrea; Kuijpers, Antoon
2017-04-01
The elemental composition of sediments from gravity core HOLOVAR11-03 provides a ca. 40 ka record of past climate variability in the Strait of Yucatan, between the Caribbean Sea and the Gulf of Mexico, a region where precipitation variability is determined by the seasonal position of the Intertropical Convergence Zone (ITCZ). Within this region, sea level pressure decreases and rainfall increases as the ITCZ moves north of the equator in response to increased solar insolation in the Northern Hemisphere during boreal summer. In contrast, as the ITCZ retracts southward towards the equator during boreal winter, rainfall diminishes and the regional sea level pressure gradient strengthens. On interannual, multidecadal and millennial timescales, fluctuations in the average latitudinal position of the ITCZ in response to insolation forcing modulate the intensity and duration of the seasonal regimens, determining average regional precipitation and, ultimately, the elemental composition of the marine sedimentary record. Regionally, higher titanium and iron content in marine sediments reflect greater terrigenous input from inland runoff, indicating greater precipitation, hence a more northerly position of the ITCZ. Correspondingly, Ti and Fe concentration data were used to reconstruct regional rainfall variability since the Last Glacial Maxima (LGM ˜24 cal ka BP). HOLOVAR11-03 age model (based on 4 AMS 14C dates obtained from multi-specific samples of planktic foraminifera) shows stable sedimentation rates in the area throughout the cored period. Nonetheless, higher terrestrial mineral input is observed since the LGM and all through the last glacial termination (24 to 12 cal ka BP), indicating a period of increased precipitation. In contrast, lower Ti and Fe values are typical for the period between 12 and 8 cal ka BP, indicating reduced precipitation. A positive trend characterizes the following interval, showing a return to wetter conditions lasting until 5 cal ka BP
A Multi-Criterion Evolutionary Approach Applied to Phylogenetic Reconstruction
Cancino, W.; Delbem, A.C.B.
2010-01-01
In this paper, we proposed an MOEA approach, called PhyloMOEA which solves the phylogenetic inference problem using maximum parsimony and maximum likelihood criteria. The PhyloMOEA's development was motivated by several studies in the literature (Huelsenbeck, 1995; Jin & Nei, 1990; Kuhner & Felsenstein, 1994; Tateno et al., 1994), which point out that various phylogenetic inference methods lead to inconsistent solutions. Techniques using parsimony and likelihood criteria yield to different tr...
On simulated annealing phase transitions in phylogeny reconstruction.
Strobl, Maximilian A R; Barker, Daniel
2016-08-01
Phylogeny reconstruction with global criteria is NP-complete or NP-hard, hence in general requires a heuristic search. We investigate the powerful, physically inspired, general-purpose heuristic simulated annealing, applied to phylogeny reconstruction. Simulated annealing mimics the physical process of annealing, where a liquid is gently cooled to form a crystal. During the search, periods of elevated specific heat occur, analogous to physical phase transitions. These simulated annealing phase transitions play a crucial role in the outcome of the search. Nevertheless, they have received comparably little attention, for phylogeny or other optimisation problems. We analyse simulated annealing phase transitions during searches for the optimal phylogenetic tree for 34 real-world multiple alignments. In the same way in which melting temperatures differ between materials, we observe distinct specific heat profiles for each input file. We propose this reflects differences in the search landscape and can serve as a measure for problem difficulty and for suitability of the algorithm's parameters. We discuss application in algorithmic optimisation and as a diagnostic to assess parameterisation before computationally costly, large phylogeny reconstructions are launched. Whilst the focus here lies on phylogeny reconstruction under maximum parsimony, it is plausible that our results are more widely applicable to optimisation procedures in science and industry. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.
Maximum likelihood inference of small trees in the presence of long branches.
Parks, Sarah L; Goldman, Nick
2014-09-01
The statistical basis of maximum likelihood (ML), its robustness, and the fact that it appears to suffer less from biases lead to it being one of the most popular methods for tree reconstruction. Despite its popularity, very few analytical solutions for ML exist, so biases suffered by ML are not well understood. One possible bias is long branch attraction (LBA), a regularly cited term generally used to describe a propensity for long branches to be joined together in estimated trees. Although initially mentioned in connection with inconsistency of parsimony, LBA has been claimed to affect all major phylogenetic reconstruction methods, including ML. Despite the widespread use of this term in the literature, exactly what LBA is and what may be causing it is poorly understood, even for simple evolutionary models and small model trees. Studies looking at LBA have focused on the effect of two long branches on tree reconstruction. However, to understand the effect of two long branches it is also important to understand the effect of just one long branch. If ML struggles to reconstruct one long branch, then this may have an impact on LBA. In this study, we look at the effect of one long branch on three-taxon tree reconstruction. We show that, counterintuitively, long branches are preferentially placed at the tips of the tree. This can be understood through the use of analytical solutions to the ML equation and distance matrix methods. We go on to look at the placement of two long branches on four-taxon trees, showing that there is no attraction between long branches, but that for extreme branch lengths long branches are joined together disproportionally often. These results illustrate that even small model trees are still interesting to help understand how ML phylogenetic reconstruction works, and that LBA is a complicated phenomenon that deserves further study. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.
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
Reconstructible phylogenetic networks: do not distinguish the indistinguishable.
Pardi, Fabio; Scornavacca, Celine
2015-04-01
Phylogenetic networks represent the evolution of organisms that have undergone reticulate events, such as recombination, hybrid speciation or lateral gene transfer. An important way to interpret a phylogenetic network is in terms of the trees it displays, which represent all the possible histories of the characters carried by the organisms in the network. Interestingly, however, different networks may display exactly the same set of trees, an observation that poses a problem for network reconstruction: from the perspective of many inference methods such networks are "indistinguishable". This is true for all methods that evaluate a phylogenetic network solely on the basis of how well the displayed trees fit the available data, including all methods based on input data consisting of clades, triples, quartets, or trees with any number of taxa, and also sequence-based approaches such as popular formalisations of maximum parsimony and maximum likelihood for networks. This identifiability problem is partially solved by accounting for branch lengths, although this merely reduces the frequency of the problem. Here we propose that network inference methods should only attempt to reconstruct what they can uniquely identify. To this end, we introduce a novel definition of what constitutes a uniquely reconstructible network. For any given set of indistinguishable networks, we define a canonical network that, under mild assumptions, is unique and thus representative of the entire set. Given data that underwent reticulate evolution, only the canonical form of the underlying phylogenetic network can be uniquely reconstructed. While on the methodological side this will imply a drastic reduction of the solution space in network inference, for the study of reticulate evolution this is a fundamental limitation that will require an important change of perspective when interpreting phylogenetic networks.
Reconstructible phylogenetic networks: do not distinguish the indistinguishable.
Directory of Open Access Journals (Sweden)
Fabio Pardi
2015-04-01
Full Text Available Phylogenetic networks represent the evolution of organisms that have undergone reticulate events, such as recombination, hybrid speciation or lateral gene transfer. An important way to interpret a phylogenetic network is in terms of the trees it displays, which represent all the possible histories of the characters carried by the organisms in the network. Interestingly, however, different networks may display exactly the same set of trees, an observation that poses a problem for network reconstruction: from the perspective of many inference methods such networks are "indistinguishable". This is true for all methods that evaluate a phylogenetic network solely on the basis of how well the displayed trees fit the available data, including all methods based on input data consisting of clades, triples, quartets, or trees with any number of taxa, and also sequence-based approaches such as popular formalisations of maximum parsimony and maximum likelihood for networks. This identifiability problem is partially solved by accounting for branch lengths, although this merely reduces the frequency of the problem. Here we propose that network inference methods should only attempt to reconstruct what they can uniquely identify. To this end, we introduce a novel definition of what constitutes a uniquely reconstructible network. For any given set of indistinguishable networks, we define a canonical network that, under mild assumptions, is unique and thus representative of the entire set. Given data that underwent reticulate evolution, only the canonical form of the underlying phylogenetic network can be uniquely reconstructed. While on the methodological side this will imply a drastic reduction of the solution space in network inference, for the study of reticulate evolution this is a fundamental limitation that will require an important change of perspective when interpreting phylogenetic networks.
Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees.
Mirzaei, Sajad; Wu, Yufeng
2016-01-01
Hybridization networks represent plausible evolutionary histories of species that are affected by reticulate evolutionary processes. An established computational problem on hybridization networks is constructing the most parsimonious hybridization network such that each of the given phylogenetic trees (called gene trees) is "displayed" in the network. There have been several previous approaches, including an exact method and several heuristics, for this NP-hard problem. However, the exact method is only applicable to a limited range of data, and heuristic methods can be less accurate and also slow sometimes. In this paper, we develop a new algorithm for constructing near parsimonious networks for multiple binary gene trees. This method is more efficient for large numbers of gene trees than previous heuristics. This new method also produces more parsimonious results on many simulated datasets as well as a real biological dataset than a previous method. We also show that our method produces topologically more accurate networks for many datasets.
Keller, Alexander; Förster, Frank; Müller, Tobias; Dandekar, Thomas; Schultz, Jörg; Wolf, Matthias
2010-01-15
In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. For the full reviews, please go to the Reviewers' comments section.
Huo, Guangming; Jiang, Guofang; Sun, Zhengli; Liu, Dianfeng; Zhang, Yalin; Lu, Lin
2007-04-01
Sequences from the mitochondrial cytochrome b gene (Cyt b) were determined for 25 species from the superfamily Acridoidae and the homologous sequences of 19 species of grasshoppers were downloaded from the GenBank data library. The purpose was to develop a molecular phylogeny of the Acrypteridae, and to interpret the phylogenetic position of the family within the superfamily Acridoidea. Phylogeny was reconstructed by Maximum-parsimony (MP) and Bayesian criteria using Yunnanites coriacea and Tagasta marginella as outgroups. The alignment length of the fragments was 384 bp after excluding ambiguous sites, including 167 parsimony informative sites. In the fragments, the percentages of A + T and G + C were 70.7% and 29.3%, respectively. The monophyly of Arcypteridae is not supported by phylogenetic trees. Within the Arcypteridae, neither Arcypterinae nor Ceracrinae is supported as a monophyletic group. The current genus Chorthippus is not a monophyletic group, and should be a polyphyletic group. The present results are significantly different from the classification scheme of Arcypteridae, which is based on morphology.
Gervais, Matthew M; Fessler, Daniel M T
2017-01-01
The target article argues that contempt is a sentiment, and that sentiments are the deep structure of social affect. The 26 commentaries meet these claims with a range of exciting extensions and applications, as well as critiques. Most significantly, we reply that construction and emergence are necessary for, not incompatible with, evolved design, while parsimony requires explanatory adequacy and predictive accuracy, not mere simplicity.
Consequence Valuing as Operation and Process: A Parsimonious Analysis of Motivation
Whelan, Robert; Barnes-Holmes, Dermot
2010-01-01
The concept of the motivating operation (MO) has been subject to 3 criticisms: (a) the terms and concepts employed do not always overlap with traditional behavior-analytic verbal practices; (b) the dual nature of the MO is unclear; and (c) there is a lack of adequate contact with empirical data. We offer a more parsimonious approach to motivation,…
Peltier, James W.; Cummins, Shannon; Pomirleanu, Nadia; Cross, James; Simon, Rob
2014-01-01
Students' desire and intention to pursue a career in sales continue to lag behind industry demand for sales professionals. This article develops and validates a reliable and parsimonious scale for measuring and predicting student intention to pursue a selling career. The instrument advances previous scales in three ways. The instrument is…
Wang, Chao; Yang, Chuan-sheng
2017-09-01
In this paper, we present a simplified parsimonious higher-order multivariate Markov chain model with new convergence condition. (TPHOMMCM-NCC). Moreover, estimation method of the parameters in TPHOMMCM-NCC is give. Numerical experiments illustrate the effectiveness of TPHOMMCM-NCC.
DEFF Research Database (Denmark)
Callot, Laurent; Kristensen, Johannes Tang
the monetary policy response to inflation and business cycle fluctuations in the US by estimating a parsimoniously time varying parameter Taylor rule.We document substantial changes in the policy response of the Fed in the 1970s and 1980s, and since 2007, but also document the stability of this response...
Time-Lapse Monitoring of Subsurface Fluid Flow using Parsimonious Seismic Interferometry
Hanafy, Sherif; Li, Jing; Schuster, Gerard T.
2017-01-01
of parsimonious seismic interferometry with the time-lapse mentoring idea with field examples, where we were able to record 30 different data sets within a 2-hour period. The recorded data are then processed to generate 30 snapshots that shows the spread of water
Parsimonious wave-equation travel-time inversion for refraction waves
Fu, Lei; Hanafy, Sherif M.; Schuster, Gerard T.
2017-01-01
We present a parsimonious wave-equation travel-time inversion technique for refraction waves. A dense virtual refraction dataset can be generated from just two reciprocal shot gathers for the sources at the endpoints of the survey line, with N
Introduction to maximum entropy
International Nuclear Information System (INIS)
Sivia, D.S.
1988-01-01
The maximum entropy (MaxEnt) principle has been successfully used in image reconstruction in a wide variety of fields. We review the need for such methods in data analysis and show, by use of a very simple example, why MaxEnt is to be preferred over other regularizing functions. This leads to a more general interpretation of the MaxEnt method, and its use is illustrated with several different examples. Practical difficulties with non-linear problems still remain, this being highlighted by the notorious phase problem in crystallography. We conclude with an example from neutron scattering, using data from a filter difference spectrometer to contrast MaxEnt with a conventional deconvolution. 12 refs., 8 figs., 1 tab
Introduction to maximum entropy
International Nuclear Information System (INIS)
Sivia, D.S.
1989-01-01
The maximum entropy (MaxEnt) principle has been successfully used in image reconstruction in a wide variety of fields. The author reviews the need for such methods in data analysis and shows, by use of a very simple example, why MaxEnt is to be preferred over other regularizing functions. This leads to a more general interpretation of the MaxEnt method, and its use is illustrated with several different examples. Practical difficulties with non-linear problems still remain, this being highlighted by the notorious phase problem in crystallography. He concludes with an example from neutron scattering, using data from a filter difference spectrometer to contrast MaxEnt with a conventional deconvolution. 12 refs., 8 figs., 1 tab
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…
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.
Wehe, André; Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver
2008-07-01
DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++. DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree
DEFF Research Database (Denmark)
Kristensen, Jakob Baek; Albrechtsen, Thomas; Dahl-Nielsen, Emil
2017-01-01
This study shows how liking politicians’ public Facebook posts can be used as an accurate measure for predicting present-day voter intention in a multiparty system. We highlight that a few, but selective digital traces produce prediction accuracies that are on par or even greater than most curren...
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...
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 ...
A class representative model for Pure Parsimony Haplotyping under uncertain data.
Directory of Open Access Journals (Sweden)
Daniele Catanzaro
Full Text Available The Pure Parsimony Haplotyping (PPH problem is a NP-hard combinatorial optimization problem that consists of finding the minimum number of haplotypes necessary to explain a given set of genotypes. PPH has attracted more and more attention in recent years due to its importance in analysis of many fine-scale genetic data. Its application fields range from mapping complex disease genes to inferring population histories, passing through designing drugs, functional genomics and pharmacogenetics. In this article we investigate, for the first time, a recent version of PPH called the Pure Parsimony Haplotype problem under Uncertain Data (PPH-UD. This version mainly arises when the input genotypes are not accurate, i.e., when some single nucleotide polymorphisms are missing or affected by errors. We propose an exact approach to solution of PPH-UD based on an extended version of Catanzaro et al.[1] class representative model for PPH, currently the state-of-the-art integer programming model for PPH. The model is efficient, accurate, compact, polynomial-sized, easy to implement, solvable with any solver for mixed integer programming, and usable in all those cases for which the parsimony criterion is well suited for haplotype estimation.
The plunge in German electricity futures prices – Analysis using a parsimonious fundamental model
International Nuclear Information System (INIS)
Kallabis, Thomas; Pape, Christian; Weber, Christoph
2016-01-01
The German market has seen a plunge in wholesale electricity prices from 2007 until 2014, with base futures prices dropping by more than 40%. This is frequently attributed to the unexpected high increase in renewable power generation. Using a parsimonious fundamental model, we determine the respective impact of supply and demand shocks on electricity futures prices. The used methodology is based on a piecewise linear approximation of the supply stack and time-varying price-inelastic demand. This parsimonious model is able to replicate electricity futures prices and discover non-linear dependencies in futures price formation. We show that emission prices have a higher impact on power prices than renewable penetration. Changes in renewables, demand and installed capacities turn out to be similarly important for explaining the decrease in operation margins of conventional power plants. We thus argue for the establishment of an independent authority to stabilize emission prices. - Highlights: •We build a parsimonious fundamental model based on a piecewise linear bid stack. •We use the model to investigate impact factors for the plunge in German futures prices. •Largest impact by CO_2 price developments followed by demand and renewable feed-in. •Power plant operating profits strongly affected by demand and renewables. •We argue that stabilizing CO_2 emission prices could provide better market signals.
Directory of Open Access Journals (Sweden)
Liran Carmel
2010-01-01
Full Text Available Evolutionary binary characters are features of species or genes, indicating the absence (value zero or presence (value one of some property. Examples include eukaryotic gene architecture (the presence or absence of an intron in a particular locus, gene content, and morphological characters. In many studies, the acquisition of such binary characters is assumed to represent a rare evolutionary event, and consequently, their evolution is analyzed using various flavors of parsimony. However, when gain and loss of the character are not rare enough, a probabilistic analysis becomes essential. Here, we present a comprehensive probabilistic model to describe the evolution of binary characters on a bifurcating phylogenetic tree. A fast software tool, EREM, is provided, using maximum likelihood to estimate the parameters of the model and to reconstruct ancestral states (presence and absence in internal nodes and events (gain and loss events along branches.
Carmel, Liran; Wolf, Yuri I; Rogozin, Igor B; Koonin, Eugene V
2010-01-01
Evolutionary binary characters are features of species or genes, indicating the absence (value zero) or presence (value one) of some property. Examples include eukaryotic gene architecture (the presence or absence of an intron in a particular locus), gene content, and morphological characters. In many studies, the acquisition of such binary characters is assumed to represent a rare evolutionary event, and consequently, their evolution is analyzed using various flavors of parsimony. However, when gain and loss of the character are not rare enough, a probabilistic analysis becomes essential. Here, we present a comprehensive probabilistic model to describe the evolution of binary characters on a bifurcating phylogenetic tree. A fast software tool, EREM, is provided, using maximum likelihood to estimate the parameters of the model and to reconstruct ancestral states (presence and absence in internal nodes) and events (gain and loss events along branches).
Shavit Grievink, Liat; Penny, David; Hendy, Michael D; Holland, Barbara R
2010-05-01
Commonly used phylogenetic models assume a homogeneous process through time in all parts of the tree. However, it is known that these models can be too simplistic as they do not account for nonhomogeneous lineage-specific properties. In particular, it is now widely recognized that as constraints on sequences evolve, the proportion and positions of variable sites can vary between lineages causing heterotachy. The extent to which this model misspecification affects tree reconstruction is still unknown. Here, we evaluate the effect of changes in the proportions and positions of variable sites on model fit and tree estimation. We consider 5 current models of nucleotide sequence evolution in a Bayesian Markov chain Monte Carlo framework as well as maximum parsimony (MP). We show that for a tree with 4 lineages where 2 nonsister taxa undergo a change in the proportion of variable sites tree reconstruction under the best-fitting model, which is chosen using a relative test, often results in the wrong tree. In this case, we found that an absolute test of model fit is a better predictor of tree estimation accuracy. We also found further evidence that MP is not immune to heterotachy. In addition, we show that increased sampling of taxa that have undergone a change in proportion and positions of variable sites is critical for accurate tree reconstruction.
Directory of Open Access Journals (Sweden)
Galperin Michael Y
2003-01-01
Full Text Available Abstract Background Comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (HGT, at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task. Results We addressed the problem of constructing parsimonious scenarios for individual sets of orthologous genes given a species tree. The orthologous sets were taken from the database of Clusters of Orthologous Groups of proteins (COGs. We show that the phyletic patterns (patterns of presence-absence in completely sequenced genomes of almost 90% of the COGs are inconsistent with the hypothetical species tree. Algorithms were developed to reconcile the phyletic patterns with the species tree by postulating gene loss, COG emergence and HGT (the latter two classes of events were collectively treated as gene gains. We prove that each of these algorithms produces a parsimonious evolutionary scenario, which can be represented as mapping of loss and gain events on the species tree. The distribution of the evolutionary events among the tree nodes substantially depends on the underlying assumptions of the reconciliation algorithm, e.g. whether or not independent gene gains (gain after loss after gain are permitted. Biological considerations suggest that, on average, gene loss might be a more likely event than gene gain. Therefore different gain penalties were used and the resulting series of reconstructed gene sets for the last universal common ancestor (LUCA of the extant life forms were analysed. The number of genes in the reconstructed LUCA gene sets grows as the gain penalty increases. However, qualitative examination of the LUCA versions reconstructed with different gain penalties
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.
Phylogenetic reconstruction of South American felids defined by protein electrophoresis.
Slattery, J P; Johnson, W E; Goldman, D; O'Brien, S J
1994-09-01
Phylogenetic associations among six closely related South American felid species were defined by changes in protein-encoding gene loci. We analyzed proteins isolated from skin fibroblasts using two-dimensional electrophoresis and allozymes extracted from blood cells. Genotypes were determined for multiple individuals of ocelot, margay, tigrina, Geoffroy's cat, kodkod, and pampas cat at 548 loci resolved by two-dimensional electrophoresis and 44 allozyme loci. Phenograms were constructed using the methods of Fitch-Margoliash and neighbor-joining on a matrix of Nei's unbiased genetic distances for all pairs of species. Results of a relative-rate test indicate changes in two-dimensional electrophoresis data are constant among all South American felids with respect to a hyena outgroup. Allelic frequencies were transformed to discrete character states for maximum parsimony analysis. Phylogenetic reconstruction indicates a major split occurred approximately 5-6 million years ago, leading to three groups within the ocelot lineage. The earliest divergence led to Leopardus tigrina, followed by a split between an ancestor of an unresolved trichotomy of three species (Oncifelis guigna, O. geoffroyi, and Lynchailuris colocolo) and a recent common ancestor of Leopardus pardalis and L. wiedii. The results suggest that modern South American felids are monophyletic and evolved rapidly after the formation of the Panama land bridge between North and South America.
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.
Beyond technology acceptance to effective technology use: a parsimonious and actionable model.
Holahan, Patricia J; Lesselroth, Blake J; Adams, Kathleen; Wang, Kai; Church, Victoria
2015-05-01
To develop and test a parsimonious and actionable model of effective technology use (ETU). Cross-sectional survey of primary care providers (n = 53) in a large integrated health care organization that recently implemented new medication reconciliation technology. Surveys assessed 5 technology-related perceptions (compatibility with work values, implementation climate, compatibility with work processes, perceived usefulness, and ease of use) and 1 outcome variable, ETU. ETU was measured as both consistency and quality of technology use. Compatibility with work values and implementation climate were found to have differential effects on consistency and quality of use. When implementation climate was strong, consistency of technology use was high. However, quality of technology use was high only when implementation climate was strong and values compatibility was high. This is an important finding and highlights the importance of users' workplace values as a key determinant of quality of use. To extend our effectiveness in implementing new health care information technology, we need parsimonious models that include actionable determinants of ETU and account for the differential effects of these determinants on the multiple dimensions of ETU. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
The scenario on the origin of translation in the RNA world: in principle of replication parsimony
Directory of Open Access Journals (Sweden)
Ma Wentao
2010-11-01
Full Text Available Abstract Background It is now believed that in the origin of life, proteins should have been "invented" in an RNA world. However, due to the complexity of a possible RNA-based proto-translation system, this evolving process seems quite complicated and the associated scenario remains very blurry. Considering that RNA can bind amino acids with specificity, it has been reasonably supposed that initial peptides might have been synthesized on "RNA templates" containing multiple amino acid binding sites. This "Direct RNA Template (DRT" mechanism is attractive because it should be the simplest mechanism for RNA to synthesize peptides, thus very likely to have been adopted initially in the RNA world. Then, how this mechanism could develop into a proto-translation system mechanism is an interesting problem. Presentation of the hypothesis Here an explanation to this problem is shown considering the principle of "replication parsimony" --- genetic information tends to be utilized in a parsimonious way under selection pressure, due to its replication cost (e.g., in the RNA world, nucleotides and ribozymes for RNA replication. Because a DRT would be quite long even for a short peptide, its replication cost would be great. Thus the diversity and the length of functional peptides synthesized by the DRT mechanism would be seriously limited. Adaptors (proto-tRNAs would arise to allow a DRT's complementary strand (called "C-DRT" here to direct the synthesis of the same peptide synthesized by the DRT itself. Because the C-DRT is a necessary part in the DRT's replication, fewer turns of the DRT's replication would be needed to synthesize definite copies of the functional peptide, thus saving the replication cost. Acting through adaptors, C-DRTs could transform into much shorter templates (called "proto-mRNAs" here and substitute the role of DRTs, thus significantly saving the replication cost. A proto-rRNA corresponding to the small subunit rRNA would then emerge
Directory of Open Access Journals (Sweden)
Kimberly J Van Meter
Full Text Available Nutrient legacies in anthropogenic landscapes, accumulated over decades of fertilizer application, lead to time lags between implementation of conservation measures and improvements in water quality. Quantification of such time lags has remained difficult, however, due to an incomplete understanding of controls on nutrient depletion trajectories after changes in land-use or management practices. In this study, we have developed a parsimonious watershed model for quantifying catchment-scale time lags based on both soil nutrient accumulations (biogeochemical legacy and groundwater travel time distributions (hydrologic legacy. The model accurately predicted the time lags observed in an Iowa watershed that had undergone a 41% conversion of area from row crop to native prairie. We explored the time scales of change for stream nutrient concentrations as a function of both natural and anthropogenic controls, from topography to spatial patterns of land-use change. Our results demonstrate that the existence of biogeochemical nutrient legacies increases time lags beyond those due to hydrologic legacy alone. In addition, we show that the maximum concentration reduction benefits vary according to the spatial pattern of intervention, with preferential conversion of land parcels having the shortest catchment-scale travel times providing proportionally greater concentration reductions as well as faster response times. In contrast, a random pattern of conversion results in a 1:1 relationship between percent land conversion and percent concentration reduction, irrespective of denitrification rates within the landscape. Our modeling framework allows for the quantification of tradeoffs between costs associated with implementation of conservation measures and the time needed to see the desired concentration reductions, making it of great value to decision makers regarding optimal implementation of watershed conservation measures.
International Nuclear Information System (INIS)
O'Sullivan, F.; Pawitan, Y.; Harrison, R.L.; Lewellen, T.K.
1990-01-01
In statistical terms, filtered backprojection can be viewed as smoothed Least Squares (LS). In this paper, the authors report on improvement in LS resolution by: incorporating locally adaptive smoothers, imposing positivity and using statistical methods for optimal selection of the resolution parameter. The resulting algorithm has high computational efficiency relative to more elaborate Maximum Likelihood (ML) type techniques (i.e. EM with sieves). Practical aspects of the procedure are discussed in the context of PET and illustrations with computer simulated and real tomograph data are presented. The relative recovery coefficients for a 9mm sphere in a computer simulated hot-spot phantom range from .3 to .6 when the number of counts ranges from 10,000 to 640,000 respectively. The authors will also present results illustrating the relative efficacy of ML and LS reconstruction techniques
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.
Entropy and transverse section reconstruction
International Nuclear Information System (INIS)
Gullberg, G.T.
1976-01-01
A new approach to the reconstruction of a transverse section using projection data from multiple views incorporates the concept of maximum entropy. The principle of maximizing information entropy embodies the assurance of minimizing bias or prejudice in the reconstruction. Using maximum entropy is a necessary condition for the reconstructed image. This entropy criterion is most appropriate for 3-D reconstruction of objects from projections where the system is underdetermined or the data are limited statistically. This is the case in nuclear medicine time limitations in patient studies do not yield sufficient projections
Permutationally invariant state reconstruction
DEFF Research Database (Denmark)
Moroder, Tobias; Hyllus, Philipp; Tóth, Géza
2012-01-01
Feasible tomography schemes for large particle numbers must possess, besides an appropriate data acquisition protocol, an efficient way to reconstruct the density operator from the observed finite data set. Since state reconstruction typically requires the solution of a nonlinear large-scale opti...... optimization, which has clear advantages regarding speed, control and accuracy in comparison to commonly employed numerical routines. First prototype implementations easily allow reconstruction of a state of 20 qubits in a few minutes on a standard computer.......-scale optimization problem, this is a major challenge in the design of scalable tomography schemes. Here we present an efficient state reconstruction scheme for permutationally invariant quantum state tomography. It works for all common state-of-the-art reconstruction principles, including, in particular, maximum...
Koepfli, Klaus-Peter; Wayne, Robert K
2003-10-01
We compared the utility of five nuclear gene segments amplified with type I sequence-tagged site (STS) primers versus the complete mitochondrial cytochrome b (cyt b) gene in resolving phylogenetic relationships within the Mustelidae, a large and ecomorphologically diverse family of mammalian carnivores. Maximum parsimony and likelihood analyses of separate and combined data sets were used to address questions regarding the levels of homoplasy, incongruence, and information content within and among loci. All loci showed limited resolution in the separate analyses because of either a low amount of informative variation (nuclear genes) or high levels of homoplasy (cyt b). Individually or combined, the nuclear gene sequences had less homoplasy, retained more signal, and were more decisive, even though cyt b contained more potentially informative variation than all the nuclear sequences combined. We obtained a well-resolved and supported phylogeny when the nuclear sequences were combined. Maximum likelihood and Bayesian phylogenetic analyses of the total combined data (nuclear and mitochondrial DNA sequences) were able to better accommodate the high levels of homoplasy in the cyt b data than was an equally weighted maximum parsimony analysis. Furthermore, partition Bremer support analyses of the total combined tree showed that the relative support of the nuclear and mitochondrial genes differed according to whether or not the homoplasy in the cyt b gene was downweighted. Although the cyt b gene contributed phylogenetic signal for most major groupings, the nuclear gene sequences were more effective in reconstructing the deeper nodes of the combined tree in the equally weighted parsimony analysis, as judged by the variable-length bootstrap method. The total combined data supported the monophyly of the Lutrinae (otters), whereas the Melinae (badgers) and Mustelinae (weasels, martens) were both paraphyletic. The American badger, Taxidea taxus (Taxidiinae), was the most
Energy Technology Data Exchange (ETDEWEB)
Ancalla, Lourdes Pilar Zaragoza
2005-04-15
The reconstruction of the distribution of density of potency pin upright in a heterogeneous combustible element, of the nucleus of a nuclear reactor, it is a subject that has been studied inside by a long time in Physics of Reactors area. Several methods exist to do this reconstruction, one of them is Maximum Entropy's Method, that besides being an optimization method that finds the best solution of all the possible solutions, it is a method also improved that uses multipliers of Lagrange to obtain the distribution of the flows in the faces of the combustible element. This distribution of the flows in the faces is used then as a contour condition in the calculations of a detailed distribution of flow inside the combustible element. In this work, in first place it was made the homogenization of the heterogeneous element. Soon after the factor of the multiplication executes and the medium values of the flow and of the liquid current they are computed, with the program NEM2D. These values medium nodal are, then, used upright in the reconstruction of the distribution pin of the flow inside the combustible element. The obtained results were acceptable, when compared with those obtained using fine mesh. (author)
Baldo, A M; Les, D H; Strausbaugh, L D
1999-11-01
Simplified DNA sequence acquisition has provided many new data sets that are useful for phylogenetic reconstruction, including single- and multiple-copy nuclear and organellar genes. Although transcribed regions receive much attention, nontranscribed regions have recently been added to the repertoire of sequences suitable for phylogenetic studies, especially for closely related taxa. We evaluated the efficacy of a small portion of the histone repeat for phylogenetic reconstruction among Drosophila species. Histone repeats in invertebrates offer distinct advantages similar to those of widely used ribosomal repeats. First, the units are tandemly repeated and undergo concerted evolution. Second, histone repeats include both highly conserved coding and variable intergenic regions. This composition facilitates application of "universal" primers spanning potentially informative sites. We examined a small region of the histone repeat, including the intergenic spacer segments of coding regions from the divergently transcribed H2A and H2B histone genes. The spacer (about 230 bp) exists as a mosaic with highly conserved functional motifs interspersed with rapidly diverging regions; the former aid in alignment of the spacer. There are no ambiguities in alignment of coding regions. Coding and noncoding regions were analyzed together and separately for phylogenetic information. Parsimony, distance, and maximum-likelihood methods successfully retrieve the corroborated phylogeny for the taxa examined. This study demonstrates the resolving power of a small histone region which may now be added to the growing collection of phylogenetically useful DNA sequences.
Li, Yuting
2017-01-01
To explore whether the dispersion of sediments in the North Atlantic can be related to modern and past Atlantic Meridional Overturning Circulation (AMOC) flow speed, particle size distributions (weight%, Sortable Silt mean grain size) and grain-size separated (0–4, 4–10, 10–20, 20–30, 30–40 and 40–63 µm) Sm-Nd isotopes and trace element concentrations are measured on 12 cores along the flow-path of Western Boundary Undercurrent and in the central North Atlantic since the Last glacial Maximum ...
International Nuclear Information System (INIS)
Anon.
1979-01-01
This chapter presents a historic overview of the establishment of radiation guidelines by various national and international agencies. The use of maximum permissible dose and maximum permissible body burden limits to derive working standards is discussed
More quality measures versus measuring what matters: a call for balance and parsimony.
Meyer, Gregg S; Nelson, Eugene C; Pryor, David B; James, Brent; Swensen, Stephen J; Kaplan, Gary S; Weissberg, Jed I; Bisognano, Maureen; Yates, Gary R; Hunt, Gordon C
2012-11-01
External groups requiring measures now include public and private payers, regulators, accreditors and others that certify performance levels for consumers, patients and payers. Although benefits have accrued from the growth in quality measurement, the recent explosion in the number of measures threatens to shift resources from improving quality to cover a plethora of quality-performance metrics that may have a limited impact on the things that patients and payers want and need (ie, better outcomes, better care, and lower per capita costs). Here we propose a policy that quality measurement should be: balanced to meet the need of end users to judge quality and cost performance and the need of providers to continuously improve the quality, outcomes and costs of their services; and parsimonious to measure quality, outcomes and costs with appropriate metrics that are selected based on end-user needs.
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.
Singular Spectrum Analysis for Astronomical Time Series: Constructing a Parsimonious Hypothesis Test
Greco, G.; Kondrashov, D.; Kobayashi, S.; Ghil, M.; Branchesi, M.; Guidorzi, C.; Stratta, G.; Ciszak, M.; Marino, F.; Ortolan, A.
We present a data-adaptive spectral method - Monte Carlo Singular Spectrum Analysis (MC-SSA) - and its modification to tackle astrophysical problems. Through numerical simulations we show the ability of the MC-SSA in dealing with 1/f β power-law noise affected by photon counting statistics. Such noise process is simulated by a first-order autoregressive, AR(1) process corrupted by intrinsic Poisson noise. In doing so, we statistically estimate a basic stochastic variation of the source and the corresponding fluctuations due to the quantum nature of light. In addition, MC-SSA test retains its effectiveness even when a significant percentage of the signal falls below a certain level of detection, e.g., caused by the instrument sensitivity. The parsimonious approach presented here may be broadly applied, from the search for extrasolar planets to the extraction of low-intensity coherent phenomena probably hidden in high energy transients.
Borths, Matthew R; Holroyd, Patricia A; Seiffert, Erik R
2016-01-01
recovered from each phylogenetic method, we reconstructed the biogeographic history of Hyaenodonta using parsimony optimization (PO), likelihood optimization (LO), and Bayesian Binary Markov chain Monte Carlo (MCMC) to examine support for the Afro-Arabian origin of Hyaenodonta. Across all analyses, we found that Hyaenodonta most likely originated in Europe, rather than Afro-Arabia. The clade is estimated by tip-dating analysis to have undergone a rapid radiation in the Late Cretaceous and Paleocene; a radiation currently not documented by fossil evidence. During the Paleocene, lineages are reconstructed as dispersing to Asia, Afro-Arabia, and North America. The place of origin of Hyainailouroidea is likely Afro-Arabia according to the Bayesian topologies but it is ambiguous using parsimony. All topologies support the constituent clades-Hyainailourinae, Apterodontinae, and Teratodontinae-as Afro-Arabian and tip-dating estimates that each clade is established in Afro-Arabia by the middle Eocene.
Directory of Open Access Journals (Sweden)
Dandekar Thomas
2010-01-01
Full Text Available Abstract Background In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. Results This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Conclusions Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. Reviewers This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber and Eugene V. Koonin. Open peer review Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber and Eugene V. Koonin. For the full reviews, please go to the Reviewers' comments section.
