Does better taxon sampling help? A new phylogenetic hypothesis for Sepsidae (Diptera: Cyclorrhapha) based on 50 new taxa and the same old mitochondrial and nuclear markers.

PubMed

Zhao, Lei; Annie, Ang Shi Hui; Amrita, Srivathsan; Yi, Su Kathy Feng; Rudolf, Meier

2013-10-01

We here present a phylogenetic hypothesis for Sepsidae (Diptera: Cyclorrhapha), a group of schizophoran flies with ca. 320 described species that is widely used in sexual selection research. The hypothesis is based on five nuclear and five mitochondrial markers totaling 8813 bp for ca. 30% of the diversity (105 sepsid taxa) and - depending on analysis - six or nine outgroup species. Maximum parsimony (MP), maximum likelihood (ML), and Bayesian inferences (BI) yield overall congruent, well-resolved, and supported trees that are largely unaffected by three different ways to partition the data in BI and ML analyses. However, there are also five areas of uncertainty that affect suprageneric relationships where different analyses yield alternate topologies and MP and ML trees have significant conflict according to Shimodaira-Hasegawa tests. Two of these were already affected by conflict in a previous analysis that was based on the same genes and a subset of 69 species. The remaining three involve newly added taxa or genera whose relationships were previously resolved with low support. We thus find that the denser taxon sample in the present analysis does not reduce the topological conflict that had been identified previously. The present study nevertheless presents a significant contribution to the understanding of sepsid relationships in that 50 additional taxa from 18 genera are added to the Tree-of-Life of Sepsidae and that the placement of most taxa is well supported and robust to different tree reconstruction techniques. Copyright © 2013 Elsevier Inc. All rights reserved.

Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes

PubMed Central

Saarela, Jeffery M.; Wysocki, William P.; Barrett, Craig F.; Soreng, Robert J.; Davis, Jerrold I.; Clark, Lynn G.; Kelchner, Scot A.; Pires, J. Chris; Edger, Patrick P.; Mayfield, Dustin R.; Duvall, Melvin R.

2015-01-01

Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some ‘early-diverging’ tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae–Meliceae and Ampelodesmeae–Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae–Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae–Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae–Loliinae clade. PMID:25940204

Soft context clustering for F0 modeling in HMM-based speech synthesis

NASA Astrophysics Data System (ADS)

Khorram, Soheil; Sameti, Hossein; King, Simon

2015-12-01

This paper proposes the use of a new binary decision tree, which we call a soft decision tree, to improve generalization performance compared to the conventional `hard' decision tree method that is used to cluster context-dependent model parameters in statistical parametric speech synthesis. We apply the method to improve the modeling of fundamental frequency, which is an important factor in synthesizing natural-sounding high-quality speech. Conventionally, hard decision tree-clustered hidden Markov models (HMMs) are used, in which each model parameter is assigned to a single leaf node. However, this `divide-and-conquer' approach leads to data sparsity, with the consequence that it suffers from poor generalization, meaning that it is unable to accurately predict parameters for models of unseen contexts: the hard decision tree is a weak function approximator. To alleviate this, we propose the soft decision tree, which is a binary decision tree with soft decisions at the internal nodes. In this soft clustering method, internal nodes select both their children with certain membership degrees; therefore, each node can be viewed as a fuzzy set with a context-dependent membership function. The soft decision tree improves model generalization and provides a superior function approximator because it is able to assign each context to several overlapped leaves. In order to use such a soft decision tree to predict the parameters of the HMM output probability distribution, we derive the smoothest (maximum entropy) distribution which captures all partial first-order moments and a global second-order moment of the training samples. Employing such a soft decision tree architecture with maximum entropy distributions, a novel speech synthesis system is trained using maximum likelihood (ML) parameter re-estimation and synthesis is achieved via maximum output probability parameter generation. In addition, a soft decision tree construction algorithm optimizing a log-likelihood measure is developed. Both subjective and objective evaluations were conducted and indicate a considerable improvement over the conventional method.

ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices.

PubMed

Dang, Cuong Cao; Lefort, Vincent; Le, Vinh Sy; Le, Quang Si; Gascuel, Olivier

2011-10-01

Amino acid replacement rate matrices are an essential basis of protein studies (e.g. in phylogenetics and alignment). A number of general purpose matrices have been proposed (e.g. JTT, WAG, LG) since the seminal work of Margaret Dayhoff and co-workers. However, it has been shown that matrices specific to certain protein groups (e.g. mitochondrial) or life domains (e.g. viruses) differ significantly from general average matrices, and thus perform better when applied to the data to which they are dedicated. This Web server implements the maximum-likelihood estimation procedure that was used to estimate LG, and provides a number of tools and facilities. Users upload a set of multiple protein alignments from their domain of interest and receive the resulting matrix by email, along with statistics and comparisons with other matrices. A non-parametric bootstrap is performed optionally to assess the variability of replacement rate estimates. Maximum-likelihood trees, inferred using the estimated rate matrix, are also computed optionally for each input alignment. Finely tuned procedures and up-to-date ML software (PhyML 3.0, XRATE) are combined to perform all these heavy calculations on our clusters. http://www.atgc-montpellier.fr/ReplacementMatrix/ olivier.gascuel@lirmm.fr Supplementary data are available at http://www.atgc-montpellier.fr/ReplacementMatrix/

Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood.

PubMed

Wu, Yufeng

2012-03-01

Incomplete lineage sorting can cause incongruence between the phylogenetic history of genes (the gene tree) and that of the species (the species tree), which can complicate the inference of phylogenies. In this article, I present a new coalescent-based algorithm for species tree inference with maximum likelihood. I first describe an improved method for computing the probability of a gene tree topology given a species tree, which is much faster than an existing algorithm by Degnan and Salter (2005). Based on this method, I develop a practical algorithm that takes a set of gene tree topologies and infers species trees with maximum likelihood. This algorithm searches for the best species tree by starting from initial species trees and performing heuristic search to obtain better trees with higher likelihood. This algorithm, called STELLS (which stands for Species Tree InfErence with Likelihood for Lineage Sorting), has been implemented in a program that is downloadable from the author's web page. The simulation results show that the STELLS algorithm is more accurate than an existing maximum likelihood method for many datasets, especially when there is noise in gene trees. I also show that the STELLS algorithm is efficient and can be applied to real biological datasets. © 2011 The Author. Evolution© 2011 The Society for the Study of Evolution.

Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics

PubMed Central

Kolaczkowski, Bryan; Thornton, Joseph W.

2009-01-01

Bayesian inference (BI) of phylogenetic relationships uses the same probabilistic models of evolution as its precursor maximum likelihood (ML), so BI has generally been assumed to share ML's desirable statistical properties, such as largely unbiased inference of topology given an accurate model and increasingly reliable inferences as the amount of data increases. Here we show that BI, unlike ML, is biased in favor of topologies that group long branches together, even when the true model and prior distributions of evolutionary parameters over a group of phylogenies are known. Using experimental simulation studies and numerical and mathematical analyses, we show that this bias becomes more severe as more data are analyzed, causing BI to infer an incorrect tree as the maximum a posteriori phylogeny with asymptotically high support as sequence length approaches infinity. BI's long branch attraction bias is relatively weak when the true model is simple but becomes pronounced when sequence sites evolve heterogeneously, even when this complexity is incorporated in the model. This bias—which is apparent under both controlled simulation conditions and in analyses of empirical sequence data—also makes BI less efficient and less robust to the use of an incorrect evolutionary model than ML. Surprisingly, BI's bias is caused by one of the method's stated advantages—that it incorporates uncertainty about branch lengths by integrating over a distribution of possible values instead of estimating them from the data, as ML does. Our findings suggest that trees inferred using BI should be interpreted with caution and that ML may be a more reliable framework for modern phylogenetic analysis. PMID:20011052

Long-branch attraction bias and inconsistency in Bayesian phylogenetics.

PubMed

Kolaczkowski, Bryan; Thornton, Joseph W

2009-12-09

Bayesian inference (BI) of phylogenetic relationships uses the same probabilistic models of evolution as its precursor maximum likelihood (ML), so BI has generally been assumed to share ML's desirable statistical properties, such as largely unbiased inference of topology given an accurate model and increasingly reliable inferences as the amount of data increases. Here we show that BI, unlike ML, is biased in favor of topologies that group long branches together, even when the true model and prior distributions of evolutionary parameters over a group of phylogenies are known. Using experimental simulation studies and numerical and mathematical analyses, we show that this bias becomes more severe as more data are analyzed, causing BI to infer an incorrect tree as the maximum a posteriori phylogeny with asymptotically high support as sequence length approaches infinity. BI's long branch attraction bias is relatively weak when the true model is simple but becomes pronounced when sequence sites evolve heterogeneously, even when this complexity is incorporated in the model. This bias--which is apparent under both controlled simulation conditions and in analyses of empirical sequence data--also makes BI less efficient and less robust to the use of an incorrect evolutionary model than ML. Surprisingly, BI's bias is caused by one of the method's stated advantages--that it incorporates uncertainty about branch lengths by integrating over a distribution of possible values instead of estimating them from the data, as ML does. Our findings suggest that trees inferred using BI should be interpreted with caution and that ML may be a more reliable framework for modern phylogenetic analysis.

The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data.

PubMed

Peters, Ralph S; Meusemann, Karen; Petersen, Malte; Mayer, Christoph; Wilbrandt, Jeanne; Ziesmann, Tanja; Donath, Alexander; Kjer, Karl M; Aspöck, Ulrike; Aspöck, Horst; Aberer, Andre; Stamatakis, Alexandros; Friedrich, Frank; Hünefeld, Frank; Niehuis, Oliver; Beutel, Rolf G; Misof, Bernhard

2014-03-20

Despite considerable progress in systematics, a comprehensive scenario of the evolution of phenotypic characters in the mega-diverse Holometabola based on a solid phylogenetic hypothesis was still missing. We addressed this issue by de novo sequencing transcriptome libraries of representatives of all orders of holometabolan insects (13 species in total) and by using a previously published extensive morphological dataset. We tested competing phylogenetic hypotheses by analyzing various specifically designed sets of amino acid sequence data, using maximum likelihood (ML) based tree inference and Four-cluster Likelihood Mapping (FcLM). By maximum parsimony-based mapping of the morphological data on the phylogenetic relationships we traced evolutionary transformations at the phenotypic level and reconstructed the groundplan of Holometabola and of selected subgroups. In our analysis of the amino acid sequence data of 1,343 single-copy orthologous genes, Hymenoptera are placed as sister group to all remaining holometabolan orders, i.e., to a clade Aparaglossata, comprising two monophyletic subunits Mecopterida (Amphiesmenoptera + Antliophora) and Neuropteroidea (Neuropterida + Coleopterida). The monophyly of Coleopterida (Coleoptera and Strepsiptera) remains ambiguous in the analyses of the transcriptome data, but appears likely based on the morphological data. Highly supported relationships within Neuropterida and Antliophora are Raphidioptera + (Neuroptera + monophyletic Megaloptera), and Diptera + (Siphonaptera + Mecoptera). ML tree inference and FcLM yielded largely congruent results. However, FcLM, which was applied here for the first time to large phylogenomic supermatrices, displayed additional signal in the datasets that was not identified in the ML trees. Our phylogenetic results imply that an orthognathous larva belongs to the groundplan of Holometabola, with compound eyes and well-developed thoracic legs, externally feeding on plants or fungi. Ancestral larvae of Aparaglossata were prognathous, equipped with single larval eyes (stemmata), and possibly agile and predacious. Ancestral holometabolan adults likely resembled in their morphology the groundplan of adult neopteran insects. Within Aparaglossata, the adult's flight apparatus and ovipositor underwent strong modifications. We show that the combination of well-resolved phylogenies obtained by phylogenomic analyses and well-documented extensive morphological datasets is an appropriate basis for reconstructing complex morphological transformations and for the inference of evolutionary histories.

Molecular Phylogenetics and Systematics of the Bivalve Family Ostreidae Based on rRNA Sequence-Structure Models and Multilocus Species Tree

PubMed Central

Salvi, Daniele; Macali, Armando; Mariottini, Paolo

2014-01-01

The bivalve family Ostreidae has a worldwide distribution and includes species of high economic importance. Phylogenetics and systematic of oysters based on morphology have proved difficult because of their high phenotypic plasticity. In this study we explore the phylogenetic information of the DNA sequence and secondary structure of the nuclear, fast-evolving, ITS2 rRNA and the mitochondrial 16S rRNA genes from the Ostreidae and we implemented a multi-locus framework based on four loci for oyster phylogenetics and systematics. Sequence-structure rRNA models aid sequence alignment and improved accuracy and nodal support of phylogenetic trees. In agreement with previous molecular studies, our phylogenetic results indicate that none of the currently recognized subfamilies, Crassostreinae, Ostreinae, and Lophinae, is monophyletic. Single gene trees based on Maximum likelihood (ML) and Bayesian (BA) methods and on sequence-structure ML were congruent with multilocus trees based on a concatenated (ML and BA) and coalescent based (BA) approaches and consistently supported three main clades: (i) Crassostrea, (ii) Saccostrea, and (iii) an Ostreinae-Lophinae lineage. Therefore, the subfamily Crassotreinae (including Crassostrea), Saccostreinae subfam. nov. (including Saccostrea and tentatively Striostrea) and Ostreinae (including Ostreinae and Lophinae taxa) are recognized. Based on phylogenetic and biogeographical evidence the Asian species of Crassostrea from the Pacific Ocean are assigned to Magallana gen. nov., whereas an integrative taxonomic revision is required for the genera Ostrea and Dendostrea. This study pointed out the suitability of the ITS2 marker for DNA barcoding of oyster and the relevance of using sequence-structure rRNA models and features of the ITS2 folding in molecular phylogenetics and taxonomy. The multilocus approach allowed inferring a robust phylogeny of Ostreidae providing a broad molecular perspective on their systematics. PMID:25250663

Molecular phylogenetics and systematics of the bivalve family Ostreidae based on rRNA sequence-structure models and multilocus species tree.

PubMed

Salvi, Daniele; Macali, Armando; Mariottini, Paolo

2014-01-01

The bivalve family Ostreidae has a worldwide distribution and includes species of high economic importance. Phylogenetics and systematic of oysters based on morphology have proved difficult because of their high phenotypic plasticity. In this study we explore the phylogenetic information of the DNA sequence and secondary structure of the nuclear, fast-evolving, ITS2 rRNA and the mitochondrial 16S rRNA genes from the Ostreidae and we implemented a multi-locus framework based on four loci for oyster phylogenetics and systematics. Sequence-structure rRNA models aid sequence alignment and improved accuracy and nodal support of phylogenetic trees. In agreement with previous molecular studies, our phylogenetic results indicate that none of the currently recognized subfamilies, Crassostreinae, Ostreinae, and Lophinae, is monophyletic. Single gene trees based on Maximum likelihood (ML) and Bayesian (BA) methods and on sequence-structure ML were congruent with multilocus trees based on a concatenated (ML and BA) and coalescent based (BA) approaches and consistently supported three main clades: (i) Crassostrea, (ii) Saccostrea, and (iii) an Ostreinae-Lophinae lineage. Therefore, the subfamily Crassostreinae (including Crassostrea), Saccostreinae subfam. nov. (including Saccostrea and tentatively Striostrea) and Ostreinae (including Ostreinae and Lophinae taxa) are recognized [corrected]. Based on phylogenetic and biogeographical evidence the Asian species of Crassostrea from the Pacific Ocean are assigned to Magallana gen. nov., whereas an integrative taxonomic revision is required for the genera Ostrea and Dendostrea. This study pointed out the suitability of the ITS2 marker for DNA barcoding of oyster and the relevance of using sequence-structure rRNA models and features of the ITS2 folding in molecular phylogenetics and taxonomy. The multilocus approach allowed inferring a robust phylogeny of Ostreidae providing a broad molecular perspective on their systematics.

Influence function for robust phylogenetic reconstructions.

PubMed

Bar-Hen, Avner; Mariadassou, Mahendra; Poursat, Marie-Anne; Vandenkoornhuyse, Philippe

2008-05-01

Based on the computation of the influence function, a tool to measure the impact of each piece of sampled data on the statistical inference of a parameter, we propose to analyze the support of the maximum-likelihood (ML) tree for each site. We provide a new tool for filtering data sets (nucleotides, amino acids, and others) in the context of ML phylogenetic reconstructions. Because different sites support different phylogenic topologies in different ways, outlier sites, that is, sites with a very negative influence value, are important: they can drastically change the topology resulting from the statistical inference. Therefore, these outlier sites must be clearly identified and their effects accounted for before drawing biological conclusions from the inferred tree. A matrix containing 158 fungal terminals all belonging to Chytridiomycota, Zygomycota, and Glomeromycota is analyzed. We show that removing the strongest outlier from the analysis strikingly modifies the ML topology, with a loss of as many as 20% of the internal nodes. As a result, estimating the topology on the filtered data set results in a topology with enhanced bootstrap support. From this analysis, the polyphyletic status of the fungal phyla Chytridiomycota and Zygomycota is reinforced, suggesting the necessity of revisiting the systematics of these fungal groups. We show the ability of influence function to produce new evolution hypotheses.

Assessment of phylogenetic sensitivity for reconstructing HIV-1 epidemiological relationships.

PubMed

Beloukas, Apostolos; Magiorkinis, Emmanouil; Magiorkinis, Gkikas; Zavitsanou, Asimina; Karamitros, Timokratis; Hatzakis, Angelos; Paraskevis, Dimitrios

2012-06-01

Phylogenetic analysis has been extensively used as a tool for the reconstruction of epidemiological relations for research or for forensic purposes. It was our objective to assess the sensitivity of different phylogenetic methods and various phylogenetic programs to reconstruct epidemiological links among HIV-1 infected patients that is the probability to reveal a true transmission relationship. Multiple datasets (90) were prepared consisting of HIV-1 sequences in protease (PR) and partial reverse transcriptase (RT) sampled from patients with documented epidemiological relationship (target population), and from unrelated individuals (control population) belonging to the same HIV-1 subtype as the target population. Each dataset varied regarding the number, the geographic origin and the transmission risk groups of the sequences among the control population. Phylogenetic trees were inferred by neighbor-joining (NJ), maximum likelihood heuristics (hML) and Bayesian methods. All clusters of sequences belonging to the target population were correctly reconstructed by NJ and Bayesian methods receiving high bootstrap and posterior probability (PP) support, respectively. On the other hand, TreePuzzle failed to reconstruct or provide significant support for several clusters; high puzzling step support was associated with the inclusion of control sequences from the same geographic area as the target population. In contrary, all clusters were correctly reconstructed by hML as implemented in PhyML 3.0 receiving high bootstrap support. We report that under the conditions of our study, hML using PhyML, NJ and Bayesian methods were the most sensitive for the reconstruction of epidemiological links mostly from sexually infected individuals. Copyright © 2012 Elsevier B.V. All rights reserved.

MultiPhyl: a high-throughput phylogenomics webserver using distributed computing

PubMed Central

Keane, Thomas M.; Naughton, Thomas J.; McInerney, James O.

2007-01-01

With the number of fully sequenced genomes increasing steadily, there is greater interest in performing large-scale phylogenomic analyses from large numbers of individual gene families. Maximum likelihood (ML) has been shown repeatedly to be one of the most accurate methods for phylogenetic construction. Recently, there have been a number of algorithmic improvements in maximum-likelihood-based tree search methods. However, it can still take a long time to analyse the evolutionary history of many gene families using a single computer. Distributed computing refers to a method of combining the computing power of multiple computers in order to perform some larger overall calculation. In this article, we present the first high-throughput implementation of a distributed phylogenetics platform, MultiPhyl, capable of using the idle computational resources of many heterogeneous non-dedicated machines to form a phylogenetics supercomputer. MultiPhyl allows a user to upload hundreds or thousands of amino acid or nucleotide alignments simultaneously and perform computationally intensive tasks such as model selection, tree searching and bootstrapping of each of the alignments using many desktop machines. The program implements a set of 88 amino acid models and 56 nucleotide maximum likelihood models and a variety of statistical methods for choosing between alternative models. A MultiPhyl webserver is available for public use at: http://www.cs.nuim.ie/distributed/multiphyl.php. PMID:17553837

Estimating the variance for heterogeneity in arm-based network meta-analysis.

PubMed

Piepho, Hans-Peter; Madden, Laurence V; Roger, James; Payne, Roger; Williams, Emlyn R

2018-04-19

Network meta-analysis can be implemented by using arm-based or contrast-based models. Here we focus on arm-based models and fit them using generalized linear mixed model procedures. Full maximum likelihood (ML) estimation leads to biased trial-by-treatment interaction variance estimates for heterogeneity. Thus, our objective is to investigate alternative approaches to variance estimation that reduce bias compared with full ML. Specifically, we use penalized quasi-likelihood/pseudo-likelihood and hierarchical (h) likelihood approaches. In addition, we consider a novel model modification that yields estimators akin to the residual maximum likelihood estimator for linear mixed models. The proposed methods are compared by simulation, and 2 real datasets are used for illustration. Simulations show that penalized quasi-likelihood/pseudo-likelihood and h-likelihood reduce bias and yield satisfactory coverage rates. Sum-to-zero restriction and baseline contrasts for random trial-by-treatment interaction effects, as well as a residual ML-like adjustment, also reduce bias compared with an unconstrained model when ML is used, but coverage rates are not quite as good. Penalized quasi-likelihood/pseudo-likelihood and h-likelihood are therefore recommended. Copyright © 2018 John Wiley & Sons, Ltd.

Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes.

PubMed

Saarela, Jeffery M; Wysocki, William P; Barrett, Craig F; Soreng, Robert J; Davis, Jerrold I; Clark, Lynn G; Kelchner, Scot A; Pires, J Chris; Edger, Patrick P; Mayfield, Dustin R; Duvall, Melvin R

2015-05-04

Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae-Loliinae clade. Published by Oxford University Press on behalf of the Annals of Botany Company.

Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars

PubMed Central

Shahin, Arwa; Smulders, Marinus J. M.; van Tuyl, Jaap M.; Arens, Paul; Bakker, Freek T.

2014-01-01

Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium. PMID:25368628

How many bootstrap replicates are necessary?

PubMed

Pattengale, Nicholas D; Alipour, Masoud; Bininda-Emonds, Olaf R P; Moret, Bernard M E; Stamatakis, Alexandros

2010-03-01

Phylogenetic bootstrapping (BS) is a standard technique for inferring confidence values on phylogenetic trees that is based on reconstructing many trees from minor variations of the input data, trees called replicates. BS is used with all phylogenetic reconstruction approaches, but we focus here on one of the most popular, maximum likelihood (ML). Because ML inference is so computationally demanding, it has proved too expensive to date to assess the impact of the number of replicates used in BS on the relative accuracy of the support values. For the same reason, a rather small number (typically 100) of BS replicates are computed in real-world studies. Stamatakis et al. recently introduced a BS algorithm that is 1 to 2 orders of magnitude faster than previous techniques, while yielding qualitatively comparable support values, making an experimental study possible. In this article, we propose stopping criteria--that is, thresholds computed at runtime to determine when enough replicates have been generated--and we report on the first large-scale experimental study to assess the effect of the number of replicates on the quality of support values, including the performance of our proposed criteria. We run our tests on 17 diverse real-world DNA--single-gene as well as multi-gene--datasets, which include 125-2,554 taxa. We find that our stopping criteria typically stop computations after 100-500 replicates (although the most conservative criterion may continue for several thousand replicates) while producing support values that correlate at better than 99.5% with the reference values on the best ML trees. Significantly, we also find that the stopping criteria can recommend very different numbers of replicates for different datasets of comparable sizes. Our results are thus twofold: (i) they give the first experimental assessment of the effect of the number of BS replicates on the quality of support values returned through BS, and (ii) they validate our proposals for stopping criteria. Practitioners will no longer have to enter a guess nor worry about the quality of support values; moreover, with most counts of replicates in the 100-500 range, robust BS under ML inference becomes computationally practical for most datasets. The complete test suite is available at http://lcbb.epfl.ch/BS.tar.bz2, and BS with our stopping criteria is included in the latest release of RAxML v7.2.5, available at http://wwwkramer.in.tum.de/exelixis/software.html.

Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic.

PubMed

Yebra, Gonzalo; Hodcroft, Emma B; Ragonnet-Cronin, Manon L; Pillay, Deenan; Brown, Andrew J Leigh

2016-12-23

HIV molecular epidemiology studies analyse viral pol gene sequences due to their availability, but whole genome sequencing allows to use other genes. We aimed to determine what gene(s) provide(s) the best approximation to the real phylogeny by analysing a simulated epidemic (created as part of the PANGEA_HIV project) with a known transmission tree. We sub-sampled a simulated dataset of 4662 sequences into different combinations of genes (gag-pol-env, gag-pol, gag, pol, env and partial pol) and sampling depths (100%, 60%, 20% and 5%), generating 100 replicates for each case. We built maximum-likelihood trees for each combination using RAxML (GTR + Γ), and compared their topologies to the corresponding true tree's using CompareTree. The accuracy of the trees was significantly proportional to the length of the sequences used, with the gag-pol-env datasets showing the best performance and gag and partial pol sequences showing the worst. The lowest sampling depths (20% and 5%) greatly reduced the accuracy of tree reconstruction and showed high variability among replicates, especially when using the shortest gene datasets. In conclusion, using longer sequences derived from nearly whole genomes will improve the reliability of phylogenetic reconstruction. With low sample coverage, results can be highly variable, particularly when based on short sequences.

Mapping and characterizing selected canopy tree species at the Angkor World Heritage site in Cambodia using aerial data.

PubMed

Singh, Minerva; Evans, Damian; Tan, Boun Suy; Nin, Chan Samean

2015-01-01

At present, there is very limited information on the ecology, distribution, and structure of Cambodia's tree species to warrant suitable conservation measures. The aim of this study was to assess various methods of analysis of aerial imagery for characterization of the forest mensuration variables (i.e., tree height and crown width) of selected tree species found in the forested region around the temples of Angkor Thom, Cambodia. Object-based image analysis (OBIA) was used (using multiresolution segmentation) to delineate individual tree crowns from very-high-resolution (VHR) aerial imagery and light detection and ranging (LiDAR) data. Crown width and tree height values that were extracted using multiresolution segmentation showed a high level of congruence with field-measured values of the trees (Spearman's rho 0.782 and 0.589, respectively). Individual tree crowns that were delineated from aerial imagery using multiresolution segmentation had a high level of segmentation accuracy (69.22%), whereas tree crowns delineated using watershed segmentation underestimated the field-measured tree crown widths. Both spectral angle mapper (SAM) and maximum likelihood (ML) classifications were applied to the aerial imagery for mapping of selected tree species. The latter was found to be more suitable for tree species classification. Individual tree species were identified with high accuracy. Inclusion of textural information further improved species identification, albeit marginally. Our findings suggest that VHR aerial imagery, in conjunction with OBIA-based segmentation methods (such as multiresolution segmentation) and supervised classification techniques are useful for tree species mapping and for studies of the forest mensuration variables.

Mapping and Characterizing Selected Canopy Tree Species at the Angkor World Heritage Site in Cambodia Using Aerial Data

PubMed Central

Singh, Minerva; Evans, Damian; Tan, Boun Suy; Nin, Chan Samean

2015-01-01

At present, there is very limited information on the ecology, distribution, and structure of Cambodia’s tree species to warrant suitable conservation measures. The aim of this study was to assess various methods of analysis of aerial imagery for characterization of the forest mensuration variables (i.e., tree height and crown width) of selected tree species found in the forested region around the temples of Angkor Thom, Cambodia. Object-based image analysis (OBIA) was used (using multiresolution segmentation) to delineate individual tree crowns from very-high-resolution (VHR) aerial imagery and light detection and ranging (LiDAR) data. Crown width and tree height values that were extracted using multiresolution segmentation showed a high level of congruence with field-measured values of the trees (Spearman’s rho 0.782 and 0.589, respectively). Individual tree crowns that were delineated from aerial imagery using multiresolution segmentation had a high level of segmentation accuracy (69.22%), whereas tree crowns delineated using watershed segmentation underestimated the field-measured tree crown widths. Both spectral angle mapper (SAM) and maximum likelihood (ML) classifications were applied to the aerial imagery for mapping of selected tree species. The latter was found to be more suitable for tree species classification. Individual tree species were identified with high accuracy. Inclusion of textural information further improved species identification, albeit marginally. Our findings suggest that VHR aerial imagery, in conjunction with OBIA-based segmentation methods (such as multiresolution segmentation) and supervised classification techniques are useful for tree species mapping and for studies of the forest mensuration variables. PMID:25902148

Efficient Exploration of the Space of Reconciled Gene Trees

PubMed Central

Szöllősi, Gergely J.; Rosikiewicz, Wojciech; Boussau, Bastien; Tannier, Eric; Daubin, Vincent

2013-01-01

Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and species-level events, such as speciation and extinction. Gene tree–species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species-level events. The reconstruction of gene trees based on sequence alone almost always involves choosing between statistically equivalent or weakly distinguishable relationships that could be much better resolved based on a putative species tree. To exploit this potential for accurate reconstruction of gene trees, the space of reconciled gene trees must be explored according to a joint model of sequence evolution and gene tree–species tree reconciliation. Here we present amalgamated likelihood estimation (ALE), a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (Szöllősi et al. 2013), which allows for the DTL of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees. We demonstrate using simulations that gene trees reconstructed using the joint likelihood are substantially more accurate than those reconstructed using sequence alone. Using realistic gene tree topologies, branch lengths, and alignment sizes, we demonstrate that ALE produces more accurate gene trees even if the model of sequence evolution is greatly simplified. Finally, examining 1099 gene families from 36 cyanobacterial genomes we find that joint likelihood-based inference results in a striking reduction in apparent phylogenetic discord, with respectively. 24%, 59%, and 46% reductions in the mean numbers of duplications, transfers, and losses per gene family. The open source implementation of ALE is available from https://github.com/ssolo/ALE.git. [amalgamation; gene tree reconciliation; gene tree reconstruction; lateral gene transfer; phylogeny.] PMID:23925510

Molecular phylogeny of the higher and lower taxonomy of the Fusarium genus and differences in the evolutionary histories of multiple genes

PubMed Central

2011-01-01

Background Species of the Fusarium genus are important fungi which is associated with health hazards in human and animals. The taxonomy of this genus has been a subject of controversy for many years. Although many researchers have applied molecular phylogenetic analysis to examine the taxonomy of Fusarium species, their phylogenetic relationships remain unclear only few comprehensive phylogenetic analyses of the Fusarium genus and a lack of suitable nucleotides and amino acid substitution rates. A previous stugy with whole genome comparison among Fusairum species revealed the possibility that each gene in Fusarium genomes has a unique evolutionary history, and such gene may bring difficulty to the reconstruction of phylogenetic tree of Fusarium. There is a need not only to check substitution rates of genes but also to perform the exact evaluation of each gene-evolution. Results We performed phylogenetic analyses based on the nucleotide sequences of the rDNA cluster region (rDNA cluster), and the β-tubulin gene (β-tub), the elongation factor 1α gene (EF-1α), and the aminoadipate reductase gene (lys2). Although incongruence of the tree topologies between lys2 and the other genes was detected, all genes supported the classification of Fusarium species into 7 major clades, I to VII. To obtain a reliable phylogeny for Fusarium species, we excluded the lys2 sequences from our dataset, and re-constructed a maximum likelihood (ML) tree based on the combined data of the rDNA cluster, β-tub, and EF-1α. Our ML tree indicated some interesting relationships in the higher and lower taxa of Fusarium species and related genera. Moreover, we observed a novel evolutionary history of lys2. We suggest that the unique tree topologies of lys2 are not due to an analytical artefact, but due to differences in the evolutionary history of genomes caused by positive selection of particular lineages. Conclusion This study showed the reliable species tree of the higher and lower taxonomy in the lineage of the Fusarium genus. Our ML tree clearly indicated 7 major clades within the Fusarium genus. Furthermore, this study reported differences in the evolutionary histories among multiple genes within this genus for the first time. PMID:22047111

Maximum likelihood of phylogenetic networks.