Weisrock, David W; Macey, J Robert; Matsui, Masafumi; Mulcahy, Daniel G; Papenfuss, Theodore J
2013-01-01
The salamander family Hynobiidae contains over 50 species and has been the subject of a number of molecular phylogenetic investigations aimed at reconstructing branches across the entire family. In general, studies using the greatest amount of sequence data have used reduced taxon sampling, while the study with the greatest taxon sampling has used a limited sequence data set. Here, we provide insights into the phylogenetic history of the Hynobiidae using both dense taxon sampling and a large mitochondrial DNA sequence data set. We report exclusive new mitochondrial DNA data of 2566 aligned bases (with 151 excluded sites, of included sites 1157 are variable with 957 parsimony informative). This is sampled from two genic regions encoding a 12S-16S region (the 3' end of 12S rRNA, tRNA(VAI), and the 5' end of 16S rRNA), and a ND2-COI region (ND2, tRNA(Trp), tRNA(Ala), tRNA(Asn), the origin for light strand replication--O(L), tRNA(Cys), tRNAT(Tyr), and the 5' end of COI). Analyses using parsimony, Bayesian, and maximum likelihood optimality criteria produce similar phylogenetic trees, with discordant branches generally receiving low levels of branch support. Monophyly of the Hynobiidae is strongly supported across all analyses, as is the sister relationship and deep divergence between the genus Onychodactylus with all remaining hynobiids. Within this latter grouping our phylogenetic results identify six clades that are relatively divergent from one another, but for which there is minimal support for their phylogenetic placement. This includes the genus Batrachuperus, the genus Hynobius, the genus Pachyhynobius, the genus Salamandrella, a clade containing the genera Ranodon and Paradactylodon, and a clade containing the genera Liua and Pseudohynobius. This latter clade receives low bootstrap support in the parsimony analysis, but is consistent across all three analytical methods. Our results also clarify a number of well-supported relationships within the larger
Directory of Open Access Journals (Sweden)
محمد أحمد حسن الأفندي
2018-04-01
Full Text Available There is a rich literature about the analysis of consumption behavior from the perspective of Islamic economy. The focus of such literature has been on the incorporation of the effect of moral values on individuals’ consumption behavior. However, studies on consumption did not pay enough heed to the analysis of the ultimate effect of faith values on the track of consumption behavior over time. This desired track of consumption involves showing certain hypotheses and probabilities. This study suggests a normative statement which includes the gradual disappearance of parsimony and improvidence over time. This disappearance would correct the deviation of actual consumption of society members from the desired moderate consumption level, so as to make households’ consumption behavior at the desired level which is consistent with Islamic Sharia. The study emphasizes the need to develop analysis and research in two integrated directions: i conducting more empirical studies to examine the consistency of the normative statement with evidence from real situations, and ii conducting more analysis to develop a specific measure for the desired consumption levels as well as the limits of parsimony and improvidence. Keywords: Disappearance of improvidence and parsimony limits, Desired moderate consumption level, Actual consumption, Improvidence and parsimony consumption levels, Track of households’ consumption behavior.
Li, Pui-Sze; Thomas, Daniel C; Saunders, Richard M K
2015-01-01
Taxonomic delimitation of Disepalum (Annonaceae) is contentious, with some researchers favoring a narrow circumscription following segregation of the genus Enicosanthellum. We reconstruct the phylogeny of Disepalum and related taxa based on four chloroplast and two nuclear DNA regions as a framework for clarifying taxonomic delimitation and assessing evolutionary transitions in key morphological characters. Maximum parsimony, maximum likelihood and Bayesian methods resulted in a consistent, well-resolved and strongly supported topology. Disepalum s.l. is monophyletic and strongly supported, with Disepalum s.str. and Enicosanthellum retrieved as sister groups. Although this topology is consistent with both taxonomic delimitations, the distribution of morphological synapomorphies provides greater support for the inclusion of Enicosanthellum within Disepalum s.l. We propose a novel infrageneric classification with two subgenera. Subgen. Disepalum (= Disepalum s.str.) is supported by numerous synapomorphies, including the reduction of the calyx to two sepals and connation of petals. Subgen. Enicosanthellum lacks obvious morphological synapomorphies, but possesses several diagnostic characters (symplesiomorphies), including a trimerous calyx and free petals in two whorls. We evaluate changes in petal morphology in relation to hypotheses of the genetic control of floral development and suggest that the compression of two petal whorls into one and the associated fusion of contiguous petals may be associated with the loss of the pollination chamber, which in turn may be associated with a shift in primary pollinator. We also suggest that the formation of pollen octads may be selectively advantageous when pollinator visits are infrequent, although this would only be applicable if multiple ovules could be fertilized by each octad; since the flowers are apocarpous, this would require an extragynoecial compitum to enable intercarpellary growth of pollen tubes. We furthermore
Directory of Open Access Journals (Sweden)
Pui-Sze Li
Full Text Available Taxonomic delimitation of Disepalum (Annonaceae is contentious, with some researchers favoring a narrow circumscription following segregation of the genus Enicosanthellum. We reconstruct the phylogeny of Disepalum and related taxa based on four chloroplast and two nuclear DNA regions as a framework for clarifying taxonomic delimitation and assessing evolutionary transitions in key morphological characters. Maximum parsimony, maximum likelihood and Bayesian methods resulted in a consistent, well-resolved and strongly supported topology. Disepalum s.l. is monophyletic and strongly supported, with Disepalum s.str. and Enicosanthellum retrieved as sister groups. Although this topology is consistent with both taxonomic delimitations, the distribution of morphological synapomorphies provides greater support for the inclusion of Enicosanthellum within Disepalum s.l. We propose a novel infrageneric classification with two subgenera. Subgen. Disepalum (= Disepalum s.str. is supported by numerous synapomorphies, including the reduction of the calyx to two sepals and connation of petals. Subgen. Enicosanthellum lacks obvious morphological synapomorphies, but possesses several diagnostic characters (symplesiomorphies, including a trimerous calyx and free petals in two whorls. We evaluate changes in petal morphology in relation to hypotheses of the genetic control of floral development and suggest that the compression of two petal whorls into one and the associated fusion of contiguous petals may be associated with the loss of the pollination chamber, which in turn may be associated with a shift in primary pollinator. We also suggest that the formation of pollen octads may be selectively advantageous when pollinator visits are infrequent, although this would only be applicable if multiple ovules could be fertilized by each octad; since the flowers are apocarpous, this would require an extragynoecial compitum to enable intercarpellary growth of pollen tubes
Directory of Open Access Journals (Sweden)
Müller Kai F
2005-10-01
Full Text Available Abstract Background For parsimony analyses, the most common way to estimate confidence is by resampling plans (nonparametric bootstrap, jackknife, and Bremer support (Decay indices. The recent literature reveals that parameter settings that are quite commonly employed are not those that are recommended by theoretical considerations and by previous empirical studies. The optimal search strategy to be applied during resampling was previously addressed solely via standard search strategies available in PAUP*. The question of a compromise between search extensiveness and improved support accuracy for Bremer support received even less attention. A set of experiments was conducted on different datasets to find an empirical cut-off point at which increased search extensiveness does not significantly change Bremer support and jackknife or bootstrap proportions any more. Results For the number of replicates needed for accurate estimates of support in resampling plans, a diagram is provided that helps to address the question whether apparently different support values really differ significantly. It is shown that the use of random addition cycles and parsimony ratchet iterations during bootstrapping does not translate into higher support, nor does any extension of the search extensiveness beyond the rather moderate effort of TBR (tree bisection and reconnection branch swapping plus saving one tree per replicate. Instead, in case of very large matrices, saving more than one shortest tree per iteration and using a strict consensus tree of these yields decreased support compared to saving only one tree. This can be interpreted as a small risk of overestimating support but should be more than compensated by other factors that counteract an enhanced type I error. With regard to Bremer support, a rule of thumb can be derived stating that not much is gained relative to the surplus computational effort when searches are extended beyond 20 ratchet iterations per
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.
Parsimonious data: How a single Facebook like predicts voting behavior in multiparty systems.
Directory of Open Access Journals (Sweden)
Jakob Bæk Kristensen
Full Text Available This study shows how liking politicians' public Facebook posts can be used as an accurate measure for predicting present-day voter intention in a multiparty system. We highlight that a few, but selective digital traces produce prediction accuracies that are on par or even greater than most current approaches based upon bigger and broader datasets. Combining the online and offline, we connect a subsample of surveyed respondents to their public Facebook activity and apply machine learning classifiers to explore the link between their political liking behaviour and actual voting intention. Through this work, we show that even a single selective Facebook like can reveal as much about political voter intention as hundreds of heterogeneous likes. Further, by including the entire political like history of the respondents, our model reaches prediction accuracies above previous multiparty studies (60-70%. The main contribution of this paper is to show how public like-activity on Facebook allows political profiling of individual users in a multiparty system with accuracies above previous studies. Beside increased accuracies, the paper shows how such parsimonious measures allows us to generalize our findings to the entire population of a country and even across national borders, to other political multiparty systems. The approach in this study relies on data that are publicly available, and the simple setup we propose can with some limitations, be generalized to millions of users in other multiparty systems.
An integer programming formulation of the parsimonious loss of heterozygosity problem.
Catanzaro, Daniele; Labbé, Martine; Halldórsson, Bjarni V
2013-01-01
A loss of heterozygosity (LOH) event occurs when, by the laws of Mendelian inheritance, an individual should be heterozygote at a given site but, due to a deletion polymorphism, is not. Deletions play an important role in human disease and their detection could provide fundamental insights for the development of new diagnostics and treatments. In this paper, we investigate the parsimonious loss of heterozygosity problem (PLOHP), i.e., the problem of partitioning suspected polymorphisms from a set of individuals into a minimum number of deletion areas. Specifically, we generalize Halldórsson et al.'s work by providing a more general formulation of the PLOHP and by showing how one can incorporate different recombination rates and prior knowledge about the locations of deletions. Moreover, we show that the PLOHP can be formulated as a specific version of the clique partition problem in a particular class of graphs called undirected catch-point interval graphs and we prove its general $({\\cal NP})$-hardness. Finally, we provide a state-of-the-art integer programming (IP) formulation and strengthening valid inequalities to exactly solve real instances of the PLOHP containing up to 9,000 individuals and 3,000 SNPs. Our results give perspectives on the mathematics of the PLOHP and suggest new directions on the development of future efficient exact solution approaches.
Komatitsch, Dimitri; Xie, Zhinan; Bozdağ, Ebru; de Andrade, Elliott Sales; Peter, Daniel; Liu, Qinya; Tromp, Jeroen
2016-01-01
We introduce a technique to compute exact anelastic sensitivity kernels in the time domain using parsimonious disk storage. The method is based on a reordering of the time loop of time-domain forward/adjoint wave propagation solvers combined with the use of a memory buffer. It avoids instabilities that occur when time-reversing dissipative wave propagation simulations. The total number of required time steps is unchanged compared to usual acoustic or elastic approaches. The cost is reduced by a factor of 4/3 compared to the case in which anelasticity is partially accounted for by accommodating the effects of physical dispersion. We validate our technique by performing a test in which we compare the Kα sensitivity kernel to the exact kernel obtained by saving the entire forward calculation. This benchmark confirms that our approach is also exact. We illustrate the importance of including full attenuation in the calculation of sensitivity kernels by showing significant differences with physical-dispersion-only kernels.
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.
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.
An objective and parsimonious approach for classifying natural flow regimes at a continental scale
Archfield, S. A.; Kennen, J.; Carlisle, D.; Wolock, D.
2013-12-01
Hydroecological stream classification--the process of grouping streams by similar hydrologic responses and, thereby, similar aquatic habitat--has been widely accepted and is often one of the first steps towards developing ecological flow targets. Despite its importance, the last national classification of streamgauges was completed about 20 years ago. A new classification of 1,534 streamgauges in the contiguous United States is presented using a novel and parsimonious approach to understand similarity in ecological streamflow response. This new classification approach uses seven fundamental daily streamflow statistics (FDSS) rather than winnowing down an uncorrelated subset from 200 or more ecologically relevant streamflow statistics (ERSS) commonly used in hydroecological classification studies. The results of this investigation demonstrate that the distributions of 33 tested ERSS are consistently different among the classes derived from the seven FDSS. It is further shown that classification based solely on the 33 ERSS generally does a poorer job in grouping similar streamgauges than the classification based on the seven FDSS. This new classification approach has the additional advantages of overcoming some of the subjectivity associated with the selection of the classification variables and provides a set of robust continental-scale classes of US streamgauges.
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
Maximum Acceleration Recording Circuit
Bozeman, Richard J., Jr.
1995-01-01
Coarsely digitized maximum levels recorded in blown fuses. Circuit feeds power to accelerometer and makes nonvolatile record of maximum level to which output of accelerometer rises during measurement interval. In comparison with inertia-type single-preset-trip-point mechanical maximum-acceleration-recording devices, circuit weighs less, occupies less space, and records accelerations within narrower bands of uncertainty. In comparison with prior electronic data-acquisition systems designed for same purpose, circuit simpler, less bulky, consumes less power, costs and analysis of data recorded in magnetic or electronic memory devices. Circuit used, for example, to record accelerations to which commodities subjected during transportation on trucks.
Maximum Quantum Entropy Method
Sim, Jae-Hoon; Han, Myung Joon
2018-01-01
Maximum entropy method for analytic continuation is extended by introducing quantum relative entropy. This new method is formulated in terms of matrix-valued functions and therefore invariant under arbitrary unitary transformation of input matrix. As a result, the continuation of off-diagonal elements becomes straightforward. Without introducing any further ambiguity, the Bayesian probabilistic interpretation is maintained just as in the conventional maximum entropy method. The applications o...
International Nuclear Information System (INIS)
Biondi, L.
1998-01-01
The charging for a service is a supplier's remuneration for the expenses incurred in providing it. There are currently two charges for electricity: consumption and maximum demand. While no problem arises about the former, the issue is more complicated for the latter and the analysis in this article tends to show that the annual charge for maximum demand arbitrarily discriminates among consumer groups, to the disadvantage of some [it
Density estimation by maximum quantum entropy
International Nuclear Information System (INIS)
Silver, R.N.; Wallstrom, T.; Martz, H.F.
1993-01-01
A new Bayesian method for non-parametric density estimation is proposed, based on a mathematical analogy to quantum statistical physics. The mathematical procedure is related to maximum entropy methods for inverse problems and image reconstruction. The information divergence enforces global smoothing toward default models, convexity, positivity, extensivity and normalization. The novel feature is the replacement of classical entropy by quantum entropy, so that local smoothing is enforced by constraints on differential operators. The linear response of the estimate is proportional to the covariance. The hyperparameters are estimated by type-II maximum likelihood (evidence). The method is demonstrated on textbook data sets
Ala-Aho, Pertti; Tetzlaff, Doerthe; McNamara, James P; Laudon, Hjalmar; Kormos, Patrick; Soulsby, Chris
2017-07-01
Use of stable water isotopes has become increasingly popular in quantifying water flow paths and travel times in hydrological systems using tracer-aided modeling. In snow-influenced catchments, snowmelt produces a traceable isotopic signal, which differs from original snowfall isotopic composition because of isotopic fractionation in the snowpack. These fractionation processes in snow are relatively well understood, but representing their spatiotemporal variability in tracer-aided studies remains a challenge. We present a novel, parsimonious modeling method to account for the snowpack isotope fractionation and estimate isotope ratios in snowmelt water in a fully spatially distributed manner. Our model introduces two calibration parameters that alone account for the isotopic fractionation caused by sublimation from interception and ground snow storage, and snowmelt fractionation progressively enriching the snowmelt runoff. The isotope routines are linked to a generic process-based snow interception-accumulation-melt model facilitating simulation of spatially distributed snowmelt runoff. We use a synthetic modeling experiment to demonstrate the functionality of the model algorithms in different landscape locations and under different canopy characteristics. We also provide a proof-of-concept model test and successfully reproduce isotopic ratios in snowmelt runoff sampled with snowmelt lysimeters in two long-term experimental catchment with contrasting winter conditions. To our knowledge, the method is the first such tool to allow estimation of the spatially distributed nature of isotopic fractionation in snowpacks and the resulting isotope ratios in snowmelt runoff. The method can thus provide a useful tool for tracer-aided modeling to better understand the integrated nature of flow, mixing, and transport processes in snow-influenced catchments.
Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles.
Directory of Open Access Journals (Sweden)
Bin Lu
Full Text Available The phylogenetic position of turtles within the vertebrate tree of life remains controversial. Conflicting conclusions from different studies are likely a consequence of systematic error in the tree construction process, rather than random error from small amounts of data. Using genomic data, we evaluate the phylogenetic position of turtles with both conventional concatenated data analysis and a "genes as characters" approach. Two datasets were constructed, one with seven species (human, opossum, zebra finch, chicken, green anole, Chinese pond turtle, and western clawed frog and 4584 orthologous genes, and the second with four additional species (soft-shelled turtle, Nile crocodile, royal python, and tuatara but only 1638 genes. Our concatenated data analysis strongly supported turtle as the sister-group to archosaurs (the archosaur hypothesis, similar to several recent genomic data based studies using similar methods. When using genes as characters and gene trees as character-state trees with equal weighting for each gene, however, our parsimony analysis suggested that turtles are possibly sister-group to diapsids, archosaurs, or lepidosaurs. None of these resolutions were strongly supported by bootstraps. Furthermore, our incongruence analysis clearly demonstrated that there is a large amount of inconsistency among genes and most of the conflict relates to the placement of turtles. We conclude that the uncertain placement of turtles is a reflection of the true state of nature. Concatenated data analysis of large and heterogeneous datasets likely suffers from systematic error and over-estimates of confidence as a consequence of a large number of characters. Using genes as characters offers an alternative for phylogenomic analysis. It has potential to reduce systematic error, such as data heterogeneity and long-branch attraction, and it can also avoid problems associated with computation time and model selection. Finally, treating genes as
Parsimonious model for blood glucose level monitoring in type 2 diabetes patients.
Zhao, Fang; Ma, Yan Fen; Wen, Jing Xiao; DU, Yan Fang; Li, Chun Lin; Li, Guang Wei
2014-07-01
To establish the parsimonious model for blood glucose monitoring in patients with type 2 diabetes receiving oral hypoglycemic agent treatment. One hundred and fifty-nine adult Chinese type 2 diabetes patients were randomized to receive rapid-acting or sustained-release gliclazide therapy for 12 weeks. Their blood glucose levels were measured at 10 time points in a 24 h period before and after treatment, and the 24 h mean blood glucose levels were measured. Contribution of blood glucose levels to the mean blood glucose level and HbA1c was assessed by multiple regression analysis. The correlation coefficients of blood glucose level measured at 10 time points to the daily MBG were 0.58-0.74 and 0.59-0.79, respectively, before and after treatment (Pblood glucose levels measured at 6 of the 10 time points could explain 95% and 97% of the changes in MBG before and after treatment. The three blood glucose levels, which were measured at fasting, 2 h after breakfast and before dinner, of the 10 time points could explain 84% and 86% of the changes in MBG before and after treatment, but could only explain 36% and 26% of the changes in HbA1c before and after treatment, and they had a poorer correlation with the HbA1c than with the 24 h MBG. The blood glucose levels measured at fasting, 2 h after breakfast and before dinner truly reflected the change 24 h blood glucose level, suggesting that they are appropriate for the self-monitoring of blood glucose levels in diabetes patients receiving oral anti-diabetes therapy. Copyright © 2014 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.
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
Maximum likelihood as a common computational framework in tomotherapy
International Nuclear Information System (INIS)
Olivera, G.H.; Shepard, D.M.; Reckwerdt, P.J.; Ruchala, K.; Zachman, J.; Fitchard, E.E.; Mackie, T.R.
1998-01-01
Tomotherapy is a dose delivery technique using helical or axial intensity modulated beams. One of the strengths of the tomotherapy concept is that it can incorporate a number of processes into a single piece of equipment. These processes include treatment optimization planning, dose reconstruction and kilovoltage/megavoltage image reconstruction. A common computational technique that could be used for all of these processes would be very appealing. The maximum likelihood estimator, originally developed for emission tomography, can serve as a useful tool in imaging and radiotherapy. We believe that this approach can play an important role in the processes of optimization planning, dose reconstruction and kilovoltage and/or megavoltage image reconstruction. These processes involve computations that require comparable physical methods. They are also based on equivalent assumptions, and they have similar mathematical solutions. As a result, the maximum likelihood approach is able to provide a common framework for all three of these computational problems. We will demonstrate how maximum likelihood methods can be applied to optimization planning, dose reconstruction and megavoltage image reconstruction in tomotherapy. Results for planning optimization, dose reconstruction and megavoltage image reconstruction will be presented. Strengths and weaknesses of the methodology are analysed. Future directions for this work are also suggested. (author)
Maximum likely scale estimation
DEFF Research Database (Denmark)
Loog, Marco; Pedersen, Kim Steenstrup; Markussen, Bo
2005-01-01
A maximum likelihood local scale estimation principle is presented. An actual implementation of the estimation principle uses second order moments of multiple measurements at a fixed location in the image. These measurements consist of Gaussian derivatives possibly taken at several scales and/or ...
Robust Maximum Association Estimators
A. Alfons (Andreas); C. Croux (Christophe); P. Filzmoser (Peter)
2017-01-01
textabstractThe maximum association between two multivariate variables X and Y is defined as the maximal value that a bivariate association measure between one-dimensional projections αX and αY can attain. Taking the Pearson correlation as projection index results in the first canonical correlation
Matsen, Frederick A
2010-06-01
This article introduces constNJ (constrained neighbor-joining), an algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune-regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees that must fit into a recombination, hybridization, or similar network. Rather than first finding a set of trees that are optimal according to a phylogenetic criterion (e.g., likelihood or parsimony) and then attempting to fit them into a network, constNJ estimates the trees while enforcing specified rSPR distance constraints. The primary input for constNJ is a collection of distance matrices derived from sequence blocks which are assumed to have evolved in a tree-like manner, such as blocks of an alignment which do not contain any recombination breakpoints. The other input is a set of rSPR constraint inequalities for any set of pairs of trees. constNJ is consistent and a strict generalization of the neighbor-joining algorithm; it uses the new notion of maximum agreement partitions (MAPs) to assure that the resulting trees satisfy the given rSPR distance constraints.
Urban micro-scale flood risk estimation with parsimonious hydraulic modelling and census data
Directory of Open Access Journals (Sweden)
C. Arrighi
2013-05-01
Full Text Available The adoption of 2007/60/EC Directive requires European countries to implement flood hazard and flood risk maps by the end of 2013. Flood risk is the product of flood hazard, vulnerability and exposure, all three to be estimated with comparable level of accuracy. The route to flood risk assessment is consequently much more than hydraulic modelling of inundation, that is hazard mapping. While hazard maps have already been implemented in many countries, quantitative damage and risk maps are still at a preliminary level. A parsimonious quasi-2-D hydraulic model is here adopted, having many advantages in terms of easy set-up. It is here evaluated as being accurate in flood depth estimation in urban areas with a high-resolution and up-to-date Digital Surface Model (DSM. The accuracy, estimated by comparison with marble-plate records of a historic flood in the city of Florence, is characterized in the downtown's most flooded area by a bias of a very few centimetres and a determination coefficient of 0.73. The average risk is found to be about 14 € m−2 yr−1, corresponding to about 8.3% of residents' income. The spatial distribution of estimated risk highlights a complex interaction between the flood pattern and the building characteristics. As a final example application, the estimated risk values have been used to compare different retrofitting measures. Proceeding through the risk estimation steps, a new micro-scale potential damage assessment method is proposed. This is based on the georeferenced census system as the optimal compromise between spatial detail and open availability of socio-economic data. The results of flood risk assessment at the census section scale resolve most of the risk spatial variability, and they can be easily aggregated to whatever upper scale is needed given that they are geographically defined as contiguous polygons. Damage is calculated through stage–damage curves, starting from census data on building type and
International Nuclear Information System (INIS)
Enslin, J.H.R.
1990-01-01
A well engineered renewable remote energy system, utilizing the principal of Maximum Power Point Tracking can be m ore cost effective, has a higher reliability and can improve the quality of life in remote areas. This paper reports that a high-efficient power electronic converter, for converting the output voltage of a solar panel, or wind generator, to the required DC battery bus voltage has been realized. The converter is controlled to track the maximum power point of the input source under varying input and output parameters. Maximum power point tracking for relative small systems is achieved by maximization of the output current in a battery charging regulator, using an optimized hill-climbing, inexpensive microprocessor based algorithm. Through practical field measurements it is shown that a minimum input source saving of 15% on 3-5 kWh/day systems can easily be achieved. A total cost saving of at least 10-15% on the capital cost of these systems are achievable for relative small rating Remote Area Power Supply systems. The advantages at larger temperature variations and larger power rated systems are much higher. Other advantages include optimal sizing and system monitor and control
International Nuclear Information System (INIS)
Ponman, T.J.
1984-01-01
For some years now two different expressions have been in use for maximum entropy image restoration and there has been some controversy over which one is appropriate for a given problem. Here two further entropies are presented and it is argued that there is no single correct algorithm. The properties of the four different methods are compared using simple 1D simulations with a view to showing how they can be used together to gain as much information as possible about the original object. (orig.)
National Oceanic and Atmospheric Administration, Department of Commerce — The NOAA Paleoclimatology Program archives reconstructions of past climatic conditions derived from paleoclimate proxies, in addition to the Program's large holdings...
Clark, P.U.; Dyke, A.S.; Shakun, J.D.; Carlson, A.E.; Clark, J.; Wohlfarth, B.; Mitrovica, J.X.; Hostetler, S.W.; McCabe, A.M.
2009-01-01
We used 5704 14C, 10Be, and 3He ages that span the interval from 10,000 to 50,000 years ago (10 to 50 ka) to constrain the timing of the Last Glacial Maximum (LGM) in terms of global ice-sheet and mountain-glacier extent. Growth of the ice sheets to their maximum positions occurred between 33.0 and 26.5 ka in response to climate forcing from decreases in northern summer insolation, tropical Pacific sea surface temperatures, and atmospheric CO2. Nearly all ice sheets were at their LGM positions from 26.5 ka to 19 to 20 ka, corresponding to minima in these forcings. The onset of Northern Hemisphere deglaciation 19 to 20 ka was induced by an increase in northern summer insolation, providing the source for an abrupt rise in sea level. The onset of deglaciation of the West Antarctic Ice Sheet occurred between 14 and 15 ka, consistent with evidence that this was the primary source for an abrupt rise in sea level ???14.5 ka.
Directory of Open Access Journals (Sweden)
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
Probable maximum flood control
International Nuclear Information System (INIS)
DeGabriele, C.E.; Wu, C.L.
1991-11-01
This study proposes preliminary design concepts to protect the waste-handling facilities and all shaft and ramp entries to the underground from the probable maximum flood (PMF) in the current design configuration for the proposed Nevada Nuclear Waste Storage Investigation (NNWSI) repository protection provisions were furnished by the United States Bureau of Reclamation (USSR) or developed from USSR data. Proposed flood protection provisions include site grading, drainage channels, and diversion dikes. Figures are provided to show these proposed flood protection provisions at each area investigated. These areas are the central surface facilities (including the waste-handling building and waste treatment building), tuff ramp portal, waste ramp portal, men-and-materials shaft, emplacement exhaust shaft, and exploratory shafts facility
International Nuclear Information System (INIS)
Rust, D.M.
1984-01-01
The successful retrieval and repair of the Solar Maximum Mission (SMM) satellite by Shuttle astronauts in April 1984 permitted continuance of solar flare observations that began in 1980. The SMM carries a soft X ray polychromator, gamma ray, UV and hard X ray imaging spectrometers, a coronagraph/polarimeter and particle counters. The data gathered thus far indicated that electrical potentials of 25 MeV develop in flares within 2 sec of onset. X ray data show that flares are composed of compressed magnetic loops that have come too close together. Other data have been taken on mass ejection, impacts of electron beams and conduction fronts with the chromosphere and changes in the solar radiant flux due to sunspots. 13 references
Functional Maximum Autocorrelation Factors
DEFF Research Database (Denmark)
Larsen, Rasmus; Nielsen, Allan Aasbjerg
2005-01-01
MAF outperforms the functional PCA in concentrating the interesting' spectra/shape variation in one end of the eigenvalue spectrum and allows for easier interpretation of effects. Conclusions. Functional MAF analysis is a useful methods for extracting low dimensional models of temporally or spatially......Purpose. We aim at data where samples of an underlying function are observed in a spatial or temporal layout. Examples of underlying functions are reflectance spectra and biological shapes. We apply functional models based on smoothing splines and generalize the functional PCA in......\\verb+~+\\$\\backslash\\$cite{ramsay97} to functional maximum autocorrelation factors (MAF)\\verb+~+\\$\\backslash\\$cite{switzer85,larsen2001d}. We apply the method to biological shapes as well as reflectance spectra. {\\$\\backslash\\$bf Methods}. MAF seeks linear combination of the original variables that maximize autocorrelation between...
Regularized maximum correntropy machine
Wang, Jim Jing-Yan; Wang, Yunji; Jing, Bing-Yi; Gao, Xin
2015-01-01
In this paper we investigate the usage of regularized correntropy framework for learning of classifiers from noisy labels. The class label predictors learned by minimizing transitional loss functions are sensitive to the noisy and outlying labels of training samples, because the transitional loss functions are equally applied to all the samples. To solve this problem, we propose to learn the class label predictors by maximizing the correntropy between the predicted labels and the true labels of the training samples, under the regularized Maximum Correntropy Criteria (MCC) framework. Moreover, we regularize the predictor parameter to control the complexity of the predictor. The learning problem is formulated by an objective function considering the parameter regularization and MCC simultaneously. By optimizing the objective function alternately, we develop a novel predictor learning algorithm. The experiments on two challenging pattern classification tasks show that it significantly outperforms the machines with transitional loss functions.
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.
Ma, Shuai; Wu, Qi; Hu, Yibo; Wei, Fuwen
2018-05-20
The explosive growth in genomic data has provided novel insights into the conflicting signals hidden in phylogenetic trees. Although some studies have explored the effects of the GC content and parsimony informative sites (PIS) on the phylogenetic tree, the effect of the heterogeneity of the GC content at the first/second/third codon position on parsimony informative sites (GC1/2/3 PIS ) among different species and the effect of PIS on phylogenetic tree construction remain largely unexplored. Here, we used two different mammal genomic datasets to explore the patterns of GC1/2/3 PIS heterogeneity and the effect of PIS on the phylogenetic tree of genes: (i) all GC1/2/3 PIS have obvious heterogeneity between different mammals, and the levels of heterogeneity are GC3 PIS > GC2 PIS > GC1 PIS ; (ii) the number of PIS is positively correlated with the metrics of "good" gene tree topologies, and excluding the third codon position (C3) decreases the quality of gene trees by removing too many PIS. These results provide novel insights into the heterogeneity pattern of GC1/2/3 PIS in mammals and the relationship between GC3/PIS and gene trees. Additionally, it is necessary to carefully consider whether to exclude C3 to improve the quality of gene trees, especially in the super-tree method. Copyright © 2018 Elsevier B.V. All rights reserved.
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.
International Nuclear Information System (INIS)
Ryan, J.
1981-01-01
By understanding the sun, astrophysicists hope to expand this knowledge to understanding other stars. To study the sun, NASA launched a satellite on February 14, 1980. The project is named the Solar Maximum Mission (SMM). The satellite conducted detailed observations of the sun in collaboration with other satellites and ground-based optical and radio observations until its failure 10 months into the mission. The main objective of the SMM was to investigate one aspect of solar activity: solar flares. A brief description of the flare mechanism is given. The SMM satellite was valuable in providing information on where and how a solar flare occurs. A sequence of photographs of a solar flare taken from SMM satellite shows how a solar flare develops in a particular layer of the solar atmosphere. Two flares especially suitable for detailed observations by a joint effort occurred on April 30 and May 21 of 1980. These flares and observations of the flares are discussed. Also discussed are significant discoveries made by individual experiments
International Nuclear Information System (INIS)
Lesavoy, M.A.
1985-01-01
Vaginal reconstruction can be an uncomplicated and straightforward procedure when attention to detail is maintained. The Abbe-McIndoe procedure of lining the neovaginal canal with split-thickness skin grafts has become standard. The use of the inflatable Heyer-Schulte vaginal stent provides comfort to the patient and ease to the surgeon in maintaining approximation of the skin graft. For large vaginal and perineal defects, myocutaneous flaps such as the gracilis island have been extremely useful for correction of radiation-damaged tissue of the perineum or for the reconstruction of large ablative defects. Minimal morbidity and scarring ensue because the donor site can be closed primarily. With all vaginal reconstruction, a compliant patient is a necessity. The patient must wear a vaginal obturator for a minimum of 3 to 6 months postoperatively and is encouraged to use intercourse as an excellent obturator. In general, vaginal reconstruction can be an extremely gratifying procedure for both the functional and emotional well-being of patients
... in moderate exercise and recreational activities, or play sports that put less stress on the knees. ACL reconstruction is generally recommended if: You're an athlete and want to continue in your sport, especially if the sport involves jumping, cutting or ...
Directory of Open Access Journals (Sweden)
Demirhan Erdal
2015-01-01
Full Text Available This paper aims to investigate the effect of exchange-rate stability on real export volume in Turkey, using monthly data for the period February 2001 to January 2010. The Johansen multivariate cointegration method and the parsimonious error-correction model are applied to determine long-run and short-run relationships between real export volume and its determinants. In this study, the conditional variance of the GARCH (1, 1 model is taken as a proxy for exchange-rate stability, and generalized impulse-response functions and variance-decomposition analyses are applied to analyze the dynamic effects of variables on real export volume. The empirical findings suggest that exchangerate stability has a significant positive effect on real export volume, both in the short and the long run.
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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
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Brown James
2007-12-01
Full Text Available This article aims to discuss the various defects that occur with maxillectomy with a full review of the literature and discussion of the advantages and disadvantages of the various techniques described. Reconstruction of the maxilla can be relatively simple for the standard low maxillectomy that does not involve the orbital floor (Class 2. In this situation the structure of the face is less damaged and the there are multiple reconstructive options for the restoration of the maxilla and dental alveolus. If the maxillectomy includes the orbit (Class 4 then problems involving the eye (enopthalmos, orbital dystopia, ectropion and diplopia are avoided which simplifies the reconstruction. Most controversy is associated with the maxillectomy that involves the orbital floor and dental alveolus (Class 3. A case is made for the use of the iliac crest with internal oblique as an ideal option but there are other methods, which may provide a similar result. A multidisciplinary approach to these patients is emphasised which should include a prosthodontist with a special expertise for these defects.
Large-scale runoff generation - parsimonious parameterisation using high-resolution topography
Gong, L.; Halldin, S.; Xu, C.-Y.
2011-08-01
World water resources have primarily been analysed by global-scale hydrological models in the last decades. Runoff generation in many of these models are based on process formulations developed at catchments scales. The division between slow runoff (baseflow) and fast runoff is primarily governed by slope and spatial distribution of effective water storage capacity, both acting at very small scales. Many hydrological models, e.g. VIC, account for the spatial storage variability in terms of statistical distributions; such models are generally proven to perform well. The statistical approaches, however, use the same runoff-generation parameters everywhere in a basin. The TOPMODEL concept, on the other hand, links the effective maximum storage capacity with real-world topography. Recent availability of global high-quality, high-resolution topographic data makes TOPMODEL attractive as a basis for a physically-based runoff-generation algorithm at large scales, even if its assumptions are not valid in flat terrain or for deep groundwater systems. We present a new runoff-generation algorithm for large-scale hydrology based on TOPMODEL concepts intended to overcome these problems. The TRG (topography-derived runoff generation) algorithm relaxes the TOPMODEL equilibrium assumption so baseflow generation is not tied to topography. TRG only uses the topographic index to distribute average storage to each topographic index class. The maximum storage capacity is proportional to the range of topographic index and is scaled by one parameter. The distribution of storage capacity within large-scale grid cells is obtained numerically through topographic analysis. The new topography-derived distribution function is then inserted into a runoff-generation framework similar VIC's. Different basin parts are parameterised by different storage capacities, and different shapes of the storage-distribution curves depend on their topographic characteristics. The TRG algorithm is driven by the
Large-scale runoff generation – parsimonious parameterisation using high-resolution topography
Directory of Open Access Journals (Sweden)
L. Gong
2011-08-01
Full Text Available World water resources have primarily been analysed by global-scale hydrological models in the last decades. Runoff generation in many of these models are based on process formulations developed at catchments scales. The division between slow runoff (baseflow and fast runoff is primarily governed by slope and spatial distribution of effective water storage capacity, both acting at very small scales. Many hydrological models, e.g. VIC, account for the spatial storage variability in terms of statistical distributions; such models are generally proven to perform well. The statistical approaches, however, use the same runoff-generation parameters everywhere in a basin. The TOPMODEL concept, on the other hand, links the effective maximum storage capacity with real-world topography. Recent availability of global high-quality, high-resolution topographic data makes TOPMODEL attractive as a basis for a physically-based runoff-generation algorithm at large scales, even if its assumptions are not valid in flat terrain or for deep groundwater systems. We present a new runoff-generation algorithm for large-scale hydrology based on TOPMODEL concepts intended to overcome these problems. The TRG (topography-derived runoff generation algorithm relaxes the TOPMODEL equilibrium assumption so baseflow generation is not tied to topography. TRG only uses the topographic index to distribute average storage to each topographic index class. The maximum storage capacity is proportional to the range of topographic index and is scaled by one parameter. The distribution of storage capacity within large-scale grid cells is obtained numerically through topographic analysis. The new topography-derived distribution function is then inserted into a runoff-generation framework similar VIC's. Different basin parts are parameterised by different storage capacities, and different shapes of the storage-distribution curves depend on their topographic characteristics. The TRG algorithm
Perils of parsimony: properties of reduced-rank estimates of genetic covariance matrices.
Meyer, Karin; Kirkpatrick, Mark
2008-10-01
Eigenvalues and eigenvectors of covariance matrices are important statistics for multivariate problems in many applications, including quantitative genetics. Estimates of these quantities are subject to different types of bias. This article reviews and extends the existing theory on these biases, considering a balanced one-way classification and restricted maximum-likelihood estimation. Biases are due to the spread of sample roots and arise from ignoring selected principal components when imposing constraints on the parameter space, to ensure positive semidefinite estimates or to estimate covariance matrices of chosen, reduced rank. In addition, it is shown that reduced-rank estimators that consider only the leading eigenvalues and -vectors of the "between-group" covariance matrix may be biased due to selecting the wrong subset of principal components. In a genetic context, with groups representing families, this bias is inverse proportional to the degree of genetic relationship among family members, but is independent of sample size. Theoretical results are supplemented by a simulation study, demonstrating close agreement between predicted and observed bias for large samples. It is emphasized that the rank of the genetic covariance matrix should be chosen sufficiently large to accommodate all important genetic principal components, even though, paradoxically, this may require including a number of components with negligible eigenvalues. A strategy for rank selection in practical analyses is outlined.
Maximum principle and convergence of central schemes based on slope limiters
Mehmetoglu, Orhan; Popov, Bojan
2012-01-01
A maximum principle and convergence of second order central schemes is proven for scalar conservation laws in dimension one. It is well known that to establish a maximum principle a nonlinear piecewise linear reconstruction is needed and a typical choice is the minmod limiter. Unfortunately, this implies that the scheme uses a first order reconstruction at local extrema. The novelty here is that we allow local nonlinear reconstructions which do not reduce to first order at local extrema and still prove maximum principle and convergence. © 2011 American Mathematical Society.
Xu, D.; Agee, E.; Wang, J.; Ivanov, V. Y.
2017-12-01
The increased frequency and severity of droughts in the Amazon region have emphasized the potential vulnerability of the rainforests to heat and drought-induced stresses, highlighting the need to reduce the uncertainty in estimates of regional evapotranspiration (ET) and quantify resilience of the forest. Ground-based observations for estimating ET are resource intensive, making methods based on remotely sensed observations an attractive alternative. Several methodologies have been developed to estimate ET from satellite data, but challenges remained in model parameterization and satellite limited coverage reducing their utility for monitoring biodiverse regions. In this work, we apply a novel surface energy partition method (Maximum Entropy Production; MEP) based on Bayesian probability theory and nonequilibrium thermodynamics to derive ET time series using satellite data for Amazon basin. For a large, sparsely monitored region such as the Amazon, this approach has the advantage methods of only using single level measurements of net radiation, temperature, and specific humidity data. Furthermore, it is not sensitive to the uncertainty of the input data and model parameters. In this first application of MEP theory for a tropical forest biome, we assess its performance at various spatiotemporal scales against a diverse field data sets. Specifically, the objective of this work is to test this method using eddy flux data for several locations across the Amazonia at sub-daily, monthly, and annual scales and compare the new estimates with those using traditional methods. Analyses of the derived ET time series will contribute to reducing the current knowledge gap surrounding the much debated response of the Amazon Basin region to droughts and offer a template for monitoring the long-term changes in global hydrologic cycle due to anthropogenic and natural causes.
Method for position emission mammography image reconstruction
Smith, Mark Frederick
2004-10-12
An image reconstruction method comprising accepting coincidence datat from either a data file or in real time from a pair of detector heads, culling event data that is outside a desired energy range, optionally saving the desired data for each detector position or for each pair of detector pixels on the two detector heads, and then reconstructing the image either by backprojection image reconstruction or by iterative image reconstruction. In the backprojection image reconstruction mode, rays are traced between centers of lines of response (LOR's), counts are then either allocated by nearest pixel interpolation or allocated by an overlap method and then corrected for geometric effects and attenuation and the data file updated. If the iterative image reconstruction option is selected, one implementation is to compute a grid Siddon retracing, and to perform maximum likelihood expectation maiximization (MLEM) computed by either: a) tracing parallel rays between subpixels on opposite detector heads; or b) tracing rays between randomized endpoint locations on opposite detector heads.
Credal Networks under Maximum Entropy
Lukasiewicz, Thomas
2013-01-01
We apply the principle of maximum entropy to select a unique joint probability distribution from the set of all joint probability distributions specified by a credal network. In detail, we start by showing that the unique joint distribution of a Bayesian tree coincides with the maximum entropy model of its conditional distributions. This result, however, does not hold anymore for general Bayesian networks. We thus present a new kind of maximum entropy models, which are computed sequentially. ...
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Barton Robert A
2010-01-01
Full Text Available Abstract Background Brain size is a key adaptive trait. It is often assumed that increasing brain size was a general evolutionary trend in primates, yet recent fossil discoveries have documented brain size decreases in some lineages, raising the question of how general a trend there was for brains to increase in mass over evolutionary time. We present the first systematic phylogenetic analysis designed to answer this question. Results We performed ancestral state reconstructions of three traits (absolute brain mass, absolute body mass, relative brain mass using 37 extant and 23 extinct primate species and three approaches to ancestral state reconstruction: parsimony, maximum likelihood and Bayesian Markov-chain Monte Carlo. Both absolute and relative brain mass generally increased over evolutionary time, but body mass did not. Nevertheless both absolute and relative brain mass decreased along several branches. Applying these results to the contentious case of Homo floresiensis, we find a number of scenarios under which the proposed evolution of Homo floresiensis' small brain appears to be consistent with patterns observed along other lineages, dependent on body mass and phylogenetic position. Conclusions Our results confirm that brain expansion began early in primate evolution and show that increases occurred in all major clades. Only in terms of an increase in absolute mass does the human lineage appear particularly striking, with both the rate of proportional change in mass and relative brain size having episodes of greater expansion elsewhere on the primate phylogeny. However, decreases in brain mass also occurred along branches in all major clades, and we conclude that, while selection has acted to enlarge primate brains, in some lineages this trend has been reversed. Further analyses of the phylogenetic position of Homo floresiensis and better body mass estimates are required to confirm the plausibility of the evolution of its small brain
Dohrmann, Martin; Kelley, Christopher; Kelly, Michelle; Pisera, Andrzej; Hooper, John N A; Reiswig, Henry M
2017-01-01
Glass sponges (Class Hexactinellida) are important components of deep-sea ecosystems and are of interest from geological and materials science perspectives. The reconstruction of their phylogeny with molecular data has only recently begun and shows a better agreement with morphology-based systematics than is typical for other sponge groups, likely because of a greater number of informative morphological characters. However, inconsistencies remain that have far-reaching implications for hypotheses about the evolution of their major skeletal construction types (body plans). Furthermore, less than half of all described extant genera have been sampled for molecular systematics, and several taxa important for understanding skeletal evolution are still missing. Increased taxon sampling for molecular phylogenetics of this group is therefore urgently needed. However, due to their remote habitat and often poorly preserved museum material, sequencing all 126 currently recognized extant genera will be difficult to achieve. Utilizing morphological data to incorporate unsequenced taxa into an integrative systematics framework therefore holds great promise, but it is unclear which methodological approach best suits this task. Here, we increase the taxon sampling of four previously established molecular markers (18S, 28S, and 16S ribosomal DNA, as well as cytochrome oxidase subunit I) by 12 genera, for the first time including representatives of the order Aulocalycoida and the type genus of Dactylocalycidae, taxa that are key to understanding hexactinellid body plan evolution. Phylogenetic analyses suggest that Aulocalycoida is diphyletic and provide further support for the paraphyly of order Hexactinosida; hence these orders are abolished from the Linnean classification. We further assembled morphological character matrices to integrate so far unsequenced genera into phylogenetic analyses in maximum parsimony (MP), maximum likelihood (ML), Bayesian, and morphology-based binning
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.
Eder, Wolfgang; Ives Torres-Silva, Ana; Hohenegger, Johann
2017-04-01
Phylogenetic analysis and trees based on molecular data are broadly applied and used to infer genetical and biogeographic relationship in recent larger foraminifera. Molecular phylogenetic is intensively used within recent nummulitids, however for fossil representatives these trees are only of minor informational value. Hence, within paleontological studies a phylogenetic approach through morphometric analysis is of much higher value. To tackle phylogenetic relationships within the nummulitid family, a much higher number of morphological character must be measured than are commonly used in biometric studies, where mostly parameters describing embryonic size (e.g., proloculus diameter, deuteroloculus diameter) and/or the marginal spiral (e.g., spiral diagrams, spiral indices) are studied. For this purpose 11 growth-independent and/or growth-invariant characters have been used to describe the morphological variability of equatorial thin sections of seven Carribbean nummulitid taxa (Nummulites striatoreticulatus, N. macgillavry, Palaeonummulites willcoxi, P.floridensis, P. soldadensis, P.trinitatensis and P.ocalanus) and one outgroup taxon (Ranikothalia bermudezi). Using these characters, phylogenetic trees were calculated using a restricted maximum likelihood algorithm (REML), and results are cross-checked by ordination and cluster analysis. Square-change parsimony method has been run to reconstruct ancestral states, as well as to simulate the evolution of the chosen characters along the calculated phylogenetic tree and, independent - contrast analysis was used to estimate confidence intervals. Based on these simulations, phylogenetic tendencies of certain characters proposed for nummulitids (e.g., Cope's rule or nepionic acceleration) can be tested, whether these tendencies are valid for the whole family or only for certain clades. At least, within the Carribean nummulitids, phylogenetic trends along some growth-independent characters of the embryo (e.g., first
Duchêne, Véronique; Ferdinand, Séverine; Filliol, Ingrid; Guégan, Jean François; Rastogi, Nalin; Sola, Christophe
2004-03-01
In order to compare phylogenetic methods and to reconstruct the evolutionary history of the tubercle bacilli, a set of macro-array-based genotyping data of Mycobacterium tuberculosis clinical isolates (called spoligotyping for spacer oligonucleotide typing, which assays the variability of the Direct Repeat -DR- locus), was analyzed in four settings of the Caribbean region (Guadeloupe, Martinique, Cuba and Haiti). A set of 47 alleles, split into 26 shared and 21 unique alleles) representative of 321 individual M. tuberculosis clinical isolates from patients residing in the above regions was studied. The following methods (and software in brackets) were investigated: numerical taxonomy distance methods (TAXOTRON), maximum parsimony procedure (PAUP), median-joining networks (NETWORK), and nested clade analysis (GEODIS). Results using these methods were analyzed, compared and discussed. The latter method (GEODIS) was investigated in detail by introducing geographical data together with genetic variability results to detect a link between population structure and population history, and to test the null hypothesis of no association between geography and genotypes. Irrespective of the methods used, our findings demonstrate that a core structure of four families (or clades) of M. tuberculosis strains is highly prevalent within the islands studied, indirectly reflecting passed colonization history of these different settings. Specificity of M. tuberculosis genotypes in each of the islands is discussed in the light of their respective colonial and contemporary histories.
Wang, Zhaoshan; Du, Shuhui; Dayanandan, Selvadurai; Wang, Dongsheng; Zeng, Yanfei; Zhang, Jianguo
2014-01-01
Populus (Salicaceae) is one of the most economically and ecologically important genera of forest trees. The complex reticulate evolution and lack of highly variable orthologous single-copy DNA markers have posed difficulties in resolving the phylogeny of this genus. Based on a large data set of nuclear and plastid DNA sequences, we reconstructed robust phylogeny of Populus using parsimony, maximum likelihood and Bayesian inference methods. The resulting phylogenetic trees showed better resolution at both inter- and intra-sectional level than previous studies. The results revealed that (1) the plastid-based phylogenetic tree resulted in two main clades, suggesting an early divergence of the maternal progenitors of Populus; (2) three advanced sections (Populus, Aigeiros and Tacamahaca) are of hybrid origin; (3) species of the section Tacamahaca could be divided into two major groups based on plastid and nuclear DNA data, suggesting a polyphyletic nature of the section; and (4) many species proved to be of hybrid origin based on the incongruence between plastid and nuclear DNA trees. Reticulate evolution may have played a significant role in the evolution history of Populus by facilitating rapid adaptive radiations into different environments.
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Zhaoshan Wang
Full Text Available Populus (Salicaceae is one of the most economically and ecologically important genera of forest trees. The complex reticulate evolution and lack of highly variable orthologous single-copy DNA markers have posed difficulties in resolving the phylogeny of this genus. Based on a large data set of nuclear and plastid DNA sequences, we reconstructed robust phylogeny of Populus using parsimony, maximum likelihood and Bayesian inference methods. The resulting phylogenetic trees showed better resolution at both inter- and intra-sectional level than previous studies. The results revealed that (1 the plastid-based phylogenetic tree resulted in two main clades, suggesting an early divergence of the maternal progenitors of Populus; (2 three advanced sections (Populus, Aigeiros and Tacamahaca are of hybrid origin; (3 species of the section Tacamahaca could be divided into two major groups based on plastid and nuclear DNA data, suggesting a polyphyletic nature of the section; and (4 many species proved to be of hybrid origin based on the incongruence between plastid and nuclear DNA trees. Reticulate evolution may have played a significant role in the evolution history of Populus by facilitating rapid adaptive radiations into different environments.
Breast Reconstruction After Mastectomy
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Breast reconstruction - implants
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Maximum likelihood of phylogenetic networks.
Jin, Guohua; Nakhleh, Luay; Snir, Sagi; Tuller, Tamir
2006-11-01
Horizontal gene transfer (HGT) is believed to be ubiquitous among bacteria, and plays a major role in their genome diversification as well as their ability to develop resistance to antibiotics. In light of its evolutionary significance and implications for human health, developing accurate and efficient methods for detecting and reconstructing HGT is imperative. In this article we provide a new HGT-oriented likelihood framework for many problems that involve phylogeny-based HGT detection and reconstruction. Beside the formulation of various likelihood criteria, we show that most of these problems are NP-hard, and offer heuristics for efficient and accurate reconstruction of HGT under these criteria. We implemented our heuristics and used them to analyze biological as well as synthetic data. In both cases, our criteria and heuristics exhibited very good performance with respect to identifying the correct number of HGT events as well as inferring their correct location on the species tree. Implementation of the criteria as well as heuristics and hardness proofs are available from the authors upon request. Hardness proofs can also be downloaded at http://www.cs.tau.ac.il/~tamirtul/MLNET/Supp-ML.pdf
Relan, Rishi; Tiels, Koen; Marconato, Anna; Dreesen, Philippe; Schoukens, Johan
2018-05-01
Many real world systems exhibit a quasi linear or weakly nonlinear behavior during normal operation, and a hard saturation effect for high peaks of the input signal. In this paper, a methodology to identify a parsimonious discrete-time nonlinear state space model (NLSS) for the nonlinear dynamical system with relatively short data record is proposed. The capability of the NLSS model structure is demonstrated by introducing two different initialisation schemes, one of them using multivariate polynomials. In addition, a method using first-order information of the multivariate polynomials and tensor decomposition is employed to obtain the parsimonious decoupled representation of the set of multivariate real polynomials estimated during the identification of NLSS model. Finally, the experimental verification of the model structure is done on the cascaded water-benchmark identification problem.
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.
Gray, Richard A; Pathmanathan, Pras
2016-10-01
Elucidating the underlying mechanisms of fatal cardiac arrhythmias requires a tight integration of electrophysiological experiments, models, and theory. Existing models of transmembrane action potential (AP) are complex (resulting in over parameterization) and varied (leading to dissimilar predictions). Thus, simpler models are needed to elucidate the "minimal physiological requirements" to reproduce significant observable phenomena using as few parameters as possible. Moreover, models have been derived from experimental studies from a variety of species under a range of environmental conditions (for example, all existing rabbit AP models incorporate a formulation of the rapid sodium current, INa, based on 30 year old data from chick embryo cell aggregates). Here we develop a simple "parsimonious" rabbit AP model that is mathematically identifiable (i.e., not over parameterized) by combining a novel Hodgkin-Huxley formulation of INa with a phenomenological model of repolarization similar to the voltage dependent, time-independent rectifying outward potassium current (IK). The model was calibrated using the following experimental data sets measured from the same species (rabbit) under physiological conditions: dynamic current-voltage (I-V) relationships during the AP upstroke; rapid recovery of AP excitability during the relative refractory period; and steady-state INa inactivation via voltage clamp. Simulations reproduced several important "emergent" phenomena including cellular alternans at rates > 250 bpm as observed in rabbit myocytes, reentrant spiral waves as observed on the surface of the rabbit heart, and spiral wave breakup. Model variants were studied which elucidated the minimal requirements for alternans and spiral wave break up, namely the kinetics of INa inactivation and the non-linear rectification of IK.The simplicity of the model, and the fact that its parameters have physiological meaning, make it ideal for engendering generalizable mechanistic
Maximum Entropy in Drug Discovery
Directory of Open Access Journals (Sweden)
Chih-Yuan Tseng
2014-07-01
Full Text Available Drug discovery applies multidisciplinary approaches either experimentally, computationally or both ways to identify lead compounds to treat various diseases. While conventional approaches have yielded many US Food and Drug Administration (FDA-approved drugs, researchers continue investigating and designing better approaches to increase the success rate in the discovery process. In this article, we provide an overview of the current strategies and point out where and how the method of maximum entropy has been introduced in this area. The maximum entropy principle has its root in thermodynamics, yet since Jaynes’ pioneering work in the 1950s, the maximum entropy principle has not only been used as a physics law, but also as a reasoning tool that allows us to process information in hand with the least bias. Its applicability in various disciplines has been abundantly demonstrated. We give several examples of applications of maximum entropy in different stages of drug discovery. Finally, we discuss a promising new direction in drug discovery that is likely to hinge on the ways of utilizing maximum entropy.
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
Adaptive algebraic reconstruction technique
International Nuclear Information System (INIS)
Lu Wenkai; Yin Fangfang
2004-01-01
Algebraic reconstruction techniques (ART) are iterative procedures for reconstructing objects from their projections. It is proven that ART can be computationally efficient by carefully arranging the order in which the collected data are accessed during the reconstruction procedure and adaptively adjusting the relaxation parameters. In this paper, an adaptive algebraic reconstruction technique (AART), which adopts the same projection access scheme in multilevel scheme algebraic reconstruction technique (MLS-ART), is proposed. By introducing adaptive adjustment of the relaxation parameters during the reconstruction procedure, one-iteration AART can produce reconstructions with better quality, in comparison with one-iteration MLS-ART. Furthermore, AART outperforms MLS-ART with improved computational efficiency
Maximum stellar iron core mass
Indian Academy of Sciences (India)
60, No. 3. — journal of. March 2003 physics pp. 415–422. Maximum stellar iron core mass. F W GIACOBBE. Chicago Research Center/American Air Liquide ... iron core compression due to the weight of non-ferrous matter overlying the iron cores within large .... thermal equilibrium velocities will tend to be non-relativistic.
Maximum entropy beam diagnostic tomography
International Nuclear Information System (INIS)
Mottershead, C.T.
1985-01-01
This paper reviews the formalism of maximum entropy beam diagnostic tomography as applied to the Fusion Materials Irradiation Test (FMIT) prototype accelerator. The same formalism has also been used with streak camera data to produce an ultrahigh speed movie of the beam profile of the Experimental Test Accelerator (ETA) at Livermore. 11 refs., 4 figs
Maximum entropy beam diagnostic tomography
International Nuclear Information System (INIS)
Mottershead, C.T.
1985-01-01
This paper reviews the formalism of maximum entropy beam diagnostic tomography as applied to the Fusion Materials Irradiation Test (FMIT) prototype accelerator. The same formalism has also been used with streak camera data to produce an ultrahigh speed movie of the beam profile of the Experimental Test Accelerator (ETA) at Livermore
A portable storage maximum thermometer
International Nuclear Information System (INIS)
Fayart, Gerard.
1976-01-01
A clinical thermometer storing the voltage corresponding to the maximum temperature in an analog memory is described. End of the measurement is shown by a lamp switch out. The measurement time is shortened by means of a low thermal inertia platinum probe. This portable thermometer is fitted with cell test and calibration system [fr
Neutron spectra unfolding with maximum entropy and maximum likelihood
International Nuclear Information System (INIS)
Itoh, Shikoh; Tsunoda, Toshiharu
1989-01-01
A new unfolding theory has been established on the basis of the maximum entropy principle and the maximum likelihood method. This theory correctly embodies the Poisson statistics of neutron detection, and always brings a positive solution over the whole energy range. Moreover, the theory unifies both problems of overdetermined and of underdetermined. For the latter, the ambiguity in assigning a prior probability, i.e. the initial guess in the Bayesian sense, has become extinct by virtue of the principle. An approximate expression of the covariance matrix for the resultant spectra is also presented. An efficient algorithm to solve the nonlinear system, which appears in the present study, has been established. Results of computer simulation showed the effectiveness of the present theory. (author)
Directory of Open Access Journals (Sweden)
M. Coustau
2012-04-01
Full Text Available Rainfall-runoff models are crucial tools for the statistical prediction of flash floods and real-time forecasting. This paper focuses on a karstic basin in the South of France and proposes a distributed parsimonious event-based rainfall-runoff model, coherent with the poor knowledge of both evaporative and underground fluxes. The model combines a SCS runoff model and a Lag and Route routing model for each cell of a regular grid mesh. The efficiency of the model is discussed not only to satisfactorily simulate floods but also to get powerful relationships between the initial condition of the model and various predictors of the initial wetness state of the basin, such as the base flow, the Hu2 index from the Meteo-France SIM model and the piezometric levels of the aquifer. The advantage of using meteorological radar rainfall in flood modelling is also assessed. Model calibration proved to be satisfactory by using an hourly time step with Nash criterion values, ranging between 0.66 and 0.94 for eighteen of the twenty-one selected events. The radar rainfall inputs significantly improved the simulations or the assessment of the initial condition of the model for 5 events at the beginning of autumn, mostly in September–October (mean improvement of Nash is 0.09; correction in the initial condition ranges from −205 to 124 mm, but were less efficient for the events at the end of autumn. In this period, the weak vertical extension of the precipitation system and the low altitude of the 0 °C isotherm could affect the efficiency of radar measurements due to the distance between the basin and the radar (~60 km. The model initial condition S is correlated with the three tested predictors (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
On Maximum Entropy and Inference
Directory of Open Access Journals (Sweden)
Luigi Gresele
2017-11-01
Full Text Available Maximum entropy is a powerful concept that entails a sharp separation between relevant and irrelevant variables. It is typically invoked in inference, once an assumption is made on what the relevant variables are, in order to estimate a model from data, that affords predictions on all other (dependent variables. Conversely, maximum entropy can be invoked to retrieve the relevant variables (sufficient statistics directly from the data, once a model is identified by Bayesian model selection. We explore this approach in the case of spin models with interactions of arbitrary order, and we discuss how relevant interactions can be inferred. In this perspective, the dimensionality of the inference problem is not set by the number of parameters in the model, but by the frequency distribution of the data. We illustrate the method showing its ability to recover the correct model in a few prototype cases and discuss its application on a real dataset.
Maximum Water Hammer Sensitivity Analysis
Jalil Emadi; Abbas Solemani
2011-01-01
Pressure waves and Water Hammer occur in a pumping system when valves are closed or opened suddenly or in the case of sudden failure of pumps. Determination of maximum water hammer is considered one of the most important technical and economical items of which engineers and designers of pumping stations and conveyance pipelines should take care. Hammer Software is a recent application used to simulate water hammer. The present study focuses on determining significance of ...
LCLS Maximum Credible Beam Power
International Nuclear Information System (INIS)
Clendenin, J.
2005-01-01
The maximum credible beam power is defined as the highest credible average beam power that the accelerator can deliver to the point in question, given the laws of physics, the beam line design, and assuming all protection devices have failed. For a new accelerator project, the official maximum credible beam power is determined by project staff in consultation with the Radiation Physics Department, after examining the arguments and evidence presented by the appropriate accelerator physicist(s) and beam line engineers. The definitive parameter becomes part of the project's safety envelope. This technical note will first review the studies that were done for the Gun Test Facility (GTF) at SSRL, where a photoinjector similar to the one proposed for the LCLS is being tested. In Section 3 the maximum charge out of the gun for a single rf pulse is calculated. In Section 4, PARMELA simulations are used to track the beam from the gun to the end of the photoinjector. Finally in Section 5 the beam through the matching section and injected into Linac-1 is discussed
Phylogenetic reconstruction methods: an overview.
De Bruyn, Alexandre; Martin, Darren P; Lefeuvre, Pierre
2014-01-01
Initially designed to infer evolutionary relationships based on morphological and physiological characters, phylogenetic reconstruction methods have greatly benefited from recent developments in molecular biology and sequencing technologies with a number of powerful methods having been developed specifically to infer phylogenies from macromolecular data. This chapter, while presenting an overview of basic concepts and methods used in phylogenetic reconstruction, is primarily intended as a simplified step-by-step guide to the construction of phylogenetic trees from nucleotide sequences using fairly up-to-date maximum likelihood methods implemented in freely available computer programs. While the analysis of chloroplast sequences from various Vanilla species is used as an illustrative example, the techniques covered here are relevant to the comparative analysis of homologous sequences datasets sampled from any group of organisms.
Soon, Villu; Saarma, Urmas
2011-07-01
The ignita species group within the genus Chrysis includes over 100 cuckoo wasp species, which all lead a parasitic lifestyle and exhibit very similar morphology. The lack of robust, diagnostic morphological characters has hindered phylogenetic reconstructions and contributed to frequent misidentification and inconsistent interpretations of species in this group. Therefore, molecular phylogenetic analysis is the most suitable approach for resolving the phylogeny and taxonomy of this group. We present a well-resolved phylogeny of the Chrysis ignita species group based on mitochondrial sequence data from 41 ingroup and six outgroup taxa. Although our emphasis was on European taxa, we included samples from most of the distribution range of the C. ignita species group to test for monophyly. We used a continuous mitochondrial DNA sequence consisting of 16S rRNA, tRNA(Val), 12S rRNA and ND4. The location of the ND4 gene at the 3' end of this continuous sequence, following 12S rRNA, represents a novel mitochondrial gene arrangement for insects. Due to difficulties in aligning rRNA genes, two different Bayesian approaches were employed to reconstruct phylogeny: (1) using a reduced data matrix including only those positions that could be aligned with confidence; or (2) using the full sequence dataset while estimating alignment and phylogeny simultaneously. In addition maximum-parsimony and maximum-likelihood analyses were performed to test the robustness of the Bayesian approaches. Although all approaches yielded trees with similar topology, considerably more nodes were resolved with analyses using the full data matrix. Phylogenetic analysis supported the monophyly of the C. ignita species group and divided its species into well-supported clades. The resultant phylogeny was only partly in accordance with published subgroupings based on morphology. Our results suggest that several taxa currently treated as subspecies or names treated as synonyms may in fact constitute
Noise and physical limits to maximum resolution of PET images
Energy Technology Data Exchange (ETDEWEB)
Herraiz, J.L.; Espana, S. [Dpto. Fisica Atomica, Molecular y Nuclear, Facultad de Ciencias Fisicas, Universidad Complutense de Madrid, Avda. Complutense s/n, E-28040 Madrid (Spain); Vicente, E.; Vaquero, J.J.; Desco, M. [Unidad de Medicina y Cirugia Experimental, Hospital GU ' Gregorio Maranon' , E-28007 Madrid (Spain); Udias, J.M. [Dpto. Fisica Atomica, Molecular y Nuclear, Facultad de Ciencias Fisicas, Universidad Complutense de Madrid, Avda. Complutense s/n, E-28040 Madrid (Spain)], E-mail: jose@nuc2.fis.ucm.es
2007-10-01
In this work we show that there is a limit for the maximum resolution achievable with a high resolution PET scanner, as well as for the best signal-to-noise ratio, which are ultimately related to the physical effects involved in the emission and detection of the radiation and thus they cannot be overcome with any particular reconstruction method. These effects prevent the spatial high frequency components of the imaged structures to be recorded by the scanner. Therefore, the information encoded in these high frequencies cannot be recovered by any reconstruction technique. Within this framework, we have determined the maximum resolution achievable for a given acquisition as a function of data statistics and scanner parameters, like the size of the crystals or the inter-crystal scatter. In particular, the noise level in the data as a limitation factor to yield high-resolution images in tomographs with small crystal sizes is outlined. These results have implications regarding how to decide the optimal number of voxels of the reconstructed image or how to design better PET scanners.
Noise and physical limits to maximum resolution of PET images
International Nuclear Information System (INIS)
Herraiz, J.L.; Espana, S.; Vicente, E.; Vaquero, J.J.; Desco, M.; Udias, J.M.
2007-01-01
In this work we show that there is a limit for the maximum resolution achievable with a high resolution PET scanner, as well as for the best signal-to-noise ratio, which are ultimately related to the physical effects involved in the emission and detection of the radiation and thus they cannot be overcome with any particular reconstruction method. These effects prevent the spatial high frequency components of the imaged structures to be recorded by the scanner. Therefore, the information encoded in these high frequencies cannot be recovered by any reconstruction technique. Within this framework, we have determined the maximum resolution achievable for a given acquisition as a function of data statistics and scanner parameters, like the size of the crystals or the inter-crystal scatter. In particular, the noise level in the data as a limitation factor to yield high-resolution images in tomographs with small crystal sizes is outlined. These results have implications regarding how to decide the optimal number of voxels of the reconstructed image or how to design better PET scanners
Generic maximum likely scale selection
DEFF Research Database (Denmark)
Pedersen, Kim Steenstrup; Loog, Marco; Markussen, Bo
2007-01-01
in this work is on applying this selection principle under a Brownian image model. This image model provides a simple scale invariant prior for natural images and we provide illustrative examples of the behavior of our scale estimation on such images. In these illustrative examples, estimation is based......The fundamental problem of local scale selection is addressed by means of a novel principle, which is based on maximum likelihood estimation. The principle is generally applicable to a broad variety of image models and descriptors, and provides a generic scale estimation methodology. The focus...
Stability indicators in network reconstruction.
Directory of Open Access Journals (Sweden)
Michele Filosi
Full Text Available The number of available algorithms to infer a biological network from a dataset of high-throughput measurements is overwhelming and keeps growing. However, evaluating their performance is unfeasible unless a 'gold standard' is available to measure how close the reconstructed network is to the ground truth. One measure of this is the stability of these predictions to data resampling approaches. We introduce NetSI, a family of Network Stability Indicators, to assess quantitatively the stability of a reconstructed network in terms of inference variability due to data subsampling. In order to evaluate network stability, the main NetSI methods use a global/local network metric in combination with a resampling (bootstrap or cross-validation procedure. In addition, we provide two normalized variability scores over data resampling to measure edge weight stability and node degree stability, and then introduce a stability ranking for edges and nodes. A complete implementation of the NetSI indicators, including the Hamming-Ipsen-Mikhailov (HIM network distance adopted in this paper is available with the R package nettools. We demonstrate the use of the NetSI family by measuring network stability on four datasets against alternative network reconstruction methods. First, the effect of sample size on stability of inferred networks is studied in a gold standard framework on yeast-like data from the Gene Net Weaver simulator. We also consider the impact of varying modularity on a set of structurally different networks (50 nodes, from 2 to 10 modules, and then of complex feature covariance structure, showing the different behaviours of standard reconstruction methods based on Pearson correlation, Maximum Information Coefficient (MIC and False Discovery Rate (FDR strategy. Finally, we demonstrate a strong combined effect of different reconstruction methods and phenotype subgroups on a hepatocellular carcinoma miRNA microarray dataset (240 subjects, and we
Breast reconstruction - natural tissue
... flap; TRAM; Latissimus muscle flap with a breast implant; DIEP flap; DIEAP flap; Gluteal free flap; Transverse upper gracilis flap; TUG; Mastectomy - breast reconstruction with natural tissue; Breast cancer - breast reconstruction with natural tissue
Breast reconstruction after mastectomy
Directory of Open Access Journals (Sweden)
Daniel eSchmauss
2016-01-01
Full Text Available Breast cancer is the leading cause of cancer death in women worldwide. Its surgical approach has become less and less mutilating in the last decades. However, the overall number of breast reconstructions has significantly increased lately. Nowadays breast reconstruction should be individualized at its best, first of all taking into consideration oncological aspects of the tumor, neo-/adjuvant treatment and genetic predisposition, but also its timing (immediate versus delayed breast reconstruction, as well as the patient’s condition and wish. This article gives an overview over the various possibilities of breast reconstruction, including implant- and expander-based reconstruction, flap-based reconstruction (vascularized autologous tissue, the combination of implant and flap, reconstruction using non-vascularized autologous fat, as well as refinement surgery after breast reconstruction.
Extreme Maximum Land Surface Temperatures.
Garratt, J. R.
1992-09-01
There are numerous reports in the literature of observations of land surface temperatures. Some of these, almost all made in situ, reveal maximum values in the 50°-70°C range, with a few, made in desert regions, near 80°C. Consideration of a simplified form of the surface energy balance equation, utilizing likely upper values of absorbed shortwave flux (1000 W m2) and screen air temperature (55°C), that surface temperatures in the vicinity of 90°-100°C may occur for dry, darkish soils of low thermal conductivity (0.1-0.2 W m1 K1). Numerical simulations confirm this and suggest that temperature gradients in the first few centimeters of soil may reach 0.5°-1°C mm1 under these extreme conditions. The study bears upon the intrinsic interest of identifying extreme maximum temperatures and yields interesting information regarding the comfort zone of animals (including man).
Cophylogeny reconstruction via an approximate Bayesian computation.
Baudet, C; Donati, B; Sinaimeri, B; Crescenzi, P; Gautier, C; Matias, C; Sagot, M-F
2015-05-01
Despite an increasingly vast literature on cophylogenetic reconstructions for studying host-parasite associations, understanding the common evolutionary history of such systems remains a problem that is far from being solved. Most algorithms for host-parasite reconciliation use an event-based model, where the events include in general (a subset of) cospeciation, duplication, loss, and host switch. All known parsimonious event-based methods then assign a cost to each type of event in order to find a reconstruction of minimum cost. The main problem with this approach is that the cost of the events strongly influences the reconciliation obtained. Some earlier approaches attempt to avoid this problem by finding a Pareto set of solutions and hence by considering event costs under some minimization constraints. To deal with this problem, we developed an algorithm, called Coala, for estimating the frequency of the events based on an approximate Bayesian computation approach. The benefits of this method are 2-fold: (i) it provides more confidence in the set of costs to be used in a reconciliation, and (ii) it allows estimation of the frequency of the events in cases where the data set consists of trees with a large number of taxa. We evaluate our method on simulated and on biological data sets. We show that in both cases, for the same pair of host and parasite trees, different sets of frequencies for the events lead to equally probable solutions. Moreover, often these solutions differ greatly in terms of the number of inferred events. It appears crucial to take this into account before attempting any further biological interpretation of such reconciliations. More generally, we also show that the set of frequencies can vary widely depending on the input host and parasite trees. Indiscriminately applying a standard vector of costs may thus not be a good strategy. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.
Directory of Open Access Journals (Sweden)
Walter J. Gomes
2004-12-01
Full Text Available INTRODUÇÃO: A sobrevida em pacientes com insuficiência cardíaca, assim como após a cirurgia de reconstrução do ventrículo esquerdo (VE, está relacionada ao tamanho da cavidade ventricular esquerda. Também o uso de materiais sintéticos na reconstrução ventricular poderia induzir uma reação inflamatória crônica. Relatamos a modificação da técnica de reconstrução ventricular que elimina a necessidade de retalhos intra-cavitários e de uso de material sintético no fechamento do VE. MÉTODO: Onze pacientes consecutivos com aneurisma de VE, evoluindo em classe funcional (CF III e IV da New York Heart Association foram submetidos à cirurgia de reconstrução ventricular direta sem utilização de retalhos intra-cavitários ou materiais protéticos no fechamento da incisão ventricular. RESULTADOS: Não houve mortalidade cirúrgica ou necessidade de suporte circulatório mecânico. A permanência hospitalar pós-operatória variou de 4 a 7 dias (média de 5,3 ± 1,1 dias. O ecocardiograma de controle, realizado em média 4,6 ± 1,5 meses após a operação, evidenciou redução do diâmetro diastólico de VE de 69,0 ± 7,5 mm, no pré-operatório, para 62,6 ± 5,1 mm, no pós-operatório. A fração de ejeção do VE mostrou aumento de 47,3% ± 6,6% para 56,3% ±10,5%. Com um ano de seguimento, 8 pacientes encontram-se em CF I e 3 em CF II. CONCLUSÃO: Esta técnica, com eliminação de uso de material sintético, pode contribuir para a melhora dos resultados clínicos de pacientes submetidos à reconstrução ventricular esquerda, proporcionando virtual eliminação das áreas acinéticas do VE e potencialmente atenuando, no pós-operatório tardio, a reação inflamatória crônica do miocárdio.BACKGROUND: The outcome of patients with heart failure, as well as after left ventricular reconstruction, is related to the size of the left ventricular cavity. Also the use of synthetic materials in the ventricular reconstruction could
System for memorizing maximum values
Bozeman, Richard J., Jr.
1992-08-01
The invention discloses a system capable of memorizing maximum sensed values. The system includes conditioning circuitry which receives the analog output signal from a sensor transducer. The conditioning circuitry rectifies and filters the analog signal and provides an input signal to a digital driver, which may be either linear or logarithmic. The driver converts the analog signal to discrete digital values, which in turn triggers an output signal on one of a plurality of driver output lines n. The particular output lines selected is dependent on the converted digital value. A microfuse memory device connects across the driver output lines, with n segments. Each segment is associated with one driver output line, and includes a microfuse that is blown when a signal appears on the associated driver output line.