PubMed

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

Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic

PubMed Central

Yebra, Gonzalo; Hodcroft, Emma B.; Ragonnet-Cronin, Manon L.; Pillay, Deenan; Brown, Andrew J. Leigh; Fraser, Christophe; Kellam, Paul; de Oliveira, Tulio; Dennis, Ann; Hoppe, Anne; Kityo, Cissy; Frampton, Dan; Ssemwanga, Deogratius; Tanser, Frank; Keshani, Jagoda; Lingappa, Jairam; Herbeck, Joshua; Wawer, Maria; Essex, Max; Cohen, Myron S.; Paton, Nicholas; Ratmann, Oliver; Kaleebu, Pontiano; Hayes, Richard; Fidler, Sarah; Quinn, Thomas; Novitsky, Vladimir; Haywards, Andrew; Nastouli, Eleni; Morris, Steven; Clark, Duncan; Kozlakidis, Zisis

2016-01-01

HIV molecular epidemiology studies analyse viral pol gene sequences due to their availability, but whole genome sequencing allows to use other genes. We aimed to determine what gene(s) provide(s) the best approximation to the real phylogeny by analysing a simulated epidemic (created as part of the PANGEA_HIV project) with a known transmission tree. We sub-sampled a simulated dataset of 4662 sequences into different combinations of genes (gag-pol-env, gag-pol, gag, pol, env and partial pol) and sampling depths (100%, 60%, 20% and 5%), generating 100 replicates for each case. We built maximum-likelihood trees for each combination using RAxML (GTR + Γ), and compared their topologies to the corresponding true tree’s using CompareTree. The accuracy of the trees was significantly proportional to the length of the sequences used, with the gag-pol-env datasets showing the best performance and gag and partial pol sequences showing the worst. The lowest sampling depths (20% and 5%) greatly reduced the accuracy of tree reconstruction and showed high variability among replicates, especially when using the shortest gene datasets. In conclusion, using longer sequences derived from nearly whole genomes will improve the reliability of phylogenetic reconstruction. With low sample coverage, results can be highly variable, particularly when based on short sequences. PMID:28008945

GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas.

PubMed

Vinuesa, Pablo; Ochoa-Sánchez, Luz E; Contreras-Moreira, Bruno

2018-01-01

The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia , demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.

A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

PubMed Central

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

2016-01-01

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

Multitemporal WorldView satellites imagery for mapping chestnut trees

NASA Astrophysics Data System (ADS)

Marchetti, F.; Arbelo, M.; Moreno-Ruíz, J. A.; Hernández-Leal, P. A.; Alonso-Benito, A.

2017-10-01

Chestnuts have been part of the landscape and popular culture of the Canary Islands (Spain) since the sixteenth century. Many crops of this species are in state of abandonment and an updated mapping for its study and evaluation is needed. This work proposes the elaboration of this cartography using two satellite images of very high spatial resolution captured on two different dates and representing well-differentiated phenological states of the chestnut: a WorldView-2 image of March 10th, 2015 and a WorldView-3 image of May 12th, 2015 (without and with leaves respectively). Two study areas were selected within the municipality of La Orotava (Tenerife Island). One of the areas contains chestnut trees dispersed in an agricultural and semi-urban environment and in the other one, the specimens are grouped forming a forest merged with Canarian pines and other species of Monteverde. The Maximum Likelihood (ML), the Artificial Neural Networks (ANN) and the Spectral Angle Mapper (SAM) classification algorithms were applied to the multi-temporal image resulting from the combination of both dates. The results show the benefits of using the multi-temporal image for Pinolere with the ANN algorithm and for Chasna area with ML algorithm, in both cases providing an overall accuracy close to 95%.

Nonlinear phase noise tolerance for coherent optical systems using soft-decision-aided ML carrier phase estimation enhanced with constellation partitioning

NASA Astrophysics Data System (ADS)

Li, Yan; Wu, Mingwei; Du, Xinwei; Xu, Zhuoran; Gurusamy, Mohan; Yu, Changyuan; Kam, Pooi-Yuen

2018-02-01

A novel soft-decision-aided maximum likelihood (SDA-ML) carrier phase estimation method and its simplified version, the decision-aided and soft-decision-aided maximum likelihood (DA-SDA-ML) methods are tested in a nonlinear phase noise-dominant channel. The numerical performance results show that both the SDA-ML and DA-SDA-ML methods outperform the conventional DA-ML in systems with constant-amplitude modulation formats. In addition, modified algorithms based on constellation partitioning are proposed. With partitioning, the modified SDA-ML and DA-SDA-ML are shown to be useful for compensating the nonlinear phase noise in multi-level modulation systems.

[Approach to Spodoptera (Lepidoptera: Noctuidae) phylogeny based on the sequence of the cytocrhome oxydase I (COI) mitochondrial gene].

PubMed

Saldamando, Clara Inés; Marquez, Edna Judith

2012-09-01

The genus Spodoptera includes 30 species of moths considered important pests worldwide, with a great representation in the Western Hemisphere. In general, Noctuidae species have morphological similarities that have caused some difficulties for assertive species identification by conventional methods. The purpose of this work was to generate an approach to the genus phylogeny from several species of the genus Spodoptera and the species Bombyx mori as an out group, with the use of molecular tools. For this, a total of 102 S. frugiperda larvae were obtained at random in corn, cotton, rice, grass and sorghum, during late 2006 and early 2009, from Colombia. We took ADN samples from the larval posterior part and we analyzed a fragment of 451 base pairs of the mitochondrial gene cytochrome oxydase I (COI), to produce a maximum likelihood (ML) tree by using 62 sequences (29 Colombian haplotypes were used). Our results showed a great genetic differentiation (K2 distances) amongst S. frugiperda haplotypes from Colombia and the United States, condition supported by the estimators obtained for haplotype diversity and polymorphism. The obtained ML tree clustered most of the species with bootstrapping values from 73-99% in the interior branches; with low values also observed in some of the branches. In addition, this tree clustered two species of the Eastern hemisphere (S littoralis and S. litura) and eight species of the Western hemisphere (S. androgea, S. dolichos, S. eridania, S. exigua, S. frugiperda, S. latifascia, S. ornithogalli and S. pulchella). In Colombia, S. frugiperda, S. ornithogalli and S. albula represent a group of species referred as "the Spodoptera complex" of cotton crops, and our work demonstrated that sequencing a fragment of the COI gene, allows researchers to differentiate the first two species, and thus it can be used as an alternative method to taxonomic keys based on morphology. Finally, the ML tree did not cluster S. frugiperda with S. ornithogalli, suggesting that both species do not share the same recent ancestral even though they coexist in cotton. We suggest sequencing other genes (mitochondrial and nuclear) to increase our understanding of this genus evolution.

Maximum likelihood clustering with dependent feature trees

NASA Technical Reports Server (NTRS)

Chittineni, C. B. (Principal Investigator)

1981-01-01

The decomposition of mixture density of the data into its normal component densities is considered. The densities are approximated with first order dependent feature trees using criteria of mutual information and distance measures. Expressions are presented for the criteria when the densities are Gaussian. By defining different typs of nodes in a general dependent feature tree, maximum likelihood equations are developed for the estimation of parameters using fixed point iterations. The field structure of the data is also taken into account in developing maximum likelihood equations. Experimental results from the processing of remotely sensed multispectral scanner imagery data are included.

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

PubMed Central

Xu, Bo; Yang, Ziheng

2016-01-01

The multispecies coalescent (MSC) model has emerged as a powerful framework for inferring species phylogenies while accounting for ancestral polymorphism and gene tree-species tree conflict. A number of methods have been developed in the past few years to estimate the species tree under the MSC. The full likelihood methods (including maximum likelihood and Bayesian inference) average over the unknown gene trees and accommodate their uncertainties properly but involve intensive computation. The approximate or summary coalescent methods are computationally fast and are applicable to genomic datasets with thousands of loci, but do not make an efficient use of information in the multilocus data. Most of them take the two-step approach of reconstructing the gene trees for multiple loci by phylogenetic methods and then treating the estimated gene trees as observed data, without accounting for their uncertainties appropriately. In this article we review the statistical nature of the species tree estimation problem under the MSC, and explore the conceptual issues and challenges of species tree estimation by focusing mainly on simple cases of three or four closely related species. We use mathematical analysis and computer simulation to demonstrate that large differences in statistical performance may exist between the two classes of methods. We illustrate that several counterintuitive behaviors may occur with the summary methods but they are due to inefficient use of information in the data by summary methods and vanish when the data are analyzed using full-likelihood methods. These include (i) unidentifiability of parameters in the model, (ii) inconsistency in the so-called anomaly zone, (iii) singularity on the likelihood surface, and (iv) deterioration of performance upon addition of more data. We discuss the challenges and strategies of species tree inference for distantly related species when the molecular clock is violated, and highlight the need for improving the computational efficiency and model realism of the likelihood methods as well as the statistical efficiency of the summary methods. PMID:27927902

Variational Bayesian Parameter Estimation Techniques for the General Linear Model

PubMed Central

Starke, Ludger; Ostwald, Dirk

2017-01-01

Variational Bayes (VB), variational maximum likelihood (VML), restricted maximum likelihood (ReML), and maximum likelihood (ML) are cornerstone parametric statistical estimation techniques in the analysis of functional neuroimaging data. However, the theoretical underpinnings of these model parameter estimation techniques are rarely covered in introductory statistical texts. Because of the widespread practical use of VB, VML, ReML, and ML in the neuroimaging community, we reasoned that a theoretical treatment of their relationships and their application in a basic modeling scenario may be helpful for both neuroimaging novices and practitioners alike. In this technical study, we thus revisit the conceptual and formal underpinnings of VB, VML, ReML, and ML and provide a detailed account of their mathematical relationships and implementational details. We further apply VB, VML, ReML, and ML to the general linear model (GLM) with non-spherical error covariance as commonly encountered in the first-level analysis of fMRI data. To this end, we explicitly derive the corresponding free energy objective functions and ensuing iterative algorithms. Finally, in the applied part of our study, we evaluate the parameter and model recovery properties of VB, VML, ReML, and ML, first in an exemplary setting and then in the analysis of experimental fMRI data acquired from a single participant under visual stimulation. PMID:28966572

Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting

PubMed Central

Kamneva, Olga K; Rosenberg, Noah A

2017-01-01

Hybridization events generate reticulate species relationships, giving rise to species networks rather than species trees. We report a comparative study of consensus, maximum parsimony, and maximum likelihood methods of species network reconstruction using gene trees simulated assuming a known species history. We evaluate the role of the divergence time between species involved in a hybridization event, the relative contributions of the hybridizing species, and the error in gene tree estimation. When gene tree discordance is mostly due to hybridization and not due to incomplete lineage sorting (ILS), most of the methods can detect even highly skewed hybridization events between highly divergent species. For recent divergences between hybridizing species, when the influence of ILS is sufficiently high, likelihood methods outperform parsimony and consensus methods, which erroneously identify extra hybridizations. The more sophisticated likelihood methods, however, are affected by gene tree errors to a greater extent than are consensus and parsimony. PMID:28469378

Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals

PubMed Central

Yuri, Tamaki; Kimball, Rebecca T.; Harshman, John; Bowie, Rauri C. K.; Braun, Michael J.; Chojnowski, Jena L.; Han, Kin-Lan; Hackett, Shannon J.; Huddleston, Christopher J.; Moore, William S.; Reddy, Sushma; Sheldon, Frederick H.; Steadman, David W.; Witt, Christopher C.; Braun, Edward L.

2013-01-01

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions. PMID:24832669

Fuzzy multinomial logistic regression analysis: A multi-objective programming approach

NASA Astrophysics Data System (ADS)

Abdalla, Hesham A.; El-Sayed, Amany A.; Hamed, Ramadan

2017-05-01

Parameter estimation for multinomial logistic regression is usually based on maximizing the likelihood function. For large well-balanced datasets, Maximum Likelihood (ML) estimation is a satisfactory approach. Unfortunately, ML can fail completely or at least produce poor results in terms of estimated probabilities and confidence intervals of parameters, specially for small datasets. In this study, a new approach based on fuzzy concepts is proposed to estimate parameters of the multinomial logistic regression. The study assumes that the parameters of multinomial logistic regression are fuzzy. Based on the extension principle stated by Zadeh and Bárdossy's proposition, a multi-objective programming approach is suggested to estimate these fuzzy parameters. A simulation study is used to evaluate the performance of the new approach versus Maximum likelihood (ML) approach. Results show that the new proposed model outperforms ML in cases of small datasets.

Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms.

PubMed

Speiser, Daniel I; Pankey, M Sabrina; Zaharoff, Alexander K; Battelle, Barbara A; Bracken-Grissom, Heather D; Breinholt, Jesse W; Bybee, Seth M; Cronin, Thomas W; Garm, Anders; Lindgren, Annie R; Patel, Nipam H; Porter, Megan L; Protas, Meredith E; Rivera, Ajna S; Serb, Jeanne M; Zigler, Kirk S; Crandall, Keith A; Oakley, Todd H

2014-11-19

Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to produce a computationally efficient, tree-based approach for annotating transcriptomes or new genomes that we term Phylogenetically-Informed Annotation (PIA), which places uncharacterized genes into pre-calculated phylogenies of gene families. We generated maximum likelihood trees for 109 genes from a Light Interaction Toolkit (LIT), a collection of genes that underlie the function or development of light-interacting structures in metazoans. To do so, we searched protein sequences predicted from 29 fully-sequenced genomes and built trees using tools for phylogenetic analysis in the Osiris package of Galaxy (an open-source workflow management system). Next, to rapidly annotate transcriptomes from organisms that lack sequenced genomes, we repurposed a maximum likelihood-based Evolutionary Placement Algorithm (implemented in RAxML) to place sequences of potential LIT genes on to our pre-calculated gene trees. Finally, we implemented PIA in Galaxy and used it to search for LIT genes in 28 newly-sequenced transcriptomes from the light-interacting tissues of a range of cephalopod mollusks, arthropods, and cubozoan cnidarians. Our new trees for LIT genes are available on the Bitbucket public repository ( http://bitbucket.org/osiris_phylogenetics/pia/ ) and we demonstrate PIA on a publicly-accessible web server ( http://galaxy-dev.cnsi.ucsb.edu/pia/ ). Our new trees for LIT genes will be a valuable resource for researchers studying the evolution of eyes or other light-interacting structures. We also introduce PIA, a high throughput method for using phylogenetic relationships to identify LIT genes in transcriptomes from non-model organisms. With simple modifications, our methods may be used to search for different sets of genes or to annotate data sets from taxa outside of Metazoa.

Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset

PubMed Central

Higdon, Jeff W; Bininda-Emonds, Olaf RP; Beck, Robin MD; Ferguson, Steven H

2007-01-01

Background Phylogenetic comparative methods are often improved by complete phylogenies with meaningful branch lengths (e.g., divergence dates). This study presents a dated molecular supertree for all 34 world pinniped species derived from a weighted matrix representation with parsimony (MRP) supertree analysis of 50 gene trees, each determined under a maximum likelihood (ML) framework. Divergence times were determined by mapping the same sequence data (plus two additional genes) on to the supertree topology and calibrating the ML branch lengths against a range of fossil calibrations. We assessed the sensitivity of our supertree topology in two ways: 1) a second supertree with all mtDNA genes combined into a single source tree, and 2) likelihood-based supermatrix analyses. Divergence dates were also calculated using a Bayesian relaxed molecular clock with rate autocorrelation to test the sensitivity of our supertree results further. Results The resulting phylogenies all agreed broadly with recent molecular studies, in particular supporting the monophyly of Phocidae, Otariidae, and the two phocid subfamilies, as well as an Odobenidae + Otariidae sister relationship; areas of disagreement were limited to four more poorly supported regions. Neither the supertree nor supermatrix analyses supported the monophyly of the two traditional otariid subfamilies, supporting suggestions for the need for taxonomic revision in this group. Phocid relationships were similar to other recent studies and deeper branches were generally well-resolved. Halichoerus grypus was nested within a paraphyletic Pusa, although relationships within Phocina tend to be poorly supported. Divergence date estimates for the supertree were in good agreement with other studies and the available fossil record; however, the Bayesian relaxed molecular clock divergence date estimates were significantly older. Conclusion Our results join other recent studies and highlight the need for a re-evaluation of pinniped taxonomy, especially as regards the subfamilial classification of otariids and the generic nomenclature of Phocina. Even with the recent publication of new sequence data, the available genetic sequence information for several species, particularly those in Arctocephalus, remains very limited, especially for nuclear markers. However, resolution of parts of the tree will probably remain difficult, even with additional data, due to apparent rapid radiations. Our study addresses the lack of a recent pinniped phylogeny that includes all species and robust divergence dates for all nodes, and will therefore prove indispensable to comparative and macroevolutionary studies of this group of carnivores. PMID:17996107

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

PubMed

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

2016-11-28

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

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

PubMed

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

2016-03-01

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

Identification and characterization of toll-like receptors (TLRs) in the Chinese tree shrew (Tupaia belangeri chinensis).

PubMed

Yu, Dandan; Wu, Yong; Xu, Ling; Fan, Yu; Peng, Li; Xu, Min; Yao, Yong-Gang

2016-07-01

In mammals, the toll-like receptors (TLRs) play a major role in initiating innate immune responses against pathogens. Comparison of the TLRs in different mammals may help in understanding the TLR-mediated responses and developing of animal models and efficient therapeutic measures for infectious diseases. The Chinese tree shrew (Tupaia belangeri chinensis), a small mammal with a close relationship to primates, is a viable experimental animal for studying viral and bacterial infections. In this study, we characterized the TLRs genes (tTLRs) in the Chinese tree shrew and identified 13 putative TLRs, which are orthologs of mammalian TLR1-TLR9 and TLR11-TLR13, and TLR10 was a pseudogene in tree shrew. Positive selection analyses using the Maximum likelihood (ML) method showed that tTLR8 and tTLR9 were under positive selection, which might be associated with the adaptation to the pathogen challenge. The mRNA expression levels of tTLRs presented an overall low and tissue-specific pattern, and were significantly upregulated upon Hepatitis C virus (HCV) infection. tTLR4 and tTLR9 underwent alternative splicing, which leads to different transcripts. Phylogenetic analysis and TLR structure prediction indicated that tTLRs were evolutionarily conserved, which might reflect an ancient mechanism and structure in the innate immune response system. Taken together, TLRs had both conserved and unique features in the Chinese tree shrew. Copyright © 2016 Elsevier Ltd. All rights reserved.

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures

PubMed Central

Theobald, Douglas L.; Wuttke, Deborah S.

2008-01-01

Summary THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. PMID:16777907

A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea

PubMed Central

2011-01-01

Background Cetacea (dolphins, porpoises, and whales) is a clade of aquatic species that includes the most massive, deepest diving, and largest brained mammals. Understanding the temporal pattern of diversification in the group as well as the evolution of cetacean anatomy and behavior requires a robust and well-resolved phylogenetic hypothesis. Although a large body of molecular data has accumulated over the past 20 years, DNA sequences of cetaceans have not been directly integrated with the rich, cetacean fossil record to reconcile discrepancies among molecular and morphological characters. Results We combined new nuclear DNA sequences, including segments of six genes (~2800 basepairs) from the functionally extinct Yangtze River dolphin, with an expanded morphological matrix and published genomic data. Diverse analyses of these data resolved the relationships of 74 taxa that represent all extant families and 11 extinct families of Cetacea. The resulting supermatrix (61,155 characters) and its sub-partitions were analyzed using parsimony methods. Bayesian and maximum likelihood (ML) searches were conducted on the molecular partition, and a molecular scaffold obtained from these searches was used to constrain a parsimony search of the morphological partition. Based on analysis of the supermatrix and model-based analyses of the molecular partition, we found overwhelming support for 15 extant clades. When extinct taxa are included, we recovered trees that are significantly correlated with the fossil record. These trees were used to reconstruct the timing of cetacean diversification and the evolution of characters shared by "river dolphins," a non-monophyletic set of species according to all of our phylogenetic analyses. Conclusions The parsimony analysis of the supermatrix and the analysis of morphology constrained to fit the ML/Bayesian molecular tree yielded broadly congruent phylogenetic hypotheses. In trees from both analyses, all Oligocene taxa included in our study fell outside crown Mysticeti and crown Odontoceti, suggesting that these two clades radiated in the late Oligocene or later, contra some recent molecular clock studies. Our trees also imply that many character states shared by river dolphins evolved in their oceanic ancestors, contradicting the hypothesis that these characters are convergent adaptations to fluvial habitats. PMID:21518443

Phylogeny with introgression in Habronattus jumping spiders (Araneae: Salticidae).

PubMed

Leduc-Robert, Geneviève; Maddison, Wayne P

2018-02-22

Habronattus is a diverse clade of jumping spiders with complex courtship displays and repeated evolution of Y chromosomes. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved, in part because the few genes available in past studies gave conflicting signals. Such discordant gene trees could be the result of incomplete lineage sorting (ILS) in recently diverged parts of the phylogeny, but there are indications that introgression could be a source of conflict. To infer Habronattus phylogeny and investigate the cause of gene tree discordance, we assembled transcriptomes for 34 Habronattus species and 2 outgroups. The concatenated 2.41 Mb of nuclear data (1877 loci) resolved phylogeny by Maximum Likelihood (ML) with high bootstrap support (95-100%) at most nodes, with some uncertainty surrounding the relationships of H. icenoglei, H. cambridgei, H. oregonensis, and Pellenes canadensis. Species tree analyses by ASTRAL and SVDQuartets gave almost completely congruent results. Several nodes in the ML phylogeny from 12.33 kb of mitochondrial data are incongruent with the nuclear phylogeny and indicate possible mitochondrial introgression: the internal relationships of the americanus and the coecatus groups, the relationship between the altanus, decorus, banksi, and americanus group, and between H. clypeatus and the coecatus group. To determine the relative contributions of ILS and introgression, we analyzed gene tree discordance for nuclear loci longer than 1 kb using Bayesian Concordance Analysis (BCA) for the americanus group (679 loci) and the VCCR clade (viridipes/clypeatus/coecatus/roberti groups) (517 loci) and found signals of introgression in both. Finally, we tested specifically for introgression in the concatenated nuclear matrix with Patterson's D statistics and D FOIL . We found nuclear introgression resulting in substantial admixture between americanus group species, between H. roberti and the clypeatus group, and between the clypeatus and coecatus groups. Our results indicate that the phylogenetic history of Habronattus is predominantly a diverging tree, but that hybridization may have been common between phylogenetically distant species, especially in subgroups with complex courtship displays.

A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea.

PubMed

Geisler, Jonathan H; McGowen, Michael R; Yang, Guang; Gatesy, John

2011-04-25

Cetacea (dolphins, porpoises, and whales) is a clade of aquatic species that includes the most massive, deepest diving, and largest brained mammals. Understanding the temporal pattern of diversification in the group as well as the evolution of cetacean anatomy and behavior requires a robust and well-resolved phylogenetic hypothesis. Although a large body of molecular data has accumulated over the past 20 years, DNA sequences of cetaceans have not been directly integrated with the rich, cetacean fossil record to reconcile discrepancies among molecular and morphological characters. We combined new nuclear DNA sequences, including segments of six genes (~2800 basepairs) from the functionally extinct Yangtze River dolphin, with an expanded morphological matrix and published genomic data. Diverse analyses of these data resolved the relationships of 74 taxa that represent all extant families and 11 extinct families of Cetacea. The resulting supermatrix (61,155 characters) and its sub-partitions were analyzed using parsimony methods. Bayesian and maximum likelihood (ML) searches were conducted on the molecular partition, and a molecular scaffold obtained from these searches was used to constrain a parsimony search of the morphological partition. Based on analysis of the supermatrix and model-based analyses of the molecular partition, we found overwhelming support for 15 extant clades. When extinct taxa are included, we recovered trees that are significantly correlated with the fossil record. These trees were used to reconstruct the timing of cetacean diversification and the evolution of characters shared by "river dolphins," a non-monophyletic set of species according to all of our phylogenetic analyses. The parsimony analysis of the supermatrix and the analysis of morphology constrained to fit the ML/Bayesian molecular tree yielded broadly congruent phylogenetic hypotheses. In trees from both analyses, all Oligocene taxa included in our study fell outside crown Mysticeti and crown Odontoceti, suggesting that these two clades radiated in the late Oligocene or later, contra some recent molecular clock studies. Our trees also imply that many character states shared by river dolphins evolved in their oceanic ancestors, contradicting the hypothesis that these characters are convergent adaptations to fluvial habitats.

Genetic distances and phylogenetic trees of different Awassi sheep populations based on DNA sequencing.

PubMed

Al-Atiyat, R M; Aljumaah, R S

2014-08-27

This study aimed to estimate evolutionary distances and to reconstruct phylogeny trees between different Awassi sheep populations. Thirty-two sheep individuals from three different geographical areas of Jordan and the Kingdom of Saudi Arabia (KSA) were randomly sampled. DNA was extracted from the tissue samples and sequenced using the T7 promoter universal primer. Different phylogenetic trees were reconstructed from 0.64-kb DNA sequences using the MEGA software with the best general time reverse distance model. Three methods of distance estimation were then used. The maximum composite likelihood test was considered for reconstructing maximum likelihood, neighbor-joining and UPGMA trees. The maximum likelihood tree indicated three major clusters separated by cytosine (C) and thymine (T). The greatest distance was shown between the South sheep and North sheep. On the other hand, the KSA sheep as an outgroup showed shorter evolutionary distance to the North sheep population than to the others. The neighbor-joining and UPGMA trees showed quite reliable clusters of evolutionary differentiation of Jordan sheep populations from the Saudi population. The overall results support geographical information and ecological types of the sheep populations studied. Summing up, the resulting phylogeny trees may contribute to the limited information about the genetic relatedness and phylogeny of Awassi sheep in nearby Arab countries.

Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica

PubMed Central

Vásquez-Mayorga, Marcela; Fuchs, Eric J.; Hernández, Eduardo J.; Herrera, Franklin; Hernández, Jesús; Moreira, Ileana; Arnáez, Elizabeth

2017-01-01

We estimated the genetic diversity of 50 Jatropha curcas samples from the Costa Rican germplasm bank using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable compared to worldwide values for J. curcas. The PIC (PIC = 0.274) and inbreeding coefficient (f =  − 0.102) were both low. Clustering was not related to the geographical origin of accessions. International accessions clustered independently of collection sites, suggesting a lack of genetic structure, probably due to the wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of the Jatropha curcas germplasm bank in Costa Rica. PMID:28289556

Extending the BEAGLE library to a multi-FPGA platform.

PubMed

Jin, Zheming; Bakos, Jason D

2013-01-19

Maximum Likelihood (ML)-based phylogenetic inference using Felsenstein's pruning algorithm is a standard method for estimating the evolutionary relationships amongst a set of species based on DNA sequence data, and is used in popular applications such as RAxML, PHYLIP, GARLI, BEAST, and MrBayes. The Phylogenetic Likelihood Function (PLF) and its associated scaling and normalization steps comprise the computational kernel for these tools. These computations are data intensive but contain fine grain parallelism that can be exploited by coprocessor architectures such as FPGAs and GPUs. A general purpose API called BEAGLE has recently been developed that includes optimized implementations of Felsenstein's pruning algorithm for various data parallel architectures. In this paper, we extend the BEAGLE API to a multiple Field Programmable Gate Array (FPGA)-based platform called the Convey HC-1. The core calculation of our implementation, which includes both the phylogenetic likelihood function (PLF) and the tree likelihood calculation, has an arithmetic intensity of 130 floating-point operations per 64 bytes of I/O, or 2.03 ops/byte. Its performance can thus be calculated as a function of the host platform's peak memory bandwidth and the implementation's memory efficiency, as 2.03 × peak bandwidth × memory efficiency. Our FPGA-based platform has a peak bandwidth of 76.8 GB/s and our implementation achieves a memory efficiency of approximately 50%, which gives an average throughput of 78 Gflops. This represents a ~40X speedup when compared with BEAGLE's CPU implementation on a dual Xeon 5520 and 3X speedup versus BEAGLE's GPU implementation on a Tesla T10 GPU for very large data sizes. The power consumption is 92 W, yielding a power efficiency of 1.7 Gflops per Watt. The use of data parallel architectures to achieve high performance for likelihood-based phylogenetic inference requires high memory bandwidth and a design methodology that emphasizes high memory efficiency. To achieve this objective, we integrated 32 pipelined processing elements (PEs) across four FPGAs. For the design of each PE, we developed a specialized synthesis tool to generate a floating-point pipeline with resource and throughput constraints to match the target platform. We have found that using low-latency floating-point operators can significantly reduce FPGA area and still meet timing requirement on the target platform. We found that this design methodology can achieve performance that exceeds that of a GPU-based coprocessor.

Maximum-likelihood methods in wavefront sensing: stochastic models and likelihood functions

PubMed Central

Barrett, Harrison H.; Dainty, Christopher; Lara, David

2008-01-01

Maximum-likelihood (ML) estimation in wavefront sensing requires careful attention to all noise sources and all factors that influence the sensor data. We present detailed probability density functions for the output of the image detector in a wavefront sensor, conditional not only on wavefront parameters but also on various nuisance parameters. Practical ways of dealing with nuisance parameters are described, and final expressions for likelihoods and Fisher information matrices are derived. The theory is illustrated by discussing Shack–Hartmann sensors, and computational requirements are discussed. Simulation results show that ML estimation can significantly increase the dynamic range of a Shack–Hartmann sensor with four detectors and that it can reduce the residual wavefront error when compared with traditional methods. PMID:17206255

Personal Database Management System I TRIAS

NASA Astrophysics Data System (ADS)

Yamamoto, Yoneo; Kashihara, Akihiro; Kawagishi, Keisuke

The current paper provides TRIAS (TRIple Associative System) which is a database management system for a personal use. In order to implement TRIAS, we have developed an associative database, whose format is (e,a,v) : e for entity, a for attribute, v for value. ML-TREE is used to construct (e,a,v). ML-TREE is a reversion of B+-tree that is multiway valanced tree. The paper focuses mainly on the usage of associative database, demonstrating how to use basic commands, primary functions and applcations.