Remarks on the maximum luminosity
Cardoso, Vitor; Ikeda, Taishi; Moore, Christopher J.; Yoo, Chul-Moon
2018-04-01
The quest for fundamental limitations on physical processes is old and venerable. Here, we investigate the maximum possible power, or luminosity, that any event can produce. We show, via full nonlinear simulations of Einstein's equations, that there exist initial conditions which give rise to arbitrarily large luminosities. However, the requirement that there is no past horizon in the spacetime seems to limit the luminosity to below the Planck value, LP=c5/G . Numerical relativity simulations of critical collapse yield the largest luminosities observed to date, ≈ 0.2 LP . We also present an analytic solution to the Einstein equations which seems to give an unboundedly large luminosity; this will guide future numerical efforts to investigate super-Planckian luminosities.
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.
Scintillation counter, maximum gamma aspect
International Nuclear Information System (INIS)
Thumim, A.D.
1975-01-01
A scintillation counter, particularly for counting gamma ray photons, includes a massive lead radiation shield surrounding a sample-receiving zone. The shield is disassembleable into a plurality of segments to allow facile installation and removal of a photomultiplier tube assembly, the segments being so constructed as to prevent straight-line access of external radiation through the shield into radiation-responsive areas. Provisions are made for accurately aligning the photomultiplier tube with respect to one or more sample-transmitting bores extending through the shield to the sample receiving zone. A sample elevator, used in transporting samples into the zone, is designed to provide a maximum gamma-receiving aspect to maximize the gamma detecting efficiency. (U.S.)
Maximum mutual information regularized classification
Wang, Jim Jing-Yan; Wang, Yi; Zhao, Shiguang; Gao, Xin
2014-01-01
In this paper, a novel pattern classification approach is proposed by regularizing the classifier learning to maximize mutual information between the classification response and the true class label. We argue that, with the learned classifier, the uncertainty of the true class label of a data sample should be reduced by knowing its classification response as much as possible. The reduced uncertainty is measured by the mutual information between the classification response and the true class label. To this end, when learning a linear classifier, we propose to maximize the mutual information between classification responses and true class labels of training samples, besides minimizing the classification error and reducing the classifier complexity. An objective function is constructed by modeling mutual information with entropy estimation, and it is optimized by a gradient descend method in an iterative algorithm. Experiments on two real world pattern classification problems show the significant improvements achieved by maximum mutual information regularization.
Improving parallel imaging by jointly reconstructing multi-contrast data.
Bilgic, Berkin; Kim, Tae Hyung; Liao, Congyu; Manhard, Mary Kate; Wald, Lawrence L; Haldar, Justin P; Setsompop, Kawin
2018-08-01
To develop parallel imaging techniques that simultaneously exploit coil sensitivity encoding, image phase prior information, similarities across multiple images, and complementary k-space sampling for highly accelerated data acquisition. We introduce joint virtual coil (JVC)-generalized autocalibrating partially parallel acquisitions (GRAPPA) to jointly reconstruct data acquired with different contrast preparations, and show its application in 2D, 3D, and simultaneous multi-slice (SMS) acquisitions. We extend the joint parallel imaging concept to exploit limited support and smooth phase constraints through Joint (J-) LORAKS formulation. J-LORAKS allows joint parallel imaging from limited autocalibration signal region, as well as permitting partial Fourier sampling and calibrationless reconstruction. We demonstrate highly accelerated 2D balanced steady-state free precession with phase cycling, SMS multi-echo spin echo, 3D multi-echo magnetization-prepared rapid gradient echo, and multi-echo gradient recalled echo acquisitions in vivo. Compared to conventional GRAPPA, proposed joint acquisition/reconstruction techniques provide more than 2-fold reduction in reconstruction error. JVC-GRAPPA takes advantage of additional spatial encoding from phase information and image similarity, and employs different sampling patterns across acquisitions. J-LORAKS achieves a more parsimonious low-rank representation of local k-space by considering multiple images as additional coils. Both approaches provide dramatic improvement in artifact and noise mitigation over conventional single-contrast parallel imaging reconstruction. Magn Reson Med 80:619-632, 2018. © 2018 International Society for Magnetic Resonance in Medicine. © 2018 International Society for Magnetic Resonance in Medicine.
de Beer, Alex G F; Samson, Jean-Sebastièn; Hua, Wei; Huang, Zishuai; Chen, Xiangke; Allen, Heather C; Roke, Sylvie
2011-12-14
We present a direct comparison of phase sensitive sum-frequency generation experiments with phase reconstruction obtained by the maximum entropy method. We show that both methods lead to the same complex spectrum. Furthermore, we discuss the strengths and weaknesses of each of these methods, analyzing possible sources of experimental and analytical errors. A simulation program for maximum entropy phase reconstruction is available at: http://lbp.epfl.ch/. © 2011 American Institute of Physics
A clinical perspective of accelerated statistical reconstruction
International Nuclear Information System (INIS)
Hutton, B.F.; Hudson, H.M.; Beekman, F.J.
1997-01-01
Although the potential benefits of maximum likelihood reconstruction have been recognised for many years, the technique has only recently found widespread popularity in clinical practice. Factors which have contributed to the wider acceptance include improved models for the emission process, better understanding of the properties of the algorithm and, not least, the practicality of application with the development of acceleration schemes and the improved speed of computers. The objective in this article is to present a framework for applying maximum likelihood reconstruction for a wide range of clinically based problems. The article draws particularly on the experience of the three authors in applying an acceleration scheme involving use of ordered subsets to a range of applications. The potential advantages of statistical reconstruction techniques include: (a) the ability to better model the emission and detection process, in order to make the reconstruction converge to a quantitative image, (b) the inclusion of a statistical noise model which results in better noise characteristics, and (c) the possibility to incorporate prior knowledge about the distribution being imaged. The great flexibility in adapting the reconstruction for a specific model results in these techniques having wide applicability to problems in clinical nuclear medicine. (orig.). With 8 figs., 1 tab
Twenty-five years of maximum-entropy principle
Kapur, J. N.
1983-04-01
The strengths and weaknesses of the maximum entropy principle (MEP) are examined and some challenging problems that remain outstanding at the end of the first quarter century of the principle are discussed. The original formalism of the MEP is presented and its relationship to statistical mechanics is set forth. The use of MEP for characterizing statistical distributions, in statistical inference, nonlinear spectral analysis, transportation models, population density models, models for brand-switching in marketing and vote-switching in elections is discussed. Its application to finance, insurance, image reconstruction, pattern recognition, operations research and engineering, biology and medicine, and nonparametric density estimation is considered.
Maximum entropy and Bayesian methods
International Nuclear Information System (INIS)
Smith, C.R.; Erickson, G.J.; Neudorfer, P.O.
1992-01-01
Bayesian probability theory and Maximum Entropy methods are at the core of a new view of scientific inference. These 'new' ideas, along with the revolution in computational methods afforded by modern computers allow astronomers, electrical engineers, image processors of any type, NMR chemists and physicists, and anyone at all who has to deal with incomplete and noisy data, to take advantage of methods that, in the past, have been applied only in some areas of theoretical physics. The title workshops have been the focus of a group of researchers from many different fields, and this diversity is evident in this book. There are tutorial and theoretical papers, and applications in a very wide variety of fields. Almost any instance of dealing with incomplete and noisy data can be usefully treated by these methods, and many areas of theoretical research are being enhanced by the thoughtful application of Bayes' theorem. Contributions contained in this volume present a state-of-the-art overview that will be influential and useful for many years to come
Maximum entropy deconvolution of low count nuclear medicine images
International Nuclear Information System (INIS)
McGrath, D.M.
1998-12-01
Maximum entropy is applied to the problem of deconvolving nuclear medicine images, with special consideration for very low count data. The physics of the formation of scintigraphic images is described, illustrating the phenomena which degrade planar estimates of the tracer distribution. Various techniques which are used to restore these images are reviewed, outlining the relative merits of each. The development and theoretical justification of maximum entropy as an image processing technique is discussed. Maximum entropy is then applied to the problem of planar deconvolution, highlighting the question of the choice of error parameters for low count data. A novel iterative version of the algorithm is suggested which allows the errors to be estimated from the predicted Poisson mean values. This method is shown to produce the exact results predicted by combining Poisson statistics and a Bayesian interpretation of the maximum entropy approach. A facility for total count preservation has also been incorporated, leading to improved quantification. In order to evaluate this iterative maximum entropy technique, two comparable methods, Wiener filtering and a novel Bayesian maximum likelihood expectation maximisation technique, were implemented. The comparison of results obtained indicated that this maximum entropy approach may produce equivalent or better measures of image quality than the compared methods, depending upon the accuracy of the system model used. The novel Bayesian maximum likelihood expectation maximisation technique was shown to be preferable over many existing maximum a posteriori methods due to its simplicity of implementation. A single parameter is required to define the Bayesian prior, which suppresses noise in the solution and may reduce the processing time substantially. Finally, maximum entropy deconvolution was applied as a pre-processing step in single photon emission computed tomography reconstruction of low count data. Higher contrast results were
Photoelectron holography with improved image reconstruction
Energy Technology Data Exchange (ETDEWEB)
Matsushita, Tomohiro, E-mail: matusita@spring8.or.j [Japan Synchrotron Radiation Research Institute (JASRI), SPring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun Hyogo 679-5198 (Japan); Matsui, Fumihiko; Daimon, Hiroshi [Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192 (Japan); Hayashi, Kouichi [Institute for Materials Research, Tohoku University, Sendai 980-8577 (Japan)
2010-05-15
Electron holography is a type of atomic structural analysis, and it has unique features such as element selectivity and the ability to analyze the structure around an impurity in a crystal. In this paper, we introduce the measurement system, electron holograms, a theory for the recording process of an electron hologram, and a theory for the reconstruction algorithm. We describe photoelectron holograms, Auger electron holograms, and the inverse mode of an electron hologram. The reconstruction algorithm, scattering pattern extraction algorithm (SPEA), the SPEA with maximum entropy method (SPEA-MEM), and SPEA-MEM with translational operation are also described.
Photoelectron holography with improved image reconstruction
International Nuclear Information System (INIS)
Matsushita, Tomohiro; Matsui, Fumihiko; Daimon, Hiroshi; Hayashi, Kouichi
2010-01-01
Electron holography is a type of atomic structural analysis, and it has unique features such as element selectivity and the ability to analyze the structure around an impurity in a crystal. In this paper, we introduce the measurement system, electron holograms, a theory for the recording process of an electron hologram, and a theory for the reconstruction algorithm. We describe photoelectron holograms, Auger electron holograms, and the inverse mode of an electron hologram. The reconstruction algorithm, scattering pattern extraction algorithm (SPEA), the SPEA with maximum entropy method (SPEA-MEM), and SPEA-MEM with translational operation are also described.
Maximum entropy principal for transportation
International Nuclear Information System (INIS)
Bilich, F.; Da Silva, R.
2008-01-01
In this work we deal with modeling of the transportation phenomenon for use in the transportation planning process and policy-impact studies. The model developed is based on the dependence concept, i.e., the notion that the probability of a trip starting at origin i is dependent on the probability of a trip ending at destination j given that the factors (such as travel time, cost, etc.) which affect travel between origin i and destination j assume some specific values. The derivation of the solution of the model employs the maximum entropy principle combining a priori multinomial distribution with a trip utility concept. This model is utilized to forecast trip distributions under a variety of policy changes and scenarios. The dependence coefficients are obtained from a regression equation where the functional form is derived based on conditional probability and perception of factors from experimental psychology. The dependence coefficients encode all the information that was previously encoded in the form of constraints. In addition, the dependence coefficients encode information that cannot be expressed in the form of constraints for practical reasons, namely, computational tractability. The equivalence between the standard formulation (i.e., objective function with constraints) and the dependence formulation (i.e., without constraints) is demonstrated. The parameters of the dependence-based trip-distribution model are estimated, and the model is also validated using commercial air travel data in the U.S. In addition, policy impact analyses (such as allowance of supersonic flights inside the U.S. and user surcharge at noise-impacted airports) on air travel are performed.
Accelerated Compressed Sensing Based CT Image Reconstruction.
Hashemi, SayedMasoud; Beheshti, Soosan; Gill, Patrick R; Paul, Narinder S; Cobbold, Richard S C
2015-01-01
In X-ray computed tomography (CT) an important objective is to reduce the radiation dose without significantly degrading the image quality. Compressed sensing (CS) enables the radiation dose to be reduced by producing diagnostic images from a limited number of projections. However, conventional CS-based algorithms are computationally intensive and time-consuming. We propose a new algorithm that accelerates the CS-based reconstruction by using a fast pseudopolar Fourier based Radon transform and rebinning the diverging fan beams to parallel beams. The reconstruction process is analyzed using a maximum-a-posterior approach, which is transformed into a weighted CS problem. The weights involved in the proposed model are calculated based on the statistical characteristics of the reconstruction process, which is formulated in terms of the measurement noise and rebinning interpolation error. Therefore, the proposed method not only accelerates the reconstruction, but also removes the rebinning and interpolation errors. Simulation results are shown for phantoms and a patient. For example, a 512 × 512 Shepp-Logan phantom when reconstructed from 128 rebinned projections using a conventional CS method had 10% error, whereas with the proposed method the reconstruction error was less than 1%. Moreover, computation times of less than 30 sec were obtained using a standard desktop computer without numerical optimization.
Accelerated Compressed Sensing Based CT Image Reconstruction
Directory of Open Access Journals (Sweden)
SayedMasoud Hashemi
2015-01-01
Full Text Available In X-ray computed tomography (CT an important objective is to reduce the radiation dose without significantly degrading the image quality. Compressed sensing (CS enables the radiation dose to be reduced by producing diagnostic images from a limited number of projections. However, conventional CS-based algorithms are computationally intensive and time-consuming. We propose a new algorithm that accelerates the CS-based reconstruction by using a fast pseudopolar Fourier based Radon transform and rebinning the diverging fan beams to parallel beams. The reconstruction process is analyzed using a maximum-a-posterior approach, which is transformed into a weighted CS problem. The weights involved in the proposed model are calculated based on the statistical characteristics of the reconstruction process, which is formulated in terms of the measurement noise and rebinning interpolation error. Therefore, the proposed method not only accelerates the reconstruction, but also removes the rebinning and interpolation errors. Simulation results are shown for phantoms and a patient. For example, a 512 × 512 Shepp-Logan phantom when reconstructed from 128 rebinned projections using a conventional CS method had 10% error, whereas with the proposed method the reconstruction error was less than 1%. Moreover, computation times of less than 30 sec were obtained using a standard desktop computer without numerical optimization.
Bayesian image reconstruction for improving detection performance of muon tomography.
Wang, Guobao; Schultz, Larry J; Qi, Jinyi
2009-05-01
Muon tomography is a novel technology that is being developed for detecting high-Z materials in vehicles or cargo containers. Maximum likelihood methods have been developed for reconstructing the scattering density image from muon measurements. However, the instability of maximum likelihood estimation often results in noisy images and low detectability of high-Z targets. In this paper, we propose using regularization to improve the image quality of muon tomography. We formulate the muon reconstruction problem in a Bayesian framework by introducing a prior distribution on scattering density images. An iterative shrinkage algorithm is derived to maximize the log posterior distribution. At each iteration, the algorithm obtains the maximum a posteriori update by shrinking an unregularized maximum likelihood update. Inverse quadratic shrinkage functions are derived for generalized Laplacian priors and inverse cubic shrinkage functions are derived for generalized Gaussian priors. Receiver operating characteristic studies using simulated data demonstrate that the Bayesian reconstruction can greatly improve the detection performance of muon tomography.
Selected event reconstruction algorithms for the CBM experiment at FAIR
International Nuclear Information System (INIS)
Lebedev, Semen; Höhne, Claudia; Lebedev, Andrey; Ososkov, Gennady
2014-01-01
Development of fast and efficient event reconstruction algorithms is an important and challenging task in the Compressed Baryonic Matter (CBM) experiment at the future FAIR facility. The event reconstruction algorithms have to process terabytes of input data produced in particle collisions. In this contribution, several event reconstruction algorithms are presented. Optimization of the algorithms in the following CBM detectors are discussed: Ring Imaging Cherenkov (RICH) detector, Transition Radiation Detectors (TRD) and Muon Chamber (MUCH). The ring reconstruction algorithm in the RICH is discussed. In TRD and MUCH track reconstruction algorithms are based on track following and Kalman Filter methods. All algorithms were significantly optimized to achieve maximum speed up and minimum memory consumption. Obtained results showed that a significant speed up factor for all algorithms was achieved and the reconstruction efficiency stays at high level.
A phylogenetic reconstruction and emendation of Agaricus section Duploannulatae.
Challen, Michael P; Kerrigan, Richard W; Callac, Philippe
2003-01-01
Agaricus section Duploannulatae comprises the group of species allied with A. bisporus and A. bitorquis. Disagreement exists in the literature regarding the composition of this group. We used DNA sequence data from the ITS segments of the nuclear ribosomal DNA region, in a sample of European and North American isolates, to identify characters shared by this group, to further delimit species-level taxa within the section, and to develop a phylogenetic hypothesis. Shared polymorphisms that suggest a natural limit for section Duploannulatae were found. ITS1 data were assessed using parsimony, distance and maximum likelihood methods of phylogeny. The section Duploannulatae comprised six robust clades. Five clades corresponded to well characterized species from the temperate Northern Hemisphere (A. bisporus, A. subfloccosus, A. bitorquis, A. vaporarius, A. cupressicola). The sixth clade encompassed an A. devoniensis complex. Species concepts, nomenclature, and relationships are discussed and compared with prior reports.
Statistical reconstruction for cosmic ray muon tomography.
Schultz, Larry J; Blanpied, Gary S; Borozdin, Konstantin N; Fraser, Andrew M; Hengartner, Nicolas W; Klimenko, Alexei V; Morris, Christopher L; Orum, Chris; Sossong, Michael J
2007-08-01
Highly penetrating cosmic ray muons constantly shower the earth at a rate of about 1 muon per cm2 per minute. We have developed a technique which exploits the multiple Coulomb scattering of these particles to perform nondestructive inspection without the use of artificial radiation. In prior work [1]-[3], we have described heuristic methods for processing muon data to create reconstructed images. In this paper, we present a maximum likelihood/expectation maximization tomographic reconstruction algorithm designed for the technique. This algorithm borrows much from techniques used in medical imaging, particularly emission tomography, but the statistics of muon scattering dictates differences. We describe the statistical model for multiple scattering, derive the reconstruction algorithm, and present simulated examples. We also propose methods to improve the robustness of the algorithm to experimental errors and events departing from the statistical model.
Robust statistical reconstruction for charged particle tomography
Schultz, Larry Joe; Klimenko, Alexei Vasilievich; Fraser, Andrew Mcleod; Morris, Christopher; Orum, John Christopher; Borozdin, Konstantin N; Sossong, Michael James; Hengartner, Nicolas W
2013-10-08
Systems and methods for charged particle detection including statistical reconstruction of object volume scattering density profiles from charged particle tomographic data to determine the probability distribution of charged particle scattering using a statistical multiple scattering model and determine a substantially maximum likelihood estimate of object volume scattering density using expectation maximization (ML/EM) algorithm to reconstruct the object volume scattering density. The presence of and/or type of object occupying the volume of interest can be identified from the reconstructed volume scattering density profile. The charged particle tomographic data can be cosmic ray muon tomographic data from a muon tracker for scanning packages, containers, vehicles or cargo. The method can be implemented using a computer program which is executable on a computer.
Two-dimensional maximum entropy image restoration
International Nuclear Information System (INIS)
Brolley, J.E.; Lazarus, R.B.; Suydam, B.R.; Trussell, H.J.
1977-07-01
An optical check problem was constructed to test P LOG P maximum entropy restoration of an extremely distorted image. Useful recovery of the original image was obtained. Comparison with maximum a posteriori restoration is made. 7 figures
Image Reconstruction. Chapter 13
Energy Technology Data Exchange (ETDEWEB)
Nuyts, J. [Department of Nuclear Medicine and Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven (Belgium); Matej, S. [Medical Image Processing Group, Department of Radiology, University of Pennsylvania, Philadelphia, PA (United States)
2014-12-15
This chapter discusses how 2‑D or 3‑D images of tracer distribution can be reconstructed from a series of so-called projection images acquired with a gamma camera or a positron emission tomography (PET) system [13.1]. This is often called an ‘inverse problem’. The reconstruction is the inverse of the acquisition. The reconstruction is called an inverse problem because making software to compute the true tracer distribution from the acquired data turns out to be more difficult than the ‘forward’ direction, i.e. making software to simulate the acquisition. There are basically two approaches to image reconstruction: analytical reconstruction and iterative reconstruction. The analytical approach is based on mathematical inversion, yielding efficient, non-iterative reconstruction algorithms. In the iterative approach, the reconstruction problem is reduced to computing a finite number of image values from a finite number of measurements. That simplification enables the use of iterative instead of mathematical inversion. Iterative inversion tends to require more computer power, but it can cope with more complex (and hopefully more accurate) models of the acquisition process.
Update on orbital reconstruction.
Chen, Chien-Tzung; Chen, Yu-Ray
2010-08-01
Orbital trauma is common and frequently complicated by ocular injuries. The recent literature on orbital fracture is analyzed with emphasis on epidemiological data assessment, surgical timing, method of approach and reconstruction materials. Computed tomographic (CT) scan has become a routine evaluation tool for orbital trauma, and mobile CT can be applied intraoperatively if necessary. Concomitant serious ocular injury should be carefully evaluated preoperatively. Patients presenting with nonresolving oculocardiac reflex, 'white-eyed' blowout fracture, or diplopia with a positive forced duction test and CT evidence of orbital tissue entrapment require early surgical repair. Otherwise, enophthalmos can be corrected by late surgery with a similar outcome to early surgery. The use of an endoscope-assisted approach for orbital reconstruction continues to grow, offering an alternative method. Advances in alloplastic materials have improved surgical outcome and shortened operating time. In this review of modern orbital reconstruction, several controversial issues such as surgical indication, surgical timing, method of approach and choice of reconstruction material are discussed. Preoperative fine-cut CT image and thorough ophthalmologic examination are key elements to determine surgical indications. The choice of surgical approach and reconstruction materials much depends on the surgeon's experience and the reconstruction area. Prefabricated alloplastic implants together with image software and stereolithographic models are significant advances that help to more accurately reconstruct the traumatized orbit. The recent evolution of orbit reconstruction improves functional and aesthetic results and minimizes surgical complications.
Energy Technology Data Exchange (ETDEWEB)
Singh, Harpreet; Arvind; Dorai, Kavita, E-mail: kavita@iisermohali.ac.in
2016-09-07
Estimation of quantum states is an important step in any quantum information processing experiment. A naive reconstruction of the density matrix from experimental measurements can often give density matrices which are not positive, and hence not physically acceptable. How do we ensure that at all stages of reconstruction, we keep the density matrix positive? Recently a method has been suggested based on maximum likelihood estimation, wherein the density matrix is guaranteed to be positive definite. We experimentally implement this protocol on an NMR quantum information processor. We discuss several examples and compare with the standard method of state estimation. - Highlights: • State estimation using maximum likelihood method was performed on an NMR quantum information processor. • Physically valid density matrices were obtained every time in contrast to standard quantum state tomography. • Density matrices of several different entangled and separable states were reconstructed for two and three qubits.
Receiver function estimated by maximum entropy deconvolution
Institute of Scientific and Technical Information of China (English)
吴庆举; 田小波; 张乃铃; 李卫平; 曾融生
2003-01-01
Maximum entropy deconvolution is presented to estimate receiver function, with the maximum entropy as the rule to determine auto-correlation and cross-correlation functions. The Toeplitz equation and Levinson algorithm are used to calculate the iterative formula of error-predicting filter, and receiver function is then estimated. During extrapolation, reflective coefficient is always less than 1, which keeps maximum entropy deconvolution stable. The maximum entropy of the data outside window increases the resolution of receiver function. Both synthetic and real seismograms show that maximum entropy deconvolution is an effective method to measure receiver function in time-domain.
PET reconstruction via nonlocal means induced prior.
Hou, Qingfeng; Huang, Jing; Bian, Zhaoying; Chen, Wufan; Ma, Jianhua
2015-01-01
The traditional Bayesian priors for maximum a posteriori (MAP) reconstruction methods usually incorporate local neighborhood interactions that penalize large deviations in parameter estimates for adjacent pixels; therefore, only local pixel differences are utilized. This limits their abilities of penalizing the image roughness. To achieve high-quality PET image reconstruction, this study investigates a MAP reconstruction strategy by incorporating a nonlocal means induced (NLMi) prior (NLMi-MAP) which enables utilizing global similarity information of image. The present NLMi prior approximates the derivative of Gibbs energy function by an NLM filtering process. Specially, the NLMi prior is obtained by subtracting the current image estimation from its NLM filtered version and feeding the residual error back to the reconstruction filter to yield the new image estimation. We tested the present NLMi-MAP method with simulated and real PET datasets. Comparison studies with conventional filtered backprojection (FBP) and a few iterative reconstruction methods clearly demonstrate that the present NLMi-MAP method performs better in lowering noise, preserving image edge and in higher signal to noise ratio (SNR). Extensive experimental results show that the NLMi-MAP method outperforms the existing methods in terms of cross profile, noise reduction, SNR, root mean square error (RMSE) and correlation coefficient (CORR).
Maximum Power from a Solar Panel
Directory of Open Access Journals (Sweden)
Michael Miller
2010-01-01
Full Text Available Solar energy has become a promising alternative to conventional fossil fuel sources. Solar panels are used to collect solar radiation and convert it into electricity. One of the techniques used to maximize the effectiveness of this energy alternative is to maximize the power output of the solar collector. In this project the maximum power is calculated by determining the voltage and the current of maximum power. These quantities are determined by finding the maximum value for the equation for power using differentiation. After the maximum values are found for each time of day, each individual quantity, voltage of maximum power, current of maximum power, and maximum power is plotted as a function of the time of day.
Voting based object boundary reconstruction
Tian, Qi; Zhang, Like; Ma, Jingsheng
2005-07-01
A voting-based object boundary reconstruction approach is proposed in this paper. Morphological technique was adopted in many applications for video object extraction to reconstruct the missing pixels. However, when the missing areas become large, the morphological processing cannot bring us good results. Recently, Tensor voting has attracted people"s attention, and it can be used for boundary estimation on curves or irregular trajectories. However, the complexity of saliency tensor creation limits its applications in real-time systems. An alternative approach based on tensor voting is introduced in this paper. Rather than creating saliency tensors, we use a "2-pass" method for orientation estimation. For the first pass, Sobel d*etector is applied on a coarse boundary image to get the gradient map. In the second pass, each pixel puts decreasing weights based on its gradient information, and the direction with maximum weights sum is selected as the correct orientation of the pixel. After the orientation map is obtained, pixels begin linking edges or intersections along their direction. The approach is applied to various video surveillance clips under different conditions, and the experimental results demonstrate significant improvement on the final extracted objects accuracy.
Hybrid spectral CT reconstruction.
Directory of Open Access Journals (Sweden)
Darin P Clark
Full Text Available Current photon counting x-ray detector (PCD technology faces limitations associated with spectral fidelity and photon starvation. One strategy for addressing these limitations is to supplement PCD data with high-resolution, low-noise data acquired with an energy-integrating detector (EID. In this work, we propose an iterative, hybrid reconstruction technique which combines the spectral properties of PCD data with the resolution and signal-to-noise characteristics of EID data. Our hybrid reconstruction technique is based on an algebraic model of data fidelity which substitutes the EID data into the data fidelity term associated with the PCD reconstruction, resulting in a joint reconstruction problem. Within the split Bregman framework, these data fidelity constraints are minimized subject to additional constraints on spectral rank and on joint intensity-gradient sparsity measured between the reconstructions of the EID and PCD data. Following a derivation of the proposed technique, we apply it to the reconstruction of a digital phantom which contains realistic concentrations of iodine, barium, and calcium encountered in small-animal micro-CT. The results of this experiment suggest reliable separation and detection of iodine at concentrations ≥ 5 mg/ml and barium at concentrations ≥ 10 mg/ml in 2-mm features for EID and PCD data reconstructed with inherent spatial resolutions of 176 μm and 254 μm, respectively (point spread function, FWHM. Furthermore, hybrid reconstruction is demonstrated to enhance spatial resolution within material decomposition results and to improve low-contrast detectability by as much as 2.6 times relative to reconstruction with PCD data only. The parameters of the simulation experiment are based on an in vivo micro-CT experiment conducted in a mouse model of soft-tissue sarcoma. Material decomposition results produced from this in vivo data demonstrate the feasibility of distinguishing two K-edge contrast agents with
Hybrid spectral CT reconstruction
Clark, Darin P.
2017-01-01
Current photon counting x-ray detector (PCD) technology faces limitations associated with spectral fidelity and photon starvation. One strategy for addressing these limitations is to supplement PCD data with high-resolution, low-noise data acquired with an energy-integrating detector (EID). In this work, we propose an iterative, hybrid reconstruction technique which combines the spectral properties of PCD data with the resolution and signal-to-noise characteristics of EID data. Our hybrid reconstruction technique is based on an algebraic model of data fidelity which substitutes the EID data into the data fidelity term associated with the PCD reconstruction, resulting in a joint reconstruction problem. Within the split Bregman framework, these data fidelity constraints are minimized subject to additional constraints on spectral rank and on joint intensity-gradient sparsity measured between the reconstructions of the EID and PCD data. Following a derivation of the proposed technique, we apply it to the reconstruction of a digital phantom which contains realistic concentrations of iodine, barium, and calcium encountered in small-animal micro-CT. The results of this experiment suggest reliable separation and detection of iodine at concentrations ≥ 5 mg/ml and barium at concentrations ≥ 10 mg/ml in 2-mm features for EID and PCD data reconstructed with inherent spatial resolutions of 176 μm and 254 μm, respectively (point spread function, FWHM). Furthermore, hybrid reconstruction is demonstrated to enhance spatial resolution within material decomposition results and to improve low-contrast detectability by as much as 2.6 times relative to reconstruction with PCD data only. The parameters of the simulation experiment are based on an in vivo micro-CT experiment conducted in a mouse model of soft-tissue sarcoma. Material decomposition results produced from this in vivo data demonstrate the feasibility of distinguishing two K-edge contrast agents with a spectral
Interval-based reconstruction for uncertainty quantification in PET
Kucharczak, Florentin; Loquin, Kevin; Buvat, Irène; Strauss, Olivier; Mariano-Goulart, Denis
2018-02-01
A new directed interval-based tomographic reconstruction algorithm, called non-additive interval based expectation maximization (NIBEM) is presented. It uses non-additive modeling of the forward operator that provides intervals instead of single-valued projections. The detailed approach is an extension of the maximum likelihood—expectation maximization algorithm based on intervals. The main motivation for this extension is that the resulting intervals have appealing properties for estimating the statistical uncertainty associated with the reconstructed activity values. After reviewing previously published theoretical concepts related to interval-based projectors, this paper describes the NIBEM algorithm and gives examples that highlight the properties and advantages of this interval valued reconstruction.
Overview of image reconstruction
International Nuclear Information System (INIS)
Marr, R.B.
1980-04-01
Image reconstruction (or computerized tomography, etc.) is any process whereby a function, f, on R/sup n/ is estimated from empirical data pertaining to its integrals, ∫f(x) dx, for some collection of hyperplanes of dimension k < n. The paper begins with background information on how image reconstruction problems have arisen in practice, and describes some of the application areas of past or current interest; these include radioastronomy, optics, radiology and nuclear medicine, electron microscopy, acoustical imaging, geophysical tomography, nondestructive testing, and NMR zeugmatography. Then the various reconstruction algorithms are discussed in five classes: summation, or simple back-projection; convolution, or filtered back-projection; Fourier and other functional transforms; orthogonal function series expansion; and iterative methods. Certain more technical mathematical aspects of image reconstruction are considered from the standpoint of uniqueness, consistency, and stability of solution. The paper concludes by presenting certain open problems. 73 references
The evolving breast reconstruction
DEFF Research Database (Denmark)
Thomsen, Jørn Bo; Gunnarsson, Gudjon Leifur
2014-01-01
The aim of this editorial is to give an update on the use of the propeller thoracodorsal artery perforator flap (TAP/TDAP-flap) within the field of breast reconstruction. The TAP-flap can be dissected by a combined use of a monopolar cautery and a scalpel. Microsurgical instruments are generally...... not needed. The propeller TAP-flap can be designed in different ways, three of these have been published: (I) an oblique upwards design; (II) a horizontal design; (III) an oblique downward design. The latissimus dorsi-flap is a good and reliable option for breast reconstruction, but has been criticized...... for oncoplastic and reconstructive breast surgery and will certainly become an invaluable addition to breast reconstructive methods....
Forging Provincial Reconstruction Teams
National Research Council Canada - National Science Library
Honore, Russel L; Boslego, David V
2007-01-01
The Provincial Reconstruction Team (PRT) training mission completed by First U.S. Army in April 2006 was a joint Service effort to meet a requirement from the combatant commander to support goals in Afghanistan...
Breast Reconstruction with Implants
... your surgical options and discuss the advantages and disadvantages of implant-based reconstruction, and may show you ... Policy Notice of Privacy Practices Notice of Nondiscrimination Advertising Mayo Clinic is a not-for-profit organization ...
Quantitative tomography simulations and reconstruction algorithms
International Nuclear Information System (INIS)
Martz, H.E.; Aufderheide, M.B.; Goodman, D.; Schach von Wittenau, A.; Logan, C.; Hall, J.; Jackson, J.; Slone, D.
2000-01-01
X-ray, neutron and proton transmission radiography and computed tomography (CT) are important diagnostic tools that are at the heart of LLNL's effort to meet the goals of the DOE's Advanced Radiography Campaign. This campaign seeks to improve radiographic simulation and analysis so that radiography can be a useful quantitative diagnostic tool for stockpile stewardship. Current radiographic accuracy does not allow satisfactory separation of experimental effects from the true features of an object's tomographically reconstructed image. This can lead to difficult and sometimes incorrect interpretation of the results. By improving our ability to simulate the whole radiographic and CT system, it will be possible to examine the contribution of system components to various experimental effects, with the goal of removing or reducing them. In this project, we are merging this simulation capability with a maximum-likelihood (constrained-conjugate-gradient-CCG) reconstruction technique yielding a physics-based, forward-model image-reconstruction code. In addition, we seek to improve the accuracy of computed tomography from transmission radiographs by studying what physics is needed in the forward model. During FY 2000, an improved version of the LLNL ray-tracing code called HADES has been coupled with a recently developed LLNL CT algorithm known as CCG. The problem of image reconstruction is expressed as a large matrix equation relating a model for the object being reconstructed to its projections (radiographs). Using a constrained-conjugate-gradient search algorithm, a maximum likelihood solution is sought. This search continues until the difference between the input measured radiographs or projections and the simulated or calculated projections is satisfactorily small
Maximum permissible voltage of YBCO coated conductors
Energy Technology Data Exchange (ETDEWEB)
Wen, J.; Lin, B.; Sheng, J.; Xu, J.; Jin, Z. [Department of Electrical Engineering, Shanghai Jiao Tong University, Shanghai (China); Hong, Z., E-mail: zhiyong.hong@sjtu.edu.cn [Department of Electrical Engineering, Shanghai Jiao Tong University, Shanghai (China); Wang, D.; Zhou, H.; Shen, X.; Shen, C. [Qingpu Power Supply Company, State Grid Shanghai Municipal Electric Power Company, Shanghai (China)
2014-06-15
Highlights: • We examine three kinds of tapes’ maximum permissible voltage. • We examine the relationship between quenching duration and maximum permissible voltage. • Continuous I{sub c} degradations under repetitive quenching where tapes reaching maximum permissible voltage. • The relationship between maximum permissible voltage and resistance, temperature. - Abstract: Superconducting fault current limiter (SFCL) could reduce short circuit currents in electrical power system. One of the most important thing in developing SFCL is to find out the maximum permissible voltage of each limiting element. The maximum permissible voltage is defined as the maximum voltage per unit length at which the YBCO coated conductors (CC) do not suffer from critical current (I{sub c}) degradation or burnout. In this research, the time of quenching process is changed and voltage is raised until the I{sub c} degradation or burnout happens. YBCO coated conductors test in the experiment are from American superconductor (AMSC) and Shanghai Jiao Tong University (SJTU). Along with the quenching duration increasing, the maximum permissible voltage of CC decreases. When quenching duration is 100 ms, the maximum permissible of SJTU CC, 12 mm AMSC CC and 4 mm AMSC CC are 0.72 V/cm, 0.52 V/cm and 1.2 V/cm respectively. Based on the results of samples, the whole length of CCs used in the design of a SFCL can be determined.
Three-dimensional sheaf of ultrasound planes reconstruction (SOUPR) of ablated volumes.
Ingle, Atul; Varghese, Tomy
2014-08-01
This paper presents an algorithm for 3-D reconstruction of tumor ablations using ultrasound shear wave imaging with electrode vibration elastography. Radio-frequency ultrasound data frames are acquired over imaging planes that form a subset of a sheaf of planes sharing a common axis of intersection. Shear wave velocity is estimated separately on each imaging plane using a piecewise linear function fitting technique with a fast optimization routine. An interpolation algorithm then computes velocity maps on a fine grid over a set of C-planes that are perpendicular to the axis of the sheaf. A full 3-D rendering of the ablation can then be created from this stack of C-planes; hence the name "Sheaf Of Ultrasound Planes Reconstruction" or SOUPR. The algorithm is evaluated through numerical simulations and also using data acquired from a tissue mimicking phantom. Reconstruction quality is gauged using contrast and contrast-to-noise ratio measurements and changes in quality from using increasing number of planes in the sheaf are quantified. The highest contrast of 5 dB is seen between the stiffest and softest regions of the phantom. Under certain idealizing assumptions on the true shape of the ablation, good reconstruction quality while maintaining fast processing rate can be obtained with as few as six imaging planes suggesting that the method is suited for parsimonious data acquisitions with very few sparsely chosen imaging planes.
Modeling Mediterranean Ocean climate of the Last Glacial Maximum
Directory of Open Access Journals (Sweden)
U. Mikolajewicz
2011-03-01
Full Text Available A regional ocean general circulation model of the Mediterranean is used to study the climate of the Last Glacial Maximum. The atmospheric forcing for these simulations has been derived from simulations with an atmospheric general circulation model, which in turn was forced with surface conditions from a coarse resolution earth system model. The model is successful in reproducing the general patterns of reconstructed sea surface temperature anomalies with the strongest cooling in summer in the northwestern Mediterranean and weak cooling in the Levantine, although the model underestimates the extent of the summer cooling in the western Mediterranean. However, there is a strong vertical gradient associated with this pattern of summer cooling, which makes the comparison with reconstructions complicated. The exchange with the Atlantic is decreased to roughly one half of its present value, which can be explained by the shallower Strait of Gibraltar as a consequence of lower global sea level. This reduced exchange causes a strong increase of salinity in the Mediterranean in spite of reduced net evaporation.
Savannah River Site radioiodine atmospheric releases and offsite maximum doses
International Nuclear Information System (INIS)
Marter, W.L.
1990-01-01
Radioisotopes of iodine have been released to the atmosphere from the Savannah River Site since 1955. The releases, mostly from the 200-F and 200-H Chemical Separations areas, consist of the isotopes, I-129 and 1-131. Small amounts of 1-131 and 1-133 have also been released from reactor facilities and the Savannah River Laboratory. This reference memorandum was issued to summarize our current knowledge of releases of radioiodines and resultant maximum offsite doses. This memorandum supplements the reference memorandum by providing more detailed supporting technical information. Doses reported in this memorandum from consumption of the milk containing the highest I-131 concentration following the 1961 1-131 release incident are about 1% higher than reported in the reference memorandum. This is the result of using unrounded 1-131 concentrations of I-131 in milk in this memo. It is emphasized here that this technical report does not constitute a dose reconstruction in the same sense as the dose reconstruction effort currently underway at Hanford. This report uses existing published data for radioiodine releases and existing transport and dosimetry models
Climate sensitivity estimated from temperature reconstructions of the Last Glacial Maximum
Schmittner, A.; Urban, N.; Shakun, J. D.; Mahowald, N. M.; Clark, P. U.; Bartlein, P. J.; Mix, A. C.; Rosell-Melé, A.
2011-12-01
In 1959 IJ Good published the discussion "Kinds of Probability" in Science. Good identified (at least) five kinds. The need for (at least) a sixth kind of probability when quantifying uncertainty in the context of climate science is discussed. This discussion brings out the differences in weather-like forecasting tasks and climate-links tasks, with a focus on the effective use both of science and of modelling in support of decision making. Good also introduced the idea of a "Dynamic probability" a probability one expects to change without any additional empirical evidence; the probabilities assigned by a chess playing program when it is only half thorough its analysis being an example. This case is contrasted with the case of "Mature probabilities" where a forecast algorithm (or model) has converged on its asymptotic probabilities and the question hinges in whether or not those probabilities are expected to change significantly before the event in question occurs, even in the absence of new empirical evidence. If so, then how might one report and deploy such immature probabilities in scientific-support of decision-making rationally? Mature Probability is suggested as a useful sixth kind, although Good would doubtlessly argue that we can get by with just one, effective communication with decision makers may be enhanced by speaking as if the others existed. This again highlights the distinction between weather-like contexts and climate-like contexts. In the former context one has access to a relevant climatology (a relevant, arguably informative distribution prior to any model simulations), in the latter context that information is not available although one can fall back on the scientific basis upon which the model itself rests, and estimate the probability that the model output is in fact misinformative. This subjective "probability of a big surprise" is one way to communicate the probability of model-based information holding in practice, the probability that the information the model-based probability is conditioned on holds. It is argued that no model-based climate-like probability forecast is complete without a quantitative estimate of its own irrelevance, and that the clear identification of model-based probability forecasts as mature or immature, are critical elements for maintaining the credibility of science-based decision support, and can shape uncertainty quantification more widely.
Revealing the Maximum Strength in Nanotwinned Copper
DEFF Research Database (Denmark)
Lu, L.; Chen, X.; Huang, Xiaoxu
2009-01-01
boundary–related processes. We investigated the maximum strength of nanotwinned copper samples with different twin thicknesses. We found that the strength increases with decreasing twin thickness, reaching a maximum at 15 nanometers, followed by a softening at smaller values that is accompanied by enhanced...
Modelling maximum canopy conductance and transpiration in ...
African Journals Online (AJOL)
There is much current interest in predicting the maximum amount of water that can be transpired by Eucalyptus trees. It is possible that industrial waste water may be applied as irrigation water to eucalypts and it is important to predict the maximum transpiration rates of these plantations in an attempt to dispose of this ...
Directory of Open Access Journals (Sweden)
Nicola Magnavita
2012-01-01
Full Text Available Purpose. To perform a parsimonious measurement of workplace psychosocial stress in routine occupational health surveillance, this study tests the psychometric properties of a short version of the original Italian effort-reward imbalance (ERI questionnaire. Methods. 1,803 employees (63 percent women from 19 service companies in the Italian region of Latium participated in a cross-sectional survey containing the short version of the ERI questionnaire (16 items and questions related to self-reported health, musculoskeletal complaints and job satisfaction. Exploratory factor analysis, internal consistency of scales and criterion validity were utilized. Results. The internal consistency of scales was satisfactory. Principal component analysis enabled to identify the model’s main factors. Significant associations with health and job satisfaction in the majority of cases support the notion of criterion validity. A high score on the effort-reward ratio was associated with an elevated odds ratio (OR = 2.71; 95% CI 1.86–3.95 of musculoskeletal complaints in the upper arm. Conclusions. The short form of the Italian ERI questionnaire provides a psychometrically useful tool for routine occupational health surveillance, although further validation is recommended.
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.
Energy Technology Data Exchange (ETDEWEB)
Ohri, Nisha [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Cordeiro, Peter G. [Department of Plastic Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Keam, Jennifer [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Ballangrud, Ase [Department of Medical Physics, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Shi Weiji; Zhang Zhigang [Department of Biostatistics and Epidemiology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Nerbun, Claire T.; Woch, Katherine M.; Stein, Nicholas F.; Zhou Ying [Department of Medical Physics, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); McCormick, Beryl; Powell, Simon N. [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Ho, Alice Y., E-mail: HoA1234@mskcc.org [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York (United States)
2012-10-01
Purpose: To assess the impact of immediate breast reconstruction on postmastectomy radiation (PMRT) using dose-volume histogram (DVH) data. Methods and Materials: Two hundred forty-seven women underwent PMRT at our center, 196 with implant reconstruction and 51 without reconstruction. Patients with reconstruction were treated with tangential photons, and patients without reconstruction were treated with en-face electron fields and customized bolus. Twenty percent of patients received internal mammary node (IMN) treatment. The DVH data were compared between groups. Ipsilateral lung parameters included V20 (% volume receiving 20 Gy), V40 (% volume receiving 40 Gy), mean dose, and maximum dose. Heart parameters included V25 (% volume receiving 25 Gy), mean dose, and maximum dose. IMN coverage was assessed when applicable. Chest wall coverage was assessed in patients with reconstruction. Propensity-matched analysis adjusted for potential confounders of laterality and IMN treatment. Results: Reconstruction was associated with lower lung V20, mean dose, and maximum dose compared with no reconstruction (all P<.0001). These associations persisted on propensity-matched analysis (all P<.0001). Heart doses were similar between groups (P=NS). Ninety percent of patients with reconstruction had excellent chest wall coverage (D95 >98%). IMN coverage was superior in patients with reconstruction (D95 >92.0 vs 75.7%, P<.001). IMN treatment significantly increased lung and heart parameters in patients with reconstruction (all P<.05) but minimally affected those without reconstruction (all P>.05). Among IMN-treated patients, only lower lung V20 in those without reconstruction persisted (P=.022), and mean and maximum heart doses were higher than in patients without reconstruction (P=.006, P=.015, respectively). Conclusions: Implant reconstruction does not compromise the technical quality of PMRT when the IMNs are untreated. Treatment technique, not reconstruction, is the primary
International Nuclear Information System (INIS)
Manglos, S.H.
1992-01-01
Transverse image truncation can be a serious problem for human imaging using cone-beam transmission CT (CB-CT) implemented on a conventional rotating gamma camera. This paper presents a reconstruction method to reduce or eliminate the artifacts resulting from the truncation. The method uses a previously published transmission maximum likelihood EM algorithm, adapted to the cone-beam geometry. The reconstruction method is evaluated qualitatively using three human subjects of various dimensions and various degrees of truncation. (author)
Industrial dynamic tomographic reconstruction
International Nuclear Information System (INIS)
Oliveira, Eric Ferreira de
2016-01-01
The state of the art methods applied to industrial processes is currently based on the principles of classical tomographic reconstructions developed for tomographic patterns of static distributions, or is limited to cases of low variability of the density distribution function of the tomographed object. Noise and motion artifacts are the main problems caused by a mismatch in the data from views acquired in different instants. All of these add to the known fact that using a limited amount of data can result in the presence of noise, artifacts and some inconsistencies with the distribution under study. One of the objectives of the present work is to discuss the difficulties that arise from implementing reconstruction algorithms in dynamic tomography that were originally developed for static distributions. Another objective is to propose solutions that aim at reducing a temporal type of information loss caused by employing regular acquisition systems to dynamic processes. With respect to dynamic image reconstruction it was conducted a comparison between different static reconstruction methods, like MART and FBP, when used for dynamic scenarios. This comparison was based on a MCNPx simulation as well as an analytical setup of an aluminum cylinder that moves along the section of a riser during the process of acquisition, and also based on cross section images from CFD techniques. As for the adaptation of current tomographic acquisition systems for dynamic processes, this work established a sequence of tomographic views in a just-in-time fashion for visualization purposes, a form of visually disposing density information as soon as it becomes amenable to image reconstruction. A third contribution was to take advantage of the triple color channel necessary to display colored images in most displays, so that, by appropriately scaling the acquired values of each view in the linear system of the reconstruction, it was possible to imprint a temporal trace into the regularly
Alternative reconstruction after pancreaticoduodenectomy
Directory of Open Access Journals (Sweden)
Cooperman Avram M
2008-01-01
Full Text Available Abstract Background Pancreaticoduodenectomy is the procedure of choice for tumors of the head of the pancreas and periampulla. Despite advances in surgical technique and postoperative care, the procedure continues to carry a high morbidity rate. One of the most common morbidities is delayed gastric emptying with rates of 15%–40%. Following two prolonged cases of delayed gastric emptying, we altered our reconstruction to avoid this complication altogether. Subsequently, our patients underwent a classic pancreaticoduodenectomy with an undivided Roux-en-Y technique for reconstruction. Methods We reviewed the charts of our last 13 Whipple procedures evaluating them for complications, specifically delayed gastric emptying. We compared the outcomes of those patients to a control group of 15 patients who underwent the Whipple procedure with standard reconstruction. Results No instances of delayed gastric emptying occurred in patients who underwent an undivided Roux-en-Y technique for reconstruction. There was 1 wound infection (8%, 1 instance of pneumonia (8%, and 1 instance of bleeding from the gastrojejunal staple line (8%. There was no operative mortality. Conclusion Use of the undivided Roux-en-Y technique for reconstruction following the Whipple procedure may decrease the incidence of delayed gastric emptying. In addition, it has the added benefit of eliminating bile reflux gastritis. Future randomized control trials are recommended to further evaluate the efficacy of the procedure.
International Nuclear Information System (INIS)
Verhaeghe, Jeroen; D'Asseler, Yves; Vandenberghe, Stefaan; Staelens, Steven; Lemahieu, Ignace
2007-01-01
The use of a temporal B-spline basis for the reconstruction of dynamic positron emission tomography data was investigated. Maximum likelihood (ML) reconstructions using an expectation maximization framework and maximum A-posteriori (MAP) reconstructions using the generalized expectation maximization framework were evaluated. Different parameters of the B-spline basis of such as order, number of basis functions and knot placing were investigated in a reconstruction task using simulated dynamic list-mode data. We found that a higher order basis reduced both the bias and variance. Using a higher number of basis functions in the modeling of the time activity curves (TACs) allowed the algorithm to model faster changes of the TACs, however, the TACs became noisier. We have compared ML, Gaussian postsmoothed ML and MAP reconstructions. The noise level in the ML reconstructions was controlled by varying the number of basis functions. The MAP algorithm penalized the integrated squared curvature of the reconstructed TAC. The postsmoothed ML was always outperformed in terms of bias and variance properties by the MAP and ML reconstructions. A simple adaptive knot placing strategy was also developed and evaluated. It is based on an arc length redistribution scheme during the reconstruction. The free knot reconstruction allowed a more accurate reconstruction while reducing the noise level especially for fast changing TACs such as blood input functions. Limiting the number of temporal basis functions combined with the adaptive knot placing strategy is in this case advantageous for regularization purposes when compared to the other regularization techniques
International Nuclear Information System (INIS)
Yeong, C.L.; Torquato, S.
1998-01-01
We formulate a procedure to reconstruct the structure of general random heterogeneous media from limited morphological information by extending the methodology of Rintoul and Torquato [J. Colloid Interface Sci. 186, 467 (1997)] developed for dispersions. The procedure has the advantages that it is simple to implement and generally applicable to multidimensional, multiphase, and anisotropic structures. Furthermore, an extremely useful feature is that it can incorporate any type and number of correlation functions in order to provide as much morphological information as is necessary for accurate reconstruction. We consider a variety of one- and two-dimensional reconstructions, including periodic and random arrays of rods, various distribution of disks, Debye random media, and a Fontainebleau sandstone sample. We also use our algorithm to construct heterogeneous media from specified hypothetical correlation functions, including an exponentially damped, oscillating function as well as physically unrealizable ones. copyright 1998 The American Physical Society
Delayed breast implant reconstruction
DEFF Research Database (Denmark)
Hvilsom, Gitte B.; Hölmich, Lisbet R.; Steding-Jessen, Marianne
2012-01-01
We evaluated the association between radiation therapy and severe capsular contracture or reoperation after 717 delayed breast implant reconstruction procedures (288 1- and 429 2-stage procedures) identified in the prospective database of the Danish Registry for Plastic Surgery of the Breast during...... of radiation therapy was associated with a non-significantly increased risk of reoperation after both 1-stage (HR = 1.4; 95% CI: 0.7-2.5) and 2-stage (HR = 1.6; 95% CI: 0.9-3.1) procedures. Reconstruction failure was highest (13.2%) in the 2-stage procedures with a history of radiation therapy. Breast...... reconstruction approaches other than implants should be seriously considered among women who have received radiation therapy....
MXLKID: a maximum likelihood parameter identifier
International Nuclear Information System (INIS)
Gavel, D.T.
1980-07-01
MXLKID (MaXimum LiKelihood IDentifier) is a computer program designed to identify unknown parameters in a nonlinear dynamic system. Using noisy measurement data from the system, the maximum likelihood identifier computes a likelihood function (LF). Identification of system parameters is accomplished by maximizing the LF with respect to the parameters. The main body of this report briefly summarizes the maximum likelihood technique and gives instructions and examples for running the MXLKID program. MXLKID is implemented LRLTRAN on the CDC7600 computer at LLNL. A detailed mathematical description of the algorithm is given in the appendices. 24 figures, 6 tables
Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states
Directory of Open Access Journals (Sweden)
Grünewald Stefan
2011-01-01
Full Text Available Abstract Background As one of the most widely used parsimony methods for ancestral reconstruction, the Fitch method minimizes the total number of hypothetical substitutions along all branches of a tree to explain the evolution of a character. Due to the extensive usage of this method, it has become a scientific endeavor in recent years to study the reconstruction accuracies of the Fitch method. However, most studies are restricted to 2-state evolutionary models and a study for higher-state models is needed since DNA sequences take the format of 4-state series and protein sequences even have 20 states. Results In this paper, the ambiguous and unambiguous reconstruction accuracy of the Fitch method are studied for N-state evolutionary models. Given an arbitrary phylogenetic tree, a recurrence system is first presented to calculate iteratively the two accuracies. As complete binary tree and comb-shaped tree are the two extremal evolutionary tree topologies according to balance, we focus on the reconstruction accuracies on these two topologies and analyze their asymptotic properties. Then, 1000 Yule trees with 1024 leaves are generated and analyzed to simulate real evolutionary scenarios. It is known that more taxa not necessarily increase the reconstruction accuracies under 2-state models. The result under N-state models is also tested. Conclusions In a large tree with many leaves, the reconstruction accuracies of using all taxa are sometimes less than those of using a leaf subset under N-state models. For complete binary trees, there always exists an equilibrium interval [a, b] of conservation probability, in which the limiting ambiguous reconstruction accuracy equals to the probability of randomly picking a state. The value b decreases with the increase of the number of states, and it seems to converge. When the conservation probability is greater than b, the reconstruction accuracies of the Fitch method increase rapidly. The reconstruction
First results of genetic algorithm application in ML image reconstruction in emission tomography
International Nuclear Information System (INIS)
Smolik, W.
1999-01-01
This paper concerns application of genetic algorithm in maximum likelihood image reconstruction in emission tomography. The example of genetic algorithm for image reconstruction is presented. The genetic algorithm was based on the typical genetic scheme modified due to the nature of solved problem. The convergence of algorithm was examined. The different adaption functions, selection and crossover methods were verified. The algorithm was tested on simulated SPECT data. The obtained results of image reconstruction are discussed. (author)
HEEL BONE RECONSTRUCTIVE OSTEOSYNTHESIS
Directory of Open Access Journals (Sweden)
A. N. Svetashov
2010-01-01
Full Text Available To detect the most appropriate to heel bone injury severity variants of reconstructive osteosynthesis it was analyzed treatment results of 56 patients. In 15 (26.8% patients classic methods of surgical service were applied, in 41 (73.2% cases to restore the defect porous implants were used. Osteosynthesis without heel bone plastic restoration accomplishment was ineffective in 60% patients from control group. Reconstructive osteosynthesis method ensures long-term good functional effect of rehabilitation in 96.4% patients from the basic group.
International Nuclear Information System (INIS)
Chabanat, E.; D'Hondt, J.; Estre, N.; Fruehwirth, R.; Prokofiev, K.; Speer, T.; Vanlaer, P.; Waltenberger, W.
2005-01-01
Due to the high track multiplicity in the final states expected in proton collisions at the LHC experiments, novel vertex reconstruction algorithms are required. The vertex reconstruction problem can be decomposed into a pattern recognition problem ('vertex finding') and an estimation problem ('vertex fitting'). Starting from least-squares methods, robustifications of the classical algorithms are discussed and the statistical properties of the novel methods are shown. A whole set of different approaches for the vertex finding problem is presented and compared in relevant physics channels
Chabanat, E; D'Hondt, J; Vanlaer, P; Prokofiev, K; Speer, T; Frühwirth, R; Waltenberger, W
2005-01-01
Because of the high track multiplicity in the final states expected in proton collisions at the LHC experiments, novel vertex reconstruction algorithms are required. The vertex reconstruction problem can be decomposed into a pattern recognition problem ("vertex finding") and an estimation problem ("vertex fitting"). Starting from least-square methods, ways to render the classical algorithms more robust are discussed and the statistical properties of the novel methods are shown. A whole set of different approaches for the vertex finding problem is presented and compared in relevant physics channels.
A Bayesian nonparametric approach to reconstruction and prediction of random dynamical systems
Merkatas, Christos; Kaloudis, Konstantinos; Hatjispyros, Spyridon J.
2017-06-01
We propose a Bayesian nonparametric mixture model for the reconstruction and prediction from observed time series data, of discretized stochastic dynamical systems, based on Markov Chain Monte Carlo methods. Our results can be used by researchers in physical modeling interested in a fast and accurate estimation of low dimensional stochastic models when the size of the observed time series is small and the noise process (perhaps) is non-Gaussian. The inference procedure is demonstrated specifically in the case of polynomial maps of an arbitrary degree and when a Geometric Stick Breaking mixture process prior over the space of densities, is applied to the additive errors. Our method is parsimonious compared to Bayesian nonparametric techniques based on Dirichlet process mixtures, flexible and general. Simulations based on synthetic time series are presented.
A Bayesian nonparametric approach to reconstruction and prediction of random dynamical systems.
Merkatas, Christos; Kaloudis, Konstantinos; Hatjispyros, Spyridon J
2017-06-01
We propose a Bayesian nonparametric mixture model for the reconstruction and prediction from observed time series data, of discretized stochastic dynamical systems, based on Markov Chain Monte Carlo methods. Our results can be used by researchers in physical modeling interested in a fast and accurate estimation of low dimensional stochastic models when the size of the observed time series is small and the noise process (perhaps) is non-Gaussian. The inference procedure is demonstrated specifically in the case of polynomial maps of an arbitrary degree and when a Geometric Stick Breaking mixture process prior over the space of densities, is applied to the additive errors. Our method is parsimonious compared to Bayesian nonparametric techniques based on Dirichlet process mixtures, flexible and general. Simulations based on synthetic time series are presented.
Primary Vertex Reconstruction for Upgrade at LHCb
Wanczyk, Joanna
2016-01-01
The aim of the LHCb experiment is the study of beauty and charm hadron decays with the main focus on CP violating phenomena and searches for physics beyond the Standard Model through rare decays. At the present, the second data taking period is ongoing, which is called Run II. After 2018 during the long shutdown, the replacement of signicant parts of the LHCb detector is planned. One of main changes is upgrade of the present software and hardware trigger to a more rapid full software trigger. Primary Vertex (PV) is a basis for the further tracking and it is sensitive to the LHC running conditions, which are going to change for the Upgrade. In particular, the center-of-mass collision energy should reach the maximum value of 14 TeV. As a result the quality of the reconstruction has to be studied and the reconstruction algorithms have to be optimized.
Maximum neutron flux in thermal reactors
International Nuclear Information System (INIS)
Strugar, P.V.
1968-12-01
Direct approach to the problem is to calculate spatial distribution of fuel concentration if the reactor core directly using the condition of maximum neutron flux and comply with thermal limitations. This paper proved that the problem can be solved by applying the variational calculus, i.e. by using the maximum principle of Pontryagin. Mathematical model of reactor core is based on the two-group neutron diffusion theory with some simplifications which make it appropriate from maximum principle point of view. Here applied theory of maximum principle are suitable for application. The solution of optimum distribution of fuel concentration in the reactor core is obtained in explicit analytical form. The reactor critical dimensions are roots of a system of nonlinear equations and verification of optimum conditions can be done only for specific examples
Maximum allowable load on wheeled mobile manipulators
International Nuclear Information System (INIS)
Habibnejad Korayem, M.; Ghariblu, H.
2003-01-01
This paper develops a computational technique for finding the maximum allowable load of mobile manipulator during a given trajectory. The maximum allowable loads which can be achieved by a mobile manipulator during a given trajectory are limited by the number of factors; probably the dynamic properties of mobile base and mounted manipulator, their actuator limitations and additional constraints applied to resolving the redundancy are the most important factors. To resolve extra D.O.F introduced by the base mobility, additional constraint functions are proposed directly in the task space of mobile manipulator. Finally, in two numerical examples involving a two-link planar manipulator mounted on a differentially driven mobile base, application of the method to determining maximum allowable load is verified. The simulation results demonstrates the maximum allowable load on a desired trajectory has not a unique value and directly depends on the additional constraint functions which applies to resolve the motion redundancy
Maximum phytoplankton concentrations in the sea
DEFF Research Database (Denmark)
Jackson, G.A.; Kiørboe, Thomas
2008-01-01
A simplification of plankton dynamics using coagulation theory provides predictions of the maximum algal concentration sustainable in aquatic systems. These predictions have previously been tested successfully against results from iron fertilization experiments. We extend the test to data collect...
Pollen-based biome reconstruction for southern Europe and Africa 18,000 yr BP
Elenga, H; Peyron, O; Bonnefille, R; Jolly, D; Cheddadi, R; Guiot, J; Andrieu, [No Value; Bottema, S; Buchet, G; de Beaulieu, JL; Hamilton, AC; Maley, J; Marchant, R; Perez-Obiol, R; Reille, M; Riollet, G; Scott, L; Straka, H; Taylor, D; Van Campo, E; Vincens, A; Laarif, F; Jonson, H
Pollen data from 18,000 C-14 yr sp were compiled in order to reconstruct biome distributions at the last glacial maximum in southern Europe and Africa. Biome reconstructions were made using the objective biomization method applied to pollen counts using a complete list of dryland taxa wherever
Climatic reconstruction in Europe for 18,000 yr B.P. from pollen data
Peyron, O; Guiot, J; Cheddadi, R; Tarasov, P; Reille, M; de Beaulieu, JL; Bottema, S; Andrieu, [No Value
An improved concept of the best analogs method is used to reconstruct the climate of the last glacial maximum from pollen data in Europe. In order to deal with the lack of perfect analogs of fossil assemblages and therefore to obtain a more accurate climate reconstruction, we used a combination of
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.
Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets.
Directory of Open Access Journals (Sweden)
Aitor Blanco-Míguez
2016-12-01
Full Text Available Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains. To address this problem, we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptides. These can be further investigated using in vitro approaches, laying a foundation for the development of biomarker detection and application-specific methods. This novel method aims at reducing large amounts of comparative peptide data to binary matrices while maintaining a high phylogenetic resolution. The underlying case study concerns the Bacillus cereus group, namely the differentiation of Bacillus thuringiensis, Bacillus anthracis and Bacillus cereus strains. Results show that trees based on cytoplasmic and extracellular peptidomes are only marginally in conflict with those based on whole proteomes, as inferred by the established Genome-BLAST Distance Phylogeny (GBDP method. Hence, these results indicate that the two approaches can most likely be used complementarily even in other organismal groups. The obtained results confirm previous reports about the misclassification of many strains within the B. cereus group. Moreover, our method was able to separate the B. anthracis strains with high resolution, similarly to the GBDP results as benchmarked via Bayesian inference and both Maximum Likelihood and Maximum Parsimony. In addition to the presented phylogenomic applications, whole-peptide fingerprinting might also become a valuable complementary technique to digital DNA-DNA hybridization, notably for bacterial classification at the species and subspecies level in the future.
Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets.
Blanco-Míguez, Aitor; Meier-Kolthoff, Jan P; Gutiérrez-Jácome, Alberto; Göker, Markus; Fdez-Riverola, Florentino; Sánchez, Borja; Lourenço, Anália
2016-12-01
Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains. To address this problem, we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptides. These can be further investigated using in vitro approaches, laying a foundation for the development of biomarker detection and application-specific methods. This novel method aims at reducing large amounts of comparative peptide data to binary matrices while maintaining a high phylogenetic resolution. The underlying case study concerns the Bacillus cereus group, namely the differentiation of Bacillus thuringiensis, Bacillus anthracis and Bacillus cereus strains. Results show that trees based on cytoplasmic and extracellular peptidomes are only marginally in conflict with those based on whole proteomes, as inferred by the established Genome-BLAST Distance Phylogeny (GBDP) method. Hence, these results indicate that the two approaches can most likely be used complementarily even in other organismal groups. The obtained results confirm previous reports about the misclassification of many strains within the B. cereus group. Moreover, our method was able to separate the B. anthracis strains with high resolution, similarly to the GBDP results as benchmarked via Bayesian inference and both Maximum Likelihood and Maximum Parsimony. In addition to the presented phylogenomic applications, whole-peptide fingerprinting might also become a valuable complementary technique to digital DNA-DNA hybridization, notably for bacterial classification at the species and subspecies level in the future.
Jackson-Blake, L. A.; Sample, J. E.; Wade, A. J.; Helliwell, R. C.; Skeffington, R. A.
2017-07-01
Catchment-scale water quality models are increasingly popular tools for exploring the potential effects of land management, land use change and climate change on water quality. However, the dynamic, catchment-scale nutrient models in common usage are complex, with many uncertain parameters requiring calibration, limiting their usability and robustness. A key question is whether this complexity is justified. To explore this, we developed a parsimonious phosphorus model, SimplyP, incorporating a rainfall-runoff model and a biogeochemical model able to simulate daily streamflow, suspended sediment, and particulate and dissolved phosphorus dynamics. The model's complexity was compared to one popular nutrient model, INCA-P, and the performance of the two models was compared in a small rural catchment in northeast Scotland. For three land use classes, less than six SimplyP parameters must be determined through calibration, the rest may be based on measurements, while INCA-P has around 40 unmeasurable parameters. Despite substantially simpler process-representation, SimplyP performed comparably to INCA-P in both calibration and validation and produced similar long-term projections in response to changes in land management. Results support the hypothesis that INCA-P is overly complex for the study catchment. We hope our findings will help prompt wider model comparison exercises, as well as debate among the water quality modeling community as to whether today's models are fit for purpose. Simpler models such as SimplyP have the potential to be useful management and research tools, building blocks for future model development (prototype code is freely available), or benchmarks against which more complex models could be evaluated.
Frisch, Amos; Colombo, Roberto; Michaelovsky, Elena; Karpati, Mazal; Goldman, Boleslaw; Peleg, Leah
2004-03-01
The 1278insTATC is the most prevalent beta-hexosaminidase A ( HEXA) gene mutation causing Tay-Sachs disease (TSD), one of the four lysosomal storage diseases (LSDs) occurring at elevated frequencies among Ashkenazi Jews (AJs). To investigate the genetic history of this mutation in the AJ population, a conserved haplotype (D15S981:175-D15S131:240-D15S1050:284-D15S197:144-D15S188:418) was identified in 1278insTATC chromosomes from 55 unrelated AJ individuals (15 homozygotes and 40 heterozygotes for the TSD mutation), suggesting the occurrence of a common founder. When two methods were used for analysis of linkage disequilibrium (LD) between flanking polymorphic markers and the disease locus and for the study of the decay of LD over time, the estimated age of the insertion was found to be 40+/-12 generations (95% confidence interval: 30-50 generations), so that the most recent common ancestor of the mutation-bearing chromosomes would date to the 8th-9th century. This corresponds with the demographic expansion of AJs in central Europe, following the founding of the Ashkenaz settlement in the early Middle Ages. The results are consistent with the geographic distribution of the main TSD mutation, 1278insTATC being more common in central Europe, and with the coalescent times of mutations causing two other LSDs, Gaucher disease and mucolipidosis type IV. Evidence for the absence of a determinant positive selection (heterozygote advantage) over the mutation is provided by a comparison between the estimated age of 1278insTATC and the probability of the current AJ frequency of the mutant allele as a function of its age, calculated by use of a branching-process model. Therefore, the founder effect in a rapidly expanding population arising from a bottleneck provides a robust parsimonious hypothesis explaining the spread of 1278insTATC-linked TSD in AJ individuals.
Reconstructing Neutrino Mass Spectrum
Smirnov, A. Yu.
1999-01-01
Reconstruction of the neutrino mass spectrum and lepton mixing is one of the fundamental problems of particle physics. In this connection we consider two central topics: (i) the origin of large lepton mixing, (ii) possible existence of new (sterile) neutrino states. We discuss also possible relation between large mixing and existence of sterile neutrinos.
Position reconstruction in LUX
Akerib, D. S.; Alsum, S.; Araújo, H. M.; Bai, X.; Bailey, A. J.; Balajthy, J.; Beltrame, P.; Bernard, E. P.; Bernstein, A.; Biesiadzinski, T. P.; Boulton, E. M.; Brás, P.; Byram, D.; Cahn, S. B.; Carmona-Benitez, M. C.; Chan, C.; Currie, A.; Cutter, J. E.; Davison, T. J. R.; Dobi, A.; Druszkiewicz, E.; Edwards, B. N.; Fallon, S. R.; Fan, A.; Fiorucci, S.; Gaitskell, R. J.; Genovesi, J.; Ghag, C.; Gilchriese, M. G. D.; Hall, C. R.; Hanhardt, M.; Haselschwardt, S. J.; Hertel, S. A.; Hogan, D. P.; Horn, M.; Huang, D. Q.; Ignarra, C. M.; Jacobsen, R. G.; Ji, W.; Kamdin, K.; Kazkaz, K.; Khaitan, D.; Knoche, R.; Larsen, N. A.; Lenardo, B. G.; Lesko, K. T.; Lindote, A.; Lopes, M. I.; Manalaysay, A.; Mannino, R. L.; Marzioni, M. F.; McKinsey, D. N.; Mei, D.-M.; Mock, J.; Moongweluwan, M.; Morad, J. A.; Murphy, A. St. J.; Nehrkorn, C.; Nelson, H. N.; Neves, F.; O'Sullivan, K.; Oliver-Mallory, K. C.; Palladino, K. J.; Pease, E. K.; Rhyne, C.; Shaw, S.; Shutt, T. A.; Silva, C.; Solmaz, M.; Solovov, V. N.; Sorensen, P.; Sumner, T. J.; Szydagis, M.; Taylor, D. J.; Taylor, W. C.; Tennyson, B. P.; Terman, P. A.; Tiedt, D. R.; To, W. H.; Tripathi, M.; Tvrznikova, L.; Uvarov, S.; Velan, V.; Verbus, J. R.; Webb, R. C.; White, J. T.; Whitis, T. J.; Witherell, M. S.; Wolfs, F. L. H.; Xu, J.; Yazdani, K.; Young, S. K.; Zhang, C.
2018-02-01
The (x, y) position reconstruction method used in the analysis of the complete exposure of the Large Underground Xenon (LUX) experiment is presented. The algorithm is based on a statistical test that makes use of an iterative method to recover the photomultiplier tube (PMT) light response directly from the calibration data. The light response functions make use of a two dimensional functional form to account for the photons reflected on the inner walls of the detector. To increase the resolution for small pulses, a photon counting technique was employed to describe the response of the PMTs. The reconstruction was assessed with calibration data including 83mKr (releasing a total energy of 41.5 keV) and 3H (β- with Q = 18.6 keV) decays, and a deuterium-deuterium (D-D) neutron beam (2.45 MeV) . Within the detector's fiducial volume, the reconstruction has achieved an (x, y) position uncertainty of σ = 0.82 cm and σ = 0.17 cm for events of only 200 and 4,000 detected electroluminescence photons respectively. Such signals are associated with electron recoils of energies ~0.25 keV and ~10 keV, respectively. The reconstructed position of the smallest events with a single electron emitted from the liquid surface (22 detected photons) has a horizontal (x, y) uncertainty of 2.13 cm.
CAT reconstruction and potting comparison of a LMFBR fuel bundle
International Nuclear Information System (INIS)
Betten, P.R.; Tow, D.M.
1984-04-01
A standard Liquid Metal Fast Breeder Reactor (LMFBR) subassembly used in the Experimental Breeder Reactor II (EBR-II) was investigated, by remote techniques, for fuel bundle distortion by both nondestructive and destructive methods, and the results from both methods were compared. The non-destructive method employed neutron tomography to reconstruct the locations of fuel elements through the use of a maximum entropy reconstruction algorithm known as MENT. The destructive method consisted of ''potting'' (a technique that embeds and permanently fixes the fuel elements in a solid matrix) the subassembly, and then cutting and polishing the individual sections. The comparison indicated that the tomography reconstruction provided good results in describing the bundle geometry and spacer-wire locations, with the overall resolution being on the order of a spacer-wire diameter. A dimensional consistency check indicated that the element and spacer-wire dimensions were accurately reproduced in the reconstruction
Muon track reconstruction and data selection techniques in AMANDA
International Nuclear Information System (INIS)
Ahrens, J.; Bai, X.; Bay, R.; Barwick, S.W.; Becka, T.; Becker, J.K.; Becker, K.-H.; Bernardini, E.; Bertrand, D.; Biron, A.; Boersma, D.J.; Boeser, S.; Botner, O.; Bouchta, A.; Bouhali, O.; Burgess, T.; Carius, S.; Castermans, T.; Chirkin, D.; Collin, B.; Conrad, J.; Cooley, J.; Cowen, D.F.; Davour, A.; De Clercq, C.; DeYoung, T.; Desiati, P.; Dewulf, J.-P.; Ekstroem, P.; Feser, T.; Gaug, M.; Gaisser, T.K.; Ganugapati, R.; Geenen, H.; Gerhardt, L.; Gross, A.; Goldschmidt, A.; Hallgren, A.; Halzen, F.; Hanson, K.; Hardtke, R.; Harenberg, T.; Hauschildt, T.; Helbing, K.; Hellwig, M.; Herquet, P.; Hill, G.C.; Hubert, D.; Hughey, B.; Hulth, P.O.; Hultqvist, K.; Hundertmark, S.; Jacobsen, J.; Karle, A.; Kestel, M.; Koepke, L.; Kowalski, M.; Kuehn, K.; Lamoureux, J.I.; Leich, H.; Leuthold, M.; Lindahl, P.; Liubarsky, I.; Madsen, J.; Marciniewski, P.; Matis, H.S.; McParland, C.P.; Messarius, T.; Minaeva, Y.; Miocinovic, P.; Mock, P.C.; Morse, R.; Muenich, K.S.; Nam, J.; Nahnhauer, R.; Neunhoeffer, T.; Niessen, P.; Nygren, D.R.; Oegelman, H.; Olbrechts, Ph.; Perez de los Heros, C.; Pohl, A.C.; Porrata, R.; Price, P.B.; Przybylski, G.T.; Rawlins, K.; Resconi, E.; Rhode, W.; Ribordy, M.; Richter, S.; Rodriguez Martino, J.; Ross, D.; Sander, H.-G.; Schinarakis, K.; Schlenstedt, S.; Schmidt, T.; Schneider, D.; Schwarz, R.; Silvestri, A.; Solarz, M.; Spiczak, G.M.; Spiering, C.; Stamatikos, M.; Steele, D.; Steffen, P.; Stokstad, R.G.; Sulanke, K.-H.; Streicher, O.; Taboada, I.; Thollander, L.; Tilav, S.; Wagner, W.; Walck, C.; Wang, Y.-R.; Wiebusch, C.H.; Wiedemann, C.; Wischnewski, R.; Wissing, H.; Woschnagg, K.; Yodh, G.