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

PubMed Central

2010-01-01

Background Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. "Phylogenetic placement," where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way to bring the inferential power offered by likelihood-based approaches to large data sets. Results This paper introduces pplacer, a software package for phylogenetic placement and subsequent visualization. The algorithm can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, has essentially linear time and memory complexity in the number of reference taxa, and is easy to run in parallel. Pplacer features calculation of the posterior probability of a placement on an edge, which is a statistically rigorous way of quantifying uncertainty on an edge-by-edge basis. It also can inform the user of the positional uncertainty for query sequences by calculating expected distance between placement locations, which is crucial in the estimation of uncertainty with a well-sampled reference tree. The software provides visualizations using branch thickness and color to represent number of placements and their uncertainty. A simulation study using reads generated from 631 COG alignments shows a high level of accuracy for phylogenetic placement over a wide range of alignment diversity, and the power of edge uncertainty estimates to measure placement confidence. Conclusions Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service. PMID:21034504

Portable Language-Independent Adaptive Translation from OCR. Phase 1

DTIC Science & Technology

2009-04-01

including brute-force k-Nearest Neighbors ( kNN ), fast approximate kNN using hashed k-d trees, classification and regression trees, and locality...achieved by refinements in ground-truthing protocols. Recent algorithmic improvements to our approximate kNN classifier using hashed k-D trees allows...recent years discriminative training has been shown to outperform phonetic HMMs estimated using ML for speech recognition. Standard ML estimation

Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes

PubMed Central

Kikugawa, Kanae; Katoh, Kazutaka; Kuraku, Shigehiro; Sakurai, Hiroshi; Ishida, Osamu; Iwabe, Naoyuki; Miyata, Takashi

2004-01-01

Background Phylogenetic analyses of jawed vertebrates based on mitochondrial sequences often result in confusing inferences which are obviously inconsistent with generally accepted trees. In particular, in a hypothesis by Rasmussen and Arnason based on mitochondrial trees, cartilaginous fishes have a terminal position in a paraphyletic cluster of bony fishes. No previous analysis based on nuclear DNA-coded genes could significantly reject the mitochondrial trees of jawed vertebrates. Results We have cloned and sequenced seven nuclear DNA-coded genes from 13 vertebrate species. These sequences, together with sequences available from databases including 13 jawed vertebrates from eight major groups (cartilaginous fishes, bichir, chondrosteans, gar, bowfin, teleost fishes, lungfishes and tetrapods) and an outgroup (a cyclostome and a lancelet), have been subjected to phylogenetic analyses based on the maximum likelihood method. Conclusion Cartilaginous fishes have been inferred to be basal to other jawed vertebrates, which is consistent with the generally accepted view. The minimum log-likelihood difference between the maximum likelihood tree and trees not supporting the basal position of cartilaginous fishes is 18.3 ± 13.1. The hypothesis by Rasmussen and Arnason has been significantly rejected with the minimum log-likelihood difference of 123 ± 23.3. Our tree has also shown that living holosteans, comprising bowfin and gar, form a monophyletic group which is the sister group to teleost fishes. This is consistent with a formerly prevalent view of vertebrate classification, although inconsistent with both of the current morphology-based and mitochondrial sequence-based trees. Furthermore, the bichir has been shown to be the basal ray-finned fish. Tetrapods and lungfish have formed a monophyletic cluster in the tree inferred from the concatenated alignment, being consistent with the currently prevalent view. It also remains possible that tetrapods are more closely related to ray-finned fishes than to lungfishes. PMID:15070407

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures.

PubMed

Theobald, Douglas L; Wuttke, Deborah S

2006-09-01

THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. ANSI C source code and selected binaries for various computing platforms are available under the GNU open source license from http://monkshood.colorado.edu/theseus/ or http://www.theseus3d.org.

Effectivity of Azotobacter chroococcum and arbuscular mycorrhiza fungi on physiological characteristics and growth of cocoa seedlings

NASA Astrophysics Data System (ADS)

Nasaruddin; Ridwan, I.

2018-05-01

This study aims to study the effectiveness of Azotobacter chroococcum bacteria and Arbuscula mycorrhiza on some physiological characteristics and growth of cocoa seedlings. The study was conducted from March to October 2015, designed in the form of a two factors experiment based on the Randomized Block Design in a screen house. Inoculation of A chroococcum as the first factor consisted of control, inoculation of 104 CFU ml-1 water and 106 CFU ml-1 water per tree given as much as 40 ml. Inoculation of arbuscula mycorrhiza as a second factor consisted of control, inoculation of 3.0 g, 6.0 g and 9.0 g per tree, respectively. The experimental results show that inoculation of Azotobacter chroococcum 106 CFU ml-1 water tree-1 and the arbuscular mycorrhizal fungi 6.0 g tree-1 resulted in higher chlorophyll a, b and total leaf chlorophyll content, increased light absorption rate, leaf stomatal conductance and better seedling growth.

Maximum Likelihood Shift Estimation Using High Resolution Polarimetric SAR Clutter Model

NASA Astrophysics Data System (ADS)

Harant, Olivier; Bombrun, Lionel; Vasile, Gabriel; Ferro-Famil, Laurent; Gay, Michel

2011-03-01

This paper deals with a Maximum Likelihood (ML) shift estimation method in the context of High Resolution (HR) Polarimetric SAR (PolSAR) clutter. Texture modeling is exposed and the generalized ML texture tracking method is extended to the merging of various sensors. Some results on displacement estimation on the Argentiere glacier in the Mont Blanc massif using dual-pol TerraSAR-X (TSX) and quad-pol RADARSAT-2 (RS2) sensors are finally discussed.

Phylodynamic Analysis Revealed That Epidemic of CRF07_BC Strain in Men Who Have Sex with Men Drove Its Second Spreading Wave in China.

PubMed

Zhang, Min; Jia, Dijing; Li, Hanping; Gui, Tao; Jia, Lei; Wang, Xiaolin; Li, Tianyi; Liu, Yongjian; Bao, Zuoyi; Liu, Siyang; Zhuang, Daomin; Li, Jingyun; Li, Lin

2017-10-01

CRF07_BC was originally formed in Yunnan province of China in 1980s and spread quickly in injecting drug users (IDUs). In recent years, it has been introduced into men who have sex with men (MSM) and become the most dominant strain in China. In this study, we performed a comprehensively phylodynamic analysis of CRF07_BC sequences from China. All CRF07_BC sequences identified in China were retrieved from database. More sequences obtained in our laboratory were added to make the dataset more representative. A maximum-likelihood (ML) tree was constructed with PhyML3.0. Maximum clade credibility (MCC) tree and effective population size were predicted by using Markov Chains Monte Carlo sampling method with Beast software. A total of 610 CRF07_BC sequences coving 1,473 bp of the gag gene (from 817 to 2,289 according to HXB2 calculator) were included into the dataset. Three epidemic clusters were identified; two clusters comprised sequences from IDUs, while one cluster mainly contained sequences from MSMs. The time of the most recent common ancestor of clusters that composed of sequences from MSMs was estimated to be in 2000. Two rapid spreading waves of effective population size of CRF07_BC infections were identified in the skyline plot. The second wave coincided with the expanding of MSM cluster. The results indicated that the control of CRF07_BC infections in MSMs would help to decrease its epidemic in China.

Predicting the risk of patients with biopsy Gleason score 6 to harbor a higher grade cancer.

PubMed

Gofrit, Ofer N; Zorn, Kevin C; Taxy, Jerome B; Lin, Shang; Zagaja, Gregory P; Steinberg, Gary D; Shalhav, Arieh L

2007-11-01

Prostate cancer Gleason score 3 + 3 = 6 is currently the most common score assigned on prostatic biopsies. We analyzed the clinical variables that predict the likelihood of a patient with biopsy Gleason score 6 to harbor a higher grade tumor. The study population consisted of 448 patients with a mean age of 59.1 years who underwent radical prostatectomy between February 2003 to October 2006 for Gleason score 6 adenocarcinoma. The effect of preoperative variables on the probability of a Gleason score upgrade on final pathological evaluation was evaluated using logistic regression, and classification and regression tree analysis. Gleason score upgrade was found in 91 of 448 patients (20.3%). Logistic regression showed that only serum prostate specific antigen and the greatest percent of cancer in a core were significantly associated with a score upgrade (p = 0.0014 and 0.023, respectively). Classification and regression tree analysis showed that the risk of a Gleason score upgrade was 62% when serum prostate specific antigen was higher than 12 ng/ml and 18% when serum prostate specific antigen was 12 ng/ml or less. In patients with serum prostate specific antigen lower than 12 ng/ml the risk of a score upgrade could be dichotomized at a greatest percent of cancer in a core of 5%. The risk was 22.6% and 10.5% when the greatest percent of cancer in a core was higher than 5% and 5% or lower, respectively. The probability of patients with a prostate biopsy Gleason score of 6 to conceal a Gleason score of 7 or higher can be predicted using serum prostate specific antigen and the greatest percent of cancer in a core. With these parameters it is possible to predict upgrade rates as high as 62% and as low as 10.5%.

Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous character data: a case study with the lizard Anolis roosevelti.

PubMed

Revell, Liam J; Mahler, D Luke; Reynolds, R Graham; Slater, Graham J

2015-04-01

In recent years, enormous effort and investment has been put into assembling the tree of life: a phylogenetic history for all species on Earth. Overwhelmingly, this progress toward building an ever increasingly complete phylogeny of living things has been accomplished through sophisticated analysis of molecular data. In the modern genomic age, molecular genetic data have become very easy and inexpensive to obtain for many species. However, some lineages are poorly represented in or absent from tissue collections, or are unavailable for molecular analysis for other reasons such as restrictive biological sample export laws. Other species went extinct recently and are only available in formalin museum preparations or perhaps even as subfossils. In this brief communication we present a new method for placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny of extant taxa using continuous character data. This method is based on a relatively simple modification of an established maximum likelihood (ML) method for phylogeny inference from continuous traits. We show that the method works well on simulated trees and data. We then apply it to the case of placing the Culebra Island Giant Anole (Anolis roosevelti) into a phylogeny of Caribbean anoles. Anolis roosevelti is a "crown-giant" ecomorph anole hypothesized to have once been found throughout the Spanish, United States, and British Virgin Islands, but that has not been encountered or collected since the 1930s. Although this species is widely thought to be closely related to the Puerto Rican giant anole, A. cuvieri, our ML method actually places A. roosevelti in a different part of the tree and closely related to a clade of morphologically similar species. We are unable, however, to reject a phylogenetic position for A. roosevelti that places it as sister taxon to A. cuvieri; although close relationship with the remainder of Puerto Rican anole species is strongly rejected by our method. © 2015 The Author(s).

Likelihood of Tree Topologies with Fossils and Diversification Rate Estimation.

PubMed

Didier, Gilles; Fau, Marine; Laurin, Michel

2017-11-01

Since the diversification process cannot be directly observed at the human scale, it has to be studied from the information available, namely the extant taxa and the fossil record. In this sense, phylogenetic trees including both extant taxa and fossils are the most complete representations of the diversification process that one can get. Such phylogenetic trees can be reconstructed from molecular and morphological data, to some extent. Among the temporal information of such phylogenetic trees, fossil ages are by far the most precisely known (divergence times are inferences calibrated mostly with fossils). We propose here a method to compute the likelihood of a phylogenetic tree with fossils in which the only considered time information is the fossil ages, and apply it to the estimation of the diversification rates from such data. Since it is required in our computation, we provide a method for determining the probability of a tree topology under the standard diversification model. Testing our approach on simulated data shows that the maximum likelihood rate estimates from the phylogenetic tree topology and the fossil dates are almost as accurate as those obtained by taking into account all the data, including the divergence times. Moreover, they are substantially more accurate than the estimates obtained only from the exact divergence times (without taking into account the fossil record). We also provide an empirical example composed of 50 Permo-Carboniferous eupelycosaur (early synapsid) taxa ranging in age from about 315 Ma (Late Carboniferous) to 270 Ma (shortly after the end of the Early Permian). Our analyses suggest a speciation (cladogenesis, or birth) rate of about 0.1 per lineage and per myr, a marginally lower extinction rate, and a considerable hidden paleobiodiversity of early synapsids. [Extinction rate; fossil ages; maximum likelihood estimation; speciation rate.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Phylogenetic position of Loricifera inferred from nearly complete 18S and 28S rRNA gene sequences.

PubMed

Yamasaki, Hiroshi; Fujimoto, Shinta; Miyazaki, Katsumi

2015-01-01

Loricifera is an enigmatic metazoan phylum; its morphology appeared to place it with Priapulida and Kinorhyncha in the group Scalidophora which, along with Nematoida (Nematoda and Nematomorpha), comprised the group Cycloneuralia. Scarce molecular data have suggested an alternative phylogenetic hypothesis, that the phylum Loricifera is a sister taxon to Nematomorpha, although the actual phylogenetic position of the phylum remains unclear. Ecdysozoan phylogeny was reconstructed through maximum-likelihood (ML) and Bayesian inference (BI) analyses of nuclear 18S and 28S rRNA gene sequences from 60 species representing all eight ecdysozoan phyla, and including a newly collected loriciferan species. Ecdysozoa comprised two clades with high support values in both the ML and BI trees. One consisted of Priapulida and Kinorhyncha, and the other of Loricifera, Nematoida, and Panarthropoda (Tardigrada, Onychophora, and Arthropoda). The relationships between Loricifera, Nematoida, and Panarthropoda were not well resolved. Loricifera appears to be closely related to Nematoida and Panarthropoda, rather than grouping with Priapulida and Kinorhyncha, as had been suggested by previous studies. Thus, both Scalidophora and Cycloneuralia are a polyphyletic or paraphyletic groups. In addition, Loricifera and Nematomorpha did not emerge as sister groups.

Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures.

PubMed

Stamatakis, Alexandros; Ott, Michael

2008-12-27

The continuous accumulation of sequence data, for example, due to novel wet-laboratory techniques such as pyrosequencing, coupled with the increasing popularity of multi-gene phylogenies and emerging multi-core processor architectures that face problems of cache congestion, poses new challenges with respect to the efficient computation of the phylogenetic maximum-likelihood (ML) function. Here, we propose two approaches that can significantly speed up likelihood computations that typically represent over 95 per cent of the computational effort conducted by current ML or Bayesian inference programs. Initially, we present a method and an appropriate data structure to efficiently compute the likelihood score on 'gappy' multi-gene alignments. By 'gappy' we denote sampling-induced gaps owing to missing sequences in individual genes (partitions), i.e. not real alignment gaps. A first proof-of-concept implementation in RAXML indicates that this approach can accelerate inferences on large and gappy alignments by approximately one order of magnitude. Moreover, we present insights and initial performance results on multi-core architectures obtained during the transition from an OpenMP-based to a Pthreads-based fine-grained parallelization of the ML function.

A broad scale analysis of tree risk, mitigation and potential habitat for cavity-nesting birds

Treesearch

Brian Kane; Paige S. Warren; Susannah B. Lerman

2015-01-01

Trees in towns and cities provide habitat for wildlife. In particular, cavity-nesting birds nest in the deadand decayed stems and branches of these trees. The same dead and decayed stems and branches alsohave a greater likelihood of failure, which, in some circumstances, increases risk. We examined 1760trees in Baltimore, MD, USA and western MA, USA, assessing tree...

Evolution of complex fruiting-body morphologies in homobasidiomycetes.

PubMed Central

Hibbett, David S; Binder, Manfred

2002-01-01

The fruiting bodies of homobasidiomycetes include some of the most complex forms that have evolved in the fungi, such as gilled mushrooms, bracket fungi and puffballs ('pileate-erect') forms. Homobasidiomycetes also include relatively simple crust-like 'resupinate' forms, however, which account for ca. 13-15% of the described species in the group. Resupinate homobasidiomycetes have been interpreted either as a paraphyletic grade of plesiomorphic forms or a polyphyletic assemblage of reduced forms. The former view suggests that morphological evolution in homobasidiomycetes has been marked by independent elaboration in many clades, whereas the latter view suggests that parallel simplification has been a common mode of evolution. To infer patterns of morphological evolution in homobasidiomycetes, we constructed phylogenetic trees from a dataset of 481 species and performed ancestral state reconstruction (ASR) using parsimony and maximum likelihood (ML) methods. ASR with both parsimony and ML implies that the ancestor of the homobasidiomycetes was resupinate, and that there have been multiple gains and losses of complex forms in the homobasidiomycetes. We also used ML to address whether there is an asymmetry in the rate of transformations between simple and complex forms. Models of morphological evolution inferred with ML indicate that the rate of transformations from simple to complex forms is about three to six times greater than the rate of transformations in the reverse direction. A null model of morphological evolution, in which there is no asymmetry in transformation rates, was rejected. These results suggest that there is a 'driven' trend towards the evolution of complex forms in homobasidiomycetes. PMID:12396494

Extending the BEAGLE library to a multi-FPGA platform

PubMed Central

2013-01-01

Background Maximum Likelihood (ML)-based phylogenetic inference using Felsenstein’s pruning algorithm is a standard method for estimating the evolutionary relationships amongst a set of species based on DNA sequence data, and is used in popular applications such as RAxML, PHYLIP, GARLI, BEAST, and MrBayes. The Phylogenetic Likelihood Function (PLF) and its associated scaling and normalization steps comprise the computational kernel for these tools. These computations are data intensive but contain fine grain parallelism that can be exploited by coprocessor architectures such as FPGAs and GPUs. A general purpose API called BEAGLE has recently been developed that includes optimized implementations of Felsenstein’s pruning algorithm for various data parallel architectures. In this paper, we extend the BEAGLE API to a multiple Field Programmable Gate Array (FPGA)-based platform called the Convey HC-1. Results The core calculation of our implementation, which includes both the phylogenetic likelihood function (PLF) and the tree likelihood calculation, has an arithmetic intensity of 130 floating-point operations per 64 bytes of I/O, or 2.03 ops/byte. Its performance can thus be calculated as a function of the host platform’s peak memory bandwidth and the implementation’s memory efficiency, as 2.03 × peak bandwidth × memory efficiency. Our FPGA-based platform has a peak bandwidth of 76.8 GB/s and our implementation achieves a memory efficiency of approximately 50%, which gives an average throughput of 78 Gflops. This represents a ~40X speedup when compared with BEAGLE’s CPU implementation on a dual Xeon 5520 and 3X speedup versus BEAGLE’s GPU implementation on a Tesla T10 GPU for very large data sizes. The power consumption is 92 W, yielding a power efficiency of 1.7 Gflops per Watt. Conclusions The use of data parallel architectures to achieve high performance for likelihood-based phylogenetic inference requires high memory bandwidth and a design methodology that emphasizes high memory efficiency. To achieve this objective, we integrated 32 pipelined processing elements (PEs) across four FPGAs. For the design of each PE, we developed a specialized synthesis tool to generate a floating-point pipeline with resource and throughput constraints to match the target platform. We have found that using low-latency floating-point operators can significantly reduce FPGA area and still meet timing requirement on the target platform. We found that this design methodology can achieve performance that exceeds that of a GPU-based coprocessor. PMID:23331707

L.U.St: a tool for approximated maximum likelihood supertree reconstruction.

PubMed

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.

Profile-Likelihood Approach for Estimating Generalized Linear Mixed Models with Factor Structures

ERIC Educational Resources Information Center

Jeon, Minjeong; Rabe-Hesketh, Sophia

2012-01-01

In this article, the authors suggest a profile-likelihood approach for estimating complex models by maximum likelihood (ML) using standard software and minimal programming. The method works whenever setting some of the parameters of the model to known constants turns the model into a standard model. An important class of models that can be…

Reconstructing the evolutionary history of the Lorisidae using morphological, molecular, and geological data.

PubMed

Masters, J C; Anthony, N M; de Wit, M J; Mitchell, A

2005-08-01

Major aspects of lorisid phylogeny and systematics remain unresolved, despite several studies (involving morphology, histology, karyology, immunology, and DNA sequencing) aimed at elucidating them. Our study is the first to investigate the evolution of this enigmatic group using molecular and morphological data for all four well-established genera: Arctocebus, Loris, Nycticebus, and Perodicticus. Data sets consisting of 386 bp of 12S rRNA, 535 bp of 16S rRNA, and 36 craniodental characters were analyzed separately and in combination, using maximum parsimony and maximum likelihood. Outgroups, consisting of two galagid taxa (Otolemur and Galagoides) and a lemuroid (Microcebus), were also varied. The morphological data set yielded a paraphyletic lorisid clade with the robust Nycticebus and Perodicticus grouped as sister taxa, and the galagids allied with Arctocebus. All molecular analyses maximum parsimony (MP) or maximum likelihood (ML) which included Microcebus as an outgroup rendered a paraphyletic lorisid clade, with one exception: the 12S + 16S data set analyzed with ML. The position of the galagids in these paraphyletic topologies was inconsistent, however, and bootstrap values were low. Exclusion of Microcebus generated a monophyletic Lorisidae with Asian and African subclades; bootstrap values for all three clades in the total evidence tree were over 90%. We estimated mean genetic distances for lemuroids vs. lorisoids, lorisids vs. galagids, and Asian vs. African lorisids as a guide to relative divergence times. We present information regarding a temporary land bridge that linked the two now widely separated regions inhabited by lorisids that may explain their distribution. Finally, we make taxonomic recommendations based on our results. (c) 2005 Wiley-Liss, Inc.

Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pražnikar, Jure; University of Primorska,; Turk, Dušan, E-mail: dusan.turk@ijs.si

2014-12-01

The maximum-likelihood free-kick target, which calculates model error estimates from the work set and a randomly displaced model, proved superior in the accuracy and consistency of refinement of crystal structures compared with the maximum-likelihood cross-validation target, which calculates error estimates from the test set and the unperturbed model. The refinement of a molecular model is a computational procedure by which the atomic model is fitted to the diffraction data. The commonly used target in the refinement of macromolecular structures is the maximum-likelihood (ML) function, which relies on the assessment of model errors. The current ML functions rely on cross-validation. Theymore » utilize phase-error estimates that are calculated from a small fraction of diffraction data, called the test set, that are not used to fit the model. An approach has been developed that uses the work set to calculate the phase-error estimates in the ML refinement from simulating the model errors via the random displacement of atomic coordinates. It is called ML free-kick refinement as it uses the ML formulation of the target function and is based on the idea of freeing the model from the model bias imposed by the chemical energy restraints used in refinement. This approach for the calculation of error estimates is superior to the cross-validation approach: it reduces the phase error and increases the accuracy of molecular models, is more robust, provides clearer maps and may use a smaller portion of data for the test set for the calculation of R{sub free} or may leave it out completely.« less

Indicators of Terrorism Vulnerability in Africa

DTIC Science & Technology

2015-03-26

the terror threat and vulnerabilities across Africa. Key words: Terrorism, Africa, Negative Binomial Regression, Classification Tree iv I would like...31 Metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 Log -likelihood...70 viii Page 5.3 Classification Tree Description

Decision-Tree Program

NASA Technical Reports Server (NTRS)

Buntine, Wray

1994-01-01

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

Photo guide for estimating risk to hardwood trees during prescribed burning operations in eastern oak forests

Treesearch

Patrick H. Brose

2009-01-01

A field guide of 40 photographs of common hardwood trees of eastern oak forests and fuel loadings surrounding their bases. The guide contains instructions on how to rapidly assess a tree's likelihood to be damaged or killed by prescribed burning.

Maximum likelihood decoding analysis of accumulate-repeat-accumulate codes

NASA Technical Reports Server (NTRS)

Abbasfar, A.; Divsalar, D.; Yao, K.

2004-01-01

In this paper, the performance of the repeat-accumulate codes with (ML) decoding are analyzed and compared to random codes by very tight bounds. Some simple codes are shown that perform very close to Shannon limit with maximum likelihood decoding.

Selecting informative subsets of sparse supermatrices increases the chance to find correct trees.

PubMed

Misof, Bernhard; Meyer, Benjamin; von Reumont, Björn Marcus; Kück, Patrick; Misof, Katharina; Meusemann, Karen

2013-12-03

Character matrices with extensive missing data are frequently used in phylogenomics with potentially detrimental effects on the accuracy and robustness of tree inference. Therefore, many investigators select taxa and genes with high data coverage. Drawbacks of these selections are their exclusive reliance on data coverage without consideration of actual signal in the data which might, thus, not deliver optimal data matrices in terms of potential phylogenetic signal. In order to circumvent this problem, we have developed a heuristics implemented in a software called mare which (1) assesses information content of genes in supermatrices using a measure of potential signal combined with data coverage and (2) reduces supermatrices with a simple hill climbing procedure to submatrices with high total information content. We conducted simulation studies using matrices of 50 taxa × 50 genes with heterogeneous phylogenetic signal among genes and data coverage between 10-30%. With matrices of 50 taxa × 50 genes with heterogeneous phylogenetic signal among genes and data coverage between 10-30% Maximum Likelihood (ML) tree reconstructions failed to recover correct trees. A selection of a data subset with the herein proposed approach increased the chance to recover correct partial trees more than 10-fold. The selection of data subsets with the herein proposed simple hill climbing procedure performed well either considering the information content or just a simple presence/absence information of genes. We also applied our approach on an empirical data set, addressing questions of vertebrate systematics. With this empirical dataset selecting a data subset with high information content and supporting a tree with high average boostrap support was most successful if information content of genes was considered. Our analyses of simulated and empirical data demonstrate that sparse supermatrices can be reduced on a formal basis outperforming the usually used simple selections of taxa and genes with high data coverage.

An Investigation of the Sample Performance of Two Nonnormality Corrections for RMSEA

ERIC Educational Resources Information Center

Brosseau-Liard, Patricia E.; Savalei, Victoria; Li, Libo

2012-01-01

The root mean square error of approximation (RMSEA) is a popular fit index in structural equation modeling (SEM). Typically, RMSEA is computed using the normal theory maximum likelihood (ML) fit function. Under nonnormality, the uncorrected sample estimate of the ML RMSEA tends to be inflated. Two robust corrections to the sample ML RMSEA have…

Molecular Characterization of the Meyer Lemon Isolate of Citrus Tatter Leaf Virus: Complete Genome Sequence and Development of Biologically Active In Vitro Transcripts

USDA-ARS?s Scientific Manuscript database

Citrus tatter leaf virus isolated from Meyer lemon trees (CTLV-ML) from California and Florida induces bud union incompatibility of citrus trees grafted on the widely used trifoliate and trifoliate hybrid rootstocks. The complete genome sequence of CTLV-ML was determined to be 6,495 nucleotides (nts...

A survival tree method for the analysis of discrete event times in clinical and epidemiological studies.

PubMed

Schmid, Matthias; Küchenhoff, Helmut; Hoerauf, Achim; Tutz, Gerhard

2016-02-28

Survival trees are a popular alternative to parametric survival modeling when there are interactions between the predictor variables or when the aim is to stratify patients into prognostic subgroups. A limitation of classical survival tree methodology is that most algorithms for tree construction are designed for continuous outcome variables. Hence, classical methods might not be appropriate if failure time data are measured on a discrete time scale (as is often the case in longitudinal studies where data are collected, e.g., quarterly or yearly). To address this issue, we develop a method for discrete survival tree construction. The proposed technique is based on the result that the likelihood of a discrete survival model is equivalent to the likelihood of a regression model for binary outcome data. Hence, we modify tree construction methods for binary outcomes such that they result in optimized partitions for the estimation of discrete hazard functions. By applying the proposed method to data from a randomized trial in patients with filarial lymphedema, we demonstrate how discrete survival trees can be used to identify clinically relevant patient groups with similar survival behavior. Copyright © 2015 John Wiley & Sons, Ltd.

Two C++ Libraries for Counting Trees on a Phylogenetic Terrace.

PubMed

Biczok, R; Bozsoky, P; Eisenmann, P; Ernst, J; Ribizel, T; Scholz, F; Trefzer, A; Weber, F; Hamann, M; Stamatakis, A

2018-05-08

The presence of terraces in phylogenetic tree space, that is, a potentially large number of distinct tree topologies that have exactly the same analytical likelihood score, was first described by Sanderson et al. (2011). However, popular software tools for maximum likelihood and Bayesian phylogenetic inference do not yet routinely report, if inferred phylogenies reside on a terrace, or not. We believe, this is due to the lack of an efficient library to (i) determine if a tree resides on a terrace, (ii) calculate how many trees reside on a terrace, and (iii) enumerate all trees on a terrace. In our bioinformatics practical that is set up as a programming contest we developed two efficient and independent C++ implementations of the SUPERB algorithm by Constantinescu and Sankoff (1995) for counting and enumerating trees on a terrace. Both implementations yield exactly the same results, are more than one order of magnitude faster, and require one order of magnitude less memory than a previous 3rd party python implementation. The source codes are available under GNU GPL at https://github.com/terraphast. Alexandros.Stamatakis@h-its.org. Supplementary data are available at Bioinformatics online.

Climate variability drives recent tree mortality in Europe.

PubMed

Neumann, Mathias; Mues, Volker; Moreno, Adam; Hasenauer, Hubert; Seidl, Rupert

2017-11-01

Tree mortality is an important process in forest ecosystems, frequently hypothesized to be highly climate sensitive. Yet, tree death remains one of the least understood processes of forest dynamics. Recently, changes in tree mortality have been observed in forests around the globe, which could profoundly affect ecosystem functioning and services provisioning to society. We describe continental-scale patterns of recent tree mortality from the only consistent pan-European forest monitoring network, identifying recent mortality hotspots in southern and northern Europe. Analyzing 925,462 annual observations of 235,895 trees between 2000 and 2012, we determine the influence of climate variability and tree age on interannual variation in tree mortality using Cox proportional hazard models. Warm summers as well as high seasonal variability in precipitation increased the likelihood of tree death. However, our data also suggest that reduced cold-induced mortality could compensate increased mortality related to peak temperatures in a warming climate. Besides climate variability, age was an important driver of tree mortality, with individual mortality probability decreasing with age over the first century of a trees life. A considerable portion of the observed variation in tree mortality could be explained by satellite-derived net primary productivity, suggesting that widely available remote sensing products can be used as an early warning indicator of widespread tree mortality. Our findings advance the understanding of patterns of large-scale tree mortality by demonstrating the influence of seasonal and diurnal climate variation, and highlight the potential of state-of-the-art remote sensing to anticipate an increased likelihood of tree mortality in space and time. © 2017 John Wiley & Sons Ltd.

Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent

PubMed Central

Zhu, Sha; Degnan, James H.

2017-01-01

Abstract Recent work in estimating species relationships from gene trees has included inferring networks assuming that past hybridization has occurred between species. Probabilistic models using the multispecies coalescent can be used in this framework for likelihood-based inference of both network topologies and parameters, including branch lengths and hybridization parameters. A difficulty for such methods is that it is not always clear whether, or to what extent, networks are identifiable—that is whether there could be two distinct networks that lead to the same distribution of gene trees. For cases in which incomplete lineage sorting occurs in addition to hybridization, we demonstrate a new representation of the species network likelihood that expresses the probability distribution of the gene tree topologies as a linear combination of gene tree distributions given a set of species trees. This representation makes it clear that in some cases in which two distinct networks give the same distribution of gene trees when sampling one allele per species, the two networks can be distinguished theoretically when multiple individuals are sampled per species. This result means that network identifiability is not only a function of the trees displayed by the networks but also depends on allele sampling within species. We additionally give an example in which two networks that display exactly the same trees can be distinguished from their gene trees even when there is only one lineage sampled per species. PMID:27780899

Tree age, fruit size and storage conditions affect levels of ascorbic acid, total phenolic concentrations and total antioxidant activity of 'Kinnow' mandarin juice.

PubMed

Khalid, Samina; Malik, Aman U; Khan, Ahmad S; Shahid, Muhammad; Shafique, Muhammad

2016-03-15

Bioactive compounds (ascorbic acid, total phenolics and total antioxidants) are important constituents of citrus fruit juice; however, information with regard to their concentrations and changes in relation to tree age and storage conditions is limited. 'Kinnow' (Citrus nobilis Lour × Citrus deliciosa Tenora) mandarin juice from fruit of three tree ages (6, 18 and 35 years old) and fruit sizes (large, medium and small) were examined for their bioactive compounds during 7 days under ambient storage conditions (20 ± 2 °C and 60-65% relative humidity (RH)) and during 60 days under cold storage (4 ± 1 °C and 75-80% RH) conditions. Under ambient conditions, a reduction in total phenolic concentrations (TPC) and in total antioxidant activity (TAA) was found for the juice from all tree ages and fruit sizes. Overall, fruit from 18-year-old trees had higher mean TPC (95.86 µg mL(-1) ) and TAA (93.68 mg L(-1) ), as compared to 6 and 35-year-old trees. Likewise, in cold storage, TAA decreased in all fruit size groups from 18 and 35-year-old trees. In all tree age and fruit size groups, TPC decreased initially during 15 days of cold storage and then increased gradually with increase in storage duration. Ascorbic acid concentrations showed an increasing trend in all fruit size groups from 35-year-old trees. Overall, during cold storage, fruit from 18-year-old trees maintained higher mean ascorbic acid (33.05 mg 100 mL(-1) ) concentrations, whereas fruit from 6-year-old trees had higher TAA (153.1 mg L(-1) ) and TPC (115.1 µg mL(-1) ). Large-sized fruit had higher ascorbic acid (32.08 mg 100 mL(-1) ) concentrations and TAA (157.5 mg L(-1) ). Fruit from 18-year-old trees maintained higher TPC and TAA under ambient storage conditions, whereas fruit from 6-year-old trees maintained higher TPC and TAA during cold storage. Small-sized fruit had higher TPC after ambient temperature storage, whereas large fruit size showed higher ascorbic acid concentrations and TAA after cold storage. © 2015 Society of Chemical Industry.

Implementation of a Goal-Based Systems Engineering Process Using the Systems Modeling Language (SysML)

NASA Technical Reports Server (NTRS)

Patterson, Jonathan D.; Breckenridge, Jonathan T.; Johnson, Stephen B.

2013-01-01

Building upon the purpose, theoretical approach, and use of a Goal-Function Tree (GFT) being presented by Dr. Stephen B. Johnson, described in a related Infotech 2013 ISHM abstract titled "Goal-Function Tree Modeling for Systems Engineering and Fault Management", this paper will describe the core framework used to implement the GFTbased systems engineering process using the Systems Modeling Language (SysML). These two papers are ideally accepted and presented together in the same Infotech session. Statement of problem: SysML, as a tool, is currently not capable of implementing the theoretical approach described within the "Goal-Function Tree Modeling for Systems Engineering and Fault Management" paper cited above. More generally, SysML's current capabilities to model functional decompositions in the rigorous manner required in the GFT approach are limited. The GFT is a new Model-Based Systems Engineering (MBSE) approach to the development of goals and requirements, functions, and its linkage to design. As a growing standard for systems engineering, it is important to develop methods to implement GFT in SysML. Proposed Method of Solution: Many of the central concepts of the SysML language are needed to implement a GFT for large complex systems. In the implementation of those central concepts, the following will be described in detail: changes to the nominal SysML process, model view definitions and examples, diagram definitions and examples, and detailed SysML construct and stereotype definitions.

A United States national prioritization framework for tree species vulnerability to climate change

Treesearch

Kevin M. Potter; Barbara S. Crane; William W. Hargrove

2017-01-01

Climate change is one of several threats that will increase the likelihood that forest tree species could experience population-level extirpation or species-level extinction. Scientists and managers from throughout the United States Forest Service have cooperated to develop a framework for conservation priority-setting assessments of forest tree species. This framework...

Silviculture and the assessment of climate change genetic risk for southern Appalachian forest tree species

Treesearch

Kevin M. Potter; Barbara S. Crane

2012-01-01

Changing climate conditions and increasing insect and pathogen infestations will increase the likelihood that forest trees could experience population-level extirpation or species-level extinction during the next century. Gene conservation and silvicultural efforts to preserve forest tree genetic diversity present a particular challenge in species-rich regions such as...

Reliable and More Powerful Methods for Power Analysis in Structural Equation Modeling

ERIC Educational Resources Information Center

Yuan, Ke-Hai; Zhang, Zhiyong; Zhao, Yanyun

2017-01-01

The normal-distribution-based likelihood ratio statistic T[subscript ml] = nF[subscript ml] is widely used for power analysis in structural Equation modeling (SEM). In such an analysis, power and sample size are computed by assuming that T[subscript ml] follows a central chi-square distribution under H[subscript 0] and a noncentral chi-square…

Identification of multiple leaks in pipeline: Linearized model, maximum likelihood, and super-resolution localization

NASA Astrophysics Data System (ADS)

Wang, Xun; Ghidaoui, Mohamed S.

2018-07-01

This paper considers the problem of identifying multiple leaks in a water-filled pipeline based on inverse transient wave theory. The analytical solution to this problem involves nonlinear interaction terms between the various leaks. This paper shows analytically and numerically that these nonlinear terms are of the order of the leak sizes to the power two and; thus, negligible. As a result of this simplification, a maximum likelihood (ML) scheme that identifies leak locations and leak sizes separately is formulated and tested. It is found that the ML estimation scheme is highly efficient and robust with respect to noise. In addition, the ML method is a super-resolution leak localization scheme because its resolvable leak distance (approximately 0.15λmin , where λmin is the minimum wavelength) is below the Nyquist-Shannon sampling theorem limit (0.5λmin). Moreover, the Cramér-Rao lower bound (CRLB) is derived and used to show the efficiency of the ML scheme estimates. The variance of the ML estimator approximates the CRLB proving that the ML scheme belongs to class of best unbiased estimator of leak localization methods.

Estimation of Dynamic Discrete Choice Models by Maximum Likelihood and the Simulated Method of Moments

PubMed Central

Eisenhauer, Philipp; Heckman, James J.; Mosso, Stefano

2015-01-01

We compare the performance of maximum likelihood (ML) and simulated method of moments (SMM) estimation for dynamic discrete choice models. We construct and estimate a simplified dynamic structural model of education that captures some basic features of educational choices in the United States in the 1980s and early 1990s. We use estimates from our model to simulate a synthetic dataset and assess the ability of ML and SMM to recover the model parameters on this sample. We investigate the performance of alternative tuning parameters for SMM. PMID:26494926

Characterizing the phylogenetic tree-search problem.

PubMed

Money, Daniel; Whelan, Simon

2012-03-01

Phylogenetic trees are important in many areas of biological research, ranging from systematic studies to the methods used for genome annotation. Finding the best scoring tree under any optimality criterion is an NP-hard problem, which necessitates the use of heuristics for tree-search. Although tree-search plays a major role in obtaining a tree estimate, there remains a limited understanding of its characteristics and how the elements of the statistical inferential procedure interact with the algorithms used. This study begins to answer some of these questions through a detailed examination of maximum likelihood tree-search on a wide range of real genome-scale data sets. We examine all 10,395 trees for each of the 106 genes of an eight-taxa yeast phylogenomic data set, then apply different tree-search algorithms to investigate their performance. We extend our findings by examining two larger genome-scale data sets and a large disparate data set that has been previously used to benchmark the performance of tree-search programs. We identify several broad trends occurring during tree-search that provide an insight into the performance of heuristics and may, in the future, aid their development. These trends include a tendency for the true maximum likelihood (best) tree to also be the shortest tree in terms of branch lengths, a weak tendency for tree-search to recover the best tree, and a tendency for tree-search to encounter fewer local optima in genes that have a high information content. When examining current heuristics for tree-search, we find that nearest-neighbor-interchange performs poorly, and frequently finds trees that are significantly different from the best tree. In contrast, subtree-pruning-and-regrafting tends to perform well, nearly always finding trees that are not significantly different to the best tree. Finally, we demonstrate that the precise implementation of a tree-search strategy, including when and where parameters are optimized, can change the character of tree-search, and that good strategies for tree-search may combine existing tree-search programs.

Genetic variations in two seahorse species (Hippocampus mohnikei and Hippocampus trimaculatus): evidence for middle Pleistocene population expansion.

PubMed

Zhang, Yanhong; Pham, Nancy Kim; Zhang, Huixian; Lin, Junda; Lin, Qiang

2014-01-01

Population genetic of seahorses is confidently influenced by their species-specific ecological requirements and life-history traits. In the present study, partial sequences of mitochondrial cytochrome b (cytb) and control region (CR) were obtained from 50 Hippocampus mohnikei and 92 H. trimaculatus from four zoogeographical zones. A total of 780 base pairs of cytb gene were sequenced to characterize mitochondrial DNA (mtDNA) diversity. The mtDNA marker revealed high haplotype diversity, low nucleotide diversity, and a lack of population structure across both populations of H. mohnikei and H. trimaculatus. A neighbour-joining (NJ) tree of cytb gene sequences showed that H. mohnikei haplotypes formed one cluster. A maximum likelihood (ML) tree of cytb gene sequences showed that H. trimaculatus belonged to one lineage. The star-like pattern median-joining network of cytb and CR markers indicated a previous demographic expansion of H. mohnikei and H. trimaculatus. The cytb and CR data sets exhibited a unimodal mismatch distribution, which may have resulted from population expansion. Mismatch analysis suggested that the expansion was initiated about 276,000 years ago for H. mohnikei and about 230,000 years ago for H. trimaculatus during the middle Pleistocene period. This study indicates a possible signature of genetic variation and population expansion in two seahorses under complex marine environments.

A comparison of minimum distance and maximum likelihood techniques for proportion estimation

NASA Technical Reports Server (NTRS)

Woodward, W. A.; Schucany, W. R.; Lindsey, H.; Gray, H. L.

1982-01-01

The estimation of mixing proportions P sub 1, P sub 2,...P sub m in the mixture density f(x) = the sum of the series P sub i F sub i(X) with i = 1 to M is often encountered in agricultural remote sensing problems in which case the p sub i's usually represent crop proportions. In these remote sensing applications, component densities f sub i(x) have typically been assumed to be normally distributed, and parameter estimation has been accomplished using maximum likelihood (ML) techniques. Minimum distance (MD) estimation is examined as an alternative to ML where, in this investigation, both procedures are based upon normal components. Results indicate that ML techniques are superior to MD when component distributions actually are normal, while MD estimation provides better estimates than ML under symmetric departures from normality. When component distributions are not symmetric, however, it is seen that neither of these normal based techniques provides satisfactory results.

Soil spot herbicides for single-stem hardwood control

Treesearch

James H. Miller

1988-01-01

Soil spot treatments of undiluted Velpar® L and a concentrated mixture of Spike® 80W were applied aorund test trees of five hardwood species. The test rates were 2, 4, and 6 ml of herbicidelin, of dbh applied to the soil within 3ft of each tree. Hardwood topkill was assessed after two growing seasons. The 4-ml rate of Velpar L was required to achieve...

Project CAPTURE: using forest inventory and analysis data to prioritize tree species for conservation, management, and restoration

Treesearch

Kevin M. Potter; Barbara S. Crane; William W. Hargrove

2015-01-01

A variety of threats, most importantly climate change and insect and disease infestation, will increase the likelihood that forest tree species could experience population-level extirpation or species-level extinction during the next century. Project CAPTURE (Conservation Assessment and Prioritization of Forest Trees Under Risk of Extirpation) is a cooperative effort...

Phylogenetic Reconstruction and DNA Barcoding for Closely Related Pine Moth Species (Dendrolimus) in China with Multiple Gene Markers

PubMed Central

Dai, Qing-Yan; Gao, Qiang; Wu, Chun-Sheng; Chesters, Douglas; Zhu, Chao-Dong; Zhang, Ai-Bing

2012-01-01

Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI) gene and two alternative internal transcribed spacer (ITS) genes (ITS1 and ITS2). Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML)/Neighbor-joining (NJ), “best close match” (BCM), Minimum distance (MD), and BP-based method (BP)), representing commonly used methodology (tree-based and non-tree based) in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10–97.40%, while ITS1 and ITS2 obtained a success rate of 64.70–81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In addition, our results indicate that the most closely related species D. punctatus, D. tabulaeformis, and D. spectabilis, may be still in the process of incomplete lineage sorting, with occasional hybridizations occurring among them. PMID:22509245

Fault Tree Analysis as a Planning and Management Tool: A Case Study

ERIC Educational Resources Information Center

Witkin, Belle Ruth

1977-01-01

Fault Tree Analysis is an operations research technique used to analyse the most probable modes of failure in a system, in order to redesign or monitor the system more closely in order to increase its likelihood of success. (Author)

Inverse problems-based maximum likelihood estimation of ground reflectivity for selected regions of interest from stripmap SAR data [Regularized maximum likelihood estimation of ground reflectivity from stripmap SAR data

DOE Office of Scientific and Technical Information (OSTI.GOV)

West, R. Derek; Gunther, Jacob H.; Moon, Todd K.

In this study, we derive a comprehensive forward model for the data collected by stripmap synthetic aperture radar (SAR) that is linear in the ground reflectivity parameters. It is also shown that if the noise model is additive, then the forward model fits into the linear statistical model framework, and the ground reflectivity parameters can be estimated by statistical methods. We derive the maximum likelihood (ML) estimates for the ground reflectivity parameters in the case of additive white Gaussian noise. Furthermore, we show that obtaining the ML estimates of the ground reflectivity requires two steps. The first step amounts tomore » a cross-correlation of the data with a model of the data acquisition parameters, and it is shown that this step has essentially the same processing as the so-called convolution back-projection algorithm. The second step is a complete system inversion that is capable of mitigating the sidelobes of the spatially variant impulse responses remaining after the correlation processing. We also state the Cramer-Rao lower bound (CRLB) for the ML ground reflectivity estimates.We show that the CRLB is linked to the SAR system parameters, the flight path of the SAR sensor, and the image reconstruction grid.We demonstrate the ML image formation and the CRLB bound for synthetically generated data.« less

Inverse problems-based maximum likelihood estimation of ground reflectivity for selected regions of interest from stripmap SAR data [Regularized maximum likelihood estimation of ground reflectivity from stripmap SAR data

DOE PAGES

West, R. Derek; Gunther, Jacob H.; Moon, Todd K.

2016-12-01

In this study, we derive a comprehensive forward model for the data collected by stripmap synthetic aperture radar (SAR) that is linear in the ground reflectivity parameters. It is also shown that if the noise model is additive, then the forward model fits into the linear statistical model framework, and the ground reflectivity parameters can be estimated by statistical methods. We derive the maximum likelihood (ML) estimates for the ground reflectivity parameters in the case of additive white Gaussian noise. Furthermore, we show that obtaining the ML estimates of the ground reflectivity requires two steps. The first step amounts tomore » a cross-correlation of the data with a model of the data acquisition parameters, and it is shown that this step has essentially the same processing as the so-called convolution back-projection algorithm. The second step is a complete system inversion that is capable of mitigating the sidelobes of the spatially variant impulse responses remaining after the correlation processing. We also state the Cramer-Rao lower bound (CRLB) for the ML ground reflectivity estimates.We show that the CRLB is linked to the SAR system parameters, the flight path of the SAR sensor, and the image reconstruction grid.We demonstrate the ML image formation and the CRLB bound for synthetically generated data.« less

A likelihood-based time series modeling approach for application in dendrochronology to examine the growth-climate relations and forest disturbance history.

PubMed

Lee, E Henry; Wickham, Charlotte; Beedlow, Peter A; Waschmann, Ronald S; Tingey, David T

2017-10-01

A time series intervention analysis (TSIA) of dendrochronological data to infer the tree growth-climate-disturbance relations and forest disturbance history is described. Maximum likelihood is used to estimate the parameters of a structural time series model with components for climate and forest disturbances (i.e., pests, diseases, fire). The statistical method is illustrated with a tree-ring width time series for a mature closed-canopy Douglas-fir stand on the west slopes of the Cascade Mountains of Oregon, USA that is impacted by Swiss needle cast disease caused by the foliar fungus, Phaecryptopus gaeumannii (Rhode) Petrak. The likelihood-based TSIA method is proposed for the field of dendrochronology to understand the interaction of temperature, water, and forest disturbances that are important in forest ecology and climate change studies.

A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases.

PubMed

Cummins, Carla A; McInerney, James O

2011-12-01

Current phylogenetic methods attempt to account for evolutionary rate variation across characters in a matrix. This is generally achieved by the use of sophisticated evolutionary models, combined with dense sampling of large numbers of characters. However, systematic biases and superimposed substitutions make this task very difficult. Model adequacy can sometimes be achieved at the cost of adding large numbers of free parameters, with each parameter being optimized according to some criterion, resulting in increased computation times and large variances in the model estimates. In this study, we develop a simple approach that estimates the relative evolutionary rate of each homologous character. The method that we describe uses the similarity between characters as a proxy for evolutionary rate. In this article, we work on the premise that if the character-state distribution of a homologous character is similar to many other characters, then this character is likely to be relatively slowly evolving. If the character-state distribution of a homologous character is not similar to many or any of the rest of the characters in a data set, then it is likely to be the result of rapid evolution. We show that in some test cases, at least, the premise can hold and the inferences are robust. Importantly, the method does not use a "starting tree" to make the inference and therefore is tree independent. We demonstrate that this approach can work as well as a maximum likelihood (ML) approach, though the ML method needs to have a known phylogeny, or at least a very good estimate of that phylogeny. We then demonstrate some uses for this method of analysis, including the improvement in phylogeny reconstruction for both deep-level and recent relationships and overcoming systematic biases such as base composition bias. Furthermore, we compare this approach to two well-established methods for reweighting or removing characters. These other methods are tree-based and we show that they can be systematically biased. We feel this method can be useful for phylogeny reconstruction, understanding evolutionary rate variation, and for understanding selection variation on different characters.

Measurement and Structural Model Class Separation in Mixture CFA: ML/EM versus MCMC

ERIC Educational Resources Information Center

Depaoli, Sarah

2012-01-01

Parameter recovery was assessed within mixture confirmatory factor analysis across multiple estimator conditions under different simulated levels of mixture class separation. Mixture class separation was defined in the measurement model (through factor loadings) and the structural model (through factor variances). Maximum likelihood (ML) via the…

Empirical Correction to the Likelihood Ratio Statistic for Structural Equation Modeling with Many Variables.

PubMed

Yuan, Ke-Hai; Tian, Yubin; Yanagihara, Hirokazu

2015-06-01

Survey data typically contain many variables. Structural equation modeling (SEM) is commonly used in analyzing such data. The most widely used statistic for evaluating the adequacy of a SEM model is T ML, a slight modification to the likelihood ratio statistic. Under normality assumption, T ML approximately follows a chi-square distribution when the number of observations (N) is large and the number of items or variables (p) is small. However, in practice, p can be rather large while N is always limited due to not having enough participants. Even with a relatively large N, empirical results show that T ML rejects the correct model too often when p is not too small. Various corrections to T ML have been proposed, but they are mostly heuristic. Following the principle of the Bartlett correction, this paper proposes an empirical approach to correct T ML so that the mean of the resulting statistic approximately equals the degrees of freedom of the nominal chi-square distribution. Results show that empirically corrected statistics follow the nominal chi-square distribution much more closely than previously proposed corrections to T ML, and they control type I errors reasonably well whenever N ≥ max(50,2p). The formulations of the empirically corrected statistics are further used to predict type I errors of T ML as reported in the literature, and they perform well.

Bias and Efficiency in Structural Equation Modeling: Maximum Likelihood versus Robust Methods

ERIC Educational Resources Information Center

Zhong, Xiaoling; Yuan, Ke-Hai

2011-01-01

In the structural equation modeling literature, the normal-distribution-based maximum likelihood (ML) method is most widely used, partly because the resulting estimator is claimed to be asymptotically unbiased and most efficient. However, this may not hold when data deviate from normal distribution. Outlying cases or nonnormally distributed data,…

Five Methods for Estimating Angoff Cut Scores with IRT

ERIC Educational Resources Information Center

Wyse, Adam E.

2017-01-01

This article illustrates five different methods for estimating Angoff cut scores using item response theory (IRT) models. These include maximum likelihood (ML), expected a priori (EAP), modal a priori (MAP), and weighted maximum likelihood (WML) estimators, as well as the most commonly used approach based on translating ratings through the test…

Estimation of Complex Generalized Linear Mixed Models for Measurement and Growth

ERIC Educational Resources Information Center

Jeon, Minjeong

2012-01-01

Maximum likelihood (ML) estimation of generalized linear mixed models (GLMMs) is technically challenging because of the intractable likelihoods that involve high dimensional integrations over random effects. The problem is magnified when the random effects have a crossed design and thus the data cannot be reduced to small independent clusters. A…

On the error probability of general tree and trellis codes with applications to sequential decoding

NASA Technical Reports Server (NTRS)

Johannesson, R.

1973-01-01

An upper bound on the average error probability for maximum-likelihood decoding of the ensemble of random binary tree codes is derived and shown to be independent of the length of the tree. An upper bound on the average error probability for maximum-likelihood decoding of the ensemble of random L-branch binary trellis codes of rate R = 1/n is derived which separates the effects of the tail length T and the memory length M of the code. It is shown that the bound is independent of the length L of the information sequence. This implication is investigated by computer simulations of sequential decoding utilizing the stack algorithm. These simulations confirm the implication and further suggest an empirical formula for the true undetected decoding error probability with sequential decoding.

Cramer-Rao Bound, MUSIC, and Maximum Likelihood. Effects of Temporal Phase Difference

DTIC Science & Technology

1990-11-01

Technical Report 1373 November 1990 Cramer-Rao Bound, MUSIC , And Maximum Likelihood Effects of Temporal Phase o Difference C. V. TranI OTIC Approved... MUSIC , and Maximum Likelihood (ML) asymptotic variances corresponding to the two-source direction-of-arrival estimation where sources were modeled as...1pI = 1.00, SNR = 20 dB ..................................... 27 2. MUSIC for two equipowered signals impinging on a 5-element ULA (a) IpI = 0.50, SNR

Maximum Likelihood Reconstruction for Magnetic Resonance Fingerprinting

PubMed Central

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

2017-01-01

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 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. PMID:26915119

Maximum Likelihood Reconstruction for Magnetic Resonance Fingerprinting.

PubMed

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.

Inferring Phylogenetic Networks Using PhyloNet.

PubMed

Wen, Dingqiao; Yu, Yun; Zhu, Jiafan; Nakhleh, Luay

2018-07-01

PhyloNet was released in 2008 as a software package for representing and analyzing phylogenetic networks. At the time of its release, the main functionalities in PhyloNet consisted of measures for comparing network topologies and a single heuristic for reconciling gene trees with a species tree. Since then, PhyloNet has grown significantly. The software package now includes a wide array of methods for inferring phylogenetic networks from data sets of unlinked loci while accounting for both reticulation (e.g., hybridization) and incomplete lineage sorting. In particular, PhyloNet now allows for maximum parsimony, maximum likelihood, and Bayesian inference of phylogenetic networks from gene tree estimates. Furthermore, Bayesian inference directly from sequence data (sequence alignments or biallelic markers) is implemented. Maximum parsimony is based on an extension of the "minimizing deep coalescences" criterion to phylogenetic networks, whereas maximum likelihood and Bayesian inference are based on the multispecies network coalescent. All methods allow for multiple individuals per species. As computing the likelihood of a phylogenetic network is computationally hard, PhyloNet allows for evaluation and inference of networks using a pseudolikelihood measure. PhyloNet summarizes the results of the various analyzes and generates phylogenetic networks in the extended Newick format that is readily viewable by existing visualization software.

A likelihood-based time series modeling approach for application in dendrochronology to examine the growth-climate relations and forest disturbance history

EPA Science Inventory

A time series intervention analysis (TSIA) of dendrochronological data to infer the tree growth-climate-disturbance relations and forest disturbance history is described. Maximum likelihood is used to estimate the parameters of a structural time series model with components for ...

Maximum Likelihood Analysis of a Two-Level Nonlinear Structural Equation Model with Fixed Covariates

ERIC Educational Resources Information Center

Lee, Sik-Yum; Song, Xin-Yuan

2005-01-01

In this article, a maximum likelihood (ML) approach for analyzing a rather general two-level structural equation model is developed for hierarchically structured data that are very common in educational and/or behavioral research. The proposed two-level model can accommodate nonlinear causal relations among latent variables as well as effects…

Maximum likelihood orientation estimation of 1-D patterns in Laguerre-Gauss subspaces.

PubMed

Di Claudio, Elio D; Jacovitti, Giovanni; Laurenti, Alberto

2010-05-01

A method for measuring the orientation of linear (1-D) patterns, based on a local expansion with Laguerre-Gauss circular harmonic (LG-CH) functions, is presented. It lies on the property that the polar separable LG-CH functions span the same space as the 2-D Cartesian separable Hermite-Gauss (2-D HG) functions. Exploiting the simple steerability of the LG-CH functions and the peculiar block-linear relationship among the two expansion coefficients sets, maximum likelihood (ML) estimates of orientation and cross section parameters of 1-D patterns are obtained projecting them in a proper subspace of the 2-D HG family. It is shown in this paper that the conditional ML solution, derived by elimination of the cross section parameters, surprisingly yields the same asymptotic accuracy as the ML solution for known cross section parameters. The accuracy of the conditional ML estimator is compared to the one of state of art solutions on a theoretical basis and via simulation trials. A thorough proof of the key relationship between the LG-CH and the 2-D HG expansions is also provided.

Implementation of a Goal-Based Systems Engineering Process Using the Systems Modeling Language (SysML)

NASA Technical Reports Server (NTRS)

Breckenridge, Jonathan T.; Johnson, Stephen B.

2013-01-01

This paper describes the core framework used to implement a Goal-Function Tree (GFT) based systems engineering process using the Systems Modeling Language. It defines a set of principles built upon by the theoretical approach described in the InfoTech 2013 ISHM paper titled "Goal-Function Tree Modeling for Systems Engineering and Fault Management" presented by Dr. Stephen B. Johnson. Using the SysML language, the principles in this paper describe the expansion of the SysML language as a baseline in order to: hierarchically describe a system, describe that system functionally within success space, and allocate detection mechanisms to success functions for system protection.

Rosid radiation and the rapid rise of angiosperm-dominated forests

PubMed Central

Wang, Hengchang; Moore, Michael J.; Soltis, Pamela S.; Bell, Charles D.; Brockington, Samuel F.; Alexandre, Roolse; Davis, Charles C.; Latvis, Maribeth; Manchester, Steven R.; Soltis, Douglas E.

2009-01-01

The rosid clade (70,000 species) contains more than one-fourth of all angiosperm species and includes most lineages of extant temperate and tropical forest trees. Despite progress in elucidating relationships within the angiosperms, rosids remain the largest poorly resolved major clade; deep relationships within the rosids are particularly enigmatic. Based on parsimony and maximum likelihood (ML) analyses of separate and combined 12-gene (10 plastid genes, 2 nuclear; >18,000 bp) and plastid inverted repeat (IR; 24 genes and intervening spacers; >25,000 bp) datasets for >100 rosid species, we provide a greatly improved understanding of rosid phylogeny. Vitaceae are sister to all other rosids, which in turn form 2 large clades, each with a ML bootstrap value of 100%: (i) eurosids I (Fabidae) include the nitrogen-fixing clade, Celastrales, Huaceae, Zygophyllales, Malpighiales, and Oxalidales; and (ii) eurosids II (Malvidae) include Tapisciaceae, Brassicales, Malvales, Sapindales, Geraniales, Myrtales, Crossosomatales, and Picramniaceae. The rosid clade diversified rapidly into these major lineages, possibly over a period of <15 million years, and perhaps in as little as 4 to 5 million years. The timing of the inferred rapid radiation of rosids [108 to 91 million years ago (Mya) and 107–83 Mya for Fabidae and Malvidae, respectively] corresponds with the rapid rise of angiosperm-dominated forests and the concomitant diversification of other clades that inhabit these forests, including amphibians, ants, placental mammals, and ferns. PMID:19223592

Molecular delineation of the Agave Red Worm Comadia redtenbacheri  (Lepidoptera: Cossidae).

PubMed

CÁrdenas-Aquino, MarÍa Del Rosario; AlarcÓn-rodrÍguez, Norma Marina; Rivas-Medrano, Mario; GonzÁlez-hernÁndez, HÉctor; Vargas-hernÁndez, Mateo; SÁnchez-Arroyo, Hussein; Llanderal-cÁzares, Celina

2018-01-25

Comadia redtenbacheri (Hammerschmidt) (Agave Red Worm) is the only member of the family Cossidae that has been described as a phytophagous specialist of the plant genus Agave, which is mainly distributed in México. A new extraction protocol adapted from Stewart Via (1993) has been implemented for sequencing the COI gene from samples collected in five states of the North Central (Querétaro and Zacatecas), South Central (Estado de México) and East Central (Hidalgo and Tlaxcala) regions of México with the purpose of contributing to delineation of the species. A Maximum Likelihood (ML) tree based on these COI sequences as well as COI sequences from other Cossinae species was developed to complement the existing morphological and taxonomic approaches to delineation of this species. As expected, our Comadia samples cluster together within a monophyletic clade that includes four C. redtenbacheri sequences previously reported. This group seems to be consistent with our reconstruction, which is supported by a bootstrap value of over 99%. The closely related branches associated with the latter group include organisms known to be the plant and tree borers of the Cossinae subfamily. The COI sequences from our samples were analyzed to determine the percentage of identity among the C. redtenbacheri in a first attempt to detect differences in the sequence that matches a particular region of México.