2004-01-01
The Antarctic Muon And Neutrino Detector Array (AMANDA) is a high-energy neutrino telescope operating at the geographic South Pole. It is a lattice of photo-multiplier tubes buried deep in the polar ice between 1500 and 2000 m. The primary goal of this detector is to discover astrophysical sources of high-energy neutrinos. A high-energy muon neutrino coming through the earth from the Northern Hemisphere can be identified by the secondary muon moving upward through the detector. The muon tracks are reconstructed with a maximum likelihood method. It models the arrival times and amplitudes of Cherenkov photons registered by the photo-multipliers. This paper describes the different methods of reconstruction, which have been successfully implemented within AMANDA. Strategies for optimizing the reconstruction performance and rejecting background are presented. For a typical analysis procedure the direction of tracks are reconstructed with about 2 deg. accuracy
Spectral reconstruction for shifted-excitation Raman difference spectroscopy (SERDS).
Guo, Shuxia; Chernavskaia, Olga; Popp, Jürgen; Bocklitz, Thomas
2018-08-15
Fluorescence emission is one of the major obstacles to apply Raman spectroscopy in biological investigations. It is usually several orders more intense than Raman scattering and hampers further analysis. In cases where the fluorescence emission is too intense to be efficiently removed via routine mathematical baseline correction algorithms, an alternative approach is needed. One alternative approach is shifted-excitation Raman difference spectroscopy (SERDS), where two Raman spectra are recorded with two slightly different excitation wavelengths. Ideally, the fluorescence emission at the two excitations does not change while the Raman spectrum shifts according to the excitation wavelength. Hence the fluorescence is removed in the difference of the two recorded Raman spectra. For better interpretability a spectral reconstruction procedure is necessary to recover the fluorescence-free Raman spectrum. This is challenging due to the intensity variations between the two recorded Raman spectra caused by unavoidable experimental changes as well as the presence of noise. Existent approaches suffer from drawbacks like spectral resolution loss, fluorescence residual, and artefacts. In this contribution, we proposed a reconstruction method based on non-negative least squares (NNLS), where the intensity variations between the two measurements are utilized in the reconstruction model. The method achieved fluorescence-free reconstruction on three real-world SERDS datasets without significant information loss. Thereafter, we quantified the performance of the reconstruction based on artificial datasets from four aspects: reconstructed spectral resolution, precision of reconstruction, signal-to-noise-ratio (SNR), and fluorescence residual. The artificial datasets were constructed with varied Raman to fluorescence intensity ratio (RFIR), SNR, full-width at half-maximum (FWHM), excitation wavelength shift, and fluorescence variation between the two spectra. It was demonstrated that
Time-of-flight PET image reconstruction using origin ensembles
Wülker, Christian; Sitek, Arkadiusz; Prevrhal, Sven
2015-03-01
The origin ensemble (OE) algorithm is a novel statistical method for minimum-mean-square-error (MMSE) reconstruction of emission tomography data. This method allows one to perform reconstruction entirely in the image domain, i.e. without the use of forward and backprojection operations. We have investigated the OE algorithm in the context of list-mode (LM) time-of-flight (TOF) PET reconstruction. In this paper, we provide a general introduction to MMSE reconstruction, and a statistically rigorous derivation of the OE algorithm. We show how to efficiently incorporate TOF information into the reconstruction process, and how to correct for random coincidences and scattered events. To examine the feasibility of LM-TOF MMSE reconstruction with the OE algorithm, we applied MMSE-OE and standard maximum-likelihood expectation-maximization (ML-EM) reconstruction to LM-TOF phantom data with a count number typically registered in clinical PET examinations. We analyzed the convergence behavior of the OE algorithm, and compared reconstruction time and image quality to that of the EM algorithm. In summary, during the reconstruction process, MMSE-OE contrast recovery (CRV) remained approximately the same, while background variability (BV) gradually decreased with an increasing number of OE iterations. The final MMSE-OE images exhibited lower BV and a slightly lower CRV than the corresponding ML-EM images. The reconstruction time of the OE algorithm was approximately 1.3 times longer. At the same time, the OE algorithm can inherently provide a comprehensive statistical characterization of the acquired data. This characterization can be utilized for further data processing, e.g. in kinetic analysis and image registration, making the OE algorithm a promising approach in a variety of applications.
Maximum Entropy Method in Moessbauer Spectroscopy - a Problem of Magnetic Texture
International Nuclear Information System (INIS)
Satula, D.; Szymanski, K.; Dobrzynski, L.
2011-01-01
A reconstruction of the three dimensional distribution of the hyperfine magnetic field, isomer shift and texture parameter z from the Moessbauer spectra by the maximum entropy method is presented. The method was tested on the simulated spectrum consisting of two Gaussian hyperfine field distributions with different values of the texture parameters. It is shown that proper prior has to be chosen in order to arrive at the physically meaningful results. (authors)
Three Dimensional Sheaf of Ultrasound Planes Reconstruction (SOUPR) of Ablated Volumes
Ingle, Atul; Varghese, Tomy
2014-01-01
This paper presents an algorithm for three dimensional reconstruction of tumor ablations using ultrasound shear wave imaging with electrode vibration elastography. Radiofrequency ultrasound data frames are acquired over imaging planes that form a subset of a sheaf of planes sharing a common axis of intersection. Shear wave velocity is estimated separately on each imaging plane using a piecewise linear function fitting technique with a fast optimization routine. An interpolation algorithm then computes velocity maps on a fine grid over a set of C-planes that are perpendicular to the axis of the sheaf. A full three dimensional rendering of the ablation can then be created from this stack of C-planes; hence the name “Sheaf Of Ultrasound Planes Reconstruction” or SOUPR. The algorithm is evaluated through numerical simulations and also using data acquired from a tissue mimicking phantom. Reconstruction quality is gauged using contrast and contrast-to-noise ratio measurements and changes in quality from using increasing number of planes in the sheaf are quantified. The highest contrast of 5 dB is seen between the stiffest and softest regions of the phantom. Under certain idealizing assumptions on the true shape of the ablation, good reconstruction quality while maintaining fast processing rate can be obtained with as few as 6 imaging planes suggesting that the method is suited for parsimonious data acquisitions with very few sparsely chosen imaging planes. PMID:24808405
Maximum gravitational redshift of white dwarfs
International Nuclear Information System (INIS)
Shapiro, S.L.; Teukolsky, S.A.
1976-01-01
The stability of uniformly rotating, cold white dwarfs is examined in the framework of the Parametrized Post-Newtonian (PPN) formalism of Will and Nordtvedt. The maximum central density and gravitational redshift of a white dwarf are determined as functions of five of the nine PPN parameters (γ, β, zeta 2 , zeta 3 , and zeta 4 ), the total angular momentum J, and the composition of the star. General relativity predicts that the maximum redshifts is 571 km s -1 for nonrotating carbon and helium dwarfs, but is lower for stars composed of heavier nuclei. Uniform rotation can increase the maximum redshift to 647 km s -1 for carbon stars (the neutronization limit) and to 893 km s -1 for helium stars (the uniform rotation limit). The redshift distribution of a larger sample of white dwarfs may help determine the composition of their cores
Maximum entropy analysis of EGRET data
DEFF Research Database (Denmark)
Pohl, M.; Strong, A.W.
1997-01-01
EGRET data are usually analysed on the basis of the Maximum-Likelihood method \\cite{ma96} in a search for point sources in excess to a model for the background radiation (e.g. \\cite{hu97}). This method depends strongly on the quality of the background model, and thus may have high systematic unce...... uncertainties in region of strong and uncertain background like the Galactic Center region. Here we show images of such regions obtained by the quantified Maximum-Entropy method. We also discuss a possible further use of MEM in the analysis of problematic regions of the sky....
The Maximum Resource Bin Packing Problem
DEFF Research Database (Denmark)
Boyar, J.; Epstein, L.; Favrholdt, L.M.
2006-01-01
Usually, for bin packing problems, we try to minimize the number of bins used or in the case of the dual bin packing problem, maximize the number or total size of accepted items. This paper presents results for the opposite problems, where we would like to maximize the number of bins used...... algorithms, First-Fit-Increasing and First-Fit-Decreasing for the maximum resource variant of classical bin packing. For the on-line variant, we define maximum resource variants of classical and dual bin packing. For dual bin packing, no on-line algorithm is competitive. For classical bin packing, we find...
Shower maximum detector for SDC calorimetry
International Nuclear Information System (INIS)
Ernwein, J.
1994-01-01
A prototype for the SDC end-cap (EM) calorimeter complete with a pre-shower and a shower maximum detector was tested in beams of electrons and Π's at CERN by an SDC subsystem group. The prototype was manufactured from scintillator tiles and strips read out with 1 mm diameter wave-length shifting fibers. The design and construction of the shower maximum detector is described, and results of laboratory tests on light yield and performance of the scintillator-fiber system are given. Preliminary results on energy and position measurements with the shower max detector in the test beam are shown. (authors). 4 refs., 5 figs
Topics in Bayesian statistics and maximum entropy
International Nuclear Information System (INIS)
Mutihac, R.; Cicuttin, A.; Cerdeira, A.; Stanciulescu, C.
1998-12-01
Notions of Bayesian decision theory and maximum entropy methods are reviewed with particular emphasis on probabilistic inference and Bayesian modeling. The axiomatic approach is considered as the best justification of Bayesian analysis and maximum entropy principle applied in natural sciences. Particular emphasis is put on solving the inverse problem in digital image restoration and Bayesian modeling of neural networks. Further topics addressed briefly include language modeling, neutron scattering, multiuser detection and channel equalization in digital communications, genetic information, and Bayesian court decision-making. (author)
Algebraic reconstruction techniques for spectral reconstruction in diffuse optical tomography
International Nuclear Information System (INIS)
Brendel, Bernhard; Ziegler, Ronny; Nielsen, Tim
2008-01-01
Reconstruction in diffuse optical tomography (DOT) necessitates solving the diffusion equation, which is nonlinear with respect to the parameters that have to be reconstructed. Currently applied solving methods are based on the linearization of the equation. For spectral three-dimensional reconstruction, the emerging equation system is too large for direct inversion, but the application of iterative methods is feasible. Computational effort and speed of convergence of these iterative methods are crucial since they determine the computation time of the reconstruction. In this paper, the iterative methods algebraic reconstruction technique (ART) and conjugated gradients (CGs) as well as a new modified ART method are investigated for spectral DOT reconstruction. The aim of the modified ART scheme is to speed up the convergence by considering the specific conditions of spectral reconstruction. As a result, it converges much faster to favorable results than conventional ART and CG methods
Arctic Sea Level Reconstruction
DEFF Research Database (Denmark)
Svendsen, Peter Limkilde
Reconstruction of historical Arctic sea level is very difficult due to the limited coverage and quality of tide gauge and altimetry data in the area. This thesis addresses many of these issues, and discusses strategies to help achieve a stable and plausible reconstruction of Arctic sea level from...... 1950 to today.The primary record of historical sea level, on the order of several decades to a few centuries, is tide gauges. Tide gauge records from around the world are collected in the Permanent Service for Mean Sea Level (PSMSL) database, and includes data along the Arctic coasts. A reasonable...... amount of data is available along the Norwegian and Russian coasts since 1950, and most published research on Arctic sea level extends cautiously from these areas. Very little tide gauge data is available elsewhere in the Arctic, and records of a length of several decades,as generally recommended for sea...
Herrera, Ramón
2018-03-01
The reconstruction of a warm inflationary universe model from the scalar spectral index n_S(N) and the tensor to scalar ratio r( N) as a function of the number of e-folds N is studied. Under a general formalism we find the effective potential and the dissipative coefficient in terms of the cosmological parameters n_S and r considering the weak and strong dissipative stages under the slow roll approximation. As a specific example, we study the attractors for the index n_S given by nS-1∝ N^{-1} and for the ratio r∝ N^{-2}, in order to reconstruct the model of warm inflation. Here, expressions for the effective potential V(φ ) and the dissipation coefficient Γ (φ ) are obtained.
Jet Vertex Charge Reconstruction
Nektarijevic, Snezana; The ATLAS collaboration
2015-01-01
A newly developed algorithm called the jet vertex charge tagger, aimed at identifying the sign of the charge of jets containing $b$-hadrons, referred to as $b$-jets, is presented. In addition to the well established track-based jet charge determination, this algorithm introduces the so-called \\emph{jet vertex charge} reconstruction, which exploits the charge information associated to the displaced vertices within the jet. Furthermore, the charge of a soft muon contained in the jet is taken into account when available. All available information is combined into a multivariate discriminator. The algorithm has been developed on jets matched to generator level $b$-hadrons provided by $t\\bar{t}$ events simulated at $\\sqrt{s}$=13~TeV using the full ATLAS detector simulation and reconstruction.
Marchant, R.; Behling, H.; Berrío, J.C.; Cleef, A.M.; Duivenvoorden, J.; Hooghiemstra, H.; Kuhry, P.; Melief, B.; Schreve-Brinkman, E.; Geel, van B.; Hammen, van der T.; Reenen, van G.
2002-01-01
Colombian biomes are reconstructed at 45 sites from the modern period extending to the Last Glacial Maximum (LGM). The basis for our reconstruction is pollen data assigned to plant functional types and biomes at six 3000-yr intervals. A reconstruction of modern biomes is used to check the treatment
Segmentation-DrivenTomographic Reconstruction
DEFF Research Database (Denmark)
Kongskov, Rasmus Dalgas
such that the segmentation subsequently can be carried out by use of a simple segmentation method, for instance just a thresholding method. We tested the advantages of going from a two-stage reconstruction method to a one stage segmentation-driven reconstruction method for the phase contrast tomography reconstruction......The tomographic reconstruction problem is concerned with creating a model of the interior of an object from some measured data, typically projections of the object. After reconstructing an object it is often desired to segment it, either automatically or manually. For computed tomography (CT...
International Nuclear Information System (INIS)
Francisco, Oscar; Rangel, Murilo; Barter, William; Bursche, Albert; Potterat, Cedric; Coco, Victor
2012-01-01
Full text: The Large Hadron Collider (LHC) is the most powerful particle accelerator in the world. It has been designed to collide proton beams at an energy up to 14 TeV in the center of mass. In 2011, the data taking was done with a center of mass energy of 7 TeV, the instant luminosity has reached values greater than 4 X 10 32 cm -2 s -1 and the integrated luminosity reached the value of 1,02fb -1 on the LHCb. The jet reconstruction is fundamental to observe events that can be used to test perturbative QCD (pQCD). It also provides a way to observe standard model channels and searches for new physics like SUSY. The anti-kt algorithm is a jet reconstruction algorithm that is based on the distance of the particles on the space ηX φ and on the transverse momentum of particles. To maximize the energy resolution all information about the trackers and the colorimeters are used on the LHCb experiment to create objects called particle flow objects that are used as input to anti-kt algorithm. The LHCb is specially interesting for jets studies because its η region is complementary to the others main experiments on LHC. We will present the first results of jet reconstruction using 2011 LHCb data. (author)
Energy Technology Data Exchange (ETDEWEB)
Francisco, Oscar; Rangel, Murilo [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil); Barter, William [University of Cambridge, Cambridge (United Kingdom); Bursche, Albert [Universitat Zurich, Zurich (Switzerland); Potterat, Cedric [Universitat de Barcelona, Barcelona (Spain); Coco, Victor [Nikhef National Institute for Subatomic Physics, Amsterdam (Netherlands)
2012-07-01
Full text: The Large Hadron Collider (LHC) is the most powerful particle accelerator in the world. It has been designed to collide proton beams at an energy up to 14 TeV in the center of mass. In 2011, the data taking was done with a center of mass energy of 7 TeV, the instant luminosity has reached values greater than 4 X 10{sup 32} cm{sup -2}s{sup -1} and the integrated luminosity reached the value of 1,02fb{sup -1} on the LHCb. The jet reconstruction is fundamental to observe events that can be used to test perturbative QCD (pQCD). It also provides a way to observe standard model channels and searches for new physics like SUSY. The anti-kt algorithm is a jet reconstruction algorithm that is based on the distance of the particles on the space {eta}X {phi} and on the transverse momentum of particles. To maximize the energy resolution all information about the trackers and the colorimeters are used on the LHCb experiment to create objects called particle flow objects that are used as input to anti-kt algorithm. The LHCb is specially interesting for jets studies because its {eta} region is complementary to the others main experiments on LHC. We will present the first results of jet reconstruction using 2011 LHCb data. (author)
Nonsymmetric entropy and maximum nonsymmetric entropy principle
International Nuclear Information System (INIS)
Liu Chengshi
2009-01-01
Under the frame of a statistical model, the concept of nonsymmetric entropy which generalizes the concepts of Boltzmann's entropy and Shannon's entropy, is defined. Maximum nonsymmetric entropy principle is proved. Some important distribution laws such as power law, can be derived from this principle naturally. Especially, nonsymmetric entropy is more convenient than other entropy such as Tsallis's entropy in deriving power laws.
Maximum speed of dewetting on a fiber
Chan, Tak Shing; Gueudre, Thomas; Snoeijer, Jacobus Hendrikus
2011-01-01
A solid object can be coated by a nonwetting liquid since a receding contact line cannot exceed a critical speed. We theoretically investigate this forced wetting transition for axisymmetric menisci on fibers of varying radii. First, we use a matched asymptotic expansion and derive the maximum speed
Maximum potential preventive effect of hip protectors
van Schoor, N.M.; Smit, J.H.; Bouter, L.M.; Veenings, B.; Asma, G.B.; Lips, P.T.A.M.
2007-01-01
OBJECTIVES: To estimate the maximum potential preventive effect of hip protectors in older persons living in the community or homes for the elderly. DESIGN: Observational cohort study. SETTING: Emergency departments in the Netherlands. PARTICIPANTS: Hip fracture patients aged 70 and older who
Maximum gain of Yagi-Uda arrays
DEFF Research Database (Denmark)
Bojsen, J.H.; Schjær-Jacobsen, Hans; Nilsson, E.
1971-01-01
Numerical optimisation techniques have been used to find the maximum gain of some specific parasitic arrays. The gain of an array of infinitely thin, equispaced dipoles loaded with arbitrary reactances has been optimised. The results show that standard travelling-wave design methods are not optimum....... Yagi–Uda arrays with equal and unequal spacing have also been optimised with experimental verification....
correlation between maximum dry density and cohesion
African Journals Online (AJOL)
HOD
represents maximum dry density, signifies plastic limit and is liquid limit. Researchers [6, 7] estimate compaction parameters. Aside from the correlation existing between compaction parameters and other physical quantities there are some other correlations that have been investigated by other researchers. The well-known.
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.
The maximum-entropy method in superspace
Czech Academy of Sciences Publication Activity Database
van Smaalen, S.; Palatinus, Lukáš; Schneider, M.
2003-01-01
Roč. 59, - (2003), s. 459-469 ISSN 0108-7673 Grant - others:DFG(DE) XX Institutional research plan: CEZ:AV0Z1010914 Keywords : maximum-entropy method, * aperiodic crystals * electron density Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.558, year: 2003
Achieving maximum sustainable yield in mixed fisheries
Ulrich, Clara; Vermard, Youen; Dolder, Paul J.; Brunel, Thomas; Jardim, Ernesto; Holmes, Steven J.; Kempf, Alexander; Mortensen, Lars O.; Poos, Jan Jaap; Rindorf, Anna
2017-01-01
Achieving single species maximum sustainable yield (MSY) in complex and dynamic fisheries targeting multiple species (mixed fisheries) is challenging because achieving the objective for one species may mean missing the objective for another. The North Sea mixed fisheries are a representative example
5 CFR 534.203 - Maximum stipends.
2010-01-01
... maximum stipend established under this section. (e) A trainee at a non-Federal hospital, clinic, or medical or dental laboratory who is assigned to a Federal hospital, clinic, or medical or dental... Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY UNDER OTHER SYSTEMS Student...
Minimal length, Friedmann equations and maximum density
Energy Technology Data Exchange (ETDEWEB)
Awad, Adel [Center for Theoretical Physics, British University of Egypt,Sherouk City 11837, P.O. Box 43 (Egypt); Department of Physics, Faculty of Science, Ain Shams University,Cairo, 11566 (Egypt); Ali, Ahmed Farag [Centre for Fundamental Physics, Zewail City of Science and Technology,Sheikh Zayed, 12588, Giza (Egypt); Department of Physics, Faculty of Science, Benha University,Benha, 13518 (Egypt)
2014-06-16
Inspired by Jacobson’s thermodynamic approach, Cai et al. have shown the emergence of Friedmann equations from the first law of thermodynamics. We extend Akbar-Cai derivation http://dx.doi.org/10.1103/PhysRevD.75.084003 of Friedmann equations to accommodate a general entropy-area law. Studying the resulted Friedmann equations using a specific entropy-area law, which is motivated by the generalized uncertainty principle (GUP), reveals the existence of a maximum energy density closed to Planck density. Allowing for a general continuous pressure p(ρ,a) leads to bounded curvature invariants and a general nonsingular evolution. In this case, the maximum energy density is reached in a finite time and there is no cosmological evolution beyond this point which leaves the big bang singularity inaccessible from a spacetime prospective. The existence of maximum energy density and a general nonsingular evolution is independent of the equation of state and the spacial curvature k. As an example we study the evolution of the equation of state p=ωρ through its phase-space diagram to show the existence of a maximum energy which is reachable in a finite time.
[Reconstructive methods after Fournier gangrene].
Wallner, C; Behr, B; Ring, A; Mikhail, B D; Lehnhardt, M; Daigeler, A
2016-04-01
Fournier's gangrene is a variant of the necrotizing fasciitis restricted to the perineal and genital region. It presents as an acute life-threatening disease and demands rapid surgical debridement, resulting in large soft tissue defects. Various reconstructive methods have to be applied to reconstitute functionality and aesthetics. The objective of this work is to identify different reconstructive methods in the literature and compare them to our current concepts for reconstructing defects caused by Fournier gangrene. Analysis of the current literature and our reconstructive methods on Fournier gangrene. The Fournier gangrene is an emergency requiring rapid, calculated antibiotic treatment and radical surgical debridement. After the acute phase of the disease, appropriate reconstructive methods are indicated. The planning of the reconstruction of the defect depends on many factors, especially functional and aesthetic demands. Scrotal reconstruction requires a higher aesthetic and functional reconstructive degree than perineal cutaneous wounds. In general, thorough wound hygiene, proper pre-operative planning, and careful consideration of the patient's demands are essential for successful reconstruction. In the literature, various methods for reconstruction after Fournier gangrene are described. Reconstruction with a flap is required for a good functional result in complex regions as the scrotum and penis, while cutaneous wounds can be managed through skin grafting. Patient compliance and tissue demand are crucial factors in the decision-making process.
Quantitative SPECT reconstruction of iodine-123 data
International Nuclear Information System (INIS)
Gilland, D.R.; Jaszczak, R.J.; Greer, K.L.; Coleman, R.E.
1991-01-01
Many clinical and research studies in nuclear medicine require quantitation of iodine-123 ( 123 I) distribution for the determination of kinetics or localization. The objective of this study was to implement several reconstruction methods designed for single-photon emission computed tomography (SPECT) using 123 I and to evaluate their performance in terms of quantitative accuracy, image artifacts, and noise. The methods consisted of four attenuation and scatter compensation schemes incorporated into both the filtered backprojection/Chang (FBP) and maximum likelihood-expectation maximization (ML-EM) reconstruction algorithms. The methods were evaluated on data acquired of a phantom containing a hot sphere of 123 I activity in a lower level background 123 I distribution and nonuniform density media. For both reconstruction algorithms, nonuniform attenuation compensation combined with either scatter subtraction or Metz filtering produced images that were quantitatively accurate to within 15% of the true value. The ML-EM algorithm demonstrated quantitative accuracy comparable to FBP and smaller relative noise magnitude for all compensation schemes
Strategies of reconstruction algorithms for computerized tomography
International Nuclear Information System (INIS)
Garderet, P.
1984-10-01
Image reconstruction from projections has progressively spread out over all fields of medical imaging. As the mathematical aspects of the problem become more and more comprehensively explored a great variety of numerical solutions have been developed best suited to such-and-such imaging medical application and taking into account the physical phenomena related to data collection (a priori properties for signal and noise). The purpose of that survey is to present the general mathematical frame and the fundamental assumptions of various strategies; Fourier methods approximate explicit deterministic inversion formula for the Radon transform. Algebraic reconstruction techniques set up an a priori discrete model through a series expansion approach of the solution. The numerical system to be solved is huge when a fine grid of pixels is to be reconstructed; iterative solutions may then be found. Recently some least square procedures have been shown to be tractable which avoid the use of iterative methods. Finally maximum like hood approach incorporates accurately the Poisson nature of photon noise and are well adapted to emission computed tomography. The various strategies will be analysed from both aspects of theoretical assumptions needed for suitable use and of computing facilities, actual performance and cost. In the end we take a glimpse of the extension of the algorithms from two dimensional imaging to fully three dimensional volume analysis in preparation of the future medical imaging technologies
Diffusion archeology for diffusion progression history reconstruction.
Sefer, Emre; Kingsford, Carl
2016-11-01
Diffusion through graphs can be used to model many real-world processes, such as the spread of diseases, social network memes, computer viruses, or water contaminants. Often, a real-world diffusion cannot be directly observed while it is occurring - perhaps it is not noticed until some time has passed, continuous monitoring is too costly, or privacy concerns limit data access. This leads to the need to reconstruct how the present state of the diffusion came to be from partial diffusion data. Here, we tackle the problem of reconstructing a diffusion history from one or more snapshots of the diffusion state. This ability can be invaluable to learn when certain computer nodes are infected or which people are the initial disease spreaders to control future diffusions. We formulate this problem over discrete-time SEIRS-type diffusion models in terms of maximum likelihood. We design methods that are based on submodularity and a novel prize-collecting dominating-set vertex cover (PCDSVC) relaxation that can identify likely diffusion steps with some provable performance guarantees. Our methods are the first to be able to reconstruct complete diffusion histories accurately in real and simulated situations. As a special case, they can also identify the initial spreaders better than the existing methods for that problem. Our results for both meme and contaminant diffusion show that the partial diffusion data problem can be overcome with proper modeling and methods, and that hidden temporal characteristics of diffusion can be predicted from limited data.
Flantua, S.G.A.; Hooghiemstra, H.; van Boxel, J.H.; Cabrera, M.; González-Carranza, Z.; González-Arango, C.; Stevens, W.D.; Montiel, O.M.; Raven, P.H.
2014-01-01
We provide an innovative pollen-driven connectivity framework of the dynamic altitudinal distribution of North Andean biomes since the Last Glacial Maximum (LGM). Altitudinally changing biome distributions reconstructed from a pollen record from Lake La Cocha (2780 m) are assessed in terms of their
EM for phylogenetic topology reconstruction on nonhomogeneous data.
Ibáñez-Marcelo, Esther; Casanellas, Marta
2014-06-17
The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly dealing with the long-branch attraction problem. The correct reconstruction of 4-taxon trees is crucial for making quartet-based methods work and being able to recover large phylogenies. We adapt the well known expectation-maximization algorithm to evolutionary Markov models on phylogenetic 4-taxon trees. We then use this algorithm to estimate the substitution parameters, compute the corresponding likelihood, and to infer the most likely quartet. In this paper we consider an expectation-maximization method for maximizing the likelihood of (time nonhomogeneous) evolutionary Markov models on trees. We study its success on reconstructing 4-taxon topologies and its performance as input method in quartet-based phylogenetic reconstruction methods such as QFIT and QuartetSuite. Our results show that the method proposed here outperforms neighbor-joining and the usual (time-homogeneous continuous-time) maximum likelihood methods on 4-leaved trees with among-lineage instantaneous rate heterogeneity, and perform similarly to usual continuous-time maximum-likelihood when data satisfies the assumptions of both methods. The method presented in this paper is well suited for reconstructing the topology of any number of taxa via quartet-based methods and is highly accurate, specially regarding largely divergent trees and time nonhomogeneous data.
Adaptive multiresolution method for MAP reconstruction in electron tomography
Energy Technology Data Exchange (ETDEWEB)
Acar, Erman, E-mail: erman.acar@tut.fi [Department of Signal Processing, Tampere University of Technology, P.O. Box 553, FI-33101 Tampere (Finland); BioMediTech, Tampere University of Technology, Biokatu 10, 33520 Tampere (Finland); Peltonen, Sari; Ruotsalainen, Ulla [Department of Signal Processing, Tampere University of Technology, P.O. Box 553, FI-33101 Tampere (Finland); BioMediTech, Tampere University of Technology, Biokatu 10, 33520 Tampere (Finland)
2016-11-15
3D image reconstruction with electron tomography holds problems due to the severely limited range of projection angles and low signal to noise ratio of the acquired projection images. The maximum a posteriori (MAP) reconstruction methods have been successful in compensating for the missing information and suppressing noise with their intrinsic regularization techniques. There are two major problems in MAP reconstruction methods: (1) selection of the regularization parameter that controls the balance between the data fidelity and the prior information, and (2) long computation time. One aim of this study is to provide an adaptive solution to the regularization parameter selection problem without having additional knowledge about the imaging environment and the sample. The other aim is to realize the reconstruction using sequences of resolution levels to shorten the computation time. The reconstructions were analyzed in terms of accuracy and computational efficiency using a simulated biological phantom and publically available experimental datasets of electron tomography. The numerical and visual evaluations of the experiments show that the adaptive multiresolution method can provide more accurate results than the weighted back projection (WBP), simultaneous iterative reconstruction technique (SIRT), and sequential MAP expectation maximization (sMAPEM) method. The method is superior to sMAPEM also in terms of computation time and usability since it can reconstruct 3D images significantly faster without requiring any parameter to be set by the user. - Highlights: • An adaptive multiresolution reconstruction method is introduced for electron tomography. • The method provides more accurate results than the conventional reconstruction methods. • The missing wedge and noise problems can be compensated by the method efficiently.
International Nuclear Information System (INIS)
1991-01-01
The meaning of the term 'maximum concentration at work' in regard of various pollutants is discussed. Specifically, a number of dusts and smokes are dealt with. The valuation criteria for maximum biologically tolerable concentrations for working materials are indicated. The working materials in question are corcinogeneous substances or substances liable to cause allergies or mutate the genome. (VT) [de
2010-07-27
...-17530; Notice No. 2] RIN 2130-ZA03 Inflation Adjustment of the Ordinary Maximum and Aggravated Maximum... remains at $250. These adjustments are required by the Federal Civil Penalties Inflation Adjustment Act [email protected] . SUPPLEMENTARY INFORMATION: The Federal Civil Penalties Inflation Adjustment Act of 1990...
Blind spectrum reconstruction algorithm with L0-sparse representation
International Nuclear Information System (INIS)
Liu, Hai; Zhang, Zhaoli; Liu, Sanyan; Shu, Jiangbo; Liu, Tingting; Zhang, Tianxu
2015-01-01
Raman spectrum often suffers from band overlap and Poisson noise. This paper presents a new blind Poissonian Raman spectrum reconstruction method, which incorporates the L 0 -sparse prior together with the total variation constraint into the maximum a posteriori framework. Furthermore, the greedy analysis pursuit algorithm is adopted to solve the L 0 -based minimization problem. Simulated and real spectrum experimental results show that the proposed method can effectively preserve spectral structure and suppress noise. The reconstructed Raman spectra are easily used for interpreting unknown chemical mixtures. (paper)
Development of Image Reconstruction Algorithms in electrical Capacitance Tomography
International Nuclear Information System (INIS)
Fernandez Marron, J. L.; Alberdi Primicia, J.; Barcala Riveira, J. M.
2007-01-01
The Electrical Capacitance Tomography (ECT) has not obtained a good development in order to be used at industrial level. That is due first to difficulties in the measurement of very little capacitances (in the range of femto farads) and second to the problem of reconstruction on- line of the images. This problem is due also to the small numbers of electrodes (maximum 16), that made the usual algorithms of reconstruction has many errors. In this work it is described a new purely geometrical method that could be used for this purpose. (Author) 4 refs
3D Tomographic Image Reconstruction using CUDA C
International Nuclear Information System (INIS)
Dominguez, J. S.; Assis, J. T.; Oliveira, L. F. de
2011-01-01
This paper presents the study and implementation of a software for three dimensional reconstruction of images obtained with a tomographic system using the capabilities of Graphic Processing Units(GPU). The reconstruction by filtered back-projection method was developed using the CUDA C, for maximum utilization of the processing capabilities of GPUs to solve computational problems with large computational cost and highly parallelizable. It was discussed the potential of GPUs and shown its advantages to solving this kind of problems. The results in terms of runtime will be compared with non-parallelized implementations and must show a great reduction of processing time. (Author)
Zipf's law, power laws and maximum entropy
International Nuclear Information System (INIS)
Visser, Matt
2013-01-01
Zipf's law, and power laws in general, have attracted and continue to attract considerable attention in a wide variety of disciplines—from astronomy to demographics to software structure to economics to linguistics to zoology, and even warfare. A recent model of random group formation (RGF) attempts a general explanation of such phenomena based on Jaynes' notion of maximum entropy applied to a particular choice of cost function. In the present paper I argue that the specific cost function used in the RGF model is in fact unnecessarily complicated, and that power laws can be obtained in a much simpler way by applying maximum entropy ideas directly to the Shannon entropy subject only to a single constraint: that the average of the logarithm of the observable quantity is specified. (paper)
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 likelihood estimation for integrated diffusion processes
DEFF Research Database (Denmark)
Baltazar-Larios, Fernando; Sørensen, Michael
We propose a method for obtaining maximum likelihood estimates of parameters in diffusion models when the data is a discrete time sample of the integral of the process, while no direct observations of the process itself are available. The data are, moreover, assumed to be contaminated...... EM-algorithm to obtain maximum likelihood estimates of the parameters in the diffusion model. As part of the algorithm, we use a recent simple method for approximate simulation of diffusion bridges. In simulation studies for the Ornstein-Uhlenbeck process and the CIR process the proposed method works...... by measurement errors. Integrated volatility is an example of this type of observations. Another example is ice-core data on oxygen isotopes used to investigate paleo-temperatures. The data can be viewed as incomplete observations of a model with a tractable likelihood function. Therefore we propose a simulated...
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 entropy analysis of liquid diffraction data
International Nuclear Information System (INIS)
Root, J.H.; Egelstaff, P.A.; Nickel, B.G.
1986-01-01
A maximum entropy method for reducing truncation effects in the inverse Fourier transform of structure factor, S(q), to pair correlation function, g(r), is described. The advantages and limitations of the method are explored with the PY hard sphere structure factor as model input data. An example using real data on liquid chlorine, is then presented. It is seen that spurious structure is greatly reduced in comparison to traditional Fourier transform methods. (author)
A Maximum Resonant Set of Polyomino Graphs
Directory of Open Access Journals (Sweden)
Zhang Heping
2016-05-01
Full Text Available A polyomino graph P is a connected finite subgraph of the infinite plane grid such that each finite face is surrounded by a regular square of side length one and each edge belongs to at least one square. A dimer covering of P corresponds to a perfect matching. Different dimer coverings can interact via an alternating cycle (or square with respect to them. A set of disjoint squares of P is a resonant set if P has a perfect matching M so that each one of those squares is M-alternating. In this paper, we show that if K is a maximum resonant set of P, then P − K has a unique perfect matching. We further prove that the maximum forcing number of a polyomino graph is equal to the cardinality of a maximum resonant set. This confirms a conjecture of Xu et al. [26]. We also show that if K is a maximal alternating set of P, then P − K has a unique perfect matching.
maximum neutron flux at thermal nuclear reactors
International Nuclear Information System (INIS)
Strugar, P.
1968-10-01
Since actual research reactors are technically complicated and expensive facilities it is important to achieve savings by appropriate reactor lattice configurations. There is a number of papers, and practical examples of reactors with central reflector, dealing with spatial distribution of fuel elements which would result in higher neutron flux. Common disadvantage of all the solutions is that the choice of best solution is done starting from the anticipated spatial distributions of fuel elements. The weakness of these approaches is lack of defined optimization criteria. Direct approach is defined as follows: determine the spatial distribution of fuel concentration starting from the condition of maximum neutron flux by fulfilling the thermal constraints. Thus the problem of determining the maximum neutron flux is solving a variational problem which is beyond the possibilities of classical variational calculation. This variational problem has been successfully solved by applying the maximum principle of Pontrjagin. Optimum distribution of fuel concentration was obtained in explicit analytical form. Thus, spatial distribution of the neutron flux and critical dimensions of quite complex reactor system are calculated in a relatively simple way. In addition to the fact that the results are innovative this approach is interesting because of the optimization procedure itself [sr
Noniterative MAP reconstruction using sparse matrix representations.