Genetic Variations in Two Seahorse Species (Hippocampus mohnikei and Hippocampus trimaculatus): Evidence for Middle Pleistocene Population Expansion

PubMed Central

Zhang, Yanhong; Pham, Nancy Kim; Zhang, Huixian; Lin, Junda; Lin, Qiang

2014-01-01

Population genetic of seahorses is confidently influenced by their species-specific ecological requirements and life-history traits. In the present study, partial sequences of mitochondrial cytochrome b (cytb) and control region (CR) were obtained from 50 Hippocampus mohnikei and 92 H. trimaculatus from four zoogeographical zones. A total of 780 base pairs of cytb gene were sequenced to characterize mitochondrial DNA (mtDNA) diversity. The mtDNA marker revealed high haplotype diversity, low nucleotide diversity, and a lack of population structure across both populations of H. mohnikei and H. trimaculatus. A neighbour-joining (NJ) tree of cytb gene sequences showed that H. mohnikei haplotypes formed one cluster. A maximum likelihood (ML) tree of cytb gene sequences showed that H. trimaculatus belonged to one lineage. The star-like pattern median-joining network of cytb and CR markers indicated a previous demographic expansion of H. mohnikei and H. trimaculatus. The cytb and CR data sets exhibited a unimodal mismatch distribution, which may have resulted from population expansion. Mismatch analysis suggested that the expansion was initiated about 276,000 years ago for H. mohnikei and about 230,000 years ago for H. trimaculatus during the middle Pleistocene period. This study indicates a possible signature of genetic variation and population expansion in two seahorses under complex marine environments. PMID:25144384

Detection and phylogenetic analysis of bacteriophage WO in spiders (Araneae).

PubMed

Yan, Qian; Qiao, Huping; Gao, Jin; Yun, Yueli; Liu, Fengxiang; Peng, Yu

2015-11-01

Phage WO is a bacteriophage found in Wolbachia. Herein, we represent the first phylogenetic study of WOs that infect spiders (Araneae). Seven species of spiders (Araneus alternidens, Nephila clavata, Hylyphantes graminicola, Prosoponoides sinensis, Pholcus crypticolens, Coleosoma octomaculatum, and Nurscia albofasciata) from six families were infected by Wolbachia and WO, followed by comprehensive sequence analysis. Interestingly, WO could be only detected Wolbachia-infected spiders. The relative infection rates of those seven species of spiders were 75, 100, 88.9, 100, 62.5, 72.7, and 100 %, respectively. Our results indicated that both Wolbachia and WO were found in three different body parts of N. clavata, and WO could be passed to the next generation of H. graminicola by vertical transmission. There were three different sequences for WO infected in A. alternidens and two different WO sequences from C. octomaculatum. Only one sequence of WO was found for the other five species of spiders. The discovered sequence of WO ranged from 239 to 311 bp. Phylogenetic tree was generated using maximum likelihood (ML) based on the orf7 gene sequences. According to the phylogenetic tree, WOs in N. clavata and H. graminicola were clustered in the same group. WOs from A. alternidens (WAlt1) and C. octomaculatum (WOct2) were closely related to another clade, whereas WO in P. sinensis was classified as a sole cluster.

Maximum-likelihood estimation of parameterized wavefronts from multifocal data

PubMed Central

Sakamoto, Julia A.; Barrett, Harrison H.

2012-01-01

A method for determining the pupil phase distribution of an optical system is demonstrated. Coefficients in a wavefront expansion were estimated using likelihood methods, where the data consisted of multiple irradiance patterns near focus. Proof-of-principle results were obtained in both simulation and experiment. Large-aberration wavefronts were handled in the numerical study. Experimentally, we discuss the handling of nuisance parameters. Fisher information matrices, Cramér-Rao bounds, and likelihood surfaces are examined. ML estimates were obtained by simulated annealing to deal with numerous local extrema in the likelihood function. Rapid processing techniques were employed to reduce the computational time. PMID:22772282

Bootstrap Standard Errors for Maximum Likelihood Ability Estimates When Item Parameters Are Unknown

ERIC Educational Resources Information Center

Patton, Jeffrey M.; Cheng, Ying; Yuan, Ke-Hai; Diao, Qi

2014-01-01

When item parameter estimates are used to estimate the ability parameter in item response models, the standard error (SE) of the ability estimate must be corrected to reflect the error carried over from item calibration. For maximum likelihood (ML) ability estimates, a corrected asymptotic SE is available, but it requires a long test and the…

An Iterative Maximum a Posteriori Estimation of Proficiency Level to Detect Multiple Local Likelihood Maxima

ERIC Educational Resources Information Center

Magis, David; Raiche, Gilles

2010-01-01

In this article the authors focus on the issue of the nonuniqueness of the maximum likelihood (ML) estimator of proficiency level in item response theory (with special attention to logistic models). The usual maximum a posteriori (MAP) method offers a good alternative within that framework; however, this article highlights some drawbacks of its…

Intraspecific diversity in Sinningia speciosa (Gesneriaceae: Sinningieae), and possible origins of the cultivated florist's gloxinia

PubMed Central

Zaitlin, David

2012-01-01

Background and aims The florist's gloxinia is a familiar houseplant in the Gesneriaceae, the botanical family that includes the African violet (Saintpaulia) and other ornamental species. The gloxinia's wild progenitor is Sinningia speciosa (Lodd.) Hiern, a Brazilian endemic. Although it has been cultivated for almost 200 years, little is known about the genetic diversity in S. speciosa, how the wild populations relate to one another or even where the cultivated forms originated. Using available wild collections, preliminary phenetic and phylogenetic investigations were conducted to elucidate the interspecific relationships within S. speciosa and to infer the origins of the cultivars. Methodology Amplified fragment length polymorphism (AFLP) analysis was applied to 24 accessions of S. speciosa (17 wild collections, seven cultivars) and one accession each of Sinningia guttata and Sinningia macrophylla. A maximum likelihood (ML) tree was also calculated from an alignment of the nuclear ribosomal internal transcribed spacer sequence from the same 26 accessions. Principal results Dice/UPGMA and principal coordinates analysis of the AFLP data partitioned S. speciosa into several distinct clusters, one of which included S. macrophylla. All cultivated ‘gloxinias’ grouped together in a major cluster with plants from Rio de Janeiro. The AFLP results were compared with a phylogenetic analysis of the ribosomal spacer region, which was informative in S. speciosa. The ML tree generally supported the AFLP results, although several clades lacked strong statistical support. Conclusions Independent analyses of two different data sets show that S. speciosa is a diverse species comprised of several lineages. Genetic distance estimates calculated from the AFLP data were positively correlated with geographic distances between populations, indicating that reproductive isolation could be driving speciation in this taxon. Molecular markers are under development for population genetic studies in S. speciosa, which will make it possible to define evolutionarily significant units for purposes of conservation. PMID:23755350

Enhancing the performance of regional land cover mapping

NASA Astrophysics Data System (ADS)

Wu, Weicheng; Zucca, Claudio; Karam, Fadi; Liu, Guangping

2016-10-01

Different pixel-based, object-based and subpixel-based methods such as time-series analysis, decision-tree, and different supervised approaches have been proposed to conduct land use/cover classification. However, despite their proven advantages in small dataset tests, their performance is variable and less satisfactory while dealing with large datasets, particularly, for regional-scale mapping with high resolution data due to the complexity and diversity in landscapes and land cover patterns, and the unacceptably long processing time. The objective of this paper is to demonstrate the comparatively highest performance of an operational approach based on integration of multisource information ensuring high mapping accuracy in large areas with acceptable processing time. The information used includes phenologically contrasted multiseasonal and multispectral bands, vegetation index, land surface temperature, and topographic features. The performance of different conventional and machine learning classifiers namely Malahanobis Distance (MD), Maximum Likelihood (ML), Artificial Neural Networks (ANNs), Support Vector Machines (SVMs) and Random Forests (RFs) was compared using the same datasets in the same IDL (Interactive Data Language) environment. An Eastern Mediterranean area with complex landscape and steep climate gradients was selected to test and develop the operational approach. The results showed that SVMs and RFs classifiers produced most accurate mapping at local-scale (up to 96.85% in Overall Accuracy), but were very time-consuming in whole-scene classification (more than five days per scene) whereas ML fulfilled the task rapidly (about 10 min per scene) with satisfying accuracy (94.2-96.4%). Thus, the approach composed of integration of seasonally contrasted multisource data and sampling at subclass level followed by a ML classification is a suitable candidate to become an operational and effective regional land cover mapping method.

The use of copulas to practical estimation of multivariate stochastic differential equation mixed effects models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rupšys, P.

A system of stochastic differential equations (SDE) with mixed-effects parameters and multivariate normal copula density function were used to develop tree height model for Scots pine trees in Lithuania. A two-step maximum likelihood parameter estimation method is used and computational guidelines are given. After fitting the conditional probability density functions to outside bark diameter at breast height, and total tree height, a bivariate normal copula distribution model was constructed. Predictions from the mixed-effects parameters SDE tree height model calculated during this research were compared to the regression tree height equations. The results are implemented in the symbolic computational language MAPLE.

3D Visualization of Machine Learning Algorithms with Astronomical Data

NASA Astrophysics Data System (ADS)

Kent, Brian R.

2016-01-01

We present innovative machine learning (ML) methods using unsupervised clustering with minimum spanning trees (MSTs) to study 3D astronomical catalogs. Utilizing Python code to build trees based on galaxy catalogs, we can render the results with the visualization suite Blender to produce interactive 360 degree panoramic videos. The catalogs and their ML results can be explored in a 3D space using mobile devices, tablets or desktop browsers. We compare the statistics of the MST results to a number of machine learning methods relating to optimization and efficiency.

Addressing Data Analysis Challenges in Gravitational Wave Searches Using the Particle Swarm Optimization Algorithm

NASA Astrophysics Data System (ADS)

Weerathunga, Thilina Shihan

2017-08-01

Gravitational waves are a fundamental prediction of Einstein's General Theory of Relativity. The first experimental proof of their existence was provided by the Nobel Prize winning discovery by Taylor and Hulse of orbital decay in a binary pulsar system. The first detection of gravitational waves incident on earth from an astrophysical source was announced in 2016 by the LIGO Scientific Collaboration, launching the new era of gravitational wave (GW) astronomy. The signal detected was from the merger of two black holes, which is an example of sources called Compact Binary Coalescences (CBCs). Data analysis strategies used in the search for CBC signals are derivatives of the Maximum-Likelihood (ML) method. The ML method applied to data from a network of geographically distributed GW detectors--called fully coherent network analysis--is currently the best approach for estimating source location and GW polarization waveforms. However, in the case of CBCs, especially for lower mass systems (O(1M solar masses)) such as double neutron star binaries, fully coherent network analysis is computationally expensive. The ML method requires locating the global maximum of the likelihood function over a nine dimensional parameter space, where the computation of the likelihood at each point requires correlations involving O(104) to O(106) samples between the data and the corresponding candidate signal waveform template. Approximations, such as semi-coherent coincidence searches, are currently used to circumvent the computational barrier but incur a concomitant loss in sensitivity. We explored the effectiveness of Particle Swarm Optimization (PSO), a well-known algorithm in the field of swarm intelligence, in addressing the fully coherent network analysis problem. As an example, we used a four-detector network consisting of the two LIGO detectors at Hanford and Livingston, Virgo and Kagra, all having initial LIGO noise power spectral densities, and show that PSO can locate the global maximum with less than 240,000 likelihood evaluations for a component mass range of 1.0 to 10.0 solar masses at a realistic coherent network signal to noise ratio of 9.0. Our results show that PSO can successfully deliver a fully-coherent all-sky search with < (1/10 ) the number of likelihood evaluations needed for a grid-based search. Used as a follow-up step, the savings in the number of likelihood evaluations may also reduce latency in obtaining ML estimates of source parameters in semi-coherent searches.

Fitting power-laws in empirical data with estimators that work for all exponents

PubMed Central

Hanel, Rudolf; Corominas-Murtra, Bernat; Liu, Bo; Thurner, Stefan

2017-01-01

Most standard methods based on maximum likelihood (ML) estimates of power-law exponents can only be reliably used to identify exponents smaller than minus one. The argument that power laws are otherwise not normalizable, depends on the underlying sample space the data is drawn from, and is true only for sample spaces that are unbounded from above. Power-laws obtained from bounded sample spaces (as is the case for practically all data related problems) are always free of such limitations and maximum likelihood estimates can be obtained for arbitrary powers without restrictions. Here we first derive the appropriate ML estimator for arbitrary exponents of power-law distributions on bounded discrete sample spaces. We then show that an almost identical estimator also works perfectly for continuous data. We implemented this ML estimator and discuss its performance with previous attempts. We present a general recipe of how to use these estimators and present the associated computer codes. PMID:28245249

Additivity and maximum likelihood estimation of nonlinear component biomass models

Treesearch

David L.R. Affleck

2015-01-01

Since Parresol's (2001) seminal paper on the subject, it has become common practice to develop nonlinear tree biomass equations so as to ensure compatibility among total and component predictions and to fit equations jointly using multi-step least squares (MSLS) methods. In particular, many researchers have specified total tree biomass models by aggregating the...

Additive nonlinear biomass equations: A likelihood-based approach

Treesearch

David L. R. Affleck; Ulises Dieguez-Aranda

2016-01-01

Since Parresol’s (Can. J. For. Res. 31:865-878, 2001) seminal article on the topic, it has become standard to develop nonlinear tree biomass equations to ensure compatibility among total and component predictions and to fit these equations using multistep generalized least-squares methods. In particular, many studies have specified equations for total tree...

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

PubMed

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

2014-12-01

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

The Impact of Missing Data on Species Tree Estimation.

PubMed

Xi, Zhenxiang; Liu, Liang; Davis, Charles C

2016-03-01

Phylogeneticists are increasingly assembling genome-scale data sets that include hundreds of genes to resolve their focal clades. Although these data sets commonly include a moderate to high amount of missing data, there remains no consensus on their impact to species tree estimation. Here, using several simulated and empirical data sets, we assess the effects of missing data on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and gene rate heterogeneity. We demonstrate that concatenation (RAxML), gene-tree-based coalescent (ASTRAL, MP-EST, and STAR), and supertree (matrix representation with parsimony [MRP]) methods perform reliably, so long as missing data are randomly distributed (by gene and/or by species) and that a sufficiently large number of genes are sampled. When data sets are indecisive sensu Sanderson et al. (2010. Phylogenomics with incomplete taxon coverage: the limits to inference. BMC Evol Biol. 10:155) and/or ILS is high, however, high amounts of missing data that are randomly distributed require exhaustive levels of gene sampling, likely exceeding most empirical studies to date. Moreover, missing data become especially problematic when they are nonrandomly distributed. We demonstrate that STAR produces inconsistent results when the amount of nonrandom missing data is high, regardless of the degree of ILS and gene rate heterogeneity. Similarly, concatenation methods using maximum likelihood can be misled by nonrandom missing data in the presence of gene rate heterogeneity, which becomes further exacerbated when combined with high ILS. In contrast, ASTRAL, MP-EST, and MRP are more robust under all of these scenarios. These results underscore the importance of understanding the influence of missing data in the phylogenomics era. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

PubMed

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.

A Two-Stage Approach to Missing Data: Theory and Application to Auxiliary Variables

ERIC Educational Resources Information Center

Savalei, Victoria; Bentler, Peter M.

2009-01-01

A well-known ad-hoc approach to conducting structural equation modeling with missing data is to obtain a saturated maximum likelihood (ML) estimate of the population covariance matrix and then to use this estimate in the complete data ML fitting function to obtain parameter estimates. This 2-stage (TS) approach is appealing because it minimizes a…

The Performance of ML, GLS, and WLS Estimation in Structural Equation Modeling under Conditions of Misspecification and Nonnormality.

ERIC Educational Resources Information Center

Olsson, Ulf Henning; Foss, Tron; Troye, Sigurd V.; Howell, Roy D.

2000-01-01

Used simulation to demonstrate how the choice of estimation method affects indexes of fit and parameter bias for different sample sizes when nested models vary in terms of specification error and the data demonstrate different levels of kurtosis. Discusses results for maximum likelihood (ML), generalized least squares (GLS), and weighted least…

SEM with Missing Data and Unknown Population Distributions Using Two-Stage ML: Theory and Its Application

ERIC Educational Resources Information Center

Yuan, Ke-Hai; Lu, Laura

2008-01-01

This article provides the theory and application of the 2-stage maximum likelihood (ML) procedure for structural equation modeling (SEM) with missing data. The validity of this procedure does not require the assumption of a normally distributed population. When the population is normally distributed and all missing data are missing at random…

Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty

PubMed Central

Baele, Guy; Lemey, Philippe; Suchard, Marc A.

2016-01-01

Marginal likelihood estimates to compare models using Bayes factors frequently accompany Bayesian phylogenetic inference. Approaches to estimate marginal likelihoods have garnered increased attention over the past decade. In particular, the introduction of path sampling (PS) and stepping-stone sampling (SS) into Bayesian phylogenetics has tremendously improved the accuracy of model selection. These sampling techniques are now used to evaluate complex evolutionary and population genetic models on empirical data sets, but considerable computational demands hamper their widespread adoption. Further, when very diffuse, but proper priors are specified for model parameters, numerical issues complicate the exploration of the priors, a necessary step in marginal likelihood estimation using PS or SS. To avoid such instabilities, generalized SS (GSS) has recently been proposed, introducing the concept of “working distributions” to facilitate—or shorten—the integration process that underlies marginal likelihood estimation. However, the need to fix the tree topology currently limits GSS in a coalescent-based framework. Here, we extend GSS by relaxing the fixed underlying tree topology assumption. To this purpose, we introduce a “working” distribution on the space of genealogies, which enables estimating marginal likelihoods while accommodating phylogenetic uncertainty. We propose two different “working” distributions that help GSS to outperform PS and SS in terms of accuracy when comparing demographic and evolutionary models applied to synthetic data and real-world examples. Further, we show that the use of very diffuse priors can lead to a considerable overestimation in marginal likelihood when using PS and SS, while still retrieving the correct marginal likelihood using both GSS approaches. The methods used in this article are available in BEAST, a powerful user-friendly software package to perform Bayesian evolutionary analyses. PMID:26526428

Maximum likelihood positioning algorithm for high-resolution PET scanners

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gross-Weege, Nicolas, E-mail: nicolas.gross-weege@pmi.rwth-aachen.de, E-mail: schulz@pmi.rwth-aachen.de; Schug, David; Hallen, Patrick

2016-06-15

Purpose: In high-resolution positron emission tomography (PET), lightsharing elements are incorporated into typical detector stacks to read out scintillator arrays in which one scintillator element (crystal) is smaller than the size of the readout channel. In order to identify the hit crystal by means of the measured light distribution, a positioning algorithm is required. One commonly applied positioning algorithm uses the center of gravity (COG) of the measured light distribution. The COG algorithm is limited in spatial resolution by noise and intercrystal Compton scatter. The purpose of this work is to develop a positioning algorithm which overcomes this limitation. Methods:more » The authors present a maximum likelihood (ML) algorithm which compares a set of expected light distributions given by probability density functions (PDFs) with the measured light distribution. Instead of modeling the PDFs by using an analytical model, the PDFs of the proposed ML algorithm are generated assuming a single-gamma-interaction model from measured data. The algorithm was evaluated with a hot-rod phantom measurement acquired with the preclinical HYPERION II {sup D} PET scanner. In order to assess the performance with respect to sensitivity, energy resolution, and image quality, the ML algorithm was compared to a COG algorithm which calculates the COG from a restricted set of channels. The authors studied the energy resolution of the ML and the COG algorithm regarding incomplete light distributions (missing channel information caused by detector dead time). Furthermore, the authors investigated the effects of using a filter based on the likelihood values on sensitivity, energy resolution, and image quality. Results: A sensitivity gain of up to 19% was demonstrated in comparison to the COG algorithm for the selected operation parameters. Energy resolution and image quality were on a similar level for both algorithms. Additionally, the authors demonstrated that the performance of the ML algorithm is less prone to missing channel information. A likelihood filter visually improved the image quality, i.e., the peak-to-valley increased up to a factor of 3 for 2-mm-diameter phantom rods by rejecting 87% of the coincidences. A relative improvement of the energy resolution of up to 12.8% was also measured rejecting 91% of the coincidences. Conclusions: The developed ML algorithm increases the sensitivity by correctly handling missing channel information without influencing energy resolution or image quality. Furthermore, the authors showed that energy resolution and image quality can be improved substantially by rejecting events that do not comply well with the single-gamma-interaction model, such as Compton-scattered events.« less

Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach

PubMed Central

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 taxa, hence the quartet-based supertree methods combine many -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. PMID:25117474

Salivary flow rate and periodontal infection - a study among subjects aged 75 years or older.

PubMed

Syrjälä, A-M H; Raatikainen, L; Komulainen, K; Knuuttila, M; Ruoppi, P; Hartikainen, S; Sulkava, R; Ylöstalo, P

2011-05-01

To analyse the relation of stimulated and unstimulated salivary flow rates to periodontal infection in home-dwelling elderly people aged 75 years or older. This study was based on a subpopulation of 157 (111 women, 46 men) home-dwelling, dentate, non-smoking elderly people (mean age 79.8, SD 3.6 years) from the Geriatric Multidisciplinary Strategy for the Good Care of the Elderly Study). The data were collected by interview and oral clinical examination. Persons with very low (< 0.7 ml min⁻¹) and low stimulated salivary flow rates (0.7- < 1.0 ml min⁻¹) had a decreased likelihood of having teeth with deepened (≥ 4 mm) periodontal pockets, RR: 0.7, CI: 0.5-0.9 and RR: 0.7, CI: 0.5-0.9, respectively, when compared with those with normal stimulated salivary flow. Persons with a very low unstimulated salivary flow rate (< 0.1 ml min⁻¹) had a decreased likelihood of having teeth with deepened (≥ 4 mm) periodontal pockets, RR 0.8, CI: 0.6-1.0, when compared with subjects with low/normal unstimulated salivary flow. In a population of dentate, home-dwelling non-smokers, aged 75 years or older, low stimulated and unstimulated salivary flow rates were weakly associated with a decreased likelihood of having teeth with deep periodontal pockets. © 2010 John Wiley & Sons A/S.

FPGA Acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods.

PubMed

Zierke, Stephanie; Bakos, Jason D

2010-04-12

Likelihood (ML)-based phylogenetic inference has become a popular method for estimating the evolutionary relationships among species based on genomic sequence data. This method is used in applications such as RAxML, GARLI, MrBayes, PAML, and PAUP. The Phylogenetic Likelihood Function (PLF) is an important kernel computation for this method. The PLF consists of a loop with no conditional behavior or dependencies between iterations. As such it contains a high potential for exploiting parallelism using micro-architectural techniques. In this paper, we describe a technique for mapping the PLF and supporting logic onto a Field Programmable Gate Array (FPGA)-based co-processor. By leveraging the FPGA's on-chip DSP modules and the high-bandwidth local memory attached to the FPGA, the resultant co-processor can accelerate ML-based methods and outperform state-of-the-art multi-core processors. We use the MrBayes 3 tool as a framework for designing our co-processor. For large datasets, we estimate that our accelerated MrBayes, if run on a current-generation FPGA, achieves a 10x speedup relative to software running on a state-of-the-art server-class microprocessor. The FPGA-based implementation achieves its performance by deeply pipelining the likelihood computations, performing multiple floating-point operations in parallel, and through a natural log approximation that is chosen specifically to leverage a deeply pipelined custom architecture. Heterogeneous computing, which combines general-purpose processors with special-purpose co-processors such as FPGAs and GPUs, is a promising approach for high-performance phylogeny inference as shown by the growing body of literature in this field. FPGAs in particular are well-suited for this task because of their low power consumption as compared to many-core processors and Graphics Processor Units (GPUs).

Automation and Evaluation of the SOWH Test with SOWHAT.

PubMed

Church, Samuel H; Ryan, Joseph F; Dunn, Casey W

2015-11-01

The Swofford-Olsen-Waddell-Hillis (SOWH) test evaluates statistical support for incongruent phylogenetic topologies. It is commonly applied to determine if the maximum likelihood tree in a phylogenetic analysis is significantly different than an alternative hypothesis. The SOWH test compares the observed difference in log-likelihood between two topologies to a null distribution of differences in log-likelihood generated by parametric resampling. The test is a well-established phylogenetic method for topology testing, but it is sensitive to model misspecification, it is computationally burdensome to perform, and its implementation requires the investigator to make several decisions that each have the potential to affect the outcome of the test. We analyzed the effects of multiple factors using seven data sets to which the SOWH test was previously applied. These factors include a number of sample replicates, likelihood software, the introduction of gaps to simulated data, the use of distinct models of evolution for data simulation and likelihood inference, and a suggested test correction wherein an unresolved "zero-constrained" tree is used to simulate sequence data. To facilitate these analyses and future applications of the SOWH test, we wrote SOWHAT, a program that automates the SOWH test. We find that inadequate bootstrap sampling can change the outcome of the SOWH test. The results also show that using a zero-constrained tree for data simulation can result in a wider null distribution and higher p-values, but does not change the outcome of the SOWH test for most of the data sets tested here. These results will help others implement and evaluate the SOWH test and allow us to provide recommendations for future applications of the SOWH test. SOWHAT is available for download from https://github.com/josephryan/SOWHAT. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Delayed mortality of eastern hardwoods after prescribed fire

Treesearch

Daniel A. Yaussy; Thomas A. Waldrop

2010-01-01

The Southern Appalachian Mountain and the Ohio Hills sites of the National Fire and Fire Surrogate Study are located in hardwood dominated forests. Mortality of trees was anticipated the first year after burning but it continued for up to 4 years after burning, which was not expected. Survival analysis showed that the likelihood of mortality was related to prior tree...

Predicting Tree Mortality From Diameter Growth: A Comparison of Maximum Likelihood and Bayesian Approaches

Treesearch

Peter H. Wychoff; James S. Clark

2000-01-01

Ecologists and foresters have long noted a link between tree growth rate and mortality, and recent work suggests that i&erspecific differences in low growth tolerauce is a key force shaping forest structure. Little information is available, however, on the growth-mortality relationship for most species. We present three methods for estimating growth-mortality...

Gene expression signatures in tree shrew choroid in response to three myopiagenic conditions

PubMed Central

He, Li; Frost, Michael R.; Siegwart, John T.; Norton, Thomas T.

2014-01-01

We examined gene expression in tree shrew choroid in response to three different myopiagenic conditions: minus lens (ML) wear, form deprivation (FD), and continuous darkness (DK). Four groups of tree shrews (n = 7 per group) were used. Starting 24 days after normal eye opening (days of visual experience [DVE]), the ML group wore a monocular −5 D lens for 2 days. The FD group wore a monocular translucent diffuser for 2 days. The DK group experienced continuous darkness binocularly for 11 days, starting at 17 DVE. An age-matched normal group was examined at 26 DVE. Quantitative PCR was used to measure the relative (treated eye vs. control eye) differences in mRNA levels in the choroid for 77 candidate genes. Small myopic changes were observed in the treated eyes (relative to the control eyes) of the ML group (−1.0 ± 0.2 D; mean ± SEM) and FD group (−1.9 ± 0.2 D). A larger myopia developed in the DK group (−4.4 ± 1.0 D) relative to Normal eyes (both groups, mean of right and left eyes). In the ML group, 28 genes showed significant differential mRNA expression; eighteen were down-regulated. A very similar pattern occurred in the FD group; twenty-seven of the same genes were similarly regulated, along with five additional genes. Fewer expression differences in the DK group were significant compared to normal or the control eyes of the ML and FD groups, but the pattern was similar to that of the ML and FD differential expression patterns. These data suggest that, at the level of the choroid, the gene expression signatures produced by “GO” emmetropization signals are highly similar despite the different visual conditions. PMID:25072854

DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood.

PubMed

Kim, Tane; Hao, Weilong

2014-09-27

The study of discrete characters is crucial for the understanding of evolutionary processes. Even though great advances have been made in the analysis of nucleotide sequences, computer programs for non-DNA discrete characters are often dedicated to specific analyses and lack flexibility. Discrete characters often have different transition rate matrices, variable rates among sites and sometimes contain unobservable states. To obtain the ability to accurately estimate a variety of discrete characters, programs with sophisticated methodologies and flexible settings are desired. DiscML performs maximum likelihood estimation for evolutionary rates of discrete characters on a provided phylogeny with the options that correct for unobservable data, rate variations, and unknown prior root probabilities from the empirical data. It gives users options to customize the instantaneous transition rate matrices, or to choose pre-determined matrices from models such as birth-and-death (BD), birth-death-and-innovation (BDI), equal rates (ER), symmetric (SYM), general time-reversible (GTR) and all rates different (ARD). Moreover, we show application examples of DiscML on gene family data and on intron presence/absence data. DiscML was developed as a unified R program for estimating evolutionary rates of discrete characters with no restriction on the number of character states, and with flexibility to use different transition models. DiscML is ideal for the analyses of binary (1s/0s) patterns, multi-gene families, and multistate discrete morphological characteristics.

A Comparison of Pseudo-Maximum Likelihood and Asymptotically Distribution-Free Dynamic Factor Analysis Parameter Estimation in Fitting Covariance Structure Models to Block-Toeplitz Matrices Representing Single-Subject Multivariate Time-Series.

ERIC Educational Resources Information Center

Molenaar, Peter C. M.; Nesselroade, John R.

1998-01-01

Pseudo-Maximum Likelihood (p-ML) and Asymptotically Distribution Free (ADF) estimation methods for estimating dynamic factor model parameters within a covariance structure framework were compared through a Monte Carlo simulation. Both methods appear to give consistent model parameter estimates, but only ADF gives standard errors and chi-square…

On the Performance of Maximum Likelihood versus Means and Variance Adjusted Weighted Least Squares Estimation in CFA

ERIC Educational Resources Information Center

Beauducel, Andre; Herzberg, Philipp Yorck

2006-01-01

This simulation study compared maximum likelihood (ML) estimation with weighted least squares means and variance adjusted (WLSMV) estimation. The study was based on confirmatory factor analyses with 1, 2, 4, and 8 factors, based on 250, 500, 750, and 1,000 cases, and on 5, 10, 20, and 40 variables with 2, 3, 4, 5, and 6 categories. There was no…

Using an EM Covariance Matrix to Estimate Structural Equation Models with Missing Data: Choosing an Adjusted Sample Size to Improve the Accuracy of Inferences

ERIC Educational Resources Information Center

Enders, Craig K.; Peugh, James L.