Cao, Guangzhi; Bouman, Charles A; Webb, Kevin J
2009-09-01
We present a method for noniterative maximum a posteriori (MAP) tomographic reconstruction which is based on the use of sparse matrix representations. Our approach is to precompute and store the inverse matrix required for MAP reconstruction. This approach has generally not been used in the past because the inverse matrix is typically large and fully populated (i.e., not sparse). In order to overcome this problem, we introduce two new ideas. The first idea is a novel theory for the lossy source coding of matrix transformations which we refer to as matrix source coding. This theory is based on a distortion metric that reflects the distortions produced in the final matrix-vector product, rather than the distortions in the coded matrix itself. The resulting algorithms are shown to require orthonormal transformations of both the measurement data and the matrix rows and columns before quantization and coding. The second idea is a method for efficiently storing and computing the required orthonormal transformations, which we call a sparse-matrix transform (SMT). The SMT is a generalization of the classical FFT in that it uses butterflies to compute an orthonormal transform; but unlike an FFT, the SMT uses the butterflies in an irregular pattern, and is numerically designed to best approximate the desired transforms. We demonstrate the potential of the noniterative MAP reconstruction with examples from optical tomography. The method requires offline computation to encode the inverse transform. However, once these offline computations are completed, the noniterative MAP algorithm is shown to reduce both storage and computation by well over two orders of magnitude, as compared to a linear iterative reconstruction methods.
Photometric Lunar Surface Reconstruction
Nefian, Ara V.; Alexandrov, Oleg; Morattlo, Zachary; Kim, Taemin; Beyer, Ross A.
2013-01-01
Accurate photometric reconstruction of the Lunar surface is important in the context of upcoming NASA robotic missions to the Moon and in giving a more accurate understanding of the Lunar soil composition. This paper describes a novel approach for joint estimation of Lunar albedo, camera exposure time, and photometric parameters that utilizes an accurate Lunar-Lambertian reflectance model and previously derived Lunar topography of the area visualized during the Apollo missions. The method introduced here is used in creating the largest Lunar albedo map (16% of the Lunar surface) at the resolution of 10 meters/pixel.
Penile surgery and reconstruction.
Perovic, Sava V; Djordjevic, Miroslav L J; Kekic, Zoran K; Djakovic, Nenad G
2002-05-01
This review will highlight recent advances in the field of penile reconstructive surgery in the paediatric and adult population. It is based on the work published during the year 2001. Besides the anatomical and histological studies of the penis, major contributions have been described in congenital and acquired penile anomalies. Also, a few new techniques and modifications of old procedures are described in order to improve the final functional and aesthetic outcome. The techniques for penile enlargement present a trend in the new millennium, but are still at the stage of investigation.
A Taxonomic Reduced-Space Pollen Model for Paleoclimate Reconstruction
Wahl, E. R.; Schoelzel, C.
2010-12-01
Paleoenvironmental reconstruction from fossil pollen often attempts to take advantage of the rich taxonomic diversity in such data. Here, a taxonomically "reduced-space" reconstruction model is explored that would be parsimonious in introducing parameters needing to be estimated within a Bayesian Hierarchical Modeling context. This work involves a refinement of the traditional pollen ratio method. This method is useful when one (or a few) dominant pollen type(s) in a region have a strong positive correlation with a climate variable of interest and another (or a few) dominant pollen type(s) have a strong negative correlation. When, e.g., counts of pollen taxa a and b (r >0) are combined with pollen types c and d (r logistic generalized linear model (GLM). The GLM can readily model this relationship in the forward form, pollen = g(climate), which is more physically realistic than inverse models often used in paleoclimate reconstruction [climate = f(pollen)]. The specification of the model is: rnum Bin(n,p), where E(r|T) = p = exp(η)/[1+exp(η)], and η = α + β(T); r is the pollen ratio formed as above, rnum is the ratio numerator, n is the ratio denominator (i.e., the sum of pollen counts), the denominator-specific count is (n - rnum), and T is the temperature at each site corresponding to a specific value of r. Ecological and empirical screening identified the model (Spruce+Birch) / (Spruce+Birch+Oak+Hickory) for use in temperate eastern N. America. α and β were estimated using both "traditional" and Bayesian GLM algorithms (in R). Although it includes only four pollen types, the ratio model yields more explained variation ( 80%) in the pollen-temperature relationship of the study region than a 64-taxon modern analog technique (MAT). Thus, the new pollen ratio method represents an information-rich, reduced space data model that can be efficiently employed in a BHM framework. The ratio model can directly reconstruct past temperature by solving the GLM equations
Progressive Reconstruction: A Methodology for Stabilization and Reconstruction Operations
National Research Council Canada - National Science Library
Rohr, Karl C
2006-01-01
... these nations in accordance with stated United States' goals. The argument follows closely current and developing United States military doctrine on stabilization, reconstruction, and counterinsurgency operations...
Evaluating low pass filters on SPECT reconstructed cardiac orientation estimation
Dwivedi, Shekhar
2009-02-01
Low pass filters can affect the quality of clinical SPECT images by smoothing. Appropriate filter and parameter selection leads to optimum smoothing that leads to a better quantification followed by correct diagnosis and accurate interpretation by the physician. This study aims at evaluating the low pass filters on SPECT reconstruction algorithms. Criteria for evaluating the filters are estimating the SPECT reconstructed cardiac azimuth and elevation angle. Low pass filters studied are butterworth, gaussian, hamming, hanning and parzen. Experiments are conducted using three reconstruction algorithms, FBP (filtered back projection), MLEM (maximum likelihood expectation maximization) and OSEM (ordered subsets expectation maximization), on four gated cardiac patient projections (two patients with stress and rest projections). Each filter is applied with varying cutoff and order for each reconstruction algorithm (only butterworth used for MLEM and OSEM). The azimuth and elevation angles are calculated from the reconstructed volume and the variation observed in the angles with varying filter parameters is reported. Our results demonstrate that behavior of hamming, hanning and parzen filter (used with FBP) with varying cutoff is similar for all the datasets. Butterworth filter (cutoff > 0.4) behaves in a similar fashion for all the datasets using all the algorithms whereas with OSEM for a cutoff < 0.4, it fails to generate cardiac orientation due to oversmoothing, and gives an unstable response with FBP and MLEM. This study on evaluating effect of low pass filter cutoff and order on cardiac orientation using three different reconstruction algorithms provides an interesting insight into optimal selection of filter parameters.
Neural network algorithm for image reconstruction using the grid friendly projections
International Nuclear Information System (INIS)
Cierniak, R.
2011-01-01
Full text: The presented paper describes a development of original approach to the reconstruction problem using a recurrent neural network. Particularly, the 'grid-friendly' angles of performed projections are selected according to the discrete Radon transform (DRT) concept to decrease the number of projections required. The methodology of our approach is consistent with analytical reconstruction algorithms. Reconstruction problem is reformulated in our approach to optimization problem. This problem is solved in present concept using method based on the maximum likelihood methodology. The reconstruction algorithm proposed in this work is consequently adapted for more practical discrete fan beam projections. Computer simulation results show that the neural network reconstruction algorithm designed to work in this way improves obtained results and outperforms conventional methods in reconstructed image quality. (author)
International Nuclear Information System (INIS)
Zeng, G.L.; Weng, Y.; Gullberg, G.T.
1997-01-01
Single photon emission computed tomography (SPECT) imaging with cone-beam collimators provides improved sensitivity and spatial resolution for imaging small objects with large field-of-view detectors. It is known that Tuy's cone-beam data sufficiency condition must be met to obtain artifact-free reconstructions. Even though Tuy's condition was derived for an attenuation-free situation, the authors hypothesize that an artifact-free reconstruction can be obtained even if the cone-beam data are attenuated, provided the imaging orbit satisfies Tuy's condition and the exact attenuation map is known. In the authors' studies, emission data are acquired using nonplanar circle-and-line orbits to acquire cone-beam data for tomographic reconstructions. An extended iterative ML-EM (maximum likelihood-expectation maximization) reconstruction algorithm is derived and used to reconstruct projection data with either a pre-acquired or assumed attenuation map. Quantitative accuracy of the attenuation corrected emission reconstruction is significantly improved
Synchronized dynamic dose reconstruction
International Nuclear Information System (INIS)
Litzenberg, Dale W.; Hadley, Scott W.; Tyagi, Neelam; Balter, James M.; Ten Haken, Randall K.; Chetty, Indrin J.
2007-01-01
Variations in target volume position between and during treatment fractions can lead to measurable differences in the dose distribution delivered to each patient. Current methods to estimate the ongoing cumulative delivered dose distribution make idealized assumptions about individual patient motion based on average motions observed in a population of patients. In the delivery of intensity modulated radiation therapy (IMRT) with a multi-leaf collimator (MLC), errors are introduced in both the implementation and delivery processes. In addition, target motion and MLC motion can lead to dosimetric errors from interplay effects. All of these effects may be of clinical importance. Here we present a method to compute delivered dose distributions for each treatment beam and fraction, which explicitly incorporates synchronized real-time patient motion data and real-time fluence and machine configuration data. This synchronized dynamic dose reconstruction method properly accounts for the two primary classes of errors that arise from delivering IMRT with an MLC: (a) Interplay errors between target volume motion and MLC motion, and (b) Implementation errors, such as dropped segments, dose over/under shoot, faulty leaf motors, tongue-and-groove effect, rounded leaf ends, and communications delays. These reconstructed dose fractions can then be combined to produce high-quality determinations of the dose distribution actually received to date, from which individualized adaptive treatment strategies can be determined
Augusto, O
2012-01-01
The Large Hadron Collider (LHC) is the most powerful particle accelerator in the world. It has been designed to collide proton beams at an energy up to 14 TeV in the center of mass. In 2011, the data taking was done with a center of mass energy of 7 TeV, the instant luminosity has reached values greater than $4 \\times 10^{32} cm^{-2} s^{-1}$ and the integrated luminosity reached the value of 1.02 $fb^{-1}$ on the LHCb. The jet reconstruction is fundamental to observe events that can be used to test pertubative QCD (pQCD). It also provides a way to observe standard model channels and searches for new physics like SUSY. The anti-kt algorithm is a jet reconstruction algorithm that is based on the distance of the particles on the space $\\eta \\times \\phi$ and on the transverse momentum of particles. To maximize the energy resolution all information about the trackers and the calo...
Three-dimensional ICT reconstruction
International Nuclear Information System (INIS)
Zhang Aidong; Li Ju; Chen Fa; Sun Lingxia
2005-01-01
The three-dimensional ICT reconstruction method is the hot topic of recent ICT technology research. In the context, qualified visual three-dimensional ICT pictures are achieved through multi-piece two-dimensional images accumulation by, combining with thresholding method and linear interpolation. Different direction and different position images of the reconstructed pictures are got by rotation and interception respectively. The convenient and quick method is significantly instructive to more complicated three-dimensional reconstruction of ICT images. (authors)
Three-dimensional ICT reconstruction
International Nuclear Information System (INIS)
Zhang Aidong; Li Ju; Chen Fa; Sun Lingxia
2004-01-01
The three-dimensional ICT reconstruction method is the hot topic of recent ICT technology research. In the context qualified visual three-dimensional ICT pictures are achieved through multi-piece two-dimensional images accumulation by order, combining with thresholding method and linear interpolation. Different direction and different position images of the reconstructed pictures are got by rotation and interception respectively. The convenient and quick method is significantly instructive to more complicated three-dimensional reconstruction of ICT images. (authors)
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.
Virtual 3-D Facial Reconstruction
Directory of Open Access Journals (Sweden)
Martin Paul Evison
2000-06-01
Full Text Available Facial reconstructions in archaeology allow empathy with people who lived in the past and enjoy considerable popularity with the public. It is a common misconception that facial reconstruction will produce an exact likeness; a resemblance is the best that can be hoped for. Research at Sheffield University is aimed at the development of a computer system for facial reconstruction that will be accurate, rapid, repeatable, accessible and flexible. This research is described and prototypical 3-D facial reconstructions are presented. Interpolation models simulating obesity, ageing and ethnic affiliation are also described. Some strengths and weaknesses in the models, and their potential for application in archaeology are discussed.
Maximum entropy decomposition of quadrupole mass spectra
International Nuclear Information System (INIS)
Toussaint, U. von; Dose, V.; Golan, A.
2004-01-01
We present an information-theoretic method called generalized maximum entropy (GME) for decomposing mass spectra of gas mixtures from noisy measurements. In this GME approach to the noisy, underdetermined inverse problem, the joint entropies of concentration, cracking, and noise probabilities are maximized subject to the measured data. This provides a robust estimation for the unknown cracking patterns and the concentrations of the contributing molecules. The method is applied to mass spectroscopic data of hydrocarbons, and the estimates are compared with those received from a Bayesian approach. We show that the GME method is efficient and is computationally fast
Maximum power operation of interacting molecular motors
DEFF Research Database (Denmark)
Golubeva, Natalia; Imparato, Alberto
2013-01-01
, as compared to the non-interacting system, in a wide range of biologically compatible scenarios. We furthermore consider the case where the motor-motor interaction directly affects the internal chemical cycle and investigate the effect on the system dynamics and thermodynamics.......We study the mechanical and thermodynamic properties of different traffic models for kinesin which are relevant in biological and experimental contexts. We find that motor-motor interactions play a fundamental role by enhancing the thermodynamic efficiency at maximum power of the motors...
On the maximum drawdown during speculative bubbles
Rotundo, Giulia; Navarra, Mauro
2007-08-01
A taxonomy of large financial crashes proposed in the literature locates the burst of speculative bubbles due to endogenous causes in the framework of extreme stock market crashes, defined as falls of market prices that are outlier with respect to the bulk of drawdown price movement distribution. This paper goes on deeper in the analysis providing a further characterization of the rising part of such selected bubbles through the examination of drawdown and maximum drawdown movement of indices prices. The analysis of drawdown duration is also performed and it is the core of the risk measure estimated here.
Multi-Channel Maximum Likelihood Pitch Estimation
DEFF Research Database (Denmark)
Christensen, Mads Græsbøll
2012-01-01
In this paper, a method for multi-channel pitch estimation is proposed. The method is a maximum likelihood estimator and is based on a parametric model where the signals in the various channels share the same fundamental frequency but can have different amplitudes, phases, and noise characteristics....... This essentially means that the model allows for different conditions in the various channels, like different signal-to-noise ratios, microphone characteristics and reverberation. Moreover, the method does not assume that a certain array structure is used but rather relies on a more general model and is hence...
Conductivity maximum in a charged colloidal suspension
Energy Technology Data Exchange (ETDEWEB)
Bastea, S
2009-01-27
Molecular dynamics simulations of a charged colloidal suspension in the salt-free regime show that the system exhibits an electrical conductivity maximum as a function of colloid charge. We attribute this behavior to two main competing effects: colloid effective charge saturation due to counterion 'condensation' and diffusion slowdown due to the relaxation effect. In agreement with previous observations, we also find that the effective transported charge is larger than the one determined by the Stern layer and suggest that it corresponds to the boundary fluid layer at the surface of the colloidal particles.
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.
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.
Multiperiod Maximum Loss is time unit invariant.
Kovacevic, Raimund M; Breuer, Thomas
2016-01-01
Time unit invariance is introduced as an additional requirement for multiperiod risk measures: for a constant portfolio under an i.i.d. risk factor process, the multiperiod risk should equal the one period risk of the aggregated loss, for an appropriate choice of parameters and independent of the portfolio and its distribution. Multiperiod Maximum Loss over a sequence of Kullback-Leibler balls is time unit invariant. This is also the case for the entropic risk measure. On the other hand, multiperiod Value at Risk and multiperiod Expected Shortfall are not time unit invariant.
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.
Evaluation of a 3D point cloud tetrahedral tomographic reconstruction method
Energy Technology Data Exchange (ETDEWEB)
Pereira, N F; Sitek, A, E-mail: nfp4@bwh.harvard.ed, E-mail: asitek@bwh.harvard.ed [Department of Radiology, Brigham and Women' s Hospital-Harvard Medical School Boston, MA (United States)
2010-09-21
Tomographic reconstruction on an irregular grid may be superior to reconstruction on a regular grid. This is achieved through an appropriate choice of the image space model, the selection of an optimal set of points and the use of any available prior information during the reconstruction process. Accordingly, a number of reconstruction-related parameters must be optimized for best performance. In this work, a 3D point cloud tetrahedral mesh reconstruction method is evaluated for quantitative tasks. A linear image model is employed to obtain the reconstruction system matrix and five point generation strategies are studied. The evaluation is performed using the recovery coefficient, as well as voxel- and template-based estimates of bias and variance measures, computed over specific regions in the reconstructed image. A similar analysis is performed for regular grid reconstructions that use voxel basis functions. The maximum likelihood expectation maximization reconstruction algorithm is used. For the tetrahedral reconstructions, of the five point generation methods that are evaluated, three use image priors. For evaluation purposes, an object consisting of overlapping spheres with varying activity is simulated. The exact parallel projection data of this object are obtained analytically using a parallel projector, and multiple Poisson noise realizations of these exact data are generated and reconstructed using the different point generation strategies. The unconstrained nature of point placement in some of the irregular mesh-based reconstruction strategies has superior activity recovery for small, low-contrast image regions. The results show that, with an appropriately generated set of mesh points, the irregular grid reconstruction methods can out-perform reconstructions on a regular grid for mathematical phantoms, in terms of the performance measures evaluated.
Evaluation of a 3D point cloud tetrahedral tomographic reconstruction method
Pereira, N. F.; Sitek, A.
2010-09-01
Tomographic reconstruction on an irregular grid may be superior to reconstruction on a regular grid. This is achieved through an appropriate choice of the image space model, the selection of an optimal set of points and the use of any available prior information during the reconstruction process. Accordingly, a number of reconstruction-related parameters must be optimized for best performance. In this work, a 3D point cloud tetrahedral mesh reconstruction method is evaluated for quantitative tasks. A linear image model is employed to obtain the reconstruction system matrix and five point generation strategies are studied. The evaluation is performed using the recovery coefficient, as well as voxel- and template-based estimates of bias and variance measures, computed over specific regions in the reconstructed image. A similar analysis is performed for regular grid reconstructions that use voxel basis functions. The maximum likelihood expectation maximization reconstruction algorithm is used. For the tetrahedral reconstructions, of the five point generation methods that are evaluated, three use image priors. For evaluation purposes, an object consisting of overlapping spheres with varying activity is simulated. The exact parallel projection data of this object are obtained analytically using a parallel projector, and multiple Poisson noise realizations of these exact data are generated and reconstructed using the different point generation strategies. The unconstrained nature of point placement in some of the irregular mesh-based reconstruction strategies has superior activity recovery for small, low-contrast image regions. The results show that, with an appropriately generated set of mesh points, the irregular grid reconstruction methods can out-perform reconstructions on a regular grid for mathematical phantoms, in terms of the performance measures evaluated.
Evaluation of a 3D point cloud tetrahedral tomographic reconstruction method
International Nuclear Information System (INIS)
Pereira, N F; Sitek, A
2010-01-01
Tomographic reconstruction on an irregular grid may be superior to reconstruction on a regular grid. This is achieved through an appropriate choice of the image space model, the selection of an optimal set of points and the use of any available prior information during the reconstruction process. Accordingly, a number of reconstruction-related parameters must be optimized for best performance. In this work, a 3D point cloud tetrahedral mesh reconstruction method is evaluated for quantitative tasks. A linear image model is employed to obtain the reconstruction system matrix and five point generation strategies are studied. The evaluation is performed using the recovery coefficient, as well as voxel- and template-based estimates of bias and variance measures, computed over specific regions in the reconstructed image. A similar analysis is performed for regular grid reconstructions that use voxel basis functions. The maximum likelihood expectation maximization reconstruction algorithm is used. For the tetrahedral reconstructions, of the five point generation methods that are evaluated, three use image priors. For evaluation purposes, an object consisting of overlapping spheres with varying activity is simulated. The exact parallel projection data of this object are obtained analytically using a parallel projector, and multiple Poisson noise realizations of these exact data are generated and reconstructed using the different point generation strategies. The unconstrained nature of point placement in some of the irregular mesh-based reconstruction strategies has superior activity recovery for small, low-contrast image regions. The results show that, with an appropriately generated set of mesh points, the irregular grid reconstruction methods can out-perform reconstructions on a regular grid for mathematical phantoms, in terms of the performance measures evaluated.
Objective Bayesianism and the Maximum Entropy Principle
Directory of Open Access Journals (Sweden)
Jon Williamson
2013-09-01
Full Text Available Objective Bayesian epistemology invokes three norms: the strengths of our beliefs should be probabilities; they should be calibrated to our evidence of physical probabilities; and they should otherwise equivocate sufficiently between the basic propositions that we can express. The three norms are sometimes explicated by appealing to the maximum entropy principle, which says that a belief function should be a probability function, from all those that are calibrated to evidence, that has maximum entropy. However, the three norms of objective Bayesianism are usually justified in different ways. In this paper, we show that the three norms can all be subsumed under a single justification in terms of minimising worst-case expected loss. This, in turn, is equivalent to maximising a generalised notion of entropy. We suggest that requiring language invariance, in addition to minimising worst-case expected loss, motivates maximisation of standard entropy as opposed to maximisation of other instances of generalised entropy. Our argument also provides a qualified justification for updating degrees of belief by Bayesian conditionalisation. However, conditional probabilities play a less central part in the objective Bayesian account than they do under the subjective view of Bayesianism, leading to a reduced role for Bayes’ Theorem.
Efficient heuristics for maximum common substructure search.
Englert, Péter; Kovács, Péter
2015-05-26
Maximum common substructure search is a computationally hard optimization problem with diverse applications in the field of cheminformatics, including similarity search, lead optimization, molecule alignment, and clustering. Most of these applications have strict constraints on running time, so heuristic methods are often preferred. However, the development of an algorithm that is both fast enough and accurate enough for most practical purposes is still a challenge. Moreover, in some applications, the quality of a common substructure depends not only on its size but also on various topological features of the one-to-one atom correspondence it defines. Two state-of-the-art heuristic algorithms for finding maximum common substructures have been implemented at ChemAxon Ltd., and effective heuristics have been developed to improve both their efficiency and the relevance of the atom mappings they provide. The implementations have been thoroughly evaluated and compared with existing solutions (KCOMBU and Indigo). The heuristics have been found to greatly improve the performance and applicability of the algorithms. The purpose of this paper is to introduce the applied methods and present the experimental results.
International Nuclear Information System (INIS)
Papoular, R.J.; Zheludev, A.; Ressouche, E.; Schweizer, J.
1995-01-01
When density distributions in crystals are reconstructed from 3D diffraction data, a problem sometimes occurs when the spatial resolution in one given direction is very small compared to that in perpendicular directions. In this case, a 2D projected density is usually reconstructed. For this task, the conventional Fourier inversion method only makes use of those structure factors measured in the projection plane. All the other structure factors contribute zero to the reconstruction of a projected density. On the contrary, the maximum-entropy method uses all the 3D data, to yield 3D-enhanced 2D projected density maps. It is even possible to reconstruct a projection in the extreme case when not one structure factor in the plane of projection is known. In the case of poor resolution along one given direction, a Fourier inversion reconstruction gives very low quality 3D densities 'smeared' in the third dimension. The application of the maximum-entropy procedure reduces the smearing significantly and reasonably well resolved projections along most directions can now be obtained from the MaxEnt 3D density. To illustrate these two ideas, particular examples based on real polarized neutron diffraction data sets are presented. (orig.)
Anatomically-aided PET reconstruction using the kernel method.
Hutchcroft, Will; Wang, Guobao; Chen, Kevin T; Catana, Ciprian; Qi, Jinyi
2016-09-21
This paper extends the kernel method that was proposed previously for dynamic PET reconstruction, to incorporate anatomical side information into the PET reconstruction model. In contrast to existing methods that incorporate anatomical information using a penalized likelihood framework, the proposed method incorporates this information in the simpler maximum likelihood (ML) formulation and is amenable to ordered subsets. The new method also does not require any segmentation of the anatomical image to obtain edge information. We compare the kernel method with the Bowsher method for anatomically-aided PET image reconstruction through a simulated data set. Computer simulations demonstrate that the kernel method offers advantages over the Bowsher method in region of interest quantification. Additionally the kernel method is applied to a 3D patient data set. The kernel method results in reduced noise at a matched contrast level compared with the conventional ML expectation maximization algorithm.
CONNJUR Workflow Builder: a software integration environment for spectral reconstruction.
Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O; Ellis, Heidi J C; Gryk, Michael R
2015-07-01
CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.
CONNJUR Workflow Builder: a software integration environment for spectral reconstruction
Energy Technology Data Exchange (ETDEWEB)
Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert [UConn Health, Department of Molecular Biology and Biophysics (United States); Martyn, Timothy O. [Rensselaer at Hartford, Department of Engineering and Science (United States); Ellis, Heidi J. C. [Western New England College, Department of Computer Science and Information Technology (United States); Gryk, Michael R., E-mail: gryk@uchc.edu [UConn Health, Department of Molecular Biology and Biophysics (United States)
2015-07-15
CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.
Accurate phylogenetic tree reconstruction from quartets: a heuristic approach.
Reaz, Rezwana; Bayzid, Md Shamsuzzoha; Rahman, M Sohel
2014-01-01
Supertree methods construct trees on a set of taxa (species) combining many smaller trees on the overlapping subsets of the entire set of taxa. A 'quartet' is an unrooted tree over 4 taxa, hence the quartet-based supertree methods combine many 4-taxon unrooted trees into a single and coherent tree over the complete set of taxa. Quartet-based phylogeny reconstruction methods have been receiving considerable attentions in the recent years. An accurate and efficient quartet-based method might be competitive with the current best phylogenetic tree reconstruction methods (such as maximum likelihood or Bayesian MCMC analyses), without being as computationally intensive. In this paper, we present a novel and highly accurate quartet-based phylogenetic tree reconstruction method. We performed an extensive experimental study to evaluate the accuracy and scalability of our approach on both simulated and biological datasets.
CONNJUR Workflow Builder: a software integration environment for spectral reconstruction
International Nuclear Information System (INIS)
Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O.; Ellis, Heidi J. C.; Gryk, Michael R.
2015-01-01
CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses
Matrix-based image reconstruction methods for tomography
International Nuclear Information System (INIS)
Llacer, J.; Meng, J.D.
1984-10-01
Matrix methods of image reconstruction have not been used, in general, because of the large size of practical matrices, ill condition upon inversion and the success of Fourier-based techniques. An exception is the work that has been done at the Lawrence Berkeley Laboratory for imaging with accelerated radioactive ions. An extension of that work into more general imaging problems shows that, with a correct formulation of the problem, positron tomography with ring geometries results in well behaved matrices which can be used for image reconstruction with no distortion of the point response in the field of view and flexibility in the design of the instrument. Maximum Likelihood Estimator methods of reconstruction, which use the system matrices tailored to specific instruments and do not need matrix inversion, are shown to result in good preliminary images. A parallel processing computer structure based on multiple inexpensive microprocessors is proposed as a system to implement the matrix-MLE methods. 14 references, 7 figures
International Nuclear Information System (INIS)
Cook, G.O. Jr.; Knight, L.
1979-07-01
The question of optimal projection angles has recently become of interest in the field of reconstruction from projections. Here, studies are concentrated on the n x n pixel space, where literative algorithms such as ART and direct matrix techniques due to Katz are considered. The best angles are determined in a Gauss--Markov statistical sense as well as with respect to a function-theoretical error bound. The possibility of making photon intensity a function of angle is also examined. Finally, the best angles to use in an ART-like algorithm are studied. A certain set of unequally spaced angles was found to be preferred in several contexts. 15 figures, 6 tables
CRUCIATE LIGAMENT RECONSTRUCTION
Directory of Open Access Journals (Sweden)
A. V. Korolev
2016-01-01
Full Text Available Purpose: To evaluate long-term results of meniscal repair during arthroscopic ACL reconstruction.Materials and methods: 45 patients who underwent meniscal repair during arthroscopic ACL reconstruction between 2007 and 2013 by the same surgeon were included in the study. In total, fifty meniscus were repaired (26 medial and 24 lateral. Procedures included use of one up to four Fast-Fix implants (Smith & Nephew. In five cases both medial and lateral meniscus were repaired. Cincinnati, IKDC and Lysholm scales were used for long-term outcome analysis.Results: 19 male and 26 female patients were included in the study aging from 15 to 59 years (mean age 33,2±1,5. Median time from injury to surgical procedure was zero months (ranging zero to one. Mean time from surgery to scale analysis was 55,9±3 months (ranged 20-102. Median Cincinnati score was 97 (ranged 90-100, with excellent results in 93% of cases (43 patients and good results in 7% (3 patients. Median IKDC score was 90,8 (ranged 86,2-95,4, with excellent outcomes in 51% of cases (23 patients, good in 33% (15 patients and satisfactory in 16% (7 patients. Median Lysholm score was 95 (ranged 90-100, with excellent outcomes in 76% of cases (34 patients and good in 24% (11 patients. Authors identified no statistical differences when comparing survey results in age, sex and time from trauma to surgery.Conclusions: Results of the present study match the data from orthopedic literature that prove meniscal repair as a safe and efficient procedure with good and excellent outcomes. All-inside meniscal repair can be used irrespectively of patients' age and is efficient even in case of delayed procedures.
Hydraulic Limits on Maximum Plant Transpiration
Manzoni, S.; Vico, G.; Katul, G. G.; Palmroth, S.; Jackson, R. B.; Porporato, A. M.
2011-12-01
Photosynthesis occurs at the expense of water losses through transpiration. As a consequence of this basic carbon-water interaction at the leaf level, plant growth and ecosystem carbon exchanges are tightly coupled to transpiration. In this contribution, the hydraulic constraints that limit transpiration rates under well-watered conditions are examined across plant functional types and climates. The potential water flow through plants is proportional to both xylem hydraulic conductivity (which depends on plant carbon economy) and the difference in water potential between the soil and the atmosphere (the driving force that pulls water from the soil). Differently from previous works, we study how this potential flux changes with the amplitude of the driving force (i.e., we focus on xylem properties and not on stomatal regulation). Xylem hydraulic conductivity decreases as the driving force increases due to cavitation of the tissues. As a result of this negative feedback, more negative leaf (and xylem) water potentials would provide a stronger driving force for water transport, while at the same time limiting xylem hydraulic conductivity due to cavitation. Here, the leaf water potential value that allows an optimum balance between driving force and xylem conductivity is quantified, thus defining the maximum transpiration rate that can be sustained by the soil-to-leaf hydraulic system. To apply the proposed framework at the global scale, a novel database of xylem conductivity and cavitation vulnerability across plant types and biomes is developed. Conductivity and water potential at 50% cavitation are shown to be complementary (in particular between angiosperms and conifers), suggesting a tradeoff between transport efficiency and hydraulic safety. Plants from warmer and drier biomes tend to achieve larger maximum transpiration than plants growing in environments with lower atmospheric water demand. The predicted maximum transpiration and the corresponding leaf water
Analogue of Pontryagin's maximum principle for multiple integrals minimization problems
Mikhail, Zelikin
2016-01-01
The theorem like Pontryagin's maximum principle for multiple integrals is proved. Unlike the usual maximum principle, the maximum should be taken not over all matrices, but only on matrices of rank one. Examples are given.
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...
Reconstruction of electric systems (ELE)
International Nuclear Information System (INIS)
Kohutovic, P.
2001-01-01
The original design of WWER-230 units consisted of a single common system EEPS (essential electric power supply system) per unit. The establishment of redundancy 2 x 100% EEPS was a global task. The task was started during the 'Small reconstruction' - MR V1, continued in 'Gradual reconstruction' and finished in the year 2000. (author)
Agaricus section Xanthodermatei: a phylogenetic reconstruction with commentary on taxa.
Kerrigan, Richard W; Callac, Philippe; Guinberteau, Jacques; Challen, Michael P; Parra, Luis A
2005-01-01
Agaricus section Xanthodermatei comprises a group of species allied to A. xanthodermus and generally characterized by basidiomata having phenolic odors, transiently yellowing discolorations in some parts of the basidiome, Schaeffer's reaction negative, and mild to substantial toxicity. The section has a global distribution, while most included species have distributions restricted to regions of single continents. Using specimens and cultures from Europe, North America, and Hawaii, we analyzed DNA sequences from the ITS1+2 region of the nuclear rDNA to identify and characterize phylogenetically distinct entities and to construct a hypothesis of relationships, both among members of the section and with representative taxa from other sections of the genus. 61 sequences from affiliated taxa, plus 20 from six (or seven) other sections of Agaricus, and one Micropsalliota sequence, were evaluated under distance, maximum parsimony and maximum likelihood methods. We recognized 21 discrete entities in Xanthodermatei, including 14 established species and 7 new ones, three of which are described elsewhere. Four species from California, New Mexico, and France deserve further study before they are described. Type studies of American taxa are particularly emphasized, and a lectotype is designated for A. californicus. Section Xanthodermatei formed a single clade in most analyses, indicating that the traditional sectional characters noted above are good unifying characters that appear to have arisen only once within Agaricus. Deep divisions within the sequence-derived structure of the section could be interpreted as subsections in Xanthodermatei; however, various considerations led us to refrain from proposing new supraspecific taxa. The nearest neighbors of section Xanthodermatei are putatively in section Duploannulati.
Image-reconstruction algorithms for positron-emission tomography systems
International Nuclear Information System (INIS)
Cheng, S.N.C.
1982-01-01
The positional uncertainty in the time-of-flight measurement of a positron-emission tomography system is modelled as a Gaussian distributed random variable and the image is assumed to be piecewise constant on a rectilinear lattice. A reconstruction algorithm using maximum-likelihood estimation is derived for the situation in which time-of-flight data are sorted as the most-likely-position array. The algorithm is formulated as a linear system described by a nonseparable, block-banded, Toeplitz matrix, and a sine-transform technique is used to implement this algorithm efficiently. The reconstruction algorithms for both the most-likely-position array and the confidence-weighted array are described by similar equations, hence similar linear systems can be used to described the reconstruction algorithm for a discrete, confidence-weighted array, when the matrix and the entries in the data array are properly identified. It is found that the mean square-error depends on the ratio of the full width at half the maximum of time-of-flight measurement over the size of a pixel. When other parameters are fixed, the larger the pixel size, the smaller is the mean square-error. In the study of resolution, parameters that affect the impulse response of time-of-flight reconstruction algorithms are identified. It is found that the larger the pixel size, the larger is the standard deviation of the impulse response. This shows that small mean square-error and fine resolution are two contradictory requirements
Breast Reconstruction Following Cancer Treatment.
Gerber, Bernd; Marx, Mario; Untch, Michael; Faridi, Andree
2015-08-31
About 8000 breast reconstructions after mastectomy are per - formed in Germany each year. It has become more difficult to advise patients because of the wide variety of heterologous and autologous techniques that are now available and because of changes in the recommendations about radiotherapy. This article is based on a review of pertinent articles (2005-2014) that were retrieved by a selective search employing the search terms "mastectomy" and "breast reconstruction." The goal of reconstruction is to achieve an oncologically safe and aestically satisfactory result for the patient over the long term. Heterologous, i.e., implant-based, breast reconstruction (IBR) and autologous breast reconstruction (ABR) are complementary techniques. Immediate reconstruction preserves the skin of the breast and its natural form and prevents the psychological trauma associated with mastectomy. If post-mastectomy radiotherapy (PMRT) is not indicated, implant-based reconstruction with or without a net/acellular dermal matrix (ADM) is a common option. Complications such as seroma formation, infection, and explantation are significantly more common when an ADM is used (15.3% vs. 5.4% ). If PMRT is performed, then the complication rate of implant-based breast reconstruction is 1 to 48% ; in particular, Baker grade III/IV capsular fibrosis occurs in 7 to 22% of patients, and the prosthesis must be explanted in 9 to 41% . Primary or, preferably, secondary autologous reconstruction is an alternative. The results of ABR are more stable over the long term, but the operation is markedly more complex. Autologous breast reconstruction after PMRT does not increase the risk of serious complications (20.5% vs. 17.9% without radiotherapy). No randomized controlled trials have yet been conducted to compare the reconstructive techniques with each other. If radiotherapy will not be performed, immediate reconstruction with an implant is recommended. On the other hand, if post-mastectomy radiotherapy
Maximum Profit Configurations of Commercial Engines
Directory of Open Access Journals (Sweden)
Yiran Chen
2011-06-01
Full Text Available An investigation of commercial engines with finite capacity low- and high-price economic subsystems and a generalized commodity transfer law [n ∝ Δ (P m] in commodity flow processes, in which effects of the price elasticities of supply and demand are introduced, is presented in this paper. Optimal cycle configurations of commercial engines for maximum profit are obtained by applying optimal control theory. In some special cases, the eventual state—market equilibrium—is solely determined by the initial conditions and the inherent characteristics of two subsystems; while the different ways of transfer affect the model in respects of the specific forms of the paths of prices and the instantaneous commodity flow, i.e., the optimal configuration.
Modelling maximum likelihood estimation of availability
International Nuclear Information System (INIS)
Waller, R.A.; Tietjen, G.L.; Rock, G.W.