2004-01-01

Two methods, direct maximum likelihood (ML) and the expectation maximization (EM) algorithm, can be used to obtain ML parameter estimates for structural equation models with missing data (MD). Although the 2 methods frequently produce identical parameter estimates, it may be easier to satisfy missing at random assumptions using EM. However, no…

Is the ML Chi-Square Ever Robust to Nonnormality? A Cautionary Note with Missing Data

ERIC Educational Resources Information Center

Savalei, Victoria

2008-01-01

Normal theory maximum likelihood (ML) is by far the most popular estimation and testing method used in structural equation modeling (SEM), and it is the default in most SEM programs. Even though this approach assumes multivariate normality of the data, its use can be justified on the grounds that it is fairly robust to the violations of the…

Coalescent-Based Analyses of Genomic Sequence Data Provide a Robust Resolution of Phylogenetic Relationships among Major Groups of Gibbons

PubMed Central

Shi, Cheng-Min; Yang, Ziheng

2018-01-01

Abstract The phylogenetic relationships among extant gibbon species remain unresolved despite numerous efforts using morphological, behavorial, and genetic data and the sequencing of whole genomes. A major challenge in reconstructing the gibbon phylogeny is the radiative speciation process, which resulted in extremely short internal branches in the species phylogeny and extensive incomplete lineage sorting with extensive gene-tree heterogeneity across the genome. Here, we analyze two genomic-scale data sets, with ∼10,000 putative noncoding and exonic loci, respectively, to estimate the species tree for the major groups of gibbons. We used the Bayesian full-likelihood method bpp under the multispecies coalescent model, which naturally accommodates incomplete lineage sorting and uncertainties in the gene trees. For comparison, we included three heuristic coalescent-based methods (mp-est, SVDQuartets, and astral) as well as concatenation. From both data sets, we infer the phylogeny for the four extant gibbon genera to be (Hylobates, (Nomascus, (Hoolock, Symphalangus))). We used simulation guided by the real data to evaluate the accuracy of the methods used. Astral, while not as efficient as bpp, performed well in estimation of the species tree even in presence of excessive incomplete lineage sorting. Concatenation, mp-est and SVDQuartets were unreliable when the species tree contains very short internal branches. Likelihood ratio test of gene flow suggests a small amount of migration from Hylobates moloch to H. pileatus, while cross-genera migration is absent or rare. Our results highlight the utility of coalescent-based methods in addressing challenging species tree problems characterized by short internal branches and rampant gene tree-species tree discordance. PMID:29087487

Approximated mutual information training for speech recognition using myoelectric signals.

PubMed

Guo, Hua J; Chan, A D C

2006-01-01

A new training algorithm called the approximated maximum mutual information (AMMI) is proposed to improve the accuracy of myoelectric speech recognition using hidden Markov models (HMMs). Previous studies have demonstrated that automatic speech recognition can be performed using myoelectric signals from articulatory muscles of the face. Classification of facial myoelectric signals can be performed using HMMs that are trained using the maximum likelihood (ML) algorithm; however, this algorithm maximizes the likelihood of the observations in the training sequence, which is not directly associated with optimal classification accuracy. The AMMI training algorithm attempts to maximize the mutual information, thereby training the HMMs to optimize their parameters for discrimination. Our results show that AMMI training consistently reduces the error rates compared to these by the ML training, increasing the accuracy by approximately 3% on average.

Probabilistic atlas based labeling of the cerebral vessel tree

NASA Astrophysics Data System (ADS)

Van de Giessen, Martijn; Janssen, Jasper P.; Brouwer, Patrick A.; Reiber, Johan H. C.; Lelieveldt, Boudewijn P. F.; Dijkstra, Jouke

2015-03-01

Preoperative imaging of the cerebral vessel tree is essential for planning therapy on intracranial stenoses and aneurysms. Usually, a magnetic resonance angiography (MRA) or computed tomography angiography (CTA) is acquired from which the cerebral vessel tree is segmented. Accurate analysis is helped by the labeling of the cerebral vessels, but labeling is non-trivial due to anatomical topological variability and missing branches due to acquisition issues. In recent literature, labeling the cerebral vasculature around the Circle of Willis has mainly been approached as a graph-based problem. The most successful method, however, requires the definition of all possible permutations of missing vessels, which limits application to subsets of the tree and ignores spatial information about the vessel locations. This research aims to perform labeling using probabilistic atlases that model spatial vessel and label likelihoods. A cerebral vessel tree is aligned to a probabilistic atlas and subsequently each vessel is labeled by computing the maximum label likelihood per segment from label-specific atlases. The proposed method was validated on 25 segmented cerebral vessel trees. Labeling accuracies were close to 100% for large vessels, but dropped to 50-60% for small vessels that were only present in less than 50% of the set. With this work we showed that using solely spatial information of the vessel labels, vessel segments from stable vessels (>50% presence) were reliably classified. This spatial information will form the basis for a future labeling strategy with a very loose topological model.

Improving Depth, Energy and Timing Estimation in PET Detectors with Deconvolution and Maximum Likelihood Pulse Shape Discrimination

PubMed Central

Berg, Eric; Roncali, Emilie; Hutchcroft, Will; Qi, Jinyi; Cherry, Simon R.

2016-01-01

In a scintillation detector, the light generated in the scintillator by a gamma interaction is converted to photoelectrons by a photodetector and produces a time-dependent waveform, the shape of which depends on the scintillator properties and the photodetector response. Several depth-of-interaction (DOI) encoding strategies have been developed that manipulate the scintillator’s temporal response along the crystal length and therefore require pulse shape discrimination techniques to differentiate waveform shapes. In this work, we demonstrate how maximum likelihood (ML) estimation methods can be applied to pulse shape discrimination to better estimate deposited energy, DOI and interaction time (for time-of-flight (TOF) PET) of a gamma ray in a scintillation detector. We developed likelihood models based on either the estimated detection times of individual photoelectrons or the number of photoelectrons in discrete time bins, and applied to two phosphor-coated crystals (LFS and LYSO) used in a previously developed TOF-DOI detector concept. Compared with conventional analytical methods, ML pulse shape discrimination improved DOI encoding by 27% for both crystals. Using the ML DOI estimate, we were able to counter depth-dependent changes in light collection inherent to long scintillator crystals and recover the energy resolution measured with fixed depth irradiation (~11.5% for both crystals). Lastly, we demonstrated how the Richardson-Lucy algorithm, an iterative, ML-based deconvolution technique, can be applied to the digitized waveforms to deconvolve the photodetector’s single photoelectron response and produce waveforms with a faster rising edge. After deconvolution and applying DOI and time-walk corrections, we demonstrated a 13% improvement in coincidence timing resolution (from 290 to 254 ps) with the LFS crystal and an 8% improvement (323 to 297 ps) with the LYSO crystal. PMID:27295658

Improving Depth, Energy and Timing Estimation in PET Detectors with Deconvolution and Maximum Likelihood Pulse Shape Discrimination.

PubMed

Berg, Eric; Roncali, Emilie; Hutchcroft, Will; Qi, Jinyi; Cherry, Simon R

2016-11-01

In a scintillation detector, the light generated in the scintillator by a gamma interaction is converted to photoelectrons by a photodetector and produces a time-dependent waveform, the shape of which depends on the scintillator properties and the photodetector response. Several depth-of-interaction (DOI) encoding strategies have been developed that manipulate the scintillator's temporal response along the crystal length and therefore require pulse shape discrimination techniques to differentiate waveform shapes. In this work, we demonstrate how maximum likelihood (ML) estimation methods can be applied to pulse shape discrimination to better estimate deposited energy, DOI and interaction time (for time-of-flight (TOF) PET) of a gamma ray in a scintillation detector. We developed likelihood models based on either the estimated detection times of individual photoelectrons or the number of photoelectrons in discrete time bins, and applied to two phosphor-coated crystals (LFS and LYSO) used in a previously developed TOF-DOI detector concept. Compared with conventional analytical methods, ML pulse shape discrimination improved DOI encoding by 27% for both crystals. Using the ML DOI estimate, we were able to counter depth-dependent changes in light collection inherent to long scintillator crystals and recover the energy resolution measured with fixed depth irradiation (~11.5% for both crystals). Lastly, we demonstrated how the Richardson-Lucy algorithm, an iterative, ML-based deconvolution technique, can be applied to the digitized waveforms to deconvolve the photodetector's single photoelectron response and produce waveforms with a faster rising edge. After deconvolution and applying DOI and time-walk corrections, we demonstrated a 13% improvement in coincidence timing resolution (from 290 to 254 ps) with the LFS crystal and an 8% improvement (323 to 297 ps) with the LYSO crystal.

Maximum likelihood inference implies a high, not a low, ancestral haploid chromosome number in Araceae, with a critique of the bias introduced by ‘x’

PubMed Central

Cusimano, Natalie; Sousa, Aretuza; Renner, Susanne S.

2012-01-01

Background and Aims For 84 years, botanists have relied on calculating the highest common factor for series of haploid chromosome numbers to arrive at a so-called basic number, x. This was done without consistent (reproducible) reference to species relationships and frequencies of different numbers in a clade. Likelihood models that treat polyploidy, chromosome fusion and fission as events with particular probabilities now allow reconstruction of ancestral chromosome numbers in an explicit framework. We have used a modelling approach to reconstruct chromosome number change in the large monocot family Araceae and to test earlier hypotheses about basic numbers in the family. Methods Using a maximum likelihood approach and chromosome counts for 26 % of the 3300 species of Araceae and representative numbers for each of the other 13 families of Alismatales, polyploidization events and single chromosome changes were inferred on a genus-level phylogenetic tree for 113 of the 117 genera of Araceae. Key Results The previously inferred basic numbers x = 14 and x = 7 are rejected. Instead, maximum likelihood optimization revealed an ancestral haploid chromosome number of n = 16, Bayesian inference of n = 18. Chromosome fusion (loss) is the predominant inferred event, whereas polyploidization events occurred less frequently and mainly towards the tips of the tree. Conclusions The bias towards low basic numbers (x) introduced by the algebraic approach to inferring chromosome number changes, prevalent among botanists, may have contributed to an unrealistic picture of ancestral chromosome numbers in many plant clades. The availability of robust quantitative methods for reconstructing ancestral chromosome numbers on molecular phylogenetic trees (with or without branch length information), with confidence statistics, makes the calculation of x an obsolete approach, at least when applied to large clades. PMID:22210850

Less-Complex Method of Classifying MPSK

NASA Technical Reports Server (NTRS)

Hamkins, Jon

2006-01-01

An alternative to an optimal method of automated classification of signals modulated with M-ary phase-shift-keying (M-ary PSK or MPSK) has been derived. The alternative method is approximate, but it offers nearly optimal performance and entails much less complexity, which translates to much less computation time. Modulation classification is becoming increasingly important in radio-communication systems that utilize multiple data modulation schemes and include software-defined or software-controlled receivers. Such a receiver may "know" little a priori about an incoming signal but may be required to correctly classify its data rate, modulation type, and forward error-correction code before properly configuring itself to acquire and track the symbol timing, carrier frequency, and phase, and ultimately produce decoded bits. Modulation classification has long been an important component of military interception of initially unknown radio signals transmitted by adversaries. Modulation classification may also be useful for enabling cellular telephones to automatically recognize different signal types and configure themselves accordingly. The concept of modulation classification as outlined in the preceding paragraph is quite general. However, at the present early stage of development, and for the purpose of describing the present alternative method, the term "modulation classification" or simply "classification" signifies, more specifically, a distinction between M-ary and M'-ary PSK, where M and M' represent two different integer multiples of 2. Both the prior optimal method and the present alternative method require the acquisition of magnitude and phase values of a number (N) of consecutive baseband samples of the incoming signal + noise. The prior optimal method is based on a maximum- likelihood (ML) classification rule that requires a calculation of likelihood functions for the M and M' hypotheses: Each likelihood function is an integral, over a full cycle of carrier phase, of a complicated sum of functions of the baseband sample values, the carrier phase, the carrier-signal and noise magnitudes, and M or M'. Then the likelihood ratio, defined as the ratio between the likelihood functions, is computed, leading to the choice of whichever hypothesis - M or M'- is more likely. In the alternative method, the integral in each likelihood function is approximated by a sum over values of the integrand sampled at a number, 1, of equally spaced values of carrier phase. Used in this way, 1 is a parameter that can be adjusted to trade computational complexity against the probability of misclassification. In the limit as 1 approaches infinity, one obtains the integral form of the likelihood function and thus recovers the ML classification. The present approximate method has been tested in comparison with the ML method by means of computational simulations. The results of the simulations have shown that the performance (as quantified by probability of misclassification) of the approximate method is nearly indistinguishable from that of the ML method (see figure).

Developing a DNA barcode library for perciform fishes in the South China Sea: Species identification, accuracy and cryptic diversity.

PubMed

Hou, Gang; Chen, Wei-Tao; Lu, Huo-Sheng; Cheng, Fei; Xie, Song-Guang

2018-01-01

DNA barcodes were studied for 1,353 specimens representing 272 morphological species belonging to 149 genera and 55 families of Perciformes from the South China Sea (SCS). The average Kimura 2-parameter (K2P) distances within species, genera and families were 0.31%, 8.71% and 14.52%, respectively. A neighbour-joining (NJ) tree, Bayesian inference (BI) and maximum-likelihood (ML) trees and Automatic Barcode Gap Discovery (ABGD) revealed 260, 253 and 259 single-species-representing clusters, respectively. Barcoding gap analysis (BGA) demonstrated that barcode gaps were present for 178 of 187 species analysed with multiple specimens (95.2%), with the minimum interspecific distance to the nearest neighbour larger than the maximum intraspecific distance. A group of three Thunnus species (T. albacares, T. obesus and T. tonggol), a pair of Gerres species (G. oyena and G. japonicus), a pair of Istiblennius species (I. edentulous and I. lineatus) and a pair of Uranoscopus species (U. oligolepis and U. kaianus) were observed with low interspecific distances and overlaps between intra- and interspecific genetic distances. Three species (Apogon ellioti, Naucrates ductor and Psenopsis anomala) showed deep intraspecific divergences and generated two lineages each, suggesting the possibility of cryptic species. Our results demonstrated that DNA barcodes are highly reliable for delineating species of Perciformes in the SCS. The DNA barcode library established in this study will shed light on further research on the diversity of Perciformes in the SCS. © 2017 John Wiley & Sons Ltd.

Minimal spanning tree algorithm for γ-ray source detection in sparse photon images: cluster parameters and selection strategies

DOE PAGES

Campana, R.; Bernieri, E.; Massaro, E.; ...

2013-05-22

We present that the minimal spanning tree (MST) algorithm is a graph-theoretical cluster-finding method. We previously applied it to γ-ray bidimensional images, showing that it is quite sensitive in finding faint sources. Possible sources are associated with the regions where the photon arrival directions clusterize. MST selects clusters starting from a particular “tree” connecting all the point of the image and performing a cut based on the angular distance between photons, with a number of events higher than a given threshold. In this paper, we show how a further filtering, based on some parameters linked to the cluster properties, canmore » be applied to reduce spurious detections. We find that the most efficient parameter for this secondary selection is the magnitudeM of a cluster, defined as the product of its number of events by its clustering degree. We test the sensitivity of the method by means of simulated and real Fermi-Large Area Telescope (LAT) fields. Our results show that √M is strongly correlated with other statistical significance parameters, derived from a wavelet based algorithm and maximum likelihood (ML) analysis, and that it can be used as a good estimator of statistical significance of MST detections. Finally, we apply the method to a 2-year LAT image at energies higher than 3 GeV, and we show the presence of new clusters, likely associated with BL Lac objects.« less

Molecular differentiation and phylogenetic relationships of three Angiostrongylus species and Angiostrongylus cantonensis geographical isolates based on a 66-kDa protein gene of A. cantonensis (Nematoda: Angiostrongylidae).

PubMed

Eamsobhana, Praphathip; Lim, Phaik Eem; Zhang, Hongman; Gan, Xiaoxian; Yong, Hoi Sen

2010-12-01

The phylogenetic relationships and molecular differentiation of three species of angiostrongylid nematodes (Angiostrongylus cantonensis, Angiostrongylus costaricensis and Angiostrongylus malaysiensis) were studied using the AC primers for a 66-kDa protein gene of A. cantonensis. The AC primers successfully amplified the genomic DNA of these angiostrongylid nematodes. No amplification was detected for the DNA of Ascaris lumbricoides, Ascaris suum, Anisakis simplex, Gnathostoma spinigerum, Toxocara canis, and Trichinella spiralis. The maximum-parsimony (MP) consensus tree and the maximum-likelihood (ML) tree both showed that the Angiostrongylus taxa could be divided into two major clades - Clade 1 (A. costaricensis) and Clade 2 (A. cantonensis and A. malaysiensis) with a full support bootstrap value. A. costaricensis is the most distant taxon. A. cantonensis is a sister group to A. malaysiensis; these two taxa (species) are clearly separated. There is no clear distinction between the A. cantonensis samples from four different geographical localities (Thailand, China, Japan and Hawaii); only some of the samples are grouped ranging from no support or low support to moderate support of bootstrap values. The published nucleotide sequences of A. cantonensis adult-specific native 66kDa protein mRNA, clone L5-400 from Taiwan (U17585) appear to be very distant from the A. cantonensis samples from Thailand, China, Japan and Hawaii, with the uncorrected p-distance values ranging from 26.87% to 29.92%.

Genetic diversity analysis of the oriental river prawn (Macrobrachium nipponense) in Huaihe River.

PubMed

Cui, Feng; Yu, Yanyan; Bao, Fangyin; Wang, Song; Xiao, Ming Song

2018-04-19

The oriental river prawn (Macrobrachium nipponense) is an economically and nutritionally important species of decapod crustaceans in China. Genetic structure and demographic history of Macrobrachium nipponense were examined using sequence data from portions of the mitochondrial DNA cytochrome oxidase subunit I (COI) gene. Samples of 191 individuals were collected from 10 localities in the upper to middle reaches of the Huaihe River. Variability was detected at a total of 42 nucleotide sites along 684 bp length of homologous sequence (6.14%), and base substitutions occurred mostly at the second codon position. Haplotype diversity (h) and nucleotide diversity (π) of all populations were 0.9136 ± 0.0116 and 0.0078 ± 0.0042, respectively. Phylogenetic tree constructed using the maximum-likelihood (ML) method showed that the 44 haplotypes were assigned to two obvious clades associated with geographic regions. Moreover, the median-joining network was similar to the topology of the phylogenetic tree with 44 haplotypes. The pairwise F ST values between the populations varied from -0.0298 to 0.2994. Generally, moderate genetic differentiation (F ST  = 0.1598, p = .0000) among different geographic populations was detected, with the significant differentiation between the Huaibin (HB) and other Macrobrachium nipponense populations. Both mismatch distribution analyses and neutrality tests suggested the early stage of Late Pleistocene population expansion 85,500 years before present for the species, which was consistent with the palaeoclimatic condition of the Huaihe River Basin.

Evaluation of properties over phylogenetic trees using stochastic logics.

PubMed

Requeno, José Ignacio; Colom, José Manuel

2016-06-14

Model checking has been recently introduced as an integrated framework for extracting information of the phylogenetic trees using temporal logics as a querying language, an extension of modal logics that imposes restrictions of a boolean formula along a path of events. The phylogenetic tree is considered a transition system modeling the evolution as a sequence of genomic mutations (we understand mutation as different ways that DNA can be changed), while this kind of logics are suitable for traversing it in a strict and exhaustive way. Given a biological property that we desire to inspect over the phylogeny, the verifier returns true if the specification is satisfied or a counterexample that falsifies it. However, this approach has been only considered over qualitative aspects of the phylogeny. In this paper, we repair the limitations of the previous framework for including and handling quantitative information such as explicit time or probability. To this end, we apply current probabilistic continuous-time extensions of model checking to phylogenetics. We reinterpret a catalog of qualitative properties in a numerical way, and we also present new properties that couldn't be analyzed before. For instance, we obtain the likelihood of a tree topology according to a mutation model. As case of study, we analyze several phylogenies in order to obtain the maximum likelihood with the model checking tool PRISM. In addition, we have adapted the software for optimizing the computation of maximum likelihoods. We have shown that probabilistic model checking is a competitive framework for describing and analyzing quantitative properties over phylogenetic trees. This formalism adds soundness and readability to the definition of models and specifications. Besides, the existence of model checking tools hides the underlying technology, omitting the extension, upgrade, debugging and maintenance of a software tool to the biologists. A set of benchmarks justify the feasibility of our approach.

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

PubMed Central

Leaché, Adam D.; Banbury, Barbara L.; Felsenstein, Joseph; de Oca, Adrián nieto-Montes; Stamatakis, Alexandros

2015-01-01

Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the presence of missing data. Phylogenetic analysis of RAD loci requires careful attention to model assumptions, especially if downstream analyses depend on branch lengths. PMID:26227865

The decision tree classifier - Design and potential. [for Landsat-1 data

NASA Technical Reports Server (NTRS)

Hauska, H.; Swain, P. H.

1975-01-01

A new classifier has been developed for the computerized analysis of remote sensor data. The decision tree classifier is essentially a maximum likelihood classifier using multistage decision logic. It is characterized by the fact that an unknown sample can be classified into a class using one or several decision functions in a successive manner. The classifier is applied to the analysis of data sensed by Landsat-1 over Kenosha Pass, Colorado. The classifier is illustrated by a tree diagram which for processing purposes is encoded as a string of symbols such that there is a unique one-to-one relationship between string and decision tree.

A Single Camera Motion Capture System for Human-Computer Interaction

NASA Astrophysics Data System (ADS)

Okada, Ryuzo; Stenger, Björn

This paper presents a method for markerless human motion capture using a single camera. It uses tree-based filtering to efficiently propagate a probability distribution over poses of a 3D body model. The pose vectors and associated shapes are arranged in a tree, which is constructed by hierarchical pairwise clustering, in order to efficiently evaluate the likelihood in each frame. Anew likelihood function based on silhouette matching is proposed that improves the pose estimation of thinner body parts, i. e. the limbs. The dynamic model takes self-occlusion into account by increasing the variance of occluded body-parts, thus allowing for recovery when the body part reappears. We present two applications of our method that work in real-time on a Cell Broadband Engine™: a computer game and a virtual clothing application.

Exploiting Non-sequence Data in Dynamic Model Learning

DTIC Science & Technology

2013-10-01

For our experiments here and in Section 3.5, we implement the proposed algorithms in MATLAB and use the maximum directed spanning tree solver...embarrassingly parallelizable, whereas PM’s maximum directed spanning tree procedure is harder to parallelize. In this experiment, our MATLAB ...some estimation problems, this approach is able to give unique and consistent estimates while the maximum- likelihood method gets entangled in

Multilevel modeling of single-case data: A comparison of maximum likelihood and Bayesian estimation.

PubMed

Moeyaert, Mariola; Rindskopf, David; Onghena, Patrick; Van den Noortgate, Wim

2017-12-01

The focus of this article is to describe Bayesian estimation, including construction of prior distributions, and to compare parameter recovery under the Bayesian framework (using weakly informative priors) and the maximum likelihood (ML) framework in the context of multilevel modeling of single-case experimental data. Bayesian estimation results were found similar to ML estimation results in terms of the treatment effect estimates, regardless of the functional form and degree of information included in the prior specification in the Bayesian framework. In terms of the variance component estimates, both the ML and Bayesian estimation procedures result in biased and less precise variance estimates when the number of participants is small (i.e., 3). By increasing the number of participants to 5 or 7, the relative bias is close to 5% and more precise estimates are obtained for all approaches, except for the inverse-Wishart prior using the identity matrix. When a more informative prior was added, more precise estimates for the fixed effects and random effects were obtained, even when only 3 participants were included. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Spatial design and strength of spatial signal: Effects on covariance estimation

USGS Publications Warehouse

Irvine, Kathryn M.; Gitelman, Alix I.; Hoeting, Jennifer A.

2007-01-01

In a spatial regression context, scientists are often interested in a physical interpretation of components of the parametric covariance function. For example, spatial covariance parameter estimates in ecological settings have been interpreted to describe spatial heterogeneity or “patchiness” in a landscape that cannot be explained by measured covariates. In this article, we investigate the influence of the strength of spatial dependence on maximum likelihood (ML) and restricted maximum likelihood (REML) estimates of covariance parameters in an exponential-with-nugget model, and we also examine these influences under different sampling designs—specifically, lattice designs and more realistic random and cluster designs—at differing intensities of sampling (n=144 and 361). We find that neither ML nor REML estimates perform well when the range parameter and/or the nugget-to-sill ratio is large—ML tends to underestimate the autocorrelation function and REML produces highly variable estimates of the autocorrelation function. The best estimates of both the covariance parameters and the autocorrelation function come under the cluster sampling design and large sample sizes. As a motivating example, we consider a spatial model for stream sulfate concentration.

An evaluation of several different classification schemes - Their parameters and performance. [maximum likelihood decision for crop identification

NASA Technical Reports Server (NTRS)

Scholz, D.; Fuhs, N.; Hixson, M.

1979-01-01

The overall objective of this study was to apply and evaluate several of the currently available classification schemes for crop identification. The approaches examined were: (1) a per point Gaussian maximum likelihood classifier, (2) a per point sum of normal densities classifier, (3) a per point linear classifier, (4) a per point Gaussian maximum likelihood decision tree classifier, and (5) a texture sensitive per field Gaussian maximum likelihood classifier. Three agricultural data sets were used in the study: areas from Fayette County, Illinois, and Pottawattamie and Shelby Counties in Iowa. The segments were located in two distinct regions of the Corn Belt to sample variability in soils, climate, and agricultural practices.

Phylogenetic tree and community structure from a Tangled Nature model.

PubMed

Canko, Osman; Taşkın, Ferhat; Argın, Kamil

2015-10-07

In evolutionary biology, the taxonomy and origination of species are widely studied subjects. An estimation of the evolutionary tree can be done via available DNA sequence data. The calculation of the tree is made by well-known and frequently used methods such as maximum likelihood and neighbor-joining. In order to examine the results of these methods, an evolutionary tree is pursued computationally by a mathematical model, called Tangled Nature. A relatively small genome space is investigated due to computational burden and it is found that the actual and predicted trees are in reasonably good agreement in terms of shape. Moreover, the speciation and the resulting community structure of the food-web are investigated by modularity. Copyright © 2015 Elsevier Ltd. All rights reserved.

Maximum likelihood: Extracting unbiased information from complex networks

NASA Astrophysics Data System (ADS)

Garlaschelli, Diego; Loffredo, Maria I.

2008-07-01

The choice of free parameters in network models is subjective, since it depends on what topological properties are being monitored. However, we show that the maximum likelihood (ML) principle indicates a unique, statistically rigorous parameter choice, associated with a well-defined topological feature. We then find that, if the ML condition is incompatible with the built-in parameter choice, network models turn out to be intrinsically ill defined or biased. To overcome this problem, we construct a class of safely unbiased models. We also propose an extension of these results that leads to the fascinating possibility to extract, only from topological data, the “hidden variables” underlying network organization, making them “no longer hidden.” We test our method on World Trade Web data, where we recover the empirical gross domestic product using only topological information.

Distribution, Predictors, and Impacts of Emerald Ash Borer (Agrilus planipennis) (Coleoptera: Buprestidae) Infestation of White Fringetree (Chionanthus virginicus).

PubMed

Peterson, Donnie L; Cipollini, Don

2017-02-01

Emerald ash borer, Agrilus planipennis (Fairmaire), is an invasive pest of ash trees (Fraxinus spp.) in North America that was recently found infesting white fringetree (Chionanthus virginicus L.). Initial reports of the infestation of white fringetree by emerald ash borer occurred in southwestern Ohio and Chicago, IL. We examined white fringetrees at additional sites in Illinois, Indiana, Ohio, and Pennsylvania in Summer and Fall 2015 and Winter 2016 for emerald ash borer infestation. Our aim was to examine white fringetrees at a limited number of sites with emerald ash borer infestation and to relate tree size, crown dieback, epicormic sprouting, tree sex, and adjacency to ash or white fringetrees with the likelihood of beetle infestation. A higher proportion of infested trees exhibited epicormic sprouting and the likelihood that a tree was infested increased with increasing crown dieback, variables that may be both predictors and responses to attack. The proportion of trees infested with emerald ash borer increased with increasing tree size. Signs consistent with emerald ash borer infestation were found in 26% of 178 white fringetrees, with at least one host infested at each site in all states. Infestation rates of white fringetrees increased with the density of white fringetrees at each site. The Chicago Botanic Garden site had a significantly lower infestation (3.7%) than other sites, which may be due to proactive management of ash. Overall, these data indicate white fringetree has been utilized by emerald ash borer throughout their overlapping ranges in the United States in ornamental settings likely due to ecological fitting. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Appendix 2: Risk-based framework and risk case studies. Risk assessment for forested habitats in northern Wisconsin.

Treesearch

Louis R. Iverson; Stephen N. Matthews; Anantha M. Prasad; Matthew P. Peters; Gary W. Yohe

2012-01-01

We used a risk matrix to assess risk from climate change for multiple forest species by discussing an example that depicts a range of risk for three tree species of northern Wisconsin. Risk is defined here as the product of the likelihood of an event occurring and the consequences or effects of that event. In the context of species habitats, likelihood is related to...

Characterization of Chronic Aortic and Mitral Regurgitation Undergoing Valve Surgery Using Cardiovascular Magnetic Resonance.

PubMed

Polte, Christian L; Gao, Sinsia A; Johnsson, Åse A; Lagerstrand, Kerstin M; Bech-Hanssen, Odd

2017-06-15

Grading of chronic aortic regurgitation (AR) and mitral regurgitation (MR) by cardiovascular magnetic resonance (CMR) is currently based on thresholds, which are neither modality nor quantification method specific. Accordingly, this study sought to identify CMR-specific and quantification method-specific thresholds for regurgitant volumes (RVols), RVol indexes, and regurgitant fractions (RFs), which denote severe chronic AR or MR with an indication for surgery. The study comprised patients with moderate and severe chronic AR (n = 38) and MR (n = 40). Echocardiography and CMR was performed at baseline and in all operated AR/MR patients (n = 23/25) 10 ± 1 months after surgery. CMR quantification of AR: direct (aortic flow) and indirect method (left ventricular stroke volume [LVSV] - pulmonary stroke volume [PuSV]); MR: 2 indirect methods (LVSV - aortic forward flow [AoFF]; mitral inflow [MiIF] - AoFF). All operated patients had severe regurgitation and benefited from surgery, indicated by a significant postsurgical reduction in end-diastolic volume index and improvement or relief of symptoms. The discriminatory ability between moderate and severe AR was strong for RVol >40 ml, RVol index >20 ml/m 2 , and RF >30% (direct method) and RVol >62 ml, RVol index >31 ml/m 2 , and RF >36% (LVSV-PuSV) with a negative likelihood ratio ≤ 0.2. In MR, the discriminatory ability was very strong for RVol >64 ml, RVol index >32 ml/m 2 , and RF >41% (LVSV-AoFF) and RVol >40 ml, RVol index >20 ml/m 2 , and RF >30% (MiIF-AoFF) with a negative likelihood ratio < 0.1. In conclusion, CMR grading of chronic AR and MR should be based on modality-specific and quantification method-specific thresholds, as they differ largely from recognized guideline criteria, to assure appropriate clinical decision-making and timing of surgery. Copyright © 2017 Elsevier Inc. All rights reserved.

Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera

PubMed Central

Mutanen, Marko; Kivelä, Sami M.; Vos, Rutger A.; Doorenweerd, Camiel; Ratnasingham, Sujeevan; Hausmann, Axel; Huemer, Peter; Dincă, Vlad; van Nieukerken, Erik J.; Lopez-Vaamonde, Carlos; Vila, Roger; Aarvik, Leif; Decaëns, Thibaud; Efetov, Konstantin A.; Hebert, Paul D. N.; Johnsen, Arild; Karsholt, Ole; Pentinsaari, Mikko; Rougerie, Rodolphe; Segerer, Andreas; Tarmann, Gerhard; Zahiri, Reza; Godfray, H. Charles J.