1975-01-01
Suppose the performance of a nuclear powered electrical generating power plant is continuously monitored to record the sequence of failure and repairs during sustained operation. The purpose of this study is to assess one method of estimating the performance of the power plant when the measure of performance is availability. That is, we determine the probability that the plant is operational at time t. To study the availability of a power plant, we first assume statistical models for the variables, X and Y, which denote the time-to-failure and the time-to-repair variables, respectively. Once those statistical models are specified, the availability, A(t), can be expressed as a function of some or all of their parameters. Usually those parameters are unknown in practice and so A(t) is unknown. This paper discusses the maximum likelihood estimator of A(t) when the time-to-failure model for X is an exponential density with parameter, lambda, and the time-to-repair model for Y is an exponential density with parameter, theta. Under the assumption of exponential models for X and Y, it follows that the instantaneous availability at time t is A(t)=lambda/(lambda+theta)+theta/(lambda+theta)exp[-[(1/lambda)+(1/theta)]t] with t>0. Also, the steady-state availability is A(infinity)=lambda/(lambda+theta). We use the observations from n failure-repair cycles of the power plant, say X 1 , X 2 , ..., Xsub(n), Y 1 , Y 2 , ..., Ysub(n) to present the maximum likelihood estimators of A(t) and A(infinity). The exact sampling distributions for those estimators and some statistical properties are discussed before a simulation model is used to determine 95% simulation intervals for A(t). The methodology is applied to two examples which approximate the operating history of two nuclear power plants. (author)
International Nuclear Information System (INIS)
Chatziioannou, A.; Qi, J.; Moore, A.; Annala, A.; Nguyen, K.; Leahy, R.M.; Cherry, S.R.
2000-01-01
We have evaluated the performance of two three dimensional reconstruction algorithms with data acquired from microPET, a high resolution tomograph dedicated to small animal imaging. The first was a linear filtered-backprojection algorithm (FBP) with reprojection of the missing data and the second was a statistical maximum-aposteriori probability algorithm (MAP). The two algorithms were evaluated in terms of their resolution performance, both in phantoms and in vivo. Sixty independent realizations of a phantom simulating the brain of a baby monkey were acquired, each containing 3 million counts. Each of these realizations was reconstructed independently with both algorithms. The ensemble of the sixty reconstructed realizations was used to estimate the standard deviation as a measure of the noise for each reconstruction algorithm. More detail was recovered in the MAP reconstruction without an increase in noise relative to FBP. Studies in a simple cylindrical compartment phantom demonstrated improved recovery of known activity ratios with MAP. Finally in vivo studies also demonstrated a clear improvement in spatial resolution using the MAP algorithm. The quantitative accuracy of the MAP reconstruction was also evaluated by comparison with autoradiography and direct well counting of tissue samples and was shown to be superior
Maximum Historical Seismic Intensity Map of S. Miguel Island (azores)
Silveira, D.; Gaspar, J. L.; Ferreira, T.; Queiroz, G.
The Azores archipelago is situated in the Atlantic Ocean where the American, African and Eurasian lithospheric plates meet. The so-called Azores Triple Junction located in the area where the Terceira Rift, a NW-SE to WNW-ESE fault system with a dextral component, intersects the Mid-Atlantic Ridge, with an approximate N-S direction, dominates its geological setting. S. Miguel Island is located in the eastern segment of the Terceira Rift, showing a high diversity of volcanic and tectonic structures. It is the largest Azorean island and includes three active trachytic central volcanoes with caldera (Sete Cidades, Fogo and Furnas) placed in the intersection of the NW-SE Ter- ceira Rift regional faults with an E-W deep fault system thought to be a relic of a Mid-Atlantic Ridge transform fault. N-S and NE-SW faults also occur in this con- text. Basaltic cinder cones emplaced along NW-SE fractures link that major volcanic structures. The easternmost part of the island comprises an inactive trachytic central volcano (Povoação) and an old basaltic volcanic complex (Nordeste). Since the settle- ment of the island, early in the XV century, several destructive earthquakes occurred in the Azores region. At least 11 events hit S. Miguel Island with high intensity, some of which caused several deaths and significant damages. The analysis of historical documents allowed reconstructing the history and the impact of all those earthquakes and new intensity maps using the 1998 European Macrosseismic Scale were produced for each event. The data was then integrated in order to obtain the maximum historical seismic intensity map of S. Miguel. This tool is regarded as an important document for hazard assessment and risk mitigation taking in account that indicates the location of dangerous seismogenic zones and provides a comprehensive set of data to be applied in land-use planning, emergency planning and building construction.
A maximum power point tracking for photovoltaic-SPE system using a maximum current controller
Energy Technology Data Exchange (ETDEWEB)
Muhida, Riza [Osaka Univ., Dept. of Physical Science, Toyonaka, Osaka (Japan); Osaka Univ., Dept. of Electrical Engineering, Suita, Osaka (Japan); Park, Minwon; Dakkak, Mohammed; Matsuura, Kenji [Osaka Univ., Dept. of Electrical Engineering, Suita, Osaka (Japan); Tsuyoshi, Akira; Michira, Masakazu [Kobe City College of Technology, Nishi-ku, Kobe (Japan)
2003-02-01
Processes to produce hydrogen from solar photovoltaic (PV)-powered water electrolysis using solid polymer electrolysis (SPE) are reported. An alternative control of maximum power point tracking (MPPT) in the PV-SPE system based on the maximum current searching methods has been designed and implemented. Based on the characteristics of voltage-current and theoretical analysis of SPE, it can be shown that the tracking of the maximum current output of DC-DC converter in SPE side will track the MPPT of photovoltaic panel simultaneously. This method uses a proportional integrator controller to control the duty factor of DC-DC converter with pulse-width modulator (PWM). The MPPT performance and hydrogen production performance of this method have been evaluated and discussed based on the results of the experiment. (Author)
Ray tracing reconstruction investigation for C-arm tomosynthesis
Malalla, Nuhad A. Y.; Chen, Ying
2016-04-01
C-arm tomosynthesis is a three dimensional imaging technique. Both x-ray source and the detector are mounted on a C-arm wheeled structure to provide wide variety of movement around the object. In this paper, C-arm tomosynthesis was introduced to provide three dimensional information over a limited view angle (less than 180o) to reduce radiation exposure and examination time. Reconstruction algorithms based on ray tracing method such as ray tracing back projection (BP), simultaneous algebraic reconstruction technique (SART) and maximum likelihood expectation maximization (MLEM) were developed for C-arm tomosynthesis. C-arm tomosynthesis projection images of simulated spherical object were simulated with a virtual geometric configuration with a total view angle of 40 degrees. This study demonstrated the sharpness of in-plane reconstructed structure and effectiveness of removing out-of-plane blur for each reconstruction algorithms. Results showed the ability of ray tracing based reconstruction algorithms to provide three dimensional information with limited angle C-arm tomosynthesis.
A new iterative algorithm to reconstruct the refractive index.
Liu, Y J; Zhu, P P; Chen, B; Wang, J Y; Yuan, Q X; Huang, W X; Shu, H; Li, E R; Liu, X S; Zhang, K; Ming, H; Wu, Z Y
2007-06-21
The latest developments in x-ray imaging are associated with techniques based on the phase contrast. However, the image reconstruction procedures demand significant improvements of the traditional methods, and/or new algorithms have to be introduced to take advantage of the high contrast and sensitivity of the new experimental techniques. In this letter, an improved iterative reconstruction algorithm based on the maximum likelihood expectation maximization technique is presented and discussed in order to reconstruct the distribution of the refractive index from data collected by an analyzer-based imaging setup. The technique considered probes the partial derivative of the refractive index with respect to an axis lying in the meridional plane and perpendicular to the propagation direction. Computer simulations confirm the reliability of the proposed algorithm. In addition, the comparison between an analytical reconstruction algorithm and the iterative method has been also discussed together with the convergent characteristic of this latter algorithm. Finally, we will show how the proposed algorithm may be applied to reconstruct the distribution of the refractive index of an epoxy cylinder containing small air bubbles of about 300 micro of diameter.
Manufacture of reconstruction-bricks in Mexico
Rojas-Valencia, Ma. Neftalí; Penagos, Armando Aguilar; Rojas, Denise Y. Fernández; López, Alberto López; Gálves, David Morillón
2017-12-01
In Mexico, around 33.600 tons of construction wastes are generated every day, Mexico City contributing for around tons/day, with fewer than 1.000 tons/day being sent to be recycled. For that reason the purpose of this study was to manufacture sustainable bricks, based on three types of wastes generated in the building industry: wood cutting residues, wastes from the excavation process (From Coapa and Cuautlancingo, Puebla, Mexico) and recycled aggregates. Water was added as kneading material, and Opuntia ficus-indica (mucilage) was supplemented as natural additive to improve the workability of the mixtures. Conventional firing process was substituted by drying in a solar drying chamber. Nine mixtures were prepared using 62% excavation wastes, 4% wood cutting residues and 11%, 17% and 34% recycled aggregates. These mixtures were classified in two groups depending on their granulometry: the first one denominated cementitious recycled aggregates only having granulometry from 25.4 mm, 9.52 mm to 6.35 mm to fines and the second group denominated all in one recycled aggregates having granulometry of 6.35 mm to fines. The quality of the sustainable bricks was evaluated according to compressive strength and water absorption parameters. The results of nine mixtures showed that the reconstruction-bricks manufactured with the mixture seven consisting of 9.52 mm and 6.35 mm construction residues (all in one) fines presented the highest strength values, lowest maximum initial absorption (4 g/min) compared to the norm NMX-C-037-ONNCCE-2013 which establishes that the maximum limit for walls exposed to the outside is 5 g/min. Using a solar desiccator made from construction residues, the bricks were dried in 11 days, the maximum temperature was 76 °C and the maximum solar radiation captured was 733.4 W/m2.
Regularization parameter selection methods for ill-posed Poisson maximum likelihood estimation
International Nuclear Information System (INIS)
Bardsley, Johnathan M; Goldes, John
2009-01-01
In image processing applications, image intensity is often measured via the counting of incident photons emitted by the object of interest. In such cases, image data noise is accurately modeled by a Poisson distribution. This motivates the use of Poisson maximum likelihood estimation for image reconstruction. However, when the underlying model equation is ill-posed, regularization is needed. Regularized Poisson likelihood estimation has been studied extensively by the authors, though a problem of high importance remains: the choice of the regularization parameter. We will present three statistically motivated methods for choosing the regularization parameter, and numerical examples will be presented to illustrate their effectiveness
Nuclear Enhanced X-ray Maximum Entropy Method Used to Analyze Local Distortions in Simple Structures
DEFF Research Database (Denmark)
Christensen, Sebastian; Bindzus, Niels; Christensen, Mogens
We introduce a novel method for reconstructing pseudo nuclear density distributions (NDDs): Nuclear Enhanced X-ray Maximum Entropy Method (NEXMEM). NEXMEM offers an alternative route to experimental NDDs, exploiting the superior quality of synchrotron X-ray data compared to neutron data. The method...... proposed to result from anharmonic phonon scattering or from local fluctuating dipoles on the Pb site.[1,2] No macroscopic symmetry change are associated with these effects, rendering them invisible to conventional crystallographic techniques. For this reason PbX was until recently believed to adopt...
Variance-based Salt Body Reconstruction
Ovcharenko, Oleg
2017-05-26
Seismic inversions of salt bodies are challenging when updating velocity models based on Born approximation- inspired gradient methods. We propose a variance-based method for velocity model reconstruction in regions complicated by massive salt bodies. The novel idea lies in retrieving useful information from simultaneous updates corresponding to different single frequencies. Instead of the commonly used averaging of single-iteration monofrequency gradients, our algorithm iteratively reconstructs salt bodies in an outer loop based on updates from a set of multiple frequencies after a few iterations of full-waveform inversion. The variance among these updates is used to identify areas where considerable cycle-skipping occurs. In such areas, we update velocities by interpolating maximum velocities within a certain region. The result of several recursive interpolations is later used as a new starting model to improve results of conventional full-waveform inversion. An application on part of the BP 2004 model highlights the evolution of the proposed approach and demonstrates its effectiveness.
Evidence-Based ACL Reconstruction
Directory of Open Access Journals (Sweden)
E. Carlos RODRIGUEZ-MERCHAN
2015-01-01
Full Text Available There is controversy in the literature regarding a number of topics related to anterior cruciate ligament (ACLreconstruction. The purpose of this article is to answer the following questions: 1 Bone patellar tendon bone (BPTB reconstruction or hamstring reconstruction (HR; 2 Double bundle or single bundle; 3 Allograft or authograft; 4 Early or late reconstruction; 5 Rate of return to sports after ACL reconstruction; 6 Rate of osteoarthritis after ACL reconstruction. A Cochrane Library and PubMed (MEDLINE search of systematic reviews and meta-analysis related to ACL reconstruction was performed. The key words were: ACL reconstruction, systematic reviews and meta-analysis. The main criteria for selection were that the articles were systematic reviews and meta-analysesfocused on the aforementioned questions. Sixty-nine articles were found, but only 26 were selected and reviewed because they had a high grade (I-II of evidence. BPTB-R was associated with better postoperative knee stability but with a higher rate of morbidity. However, the results of both procedures in terms of functional outcome in the long-term were similar. The double-bundle ACL reconstruction technique showed better outcomes in rotational laxity, although functional recovery was similar between single-bundle and double-bundle. Autograft yielded better results than allograft. There was no difference between early and delayed reconstruction. 82% of patients were able to return to some kind of sport participation. 28% of patients presented radiological signs of osteoarthritis with a follow-up of minimum 10 years.
Maximum mass of magnetic white dwarfs
International Nuclear Information System (INIS)
Paret, Daryel Manreza; Horvath, Jorge Ernesto; Martínez, Aurora Perez
2015-01-01
We revisit the problem of the maximum masses of magnetized white dwarfs (WDs). The impact of a strong magnetic field on the structure equations is addressed. The pressures become anisotropic due to the presence of the magnetic field and split into parallel and perpendicular components. We first construct stable solutions of the Tolman-Oppenheimer-Volkoff equations for parallel pressures and find that physical solutions vanish for the perpendicular pressure when B ≳ 10 13 G. This fact establishes an upper bound for a magnetic field and the stability of the configurations in the (quasi) spherical approximation. Our findings also indicate that it is not possible to obtain stable magnetized WDs with super-Chandrasekhar masses because the values of the magnetic field needed for them are higher than this bound. To proceed into the anisotropic regime, we can apply results for structure equations appropriate for a cylindrical metric with anisotropic pressures that were derived in our previous work. From the solutions of the structure equations in cylindrical symmetry we have confirmed the same bound for B ∼ 10 13 G, since beyond this value no physical solutions are possible. Our tentative conclusion is that massive WDs with masses well beyond the Chandrasekhar limit do not constitute stable solutions and should not exist. (paper)
TRENDS IN ESTIMATED MIXING DEPTH DAILY MAXIMUMS
Energy Technology Data Exchange (ETDEWEB)
Buckley, R; Amy DuPont, A; Robert Kurzeja, R; Matt Parker, M
2007-11-12
Mixing depth is an important quantity in the determination of air pollution concentrations. Fireweather forecasts depend strongly on estimates of the mixing depth as a means of determining the altitude and dilution (ventilation rates) of smoke plumes. The Savannah River United States Forest Service (USFS) routinely conducts prescribed fires at the Savannah River Site (SRS), a heavily wooded Department of Energy (DOE) facility located in southwest South Carolina. For many years, the Savannah River National Laboratory (SRNL) has provided forecasts of weather conditions in support of the fire program, including an estimated mixing depth using potential temperature and turbulence change with height at a given location. This paper examines trends in the average estimated mixing depth daily maximum at the SRS over an extended period of time (4.75 years) derived from numerical atmospheric simulations using two versions of the Regional Atmospheric Modeling System (RAMS). This allows for differences to be seen between the model versions, as well as trends on a multi-year time frame. In addition, comparisons of predicted mixing depth for individual days in which special balloon soundings were released are also discussed.
Mammographic image restoration using maximum entropy deconvolution
International Nuclear Information System (INIS)
Jannetta, A; Jackson, J C; Kotre, C J; Birch, I P; Robson, K J; Padgett, R
2004-01-01
An image restoration approach based on a Bayesian maximum entropy method (MEM) has been applied to a radiological image deconvolution problem, that of reduction of geometric blurring in magnification mammography. The aim of the work is to demonstrate an improvement in image spatial resolution in realistic noisy radiological images with no associated penalty in terms of reduction in the signal-to-noise ratio perceived by the observer. Images of the TORMAM mammographic image quality phantom were recorded using the standard magnification settings of 1.8 magnification/fine focus and also at 1.8 magnification/broad focus and 3.0 magnification/fine focus; the latter two arrangements would normally give rise to unacceptable geometric blurring. Measured point-spread functions were used in conjunction with the MEM image processing to de-blur these images. The results are presented as comparative images of phantom test features and as observer scores for the raw and processed images. Visualization of high resolution features and the total image scores for the test phantom were improved by the application of the MEM processing. It is argued that this successful demonstration of image de-blurring in noisy radiological images offers the possibility of weakening the link between focal spot size and geometric blurring in radiology, thus opening up new approaches to system optimization
Maximum Margin Clustering of Hyperspectral Data
Niazmardi, S.; Safari, A.; Homayouni, S.
2013-09-01
In recent decades, large margin methods such as Support Vector Machines (SVMs) are supposed to be the state-of-the-art of supervised learning methods for classification of hyperspectral data. However, the results of these algorithms mainly depend on the quality and quantity of available training data. To tackle down the problems associated with the training data, the researcher put effort into extending the capability of large margin algorithms for unsupervised learning. One of the recent proposed algorithms is Maximum Margin Clustering (MMC). The MMC is an unsupervised SVMs algorithm that simultaneously estimates both the labels and the hyperplane parameters. Nevertheless, the optimization of the MMC algorithm is a non-convex problem. Most of the existing MMC methods rely on the reformulating and the relaxing of the non-convex optimization problem as semi-definite programs (SDP), which are computationally very expensive and only can handle small data sets. Moreover, most of these algorithms are two-class classification, which cannot be used for classification of remotely sensed data. In this paper, a new MMC algorithm is used that solve the original non-convex problem using Alternative Optimization method. This algorithm is also extended for multi-class classification and its performance is evaluated. The results of the proposed algorithm show that the algorithm has acceptable results for hyperspectral data clustering.
Paving the road to maximum productivity.
Holland, C
1998-01-01
"Job security" is an oxymoron in today's environment of downsizing, mergers, and acquisitions. Workers find themselves living by new rules in the workplace that they may not understand. How do we cope? It is the leader's charge to take advantage of this chaos and create conditions under which his or her people can understand the need for change and come together with a shared purpose to effect that change. The clinical laboratory at Arkansas Children's Hospital has taken advantage of this chaos to down-size and to redesign how the work gets done to pave the road to maximum productivity. After initial hourly cutbacks, the workers accepted the cold, hard fact that they would never get their old world back. They set goals to proactively shape their new world through reorganizing, flexing staff with workload, creating a rapid response laboratory, exploiting information technology, and outsourcing. Today the laboratory is a lean, productive machine that accepts change as a way of life. We have learned to adapt, trust, and support each other as we have journeyed together over the rough roads. We are looking forward to paving a new fork in the road to the future.
Maximum power flux of auroral kilometric radiation
International Nuclear Information System (INIS)
Benson, R.F.; Fainberg, J.
1991-01-01
The maximum auroral kilometric radiation (AKR) power flux observed by distant satellites has been increased by more than a factor of 10 from previously reported values. This increase has been achieved by a new data selection criterion and a new analysis of antenna spin modulated signals received by the radio astronomy instrument on ISEE 3. The method relies on selecting AKR events containing signals in the highest-frequency channel (1980, kHz), followed by a careful analysis that effectively increased the instrumental dynamic range by more than 20 dB by making use of the spacecraft antenna gain diagram during a spacecraft rotation. This analysis has allowed the separation of real signals from those created in the receiver by overloading. Many signals having the appearance of AKR harmonic signals were shown to be of spurious origin. During one event, however, real second harmonic AKR signals were detected even though the spacecraft was at a great distance (17 R E ) from Earth. During another event, when the spacecraft was at the orbital distance of the Moon and on the morning side of Earth, the power flux of fundamental AKR was greater than 3 x 10 -13 W m -2 Hz -1 at 360 kHz normalized to a radial distance r of 25 R E assuming the power falls off as r -2 . A comparison of these intense signal levels with the most intense source region values (obtained by ISIS 1 and Viking) suggests that multiple sources were observed by ISEE 3
Maximum likelihood window for time delay estimation
International Nuclear Information System (INIS)
Lee, Young Sup; Yoon, Dong Jin; Kim, Chi Yup
2004-01-01
Time delay estimation for the detection of leak location in underground pipelines is critically important. Because the exact leak location depends upon the precision of the time delay between sensor signals due to leak noise and the speed of elastic waves, the research on the estimation of time delay has been one of the key issues in leak lovating with the time arrival difference method. In this study, an optimal Maximum Likelihood window is considered to obtain a better estimation of the time delay. This method has been proved in experiments, which can provide much clearer and more precise peaks in cross-correlation functions of leak signals. The leak location error has been less than 1 % of the distance between sensors, for example the error was not greater than 3 m for 300 m long underground pipelines. Apart from the experiment, an intensive theoretical analysis in terms of signal processing has been described. The improved leak locating with the suggested method is due to the windowing effect in frequency domain, which offers a weighting in significant frequencies.
Reconstructing human evolution
AUTHOR|(CDS)2074069
1999-01-01
One can reconstruct human evolution using modern genetic data and models based on the mathematical theory of evolution and its four major factors : mutation, natural selection, statistical fluctuations in finite populations (random genetic drift), and migration. Archaeology gives some help on the major dates and events of the process. Chances of studying ancient DNA are very limited but there have been a few successful results. Studying DNA instead of proteins, as was done until a few years ago, and in particular the DNA of mitochondria and of the Y chromosome which are transmitted, respectively, by the maternal line and the paternal line, has greatly simplified the analysis. It is now possible to carry the analysis on individuals, while earlier studies were of necessity based on populations. Also the evolution of ÒcultureÓ (i.e. what we learn from others), in particular that of languages, gives some help and can be greatly enlightened by genetic studies. Even though it is largely based on mechanisms of mut...
Reconstructing Topological Graphs and Continua
Gartside, Paul; Pitz, Max F.; Suabedissen, Rolf
2015-01-01
The deck of a topological space $X$ is the set $\\mathcal{D}(X)=\\{[X \\setminus \\{x\\}] \\colon x \\in X\\}$, where $[Z]$ denotes the homeomorphism class of $Z$. A space $X$ is topologically reconstructible if whenever $\\mathcal{D}(X)=\\mathcal{D}(Y)$ then $X$ is homeomorphic to $Y$. It is shown that all metrizable compact connected spaces are reconstructible. It follows that all finite graphs, when viewed as a 1-dimensional cell-complex, are reconstructible in the topological sense, and more genera...
Tomographic reconstruction of binary fields
International Nuclear Information System (INIS)
Roux, Stéphane; Leclerc, Hugo; Hild, François
2012-01-01
A novel algorithm is proposed for reconstructing binary images from their projection along a set of different orientations. Based on a nonlinear transformation of the projection data, classical back-projection procedures can be used iteratively to converge to the sought image. A multiscale implementation allows for a faster convergence. The algorithm is tested on images up to 1 Mb definition, and an error free reconstruction is achieved with a very limited number of projection data, saving a factor of about 100 on the number of projections required for classical reconstruction algorithms.
Super-Resolution Image Reconstruction Applied to Medical Ultrasound
Ellis, Michael
Ultrasound is the preferred imaging modality for many diagnostic applications due to its real-time image reconstruction and low cost. Nonetheless, conventional ultrasound is not used in many applications because of limited spatial resolution and soft tissue contrast. Most commercial ultrasound systems reconstruct images using a simple delay-and-sum architecture on receive, which is fast and robust but does not utilize all information available in the raw data. Recently, more sophisticated image reconstruction methods have been developed that make use of far more information in the raw data to improve resolution and contrast. One such method is the Time-Domain Optimized Near-Field Estimator (TONE), which employs a maximum a priori estimation to solve a highly underdetermined problem, given a well-defined system model. TONE has been shown to significantly improve both the contrast and resolution of ultrasound images when compared to conventional methods. However, TONE's lack of robustness to variations from the system model and extremely high computational cost hinder it from being readily adopted in clinical scanners. This dissertation aims to reduce the impact of TONE's shortcomings, transforming it from an academic construct to a clinically viable image reconstruction algorithm. By altering the system model from a collection of individual hypothetical scatterers to a collection of weighted, diffuse regions, dTONE is able to achieve much greater robustness to modeling errors. A method for efficient parallelization of dTONE is presented that reduces reconstruction time by more than an order of magnitude with little loss in image fidelity. An alternative reconstruction algorithm, called qTONE, is also developed and is able to reduce reconstruction times by another two orders of magnitude while simultaneously improving image contrast. Each of these methods for improving TONE are presented, their limitations are explored, and all are used in concert to reconstruct in
Morimoto, Yusuke; Ferretti, Mario; Ekdahl, Max; Smolinski, Patrick; Fu, Freddie H
2009-01-01
The purpose of this study was to compare the tibiofemoral contact area and pressure after single-bundle (SB) and double-bundle (DB) anterior cruciate ligament (ACL) reconstruction by use of 2 femoral and 2 tibial tunnels in intact cadaveric knees. Tibiofemoral contact area and mean and maximum pressures were measured by pressure-sensitive film (Fujifilm, Valhalla, NY) inserted between the tibia and femur. The knee was subjected to a 1,000-N axial load by use of a uniaxial testing machine at 0 degrees , 15 degrees , 30 degrees , and 45 degrees of flexion. Three conditions were evaluated: (1) intact ACL, (2) SB ACL reconstruction (n = 10 knees), and (3) DB ACL reconstruction (n = 9 knees). When compared with the intact knee, DB ACL reconstruction showed no significant difference in tibiofemoral contact area and mean and maximum pressures. SB ACL reconstruction had a significantly smaller contact area on the lateral and medial tibiofemoral joints at 30 degrees and 15 degrees of flexion. SB ACL reconstruction also had significantly higher mean pressures at 15 degrees of flexion on the medial tibiofemoral joint and at 0 degrees and 15 degrees of flexion on the lateral tibiofemoral joint, as well as significantly higher maximum pressures at 15 degrees of flexion on the lateral tibiofemoral joint. SB ACL reconstruction resulted in a significantly smaller tibiofemoral contact area and higher pressures. DB ACL more closely restores the normal contact area and pressure mainly at low flexion angles. Our findings suggest that the changes in the contact area and pressures after SB ACL reconstruction may be one of the causes of osteoarthritis on long-term follow-up. DB ACL reconstruction may reduce the incidence of osteoarthritis by closely restoring contact area and pressure.
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...
20 CFR 226.52 - Total annuity subject to maximum.
2010-04-01
... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Total annuity subject to maximum. 226.52... COMPUTING EMPLOYEE, SPOUSE, AND DIVORCED SPOUSE ANNUITIES Railroad Retirement Family Maximum § 226.52 Total annuity subject to maximum. The total annuity amount which is compared to the maximum monthly amount to...
Half-width at half-maximum, full-width at half-maximum analysis
Indian Academy of Sciences (India)
addition to the well-defined parameter full-width at half-maximum (FWHM). The distribution of ... optical side-lobes in the diffraction pattern resulting in steep central maxima [6], reduc- tion of effects of ... and broad central peak. The idea of.
Cosmic shear measurement with maximum likelihood and maximum a posteriori inference
Hall, Alex; Taylor, Andy
2017-06-01
We investigate the problem of noise bias in maximum likelihood and maximum a posteriori estimators for cosmic shear. We derive the leading and next-to-leading order biases and compute them in the context of galaxy ellipticity measurements, extending previous work on maximum likelihood inference for weak lensing. We show that a large part of the bias on these point estimators can be removed using information already contained in the likelihood when a galaxy model is specified, without the need for external calibration. We test these bias-corrected estimators on simulated galaxy images similar to those expected from planned space-based weak lensing surveys, with promising results. We find that the introduction of an intrinsic shape prior can help with mitigation of noise bias, such that the maximum a posteriori estimate can be made less biased than the maximum likelihood estimate. Second-order terms offer a check on the convergence of the estimators, but are largely subdominant. We show how biases propagate to shear estimates, demonstrating in our simple set-up that shear biases can be reduced by orders of magnitude and potentially to within the requirements of planned space-based surveys at mild signal-to-noise ratio. We find that second-order terms can exhibit significant cancellations at low signal-to-noise ratio when Gaussian noise is assumed, which has implications for inferring the performance of shear-measurement algorithms from simplified simulations. We discuss the viability of our point estimators as tools for lensing inference, arguing that they allow for the robust measurement of ellipticity and shear.
Directory of Open Access Journals (Sweden)
Daniel L. Rabosky
2006-01-01
Full Text Available Rates of species origination and extinction can vary over time during evolutionary radiations, and it is possible to reconstruct the history of diversification using molecular phylogenies of extant taxa only. Maximum likelihood methods provide a useful framework for inferring temporal variation in diversification rates. LASER is a package for the R programming environment that implements maximum likelihood methods based on the birth-death process to test whether diversification rates have changed over time. LASER contrasts the likelihood of phylogenetic data under models where diversification rates have changed over time to alternative models where rates have remained constant over time. Major strengths of the package include the ability to detect temporal increases in diversification rates and the inference of diversification parameters under multiple rate-variable models of diversification. The program and associated documentation are freely available from the R package archive at http://cran.r-project.org.
A maximum likelihood framework for protein design
Directory of Open Access Journals (Sweden)
Philippe Hervé
2006-06-01
Full Text Available Abstract Background The aim of protein design is to predict amino-acid sequences compatible with a given target structure. Traditionally envisioned as a purely thermodynamic question, this problem can also be understood in a wider context, where additional constraints are captured by learning the sequence patterns displayed by natural proteins of known conformation. In this latter perspective, however, we still need a theoretical formalization of the question, leading to general and efficient learning methods, and allowing for the selection of fast and accurate objective functions quantifying sequence/structure compatibility. Results We propose a formulation of the protein design problem in terms of model-based statistical inference. Our framework uses the maximum likelihood principle to optimize the unknown parameters of a statistical potential, which we call an inverse potential to contrast with classical potentials used for structure prediction. We propose an implementation based on Markov chain Monte Carlo, in which the likelihood is maximized by gradient descent and is numerically estimated by thermodynamic integration. The fit of the models is evaluated by cross-validation. We apply this to a simple pairwise contact potential, supplemented with a solvent-accessibility term, and show that the resulting models have a better predictive power than currently available pairwise potentials. Furthermore, the model comparison method presented here allows one to measure the relative contribution of each component of the potential, and to choose the optimal number of accessibility classes, which turns out to be much higher than classically considered. Conclusion Altogether, this reformulation makes it possible to test a wide diversity of models, using different forms of potentials, or accounting for other factors than just the constraint of thermodynamic stability. Ultimately, such model-based statistical analyses may help to understand the forces
Joint reconstruction of activity and attenuation in Time-of-Flight PET: A Quantitative Analysis.
Rezaei, Ahmadreza; Deroose, Christophe M; Vahle, Thomas; Boada, Fernando; Nuyts, Johan
2018-03-01
Joint activity and attenuation reconstruction methods from time of flight (TOF) positron emission tomography (PET) data provide an effective solution to attenuation correction when no (or incomplete/inaccurate) information on the attenuation is available. One of the main barriers limiting their use in clinical practice is the lack of validation of these methods on a relatively large patient database. In this contribution, we aim at validating the activity reconstructions of the maximum likelihood activity reconstruction and attenuation registration (MLRR) algorithm on a whole-body patient data set. Furthermore, a partial validation (since the scale problem of the algorithm is avoided for now) of the maximum likelihood activity and attenuation reconstruction (MLAA) algorithm is also provided. We present a quantitative comparison of the joint reconstructions to the current clinical gold-standard maximum likelihood expectation maximization (MLEM) reconstruction with CT-based attenuation correction. Methods: The whole-body TOF-PET emission data of each patient data set is processed as a whole to reconstruct an activity volume covering all the acquired bed positions, which helps to reduce the problem of a scale per bed position in MLAA to a global scale for the entire activity volume. Three reconstruction algorithms are used: MLEM, MLRR and MLAA. A maximum likelihood (ML) scaling of the single scatter simulation (SSS) estimate to the emission data is used for scatter correction. The reconstruction results are then analyzed in different regions of interest. Results: The joint reconstructions of the whole-body patient data set provide better quantification in case of PET and CT misalignments caused by patient and organ motion. Our quantitative analysis shows a difference of -4.2% (±2.3%) and -7.5% (±4.6%) between the joint reconstructions of MLRR and MLAA compared to MLEM, averaged over all regions of interest, respectively. Conclusion: Joint activity and attenuation
Rosenthal, Amir; Horowitz, Moshe; Kieckbusch, Sven; Brinkmeyer, Ernst
2007-10-01
We demonstrate experimentally, for the first time to our knowledge, a reconstruction of a highly reflecting fiber Bragg grating from its complex reflection spectrum by using a regularization algorithm. The regularization method is based on correcting the measured reflection spectrum at the Bragg zone frequencies and enables the reconstruction of the grating profile using the integral-layer-peeling algorithm. A grating with an approximately uniform profile and with a maximum reflectivity of 99.98% was accurately reconstructed by measuring only its complex reflection spectrum.
Study of DNA reconstruction enzymes
Energy Technology Data Exchange (ETDEWEB)
Sekiguchi, M [Kyushu Univ., Fukuoka (Japan). Faculty of Science
1976-12-01
Description was made of the characteristics and mechanism of 3 reconstructive enzymes which received from M. luteus or E. coli or T4, and of which natures were clarified as reconstructive enzymes of DNA irradiated with ultraviolet rays. As characteristics, the site of breaking, reaction, molecular weight, electric charge in the neutrality and a specific adhesion to DNA irradiated with ultraviolet rays were mentioned. As to mutant of ultraviolet ray sensitivity, hereditary control mechanism of removal and reconstruction by endo-nuclease activation was described, and suggestion was referred to removal and reconstruction of cells of xedoderma pigmentosum which is a hereditary disease of human. Description was also made as to the mechanism of exonuclease activation which separates dimer selectively from irradiated DNA.
Quantum Logic and Quantum Reconstruction
Stairs, Allen
2015-01-01
Quantum logic understood as a reconstruction program had real successes and genuine limitations. This paper offers a synopsis of both and suggests a way of seeing quantum logic in a larger, still thriving context.
International Nuclear Information System (INIS)
Ibarra, Alejandro
2007-01-01
In this talk we discuss the prospects to reconstruct the high-energy see-saw Lagrangian from low energy experiments in supersymmetric scenarios. We show that the model with three right-handed neutrinos could be reconstructed in theory, but not in practice. Then, we discuss the prospects to reconstruct the model with two right-handed neutrinos, which is the minimal see-saw model able to accommodate neutrino observations. We identify the relevant processes to achieve this goal, and comment on the sensitivity of future experiments to them. We find the prospects much more promising and we emphasize in particular the importance of the observation of rare leptonic decays for the reconstruction of the right-handed neutrino masses
Breast Reconstruction with Flap Surgery
... augmented with a breast implant to achieve the desired breast size. Surgical methods Autologous tissue breast reconstruction ... as long as a year or two before feeling completely healed and back to normal. Future breast ...
Rational reconstructions of modern physics
Mittelstaedt, Peter
2013-01-01
Newton’s classical physics and its underlying ontology are loaded with several metaphysical hypotheses that cannot be justified by rational reasoning nor by experimental evidence. Furthermore, it is well known that some of these hypotheses are not contained in the great theories of Modern Physics, such as the theory of Special Relativity and Quantum Mechanics. This book shows that, on the basis of Newton’s classical physics and by rational reconstruction, the theory of Special Relativity as well as Quantum Mechanics can be obtained by partly eliminating or attenuating the metaphysical hypotheses. Moreover, it is shown that these reconstructions do not require additional hypotheses or new experimental results. In the second edition the rational reconstructions are completed with respect to General Relativity and Cosmology. In addition, the statistics of quantum objects is elaborated in more detail with respect to the rational reconstruction of quantum mechanics. The new material completes the approach of t...
Petz recovery versus matrix reconstruction
Holzäpfel, Milan; Cramer, Marcus; Datta, Nilanjana; Plenio, Martin B.
2018-04-01
The reconstruction of the state of a multipartite quantum mechanical system represents a fundamental task in quantum information science. At its most basic, it concerns a state of a bipartite quantum system whose subsystems are subjected to local operations. We compare two different methods for obtaining the original state from the state resulting from the action of these operations. The first method involves quantum operations called Petz recovery maps, acting locally on the two subsystems. The second method is called matrix (or state) reconstruction and involves local, linear maps that are not necessarily completely positive. Moreover, we compare the quantities on which the maps employed in the two methods depend. We show that any state that admits Petz recovery also admits state reconstruction. However, the latter is successful for a strictly larger set of states. We also compare these methods in the context of a finite spin chain. Here, the state of a finite spin chain is reconstructed from the reduced states of a few neighbouring spins. In this setting, state reconstruction is the same as the matrix product operator reconstruction proposed by Baumgratz et al. [Phys. Rev. Lett. 111, 020401 (2013)]. Finally, we generalize both these methods so that they employ long-range measurements instead of relying solely on short-range correlations embodied in such local reduced states. Long-range measurements enable the reconstruction of states which cannot be reconstructed from measurements of local few-body observables alone and hereby we improve existing methods for quantum state tomography of quantum many-body systems.
Animated Reconstruction of Forensic Animation
Hala, Albert; Unver, Ertu
1998-01-01
An animated accident display in court can be significant evidentiary tool. Computer graphics animation reconstructions which can be shown in court are cost effective, save valuable time and illustrate complex and technical issues, are realistic and can prove or disprove arguments or theories with reference to the perplexing newtonian physics involved in many accidents: this technology may well revolutionise accident reconstruction, thus enabling prosecution and defence to be more effective in...