2016-01-01

The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service “Monophylizer” to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric—conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors. PMID:27288478

Phylogeny of Kinorhyncha Based on Morphology and Two Molecular Loci

PubMed Central

Sørensen, Martin V.; Dal Zotto, Matteo; Rho, Hyun Soo; Herranz, Maria; Sánchez, Nuria; Pardos, Fernando; Yamasaki, Hiroshi

2015-01-01

The phylogeny of Kinorhyncha was analyzed using morphology and the molecular loci 18S rRNA and 28S rRNA. The different datasets were analyzed separately and in combination, using maximum likelihood and Bayesian Inference. Bayesian inference of molecular sequence data in combination with morphology supported the division of Kinorhyncha into two major clades: Cyclorhagida comb. nov. and Allomalorhagida nom. nov. The latter clade represents a new kinorhynch class, and accommodates Dracoderes, Franciscideres, a yet undescribed genus which is closely related with Franciscideres, and the traditional homalorhagid genera. Homalorhagid monophyly was not supported by any analyses with molecular sequence data included. Analysis of the combined molecular and morphological data furthermore supported a cyclorhagid clade which included all traditional cyclorhagid taxa, except Dracoderes that no longer should be considered a cyclorhagid genus. Accordingly, Cyclorhagida is divided into three main lineages: Echinoderidae, Campyloderidae, and a large clade, ‘Kentrorhagata’, which except for species of Campyloderes, includes all species with a midterminal spine present in adult individuals. Maximum likelihood analysis of the combined datasets produced a rather unresolved tree that was not regarded in the following discussion. Results of the analyses with only molecular sequence data included were incongruent at different points. However, common for all analyses was the support of several major clades, i.e., Campyloderidae, Kentrorhagata, Echinoderidae, Dracoderidae, Pycnophyidae, and a clade with Paracentrophyes + New Genus and Franciscideres (in those analyses where the latter was included). All molecular analyses including 18S rRNA sequence data furthermore supported monophyly of Allomalorhagida. Cyclorhagid monophyly was only supported in analyses of combined 18S rRNA and 28S rRNA (both ML and BI), and only in a restricted dataset where taxa with incomplete information from 28S rRNA had been omitted. Analysis of the morphological data produced results that were similar with those from the combined molecular and morphological analysis. E.g., the morphological data also supported exclusion of Dracoderes from Cyclorhagida. The main differences between the morphological analysis and analyses based on the combined datasets include: 1) Homalorhagida appears as monophyletic in the morphological tree only, 2) the morphological analyses position Franciscideres and the new genus within Cyclorhagida near Zelinkaderidae and Cateriidae, whereas analyses including molecular data place the two genera inside Allomalorhagida, and 3) species of Campyloderes appear in a basal trichotomy within Kentrorhagata in the morphological tree, whereas analysis of the combined datasets places species of Campyloderes as a sister clade to Echinoderidae and Kentrorhagata. PMID:26200115

The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms

PubMed Central

Bausher, Michael G; Singh, Nameirakpam D; Lee, Seung-Bum; Jansen, Robert K; Daniell, Henry

2006-01-01

Background The production of Citrus, the largest fruit crop of international economic value, has recently been imperiled due to the introduction of the bacterial disease Citrus canker. No significant improvements have been made to combat this disease by plant breeding and nuclear transgenic approaches. Chloroplast genetic engineering has a number of advantages over nuclear transformation; it not only increases transgene expression but also facilitates transgene containment, which is one of the major impediments for development of transgenic trees. We have sequenced the Citrus chloroplast genome to facilitate genetic improvement of this crop and to assess phylogenetic relationships among major lineages of angiosperms. Results The complete chloroplast genome sequence of Citrus sinensis is 160,129 bp in length, and contains 133 genes (89 protein-coding, 4 rRNAs and 30 distinct tRNAs). Genome organization is very similar to the inferred ancestral angiosperm chloroplast genome. However, in Citrus the infA gene is absent. The inverted repeat region has expanded to duplicate rps19 and the first 84 amino acids of rpl22. The rpl22 gene in the IRb region has a nonsense mutation resulting in 9 stop codons. This was confirmed by PCR amplification and sequencing using primers that flank the IR/LSC boundaries. Repeat analysis identified 29 direct and inverted repeats 30 bp or longer with a sequence identity ≥ 90%. Comparison of protein-coding sequences with expressed sequence tags revealed six putative RNA edits, five of which resulted in non-synonymous modifications in petL, psbH, ycf2 and ndhA. Phylogenetic analyses using maximum parsimony (MP) and maximum likelihood (ML) methods of a dataset composed of 61 protein-coding genes for 30 taxa provide strong support for the monophyly of several major clades of angiosperms, including monocots, eudicots, rosids and asterids. The MP and ML trees are incongruent in three areas: the position of Amborella and Nymphaeales, relationship of the magnoliid genus Calycanthus, and the monophyly of the eurosid I clade. Both MP and ML trees provide strong support for the monophyly of eurosids II and for the placement of Citrus (Sapindales) sister to a clade including the Malvales/Brassicales. Conclusion This is the first complete chloroplast genome sequence for a member of the Rutaceae and Sapindales. Expansion of the inverted repeat region to include rps19 and part of rpl22 and presence of two truncated copies of rpl22 is unusual among sequenced chloroplast genomes. Availability of a complete Citrus chloroplast genome sequence provides valuable information on intergenic spacer regions and endogenous regulatory sequences for chloroplast genetic engineering. Phylogenetic analyses resolve relationships among several major clades of angiosperms and provide strong support for the monophyly of the eurosid II clade and the position of the Sapindales sister to the Brassicales/Malvales. PMID:17010212

Anatomically-Aided PET Reconstruction Using the Kernel Method

PubMed Central

Hutchcroft, Will; Wang, Guobao; Chen, Kevin T.; Catana, Ciprian; Qi, Jinyi

2016-01-01

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 (ROI) 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 (EM) algorithm. PMID:27541810

Anatomically-aided PET reconstruction using the kernel method.

PubMed

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.

Anatomically-aided PET reconstruction using the kernel method

NASA Astrophysics Data System (ADS)

Hutchcroft, Will; Wang, Guobao; Chen, Kevin T.; Catana, Ciprian; Qi, Jinyi

2016-09-01

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.

A new maximum-likelihood change estimator for two-pass SAR coherent change detection

DOE PAGES

Wahl, Daniel E.; Yocky, David A.; Jakowatz, Jr., Charles V.; ...

2016-01-11

In previous research, two-pass repeat-geometry synthetic aperture radar (SAR) coherent change detection (CCD) predominantly utilized the sample degree of coherence as a measure of the temporal change occurring between two complex-valued image collects. Previous coherence-based CCD approaches tend to show temporal change when there is none in areas of the image that have a low clutter-to-noise power ratio. Instead of employing the sample coherence magnitude as a change metric, in this paper, we derive a new maximum-likelihood (ML) temporal change estimate—the complex reflectance change detection (CRCD) metric to be used for SAR coherent temporal change detection. The new CRCD estimatormore » is a surprisingly simple expression, easy to implement, and optimal in the ML sense. As a result, this new estimate produces improved results in the coherent pair collects that we have tested.« less

Endophytic Fungi from Frankincense Tree Improves Host Growth and Produces Extracellular Enzymes and Indole Acetic Acid

PubMed Central

Khan, Abdul Latif; Al-Harrasi, Ahmed; Al-Rawahi, Ahmed; Al-Farsi, Zainab; Al-Mamari, Aza; Waqas, Muhammad; Asaf, Sajjad; Elyassi, Ali; Mabood, Fazal; Shin, Jae-Ho; Lee, In-Jung

2016-01-01

Boswellia sacra, an economically important frankincense-producing tree found in the desert woodlands of Oman, is least known for its endophytic fungal diversity and the potential of these fungi to produce extracellular enzymes and auxins. We isolated various fungal endophytes belonging to Eurotiales (11.8%), Chaetomiaceae (17.6%), Incertae sadis (29.5%), Aureobasidiaceae (17.6%), Nectriaceae (5.9%) and Sporomiaceae (17.6%) from the phylloplane (leaf) and caulosphere (stem) of the tree. Endophytes were identified using genomic DNA extraction, PCR amplification and sequencing the internal transcribed spacer regions, whereas a detailed phylogenetic analysis of the same gene fragment was made with homologous sequences. The endophytic colonization rate was significantly higher in the leaf (5.33%) than the stem (0.262%). The Shannon-Weiner diversity index was H′ 0.8729, while Simpson index was higher in the leaf (0.583) than in the stem (0.416). Regarding the endophytic fungi’s potential for extracellular enzyme production, fluorogenic 4-methylumbelliferone standards and substrates were used to determine the presence of cellulases, phosphatases and glucosidases in the pure culture. Among fungal strains, Penicillum citrinum BSL17 showed significantly higher amounts of glucosidases (62.15±1.8 μM-1min-1mL) and cellulases (62.11±1.6 μM-1min-1mL), whereas Preussia sp. BSL10 showed significantly higher secretion of glucosidases (69.4±0.79 μM-1min-1mL) and phosphatases (3.46±0.31μM-1min-1mL) compared to other strains. Aureobasidium sp. BSS6 and Preussia sp. BSL10 showed significantly higher potential for indole acetic acid production (tryptophan-dependent and independent pathways). Preussia sp. BSL10 was applied to the host B. sacra tree saplings, which exhibited significant improvements in plant growth parameters and accumulation of photosynthetic pigments. The current study concluded that endophytic microbial resources producing extracellular enzymes and auxin could establish a unique niche for ecological adaptation during symbiosis with the host Frankincense tree. PMID:27359330

Endophytic Fungi from Frankincense Tree Improves Host Growth and Produces Extracellular Enzymes and Indole Acetic Acid.

PubMed

Khan, Abdul Latif; Al-Harrasi, Ahmed; Al-Rawahi, Ahmed; Al-Farsi, Zainab; Al-Mamari, Aza; Waqas, Muhammad; Asaf, Sajjad; Elyassi, Ali; Mabood, Fazal; Shin, Jae-Ho; Lee, In-Jung

2016-01-01

Boswellia sacra, an economically important frankincense-producing tree found in the desert woodlands of Oman, is least known for its endophytic fungal diversity and the potential of these fungi to produce extracellular enzymes and auxins. We isolated various fungal endophytes belonging to Eurotiales (11.8%), Chaetomiaceae (17.6%), Incertae sadis (29.5%), Aureobasidiaceae (17.6%), Nectriaceae (5.9%) and Sporomiaceae (17.6%) from the phylloplane (leaf) and caulosphere (stem) of the tree. Endophytes were identified using genomic DNA extraction, PCR amplification and sequencing the internal transcribed spacer regions, whereas a detailed phylogenetic analysis of the same gene fragment was made with homologous sequences. The endophytic colonization rate was significantly higher in the leaf (5.33%) than the stem (0.262%). The Shannon-Weiner diversity index was H' 0.8729, while Simpson index was higher in the leaf (0.583) than in the stem (0.416). Regarding the endophytic fungi's potential for extracellular enzyme production, fluorogenic 4-methylumbelliferone standards and substrates were used to determine the presence of cellulases, phosphatases and glucosidases in the pure culture. Among fungal strains, Penicillum citrinum BSL17 showed significantly higher amounts of glucosidases (62.15±1.8 μM-1min-1mL) and cellulases (62.11±1.6 μM-1min-1mL), whereas Preussia sp. BSL10 showed significantly higher secretion of glucosidases (69.4±0.79 μM-1min-1mL) and phosphatases (3.46±0.31μM-1min-1mL) compared to other strains. Aureobasidium sp. BSS6 and Preussia sp. BSL10 showed significantly higher potential for indole acetic acid production (tryptophan-dependent and independent pathways). Preussia sp. BSL10 was applied to the host B. sacra tree saplings, which exhibited significant improvements in plant growth parameters and accumulation of photosynthetic pigments. The current study concluded that endophytic microbial resources producing extracellular enzymes and auxin could establish a unique niche for ecological adaptation during symbiosis with the host Frankincense tree.

Maximum Likelihood Time-of-Arrival Estimation of Optical Pulses via Photon-Counting Photodetectors

NASA Technical Reports Server (NTRS)

Erkmen, Baris I.; Moision, Bruce E.

2010-01-01

Many optical imaging, ranging, and communications systems rely on the estimation of the arrival time of an optical pulse. Recently, such systems have been increasingly employing photon-counting photodetector technology, which changes the statistics of the observed photocurrent. This requires time-of-arrival estimators to be developed and their performances characterized. The statistics of the output of an ideal photodetector, which are well modeled as a Poisson point process, were considered. An analytical model was developed for the mean-square error of the maximum likelihood (ML) estimator, demonstrating two phenomena that cause deviations from the minimum achievable error at low signal power. An approximation was derived to the threshold at which the ML estimator essentially fails to provide better than a random guess of the pulse arrival time. Comparing the analytic model performance predictions to those obtained via simulations, it was verified that the model accurately predicts the ML performance over all regimes considered. There is little prior art that attempts to understand the fundamental limitations to time-of-arrival estimation from Poisson statistics. This work establishes both a simple mathematical description of the error behavior, and the associated physical processes that yield this behavior. Previous work on mean-square error characterization for ML estimators has predominantly focused on additive Gaussian noise. This work demonstrates that the discrete nature of the Poisson noise process leads to a distinctly different error behavior.

[Identification of pyrrosiae folium and its adulterants based on psbA-trnH sequence].

PubMed

Zhang, Ya-Qin; Shi, Yue; Song, Ming; Lin, Yun-Han; Ma, Xiao-Xi; Sun, Wei; Xiang, Li; Liu, Xi

2014-06-01

In this study, the psbA-trnH sequence as DNA barcode was used to evaluate the accuracy and stability for identification pteridophyte medicinal material Pyrrosiae Foliumas from adulterants. Genomic DNA from 106 samples were extracted successfully. The Kimura 2-Parameter (K2P) distances and ML tree were calculated using software MEGA 6.0. The intra-specific genetic distances of 3 original plants were lower than inter-specific genetic distances of adulterants. The ML tree indicated that Pyrrosiae Folium can be distinguished from its adulterants obviously. Therefore, the psbA-trnH sequence as a barcode of the pteridophyte, can accurately and stably distinguish Pyrrosiae Folium from its adulterants.

Allometric relationships predicting foliar biomass and leaf area:sapwood area ratio from tree height in five Costa Rican rain forest species.

PubMed

Calvo-Alvarado, J C; McDowell, N G; Waring, R H

2008-11-01

We developed allometric equations to predict whole-tree leaf area (A(l)), leaf biomass (M(l)) and leaf area to sapwood area ratio (A(l):A(s)) in five rain forest tree species of Costa Rica: Pentaclethra macroloba (Willd.) Kuntze (Fabaceae/Mim), Carapa guianensis Aubl. (Meliaceae), Vochysia ferru-gi-nea Mart. (Vochysiaceae), Virola koshnii Warb. (Myristicaceae) and Tetragastris panamensis (Engl.) Kuntze (Burseraceae). By destructive analyses (n = 11-14 trees per species), we observed strong nonlinear allometric relationships (r(2) > or = 0.9) for predicting A(l) or M(l) from stem diameters or A(s) measured at breast height. Linear relationships were less accurate. In general, A(l):A(s) at breast height increased linearly with tree height except for Penta-clethra, which showed a negative trend. All species, however, showed increased total A(l) with height. The observation that four of the five species increased in A(l):A(s) with height is consistent with hypotheses about trade--offs between morphological and anatomical adaptations that favor efficient water flow through variation in the amount of leaf area supported by sapwood and those imposed by the need to respond quickly to light gaps in the canopy.

Effects of forest management on understory and overstory vegetation: a retrospective study.

Treesearch

David R. Thysell; Andrew B. Carey

2000-01-01

Management for wood production through long rotations and thinning (MT) and management for biodiversity through legacy retention, protection, and no subsequent manipulation (ML) are two approaches to managing second-growth forests in the Pacific Northwest. We describe how these two strategies have affected tree size, tree density, and native and exotic vascular plant...

A Model-Based Diagnosis Framework for Distributed Systems

DTIC Science & Technology

2002-05-04

of centralized compilation techniques as applied to [6] Marco Cadoli and Francesco M . Donini . A survey several areas, of which diagnosis is one. Our...for doing so than the family for that (1) Vi 1 ... m . Xi E 2V; (2) V ui(Xi[Xi E 1). tree-structured systems. For simplicity of notation, we will that (i...our diagnosis synthesis diagnoses using a likelihood weight ri assigned to each as- algorithm. sumable Ai, i = I, ... m . Using the likelihood algebra

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data.

PubMed

Lee, Tae-Ho; Guo, Hui; Wang, Xiyin; Kim, Changsoo; Paterson, Andrew H

2014-02-26

Phylogenetic trees are widely used for genetic and evolutionary studies in various organisms. Advanced sequencing technology has dramatically enriched data available for constructing phylogenetic trees based on single nucleotide polymorphisms (SNPs). However, massive SNP data makes it difficult to perform reliable analysis, and there has been no ready-to-use pipeline to generate phylogenetic trees from these data. We developed a new pipeline, SNPhylo, to construct phylogenetic trees based on large SNP datasets. The pipeline may enable users to construct a phylogenetic tree from three representative SNP data file formats. In addition, in order to increase reliability of a tree, the pipeline has steps such as removing low quality data and considering linkage disequilibrium. A maximum likelihood method for the inference of phylogeny is also adopted in generation of a tree in our pipeline. Using SNPhylo, users can easily produce a reliable phylogenetic tree from a large SNP data file. Thus, this pipeline can help a researcher focus more on interpretation of the results of analysis of voluminous data sets, rather than manipulations necessary to accomplish the analysis.

Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering.

PubMed

Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor; Essex, M

2015-05-01

To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice.

Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering

PubMed Central

Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor

2015-01-01

Abstract To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice. PMID:25560745

Treetrimmer: a method for phylogenetic dataset size reduction.

PubMed

Maruyama, Shinichiro; Eveleigh, Robert J M; Archibald, John M

2013-04-12

With rapid advances in genome sequencing and bioinformatics, it is now possible to generate phylogenetic trees containing thousands of operational taxonomic units (OTUs) from a wide range of organisms. However, use of rigorous tree-building methods on such large datasets is prohibitive and manual 'pruning' of sequence alignments is time consuming and raises concerns over reproducibility. There is a need for bioinformatic tools with which to objectively carry out such pruning procedures. Here we present 'TreeTrimmer', a bioinformatics procedure that removes unnecessary redundancy in large phylogenetic datasets, alleviating the size effect on more rigorous downstream analyses. The method identifies and removes user-defined 'redundant' sequences, e.g., orthologous sequences from closely related organisms and 'recently' evolved lineage-specific paralogs. Representative OTUs are retained for more rigorous re-analysis. TreeTrimmer reduces the OTU density of phylogenetic trees without sacrificing taxonomic diversity while retaining the original tree topology, thereby speeding up downstream computer-intensive analyses, e.g., Bayesian and maximum likelihood tree reconstructions, in a reproducible fashion.

Estimating Tree Height-Diameter Models with the Bayesian Method

PubMed Central

Duan, Aiguo; Zhang, Jianguo; Xiang, Congwei

2014-01-01

Six candidate height-diameter models were used to analyze the height-diameter relationships. The common methods for estimating the height-diameter models have taken the classical (frequentist) approach based on the frequency interpretation of probability, for example, the nonlinear least squares method (NLS) and the maximum likelihood method (ML). The Bayesian method has an exclusive advantage compared with classical method that the parameters to be estimated are regarded as random variables. In this study, the classical and Bayesian methods were used to estimate six height-diameter models, respectively. Both the classical method and Bayesian method showed that the Weibull model was the “best” model using data1. In addition, based on the Weibull model, data2 was used for comparing Bayesian method with informative priors with uninformative priors and classical method. The results showed that the improvement in prediction accuracy with Bayesian method led to narrower confidence bands of predicted value in comparison to that for the classical method, and the credible bands of parameters with informative priors were also narrower than uninformative priors and classical method. The estimated posterior distributions for parameters can be set as new priors in estimating the parameters using data2. PMID:24711733

Estimating tree height-diameter models with the Bayesian method.

PubMed

Zhang, Xiongqing; Duan, Aiguo; Zhang, Jianguo; Xiang, Congwei

2014-01-01

Six candidate height-diameter models were used to analyze the height-diameter relationships. The common methods for estimating the height-diameter models have taken the classical (frequentist) approach based on the frequency interpretation of probability, for example, the nonlinear least squares method (NLS) and the maximum likelihood method (ML). The Bayesian method has an exclusive advantage compared with classical method that the parameters to be estimated are regarded as random variables. In this study, the classical and Bayesian methods were used to estimate six height-diameter models, respectively. Both the classical method and Bayesian method showed that the Weibull model was the "best" model using data1. In addition, based on the Weibull model, data2 was used for comparing Bayesian method with informative priors with uninformative priors and classical method. The results showed that the improvement in prediction accuracy with Bayesian method led to narrower confidence bands of predicted value in comparison to that for the classical method, and the credible bands of parameters with informative priors were also narrower than uninformative priors and classical method. The estimated posterior distributions for parameters can be set as new priors in estimating the parameters using data2.

Phylodynamic Inference with Kernel ABC and Its Application to HIV Epidemiology.

PubMed

Poon, Art F Y

2015-09-01

The shapes of phylogenetic trees relating virus populations are determined by the adaptation of viruses within each host, and by the transmission of viruses among hosts. Phylodynamic inference attempts to reverse this flow of information, estimating parameters of these processes from the shape of a virus phylogeny reconstructed from a sample of genetic sequences from the epidemic. A key challenge to phylodynamic inference is quantifying the similarity between two trees in an efficient and comprehensive way. In this study, I demonstrate that a new distance measure, based on a subset tree kernel function from computational linguistics, confers a significant improvement over previous measures of tree shape for classifying trees generated under different epidemiological scenarios. Next, I incorporate this kernel-based distance measure into an approximate Bayesian computation (ABC) framework for phylodynamic inference. ABC bypasses the need for an analytical solution of model likelihood, as it only requires the ability to simulate data from the model. I validate this "kernel-ABC" method for phylodynamic inference by estimating parameters from data simulated under a simple epidemiological model. Results indicate that kernel-ABC attained greater accuracy for parameters associated with virus transmission than leading software on the same data sets. Finally, I apply the kernel-ABC framework to study a recent outbreak of a recombinant HIV subtype in China. Kernel-ABC provides a versatile framework for phylodynamic inference because it can fit a broader range of models than methods that rely on the computation of exact likelihoods. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A search for antiplasmodial metabolites among fungal endophytes of terrestrial and marine plants of southern India.

PubMed

Kaushik, Naveen Kumar; Murali, Thokur Sreepathy; Sahal, Dinkar; Suryanarayanan, T S

2014-10-01

Eighty four different fungal endophytes isolated from sea grasses (5), marine algae (36) and leaves or barks of forest trees (43) were grown in vitro and the secondary metabolites secreted by them were harvested by immobilizing them on XAD beads. These metabolites were eluted with methanol and screened using SYBR Green I assay for their antiplasmodial activity against blood stage Plasmodium falciparum in human red blood cell culture. Our results revealed that fungal endophytes belonging to diverse genera elaborate antiplasmodial metabolites. A Fusarium sp. (580, IC50: 1.94 μg ml(-1)) endophytic in a marine alga and a Nigrospora sp. (151, IC50: 2.88 μg ml(-1)) endophytic in a tree species were subjected to antiplasmodial activity-guided reversed phase high performance liquid chromatography separation. Purification led to potentiation as reflected in IC50 values of 0.12 μg ml(-1) and 0.15 μg ml(-1) for two of the fractions obtained from 580. Our study adds further credence to the notion that fungal endophytes are a potential storehouse for a variety of novel secondary metabolites vested with different bioactivities including some that can stall the growth of the malaria parasite.

Use of acoustic technology to monitor the time course of Rhynchophorus ferrugineus larval mortality in date palms after treatments with Beauveria bassiana

USDA-ARS?s Scientific Manuscript database

Spectral and temporal patterns of insect sound impulses were monitored daily for 23-d periods in 8, 10, or 5 small date palm trees containing larvae dipped in 0 (control), 104 (low), or 108 (high) conidia/ml doses of entomopathogenic fungus, Beauveria bassiana (Bb 203), respectively. Each tree conta...

Coalescent methods for estimating phylogenetic trees.

PubMed

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

2009-10-01

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

Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria.

PubMed

Padial, José M; Grant, Taran; Frost, Darrel R

2014-06-26

Brachycephaloidea is a monophyletic group of frogs with more than 1000 species distributed throughout the New World tropics, subtropics, and Andean regions. Recently, the group has been the target of multiple molecular phylogenetic analyses, resulting in extensive changes in its taxonomy. Here, we test previous hypotheses of phylogenetic relationships for the group by combining available molecular evidence (sequences of 22 genes representing 431 ingroup and 25 outgroup terminals) and performing a tree-alignment analysis under the parsimony optimality criterion using the program POY. To elucidate the effects of alignment and optimality criterion on phylogenetic inferences, we also used the program MAFFT to obtain a similarity-alignment for analysis under both parsimony and maximum likelihood using the programs TNT and GARLI, respectively. Although all three analytical approaches agreed on numerous points, there was also extensive disagreement. Tree-alignment under parsimony supported the monophyly of the ingroup and the sister group relationship of the monophyletic marsupial frogs (Hemiphractidae), while maximum likelihood and parsimony analyses of the MAFFT similarity-alignment did not. All three methods differed with respect to the position of Ceuthomantis smaragdinus (Ceuthomantidae), with tree-alignment using parsimony recovering this species as the sister of Pristimantis + Yunganastes. All analyses rejected the monophyly of Strabomantidae and Strabomantinae as originally defined, and the tree-alignment analysis under parsimony further rejected the recently redefined Craugastoridae and Pristimantinae. Despite the greater emphasis in the systematics literature placed on the choice of optimality criterion for evaluating trees than on the choice of method for aligning DNA sequences, we found that the topological differences attributable to the alignment method were as great as those caused by the optimality criterion. Further, the optimal tree-alignment indicates that insertions and deletions occurred in twice as many aligned positions as implied by the optimal similarity-alignment, confirming previous findings that sequence turnover through insertion and deletion events plays a greater role in molecular evolution than indicated by similarity-alignments. Our results also provide a clear empirical demonstration of the different effects of wildcard taxa produced by missing data in parsimony and maximum likelihood analyses. Specifically, maximum likelihood analyses consistently (81% bootstrap frequency) provided spurious resolution despite a lack of evidence, whereas parsimony correctly depicted the ambiguity due to missing data by collapsing unsupported nodes. We provide a new taxonomy for the group that retains previously recognized Linnaean taxa except for Ceuthomantidae, Strabomantidae, and Strabomantinae. A phenotypically diagnosable superfamily is recognized formally as Brachycephaloidea, with the informal, unranked name terrarana retained as the standard common name for these frogs. We recognize three families within Brachycephaloidea that are currently diagnosable solely on molecular grounds (Brachycephalidae, Craugastoridae, and Eleutherodactylidae), as well as five subfamilies (Craugastorinae, Eleutherodactylinae, Holoadeninae, Phyzelaphryninae, and Pristimantinae) corresponding in large part to previous families and subfamilies. Our analyses upheld the monophyly of all tested genera, but we found numerous subgeneric taxa to be non-monophyletic and modified the taxonomy accordingly.

Maintenance cost, toppling risk and size of trees in a self-thinning stand.

PubMed

Larjavaara, Markku

2010-07-07

Wind routinely topples trees during storms, and the likelihood that a tree is toppled depends critically on its allometry. Yet none of the existing theories to explain tree allometry consider wind drag on tree canopies. Since leaf area index in crowded, self-thinning stands is independent of stand density, the drag force per unit land can also be assumed to be independent of stand density, with only canopy height influencing the total toppling moment. Tree stem dimensions and the self-thinning biomass can then be computed by further assuming that the risk of toppling over and stem maintenance per unit land area are independent of stand density, and that stem maintenance cost is a linear function of stem surface area and sapwood volume. These assumptions provide a novel way to understand tree allometry and lead to a self-thinning line relating tree biomass and stand density with a power between -3/2 and -2/3 depending on the ratio of maintenance of sapwood and stem surface. (c) 2010 Elsevier Ltd. All rights reserved.

Evaluation of dynamic row-action maximum likelihood algorithm reconstruction for quantitative 15O brain PET.

PubMed

Ibaraki, Masanobu; Sato, Kaoru; Mizuta, Tetsuro; Kitamura, Keishi; Miura, Shuichi; Sugawara, Shigeki; Shinohara, Yuki; Kinoshita, Toshibumi

2009-09-01

A modified version of row-action maximum likelihood algorithm (RAMLA) using a 'subset-dependent' relaxation parameter for noise suppression, or dynamic RAMLA (DRAMA), has been proposed. The aim of this study was to assess the capability of DRAMA reconstruction for quantitative (15)O brain positron emission tomography (PET). Seventeen healthy volunteers were studied using a 3D PET scanner. The PET study included 3 sequential PET scans for C(15)O, (15)O(2) and H (2) (15) O. First, the number of main iterations (N (it)) in DRAMA was optimized in relation to image convergence and statistical image noise. To estimate the statistical variance of reconstructed images on a pixel-by-pixel basis, a sinogram bootstrap method was applied using list-mode PET data. Once the optimal N (it) was determined, statistical image noise and quantitative parameters, i.e., cerebral blood flow (CBF), cerebral blood volume (CBV), cerebral metabolic rate of oxygen (CMRO(2)) and oxygen extraction fraction (OEF) were compared between DRAMA and conventional FBP. DRAMA images were post-filtered so that their spatial resolutions were matched with FBP images with a 6-mm FWHM Gaussian filter. Based on the count recovery data, N (it) = 3 was determined as an optimal parameter for (15)O PET data. The sinogram bootstrap analysis revealed that DRAMA reconstruction resulted in less statistical noise, especially in a low-activity region compared to FBP. Agreement of quantitative values between FBP and DRAMA was excellent. For DRAMA images, average gray matter values of CBF, CBV, CMRO(2) and OEF were 46.1 +/- 4.5 (mL/100 mL/min), 3.35 +/- 0.40 (mL/100 mL), 3.42 +/- 0.35 (mL/100 mL/min) and 42.1 +/- 3.8 (%), respectively. These values were comparable to corresponding values with FBP images: 46.6 +/- 4.6 (mL/100 mL/min), 3.34 +/- 0.39 (mL/100 mL), 3.48 +/- 0.34 (mL/100 mL/min) and 42.4 +/- 3.8 (%), respectively. DRAMA reconstruction is applicable to quantitative (15)O PET study and is superior to conventional FBP in terms of image quality.

Efffect of Aeroallergen Sensitization on Asthma Control in ...

EPA Pesticide Factsheets

In African-American adolescents with persistent asthma, allergic profile predicted the likelihood of having poorly controlled asthma despite guidelines-directed therapies. Our results suggest that tree and weed pollen sensitization are independent risk factors for poorly controlled asthma in this at-risk population. The study examined African-American children with difficult to treat asthma. The findings suggest that in addition to guidelines-directed asthma therapies, targeting the allergic component, particularly tree and weed pollen, is critical to achieving optimal asthma control in this at-risk population.

The influence of ignoring secondary structure on divergence time estimates from ribosomal RNA genes.

PubMed

Dohrmann, Martin

2014-02-01

Genes coding for ribosomal RNA molecules (rDNA) are among the most popular markers in molecular phylogenetics and evolution. However, coevolution of sites that code for pairing regions (stems) in the RNA secondary structure can make it challenging to obtain accurate results from such loci. While the influence of ignoring secondary structure on multiple sequence alignment and tree topology has been investigated in numerous studies, its effect on molecular divergence time estimates is still poorly known. Here, I investigate this issue in Bayesian Markov Chain Monte Carlo (BMCMC) and penalized likelihood (PL) frameworks, using empirical datasets from dragonflies (Odonata: Anisoptera) and glass sponges (Porifera: Hexactinellida). My results indicate that highly biased inferences under substitution models that ignore secondary structure only occur if maximum-likelihood estimates of branch lengths are used as input to PL dating, whereas in a BMCMC framework and in PL dating based on Bayesian consensus branch lengths, the effect is far less severe. I conclude that accounting for coevolution of paired sites in molecular dating studies is not as important as previously suggested, as long as the estimates are based on Bayesian consensus branch lengths instead of ML point estimates. This finding is especially relevant for studies where computational limitations do not allow the use of secondary-structure specific substitution models, or where accurate consensus structures cannot be predicted. I also found that the magnitude and direction (over- vs. underestimating node ages) of bias in age estimates when secondary structure is ignored was not distributed randomly across the nodes of the phylogenies, a phenomenon that requires further investigation. Copyright © 2013 Elsevier Inc. All rights reserved.

Applying six classifiers to airborne hyperspectral imagery for detecting giant reed

USDA-ARS?s Scientific Manuscript database

This study evaluated and compared six different image classifiers, including minimum distance (MD), Mahalanobis distance (MAHD), maximum likelihood (ML), spectral angle mapper (SAM), mixture tuned matched filtering (MTMF) and support vector machine (SVM), for detecting and mapping giant reed (Arundo...

Maximum likelihood estimation in calibrating a stereo camera setup.

PubMed

Muijtjens, A M; Roos, J M; Arts, T; Hasman, A

1999-02-01

Motion and deformation of the cardiac wall may be measured by following the positions of implanted radiopaque markers in three dimensions, using two x-ray cameras simultaneously. Regularly, calibration of the position measurement system is obtained by registration of the images of a calibration object, containing 10-20 radiopaque markers at known positions. Unfortunately, an accidental change of the position of a camera after calibration requires complete recalibration. Alternatively, redundant information in the measured image positions of stereo pairs can be used for calibration. Thus, a separate calibration procedure can be avoided. In the current study a model is developed that describes the geometry of the camera setup by five dimensionless parameters. Maximum Likelihood (ML) estimates of these parameters were obtained in an error analysis. It is shown that the ML estimates can be found by application of a nonlinear least squares procedure. Compared to the standard unweighted least squares procedure, the ML method resulted in more accurate estimates without noticeable bias. The accuracy of the ML method was investigated in relation to the object aperture. The reconstruction problem appeared well conditioned as long as the object aperture is larger than 0.1 rad. The angle between the two viewing directions appeared to be the parameter that was most likely to cause major inaccuracies in the reconstruction of the 3-D positions of the markers. Hence, attempts to improve the robustness of the method should primarily focus on reduction of the error in this parameter.

Safety modeling of urban arterials in Shanghai, China.

PubMed

Wang, Xuesong; Fan, Tianxiang; Chen, Ming; Deng, Bing; Wu, Bing; Tremont, Paul

2015-10-01

Traffic safety on urban arterials is influenced by several key variables including geometric design features, land use, traffic volume, and travel speeds. This paper is an exploratory study of the relationship of these variables to safety. It uses a comparatively new method of measuring speeds by extracting GPS data from taxis operating on Shanghai's urban network. This GPS derived speed data, hereafter called Floating Car Data (FCD) was used to calculate average speeds during peak and off-peak hours, and was acquired from samples of 15,000+ taxis traveling on 176 segments over 18 major arterials in central Shanghai. Geometric design features of these arterials and surrounding land use characteristics were obtained by field investigation, and crash data was obtained from police reports. Bayesian inference using four different models, Poisson-lognormal (PLN), PLN with Maximum Likelihood priors (PLN-ML), hierarchical PLN (HPLN), and HPLN with Maximum Likelihood priors (HPLN-ML), was used to estimate crash frequencies. Results showed the HPLN-ML models had the best goodness-of-fit and efficiency, and models with ML priors yielded estimates with the lowest standard errors. Crash frequencies increased with increases in traffic volume. Higher average speeds were associated with higher crash frequencies during peak periods, but not during off-peak periods. Several geometric design features including average segment length of arterial, number of lanes, presence of non-motorized lanes, number of access points, and commercial land use, were positively related to crash frequencies. Copyright © 2015 Elsevier Ltd. All rights reserved.

An application of the lottery competition model to a montane rainforest community of two canopy trees, ohia (Metrosideros polymorpha) and koa (Acacia koa) on Mauna Loa, Hawaii

USGS Publications Warehouse

Hatfield, J.S.; Link, W.A.; Dawson, D.K.; Lindquist, E.L.

1992-01-01

This rainforest occurs on Mauna Loa at 1500-2000 m elevation. Earthwatch volunteers, studying the habitat of 8 native forest bird species (3 endangered), identified 2382 living canopy trees, and 99 dead trees, on 68 study plots, 400 m2 each. Ohia made up 88% of the canopy; koa was 12%. The two-species lottery competition model, a stochastic model in which coexistence of species results from variation in recruitment and death rates, predicts a quadratic-beta distribution for the proportion of space occupied by one species. A discrete version was fit to the live tree data and a likelihood ratio test (p=0.02) was used to test if the mean death rates were equal. This test was corroborated by a contingency table analysis (p=0.03) based on dead trees. Parameter estimates from the two analyses were similar.

Maximum-likelihood soft-decision decoding of block codes using the A* algorithm

NASA Technical Reports Server (NTRS)

Ekroot, L.; Dolinar, S.

1994-01-01

The A* algorithm finds the path in a finite depth binary tree that optimizes a function. Here, it is applied to maximum-likelihood soft-decision decoding of block codes where the function optimized over the codewords is the likelihood function of the received sequence given each codeword. The algorithm considers codewords one bit at a time, making use of the most reliable received symbols first and pursuing only the partially expanded codewords that might be maximally likely. A version of the A* algorithm for maximum-likelihood decoding of block codes has been implemented for block codes up to 64 bits in length. The efficiency of this algorithm makes simulations of codes up to length 64 feasible. This article details the implementation currently in use, compares the decoding complexity with that of exhaustive search and Viterbi decoding algorithms, and presents performance curves obtained with this implementation of the A* algorithm for several codes.

Diagnostic accuracy of a novel software technology for detecting pneumothorax in a porcine model.

PubMed

Summers, Shane M; Chin, Eric J; April, Michael D; Grisell, Ronald D; Lospinoso, Joshua A; Kheirabadi, Bijan S; Salinas, Jose; Blackbourne, Lorne H

2017-09-01

Our objective was to measure the diagnostic accuracy of a novel software technology to detect pneumothorax on Brightness (B) mode and Motion (M) mode ultrasonography. Ultrasonography fellowship-trained emergency physicians performed thoracic ultrasonography at baseline and after surgically creating a pneumothorax in eight intubated, spontaneously breathing porcine subjects. Prior to pneumothorax induction, we captured sagittal M-mode still images and B-mode videos of each intercostal space with a linear array transducer at 4cm of depth. After collection of baseline images, we placed a chest tube, injected air into the pleural space in 250mL increments, and repeated the ultrasonography for pneumothorax volumes of 250mL, 500mL, 750mL, and 1000mL. We confirmed pneumothorax with intrapleural digital manometry and ultrasound by expert sonographers. We exported collected images for interpretation by the software. We treated each individual scan as a single test for interpretation by the software. Excluding indeterminate results, we collected 338M-mode images for which the software demonstrated a sensitivity of 98% (95% confidence interval [CI] 92-99%), specificity of 95% (95% CI 86-99), positive likelihood ratio (LR+) of 21.6 (95% CI 7.1-65), and negative likelihood ratio (LR-) of 0.02 (95% CI 0.008-0.046). Among 364 B-mode videos, the software demonstrated a sensitivity of 86% (95% CI 81-90%), specificity of 85% (81-91%), LR+ of 5.7 (95% CI 3.2-10.2), and LR- of 0.17 (95% CI 0.12-0.22). This novel technology has potential as a useful adjunct to diagnose pneumothorax on thoracic ultrasonography. Published by Elsevier Inc.

Comparing methods of analysing datasets with small clusters: case studies using four paediatric datasets.

PubMed

Marston, Louise; Peacock, Janet L; Yu, Keming; Brocklehurst, Peter; Calvert, Sandra A; Greenough, Anne; Marlow, Neil

2009-07-01

Studies of prematurely born infants contain a relatively large percentage of multiple births, so the resulting data have a hierarchical structure with small clusters of size 1, 2 or 3. Ignoring the clustering may lead to incorrect inferences. The aim of this study was to compare statistical methods which can be used to analyse such data: generalised estimating equations, multilevel models, multiple linear regression and logistic regression. Four datasets which differed in total size and in percentage of multiple births (n = 254, multiple 18%; n = 176, multiple 9%; n = 10 098, multiple 3%; n = 1585, multiple 8%) were analysed. With the continuous outcome, two-level models produced similar results in the larger dataset, while generalised least squares multilevel modelling (ML GLS 'xtreg' in Stata) and maximum likelihood multilevel modelling (ML MLE 'xtmixed' in Stata) produced divergent estimates using the smaller dataset. For the dichotomous outcome, most methods, except generalised least squares multilevel modelling (ML GH 'xtlogit' in Stata) gave similar odds ratios and 95% confidence intervals within datasets. For the continuous outcome, our results suggest using multilevel modelling. We conclude that generalised least squares multilevel modelling (ML GLS 'xtreg' in Stata) and maximum likelihood multilevel modelling (ML MLE 'xtmixed' in Stata) should be used with caution when the dataset is small. Where the outcome is dichotomous and there is a relatively large percentage of non-independent data, it is recommended that these are accounted for in analyses using logistic regression with adjusted standard errors or multilevel modelling. If, however, the dataset has a small percentage of clusters greater than size 1 (e.g. a population dataset of children where there are few multiples) there appears to be less need to adjust for clustering.

Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent.

PubMed

Allman, Elizabeth S; Degnan, James H; Rhodes, John A

2011-06-01

Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals-each with many genes-splitting into new populations or species. The coalescent process, which models ancestry of gene copies within populations, is often used to model the probability distribution of gene trees given a fixed species tree. This multispecies coalescent model provides a framework for phylogeneticists to infer species trees from gene trees using maximum likelihood or Bayesian approaches. Because the coalescent models a branching process over time, all trees are typically assumed to be rooted in this setting. Often, however, gene trees inferred by traditional phylogenetic methods are unrooted. We investigate probabilities of unrooted gene trees under the multispecies coalescent model. We show that when there are four species with one gene sampled per species, the distribution of unrooted gene tree topologies identifies the unrooted species tree topology and some, but not all, information in the species tree edges (branch lengths). The location of the root on the species tree is not identifiable in this situation. However, for 5 or more species with one gene sampled per species, we show that the distribution of unrooted gene tree topologies identifies the rooted species tree topology and all its internal branch lengths. The length of any pendant branch leading to a leaf of the species tree is also identifiable for any species from which more than one gene is sampled.

Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera.

PubMed

Mutanen, Marko; Kivelä, Sami M; Vos, Rutger A; Doorenweerd, Camiel; Ratnasingham, Sujeevan; Hausmann, Axel; Huemer, Peter; Dincă, Vlad; van Nieukerken, Erik J; Lopez-Vaamonde, Carlos; Vila, Roger; Aarvik, Leif; Decaëns, Thibaud; Efetov, Konstantin A; Hebert, Paul D N; Johnsen, Arild; Karsholt, Ole; Pentinsaari, Mikko; Rougerie, Rodolphe; Segerer, Andreas; Tarmann, Gerhard; Zahiri, Reza; Godfray, H Charles J

2016-11-01

The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service "Monophylizer" to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric-conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

PoMo: An Allele Frequency-Based Approach for Species Tree Estimation

PubMed Central

De Maio, Nicola; Schrempf, Dominik; Kosiol, Carolin

2015-01-01

Incomplete lineage sorting can cause incongruencies of the overall species-level phylogenetic tree with the phylogenetic trees for individual genes or genomic segments. If these incongruencies are not accounted for, it is possible to incur several biases in species tree estimation. Here, we present a simple maximum likelihood approach that accounts for ancestral variation and incomplete lineage sorting. We use a POlymorphisms-aware phylogenetic MOdel (PoMo) that we have recently shown to efficiently estimate mutation rates and fixation biases from within and between-species variation data. We extend this model to perform efficient estimation of species trees. We test the performance of PoMo in several different scenarios of incomplete lineage sorting using simulations and compare it with existing methods both in accuracy and computational speed. In contrast to other approaches, our model does not use coalescent theory but is allele frequency based. We show that PoMo is well suited for genome-wide species tree estimation and that on such data it is more accurate than previous approaches. PMID:26209413

Reversible polymorphism-aware phylogenetic models and their application to tree inference.

PubMed

Schrempf, Dominik; Minh, Bui Quang; De Maio, Nicola; von Haeseler, Arndt; Kosiol, Carolin

2016-10-21

We present a reversible Polymorphism-Aware Phylogenetic Model (revPoMo) for species tree estimation from genome-wide data. revPoMo enables the reconstruction of large scale species trees for many within-species samples. It expands the alphabet of DNA substitution models to include polymorphic states, thereby, naturally accounting for incomplete lineage sorting. We implemented revPoMo in the maximum likelihood software IQ-TREE. A simulation study and an application to great apes data show that the runtimes of our approach and standard substitution models are comparable but that revPoMo has much better accuracy in estimating trees, divergence times and mutation rates. The advantage of revPoMo is that an increase of sample size per species improves estimations but does not increase runtime. Therefore, revPoMo is a valuable tool with several applications, from speciation dating to species tree reconstruction. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Species trees for the tree swallows (Genus Tachycineta): an alternative phylogenetic hypothesis to the mitochondrial gene tree.

PubMed

Dor, Roi; Carling, Matthew D; Lovette, Irby J; Sheldon, Frederick H; Winkler, David W

2012-10-01

The New World swallow genus Tachycineta comprises nine species that collectively have a wide geographic distribution and remarkable variation both within- and among-species in ecologically important traits. Existing phylogenetic hypotheses for Tachycineta are based on mitochondrial DNA sequences, thus they provide estimates of a single gene tree. In this study we sequenced multiple individuals from each species at 16 nuclear intron loci. We used gene concatenated approaches (Bayesian and maximum likelihood) as well as coalescent-based species tree inference to reconstruct phylogenetic relationships of the genus. We examined the concordance and conflict between the nuclear and mitochondrial trees and between concatenated and coalescent-based inferences. Our results provide an alternative phylogenetic hypothesis to the existing mitochondrial DNA estimate of phylogeny. This new hypothesis provides a more accurate framework in which to explore trait evolution and examine the evolution of the mitochondrial genome in this group. Copyright © 2012 Elsevier Inc. All rights reserved.

Phylogenetically marking the limits of the genus Fusarium for post-Article 59 usage

USDA-ARS?s Scientific Manuscript database

Fusarium (Hypocreales, Nectriaceae) is one of the most important and systematically challenging groups of mycotoxigenic, plant pathogenic, and human pathogenic fungi. We conducted maximum likelihood (ML), maximum parsimony (MP) and Bayesian (B) analyses on partial nucleotide sequences of genes encod...

Application and performance of an ML-EM algorithm in NEXT

NASA Astrophysics Data System (ADS)

Simón, A.; Lerche, C.; Monrabal, F.; Gómez-Cadenas, J. J.; Álvarez, V.; Azevedo, C. D. R.; Benlloch-Rodríguez, J. M.; Borges, F. I. G. M.; Botas, A.; Cárcel, S.; Carrión, J. V.; Cebrián, S.; Conde, C. A. N.; Díaz, J.; Diesburg, M.; Escada, J.; Esteve, R.; Felkai, R.; Fernandes, L. M. P.; Ferrario, P.; Ferreira, A. L.; Freitas, E. D. C.; Goldschmidt, A.; González-Díaz, D.; Gutiérrez, R. M.; Hauptman, J.; Henriques, C. A. O.; Hernandez, A. I.; Hernando Morata, J. A.; Herrero, V.; Jones, B. J. P.; Labarga, L.; Laing, A.; Lebrun, P.; Liubarsky, I.; López-March, N.; Losada, M.; Martín-Albo, J.; Martínez-Lema, G.; Martínez, A.; McDonald, A. D.; Monteiro, C. M. B.; Mora, F. J.; Moutinho, L. M.; Muñoz Vidal, J.; Musti, M.; Nebot-Guinot, M.; Novella, P.; Nygren, D. R.; Palmeiro, B.; Para, A.; Pérez, J.; Querol, M.; Renner, J.; Ripoll, L.; Rodríguez, J.; Rogers, L.; Santos, F. P.; dos Santos, J. M. F.; Sofka, C.; Sorel, M.; Stiegler, T.; Toledo, J. F.; Torrent, J.; Tsamalaidze, Z.; Veloso, J. F. C. A.; Webb, R.; White, J. T.; Yahlali, N.

2017-08-01

The goal of the NEXT experiment is the observation of neutrinoless double beta decay in 136Xe using a gaseous xenon TPC with electroluminescent amplification and specialized photodetector arrays for calorimetry and tracking. The NEXT Collaboration is exploring a number of reconstruction algorithms to exploit the full potential of the detector. This paper describes one of them: the Maximum Likelihood Expectation Maximization (ML-EM) method, a generic iterative algorithm to find maximum-likelihood estimates of parameters that has been applied to solve many different types of complex inverse problems. In particular, we discuss a bi-dimensional version of the method in which the photosensor signals integrated over time are used to reconstruct a transverse projection of the event. First results show that, when applied to detector simulation data, the algorithm achieves nearly optimal energy resolution (better than 0.5% FWHM at the Q value of 136Xe) for events distributed over the full active volume of the TPC.

Cramer-Rao bound analysis of wideband source localization and DOA estimation

NASA Astrophysics Data System (ADS)

Yip, Lean; Chen, Joe C.; Hudson, Ralph E.; Yao, Kung

2002-12-01

In this paper, we derive the Cramér-Rao Bound (CRB) for wideband source localization and DOA estimation. The resulting CRB formula can be decomposed into two terms: one that depends on the signal characteristic and one that depends on the array geometry. For a uniformly spaced circular array (UCA), a concise analytical form of the CRB can be given by using some algebraic approximation. We further define a DOA beamwidth based on the resulting CRB formula. The DOA beamwidth can be used to design the sampling angular spacing for the Maximum-likelihood (ML) algorithm. For a randomly distributed array, we use an elliptical model to determine the largest and smallest effective beamwidth. The effective beamwidth and the CRB analysis of source localization allow us to design an efficient algorithm for the ML estimator. Finally, our simulation results of the Approximated Maximum Likelihood (AML) algorithm are demonstrated to match well to the CRB analysis at high SNR.

Efffect of Aeroallergen Sensitization on Asthma Control in African-American Teens with Persistent Asthma

EPA Science Inventory

In African-American adolescents with persistent asthma, allergic profile predicted the likelihood of having poorly controlled asthma despite guidelines-directed therapies. Our results suggest that tree and weed pollen sensitization are independent risk factors for poorly controll...

Slowdowns in diversification rates from real phylogenies may not be real.

PubMed

Cusimano, Natalie; Renner, Susanne S

2010-07-01

Studies of diversification patterns often find a slowing in lineage accumulation toward the present. This seemingly pervasive pattern of rate downturns has been taken as evidence for adaptive radiations, density-dependent regulation, and metacommunity species interactions. The significance of rate downturns is evaluated with statistical tests (the gamma statistic and Monte Carlo constant rates (MCCR) test; birth-death likelihood models and Akaike Information Criterion [AIC] scores) that rely on null distributions, which assume that the included species are a random sample of the entire clade. Sampling in real phylogenies, however, often is nonrandom because systematists try to include early-diverging species or representatives of previous intrataxon classifications. We studied the effects of biased sampling, structured sampling, and random sampling by experimentally pruning simulated trees (60 and 150 species) as well as a completely sampled empirical tree (58 species) and then applying the gamma statistic/MCCR test and birth-death likelihood models/AIC scores to assess rate changes. For trees with random species sampling, the true model (i.e., the one fitting the complete phylogenies) could be inferred in most cases. Oversampling deep nodes, however, strongly biases inferences toward downturns, with simulations of structured and biased sampling suggesting that this occurs when sampling percentages drop below 80%. The magnitude of the effect and the sensitivity of diversification rate models is such that a useful rule of thumb may be not to infer rate downturns from real trees unless they have >80% species sampling.

Identification and Mapping of Tree Species in Urban Areas Using WORLDVIEW-2 Imagery

NASA Astrophysics Data System (ADS)

Mustafa, Y. T.; Habeeb, H. N.; Stein, A.; Sulaiman, F. Y.

2015-10-01

Monitoring and mapping of urban trees are essential to provide urban forestry authorities with timely and consistent information. Modern techniques increasingly facilitate these tasks, but require the development of semi-automatic tree detection and classification methods. In this article, we propose an approach to delineate and map the crown of 15 tree species in the city of Duhok, Kurdistan Region of Iraq using WorldView-2 (WV-2) imagery. A tree crown object is identified first and is subsequently delineated as an image object (IO) using vegetation indices and texture measurements. Next, three classification methods: Maximum Likelihood, Neural Network, and Support Vector Machine were used to classify IOs using selected IO features. The best results are obtained with Support Vector Machine classification that gives the best map of urban tree species in Duhok. The overall accuracy was between 60.93% to 88.92% and κ-coefficient was between 0.57 to 0.75. We conclude that fifteen tree species were identified and mapped at a satisfactory accuracy in urban areas of this study.

Markov-random-field-based super-resolution mapping for identification of urban trees in VHR images

NASA Astrophysics Data System (ADS)

Ardila, Juan P.; Tolpekin, Valentyn A.; Bijker, Wietske; Stein, Alfred

2011-11-01

Identification of tree crowns from remote sensing requires detailed spectral information and submeter spatial resolution imagery. Traditional pixel-based classification techniques do not fully exploit the spatial and spectral characteristics of remote sensing datasets. We propose a contextual and probabilistic method for detection of tree crowns in urban areas using a Markov random field based super resolution mapping (SRM) approach in very high resolution images. Our method defines an objective energy function in terms of the conditional probabilities of panchromatic and multispectral images and it locally optimizes the labeling of tree crown pixels. Energy and model parameter values are estimated from multiple implementations of SRM in tuning areas and the method is applied in QuickBird images to produce a 0.6 m tree crown map in a city of The Netherlands. The SRM output shows an identification rate of 66% and commission and omission errors in small trees and shrub areas. The method outperforms tree crown identification results obtained with maximum likelihood, support vector machines and SRM at nominal resolution (2.4 m) approaches.

Chloroplast variation is incongruent with classification of the Australian bloodwood eucalypts (genus Corymbia, family Myrtaceae)

PubMed Central

Schuster, Tanja M.; Setaro, Sabrina D.; Tibbits, Josquin F. G.; Batty, Erin L.; Fowler, Rachael M.; McLay, Todd G. B.; Wilcox, Stephen; Ades, Peter K.

2018-01-01

Previous molecular phylogenetic analyses have resolved the Australian bloodwood eucalypt genus Corymbia (~100 species) as either monophyletic or paraphyletic with respect to Angophora (9–10 species). Here we assess relationships of Corymbia and Angophora using a large dataset of chloroplast DNA sequences (121,016 base pairs; from 90 accessions representing 55 Corymbia and 8 Angophora species, plus 33 accessions of related genera), skimmed from high throughput sequencing of genomic DNA, and compare results with new analyses of nuclear ITS sequences (119 accessions) from previous studies. Maximum likelihood and maximum parsimony analyses of cpDNA resolve well supported trees with most nodes having >95% bootstrap support. These trees strongly reject monophyly of Corymbia, its two subgenera (Corymbia and Blakella), most taxonomic sections (Abbreviatae, Maculatae, Naviculares, Septentrionales), and several species. ITS trees weakly indicate paraphyly of Corymbia (bootstrap support <50% for maximum likelihood, and 71% for parsimony), but are highly incongruent with the cpDNA analyses, in that they support monophyly of both subgenera and some taxonomic sections of Corymbia. The striking incongruence between cpDNA trees and both morphological taxonomy and ITS trees is attributed largely to chloroplast introgression between taxa, because of geographic sharing of chloroplast clades across taxonomic groups. Such introgression has been widely inferred in studies of the related genus Eucalyptus. This is the first report of its likely prevalence in Corymbia and Angophora, but this is consistent with previous morphological inferences of hybridisation between species. Our findings (based on continent-wide sampling) highlight a need for more focussed studies to assess the extent of hybridisation and introgression in the evolutionary history of these genera, and that critical testing of the classification of Corymbia and Angophora requires additional sequence data from nuclear genomes. PMID:29668710

Physalis and physaloids: A recent and complex evolutionary history.

PubMed

Zamora-Tavares, María Del Pilar; Martínez, Mahinda; Magallón, Susana; Guzmán-Dávalos, Laura; Vargas-Ponce, Ofelia

2016-07-01

The complex evolutionary history of the subtribe Physalinae is reflected in the poor resolution of the relationships of Physalis and the physaloid genera. We hypothesize that this low resolution is caused by recent evolutionary history in a complex geographic setting. The aims of this study were twofold: (1) To determine the phylogenetic relationships of the current genera recognized in Physalinae in order to identify monophyletic groups and resolve the physaloid grade; and (2) to determine the probable causes of the recent divergence in Physalinae. We conducted phylogenetic analyses with maximum likelihood (ML) and Bayesian inference with 50 Physalinae species and 19 others as outgroups, using morphological and molecular data from five plastid and two nuclear regions. A relaxed molecular clock was obtained from the ML topology and ancestral area reconstruction was conducted using the DEC model. The genera Chamaesaracha, Leucophysalis, and Physalis subgenus Rydbergis were recovered as monophyletic. Three clades, Alkekengi-Calliphysalis, Schraderanthus-Tzeltalia, and Witheringia-Brachistus, also received good support. However, even with morphological data and that of the DNA of seven regions, the tree was not completely resolved and many clades remained unsupported. Physalinae diverged at the end of the Miocene (∼9.22Mya) with one trend indicating that the greatest diversification within the subtribe occurred during the last 5My. The Neotropical region presented the highest probability (45%) of being the ancestral area of Physalinae followed by the Mexican Transition Zone (35%). During the Pliocene and Pleistocene, the geographical areas where species were found experienced significant geological and climatic changes, giving rise to rapid and relatively recent diversification events in Physalinae. Thus, recent origin, high diversification, and morphological complexity have contributed, at least with the currently available methods, to the inability to completely disentangle the phylogenetic relationships of Physalinae. Copyright © 2016 Elsevier Inc. All rights reserved.

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

PubMed

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

2015-12-01

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

Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures

PubMed Central

Moore, Brian R.; Höhna, Sebastian; May, Michael R.; Rannala, Bruce; Huelsenbeck, John P.

2016-01-01

Bayesian analysis of macroevolutionary mixtures (BAMM) has recently taken the study of lineage diversification by storm. BAMM estimates the diversification-rate parameters (speciation and extinction) for every branch of a study phylogeny and infers the number and location of diversification-rate shifts across branches of a tree. Our evaluation of BAMM reveals two major theoretical errors: (i) the likelihood function (which estimates the model parameters from the data) is incorrect, and (ii) the compound Poisson process prior model (which describes the prior distribution of diversification-rate shifts across branches) is incoherent. Using simulation, we demonstrate that these theoretical issues cause statistical pathologies; posterior estimates of the number of diversification-rate shifts are strongly influenced by the assumed prior, and estimates of diversification-rate parameters are unreliable. Moreover, the inability to correctly compute the likelihood or to correctly specify the prior for rate-variable trees precludes the use of Bayesian approaches for testing hypotheses regarding the number and location of diversification-rate shifts using BAMM. PMID:27512038

Genetic diversity and symbiotic effectiveness of Bradyrhizobium strains nodulating selected annual grain legumes growing in Ethiopia.

PubMed

Degefu, Tulu; Wolde-Meskel, Endalkachew; Rasche, Frank

2018-01-01

Vigna unguiculata, Vigna radiata and Arachis hypogaea growing in Ethiopia are nodulated by a genetically diverse group of Bradyrhizobium strains. To determine the genetic identity and symbiotic effectiveness of these bacteria, a collection of 36 test strains originating from the root nodules of the three hosts was investigated using multilocus sequence analyses (MLSA) of core genes including 16S rRNA, recA, glnII, gyrB, atpD and dnaK. Sequence analysis of nodA and nifH genes along with tests for symbiotic effectiveness using δ 15 N analysis were also carried out. The phylogenetic trees derived from the MLSA grouped most test strains into four well-supported distinct positions designated as genospecies I-IV. The maximum likelihood (ML) tree that was constructed based on the nodA gene sequences separated the entire test strains into two lineages, where the majority of the test strains were clustered on one of a well-supported large branch that comprise Bradyrhizobium species from the tropics. This clearly suggested the monophyletic origin of the nodA genes within the bradyrhizobia of tropical origin. The δ 15 N-based symbiotic effectiveness test of seven selected strains revealed that strains GN100 (δ 15 N=0.73) and GN102 (δ 15 N=0.79) were highly effective nitrogen fixers when inoculated to cowpea, thus can be considered as inoculants in cowpea production. It was concluded that Ethiopian soils are a hotspot for rhizobial diversity. This calls for further research to unravel as yet unknown bradyrhizobia nodulating legume host species growing in the country. In this respect, prospective research should also address the mechanisms of symbiotic specificity that could lead to high nitrogen fixation in target legumes.

Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation.

PubMed

Slater, Graham J; Harmon, Luke J; Wegmann, Daniel; Joyce, Paul; Revell, Liam J; Alfaro, Michael E

2012-03-01

In recent years, a suite of methods has been developed to fit multiple rate models to phylogenetic comparative data. However, most methods have limited utility at broad phylogenetic scales because they typically require complete sampling of both the tree and the associated phenotypic data. Here, we develop and implement a new, tree-based method called MECCA (Modeling Evolution of Continuous Characters using ABC) that uses a hybrid likelihood/approximate Bayesian computation (ABC)-Markov-Chain Monte Carlo approach to simultaneously infer rates of diversification and trait evolution from incompletely sampled phylogenies and trait data. We demonstrate via simulation that MECCA has considerable power to choose among single versus multiple evolutionary rate models, and thus can be used to test hypotheses about changes in the rate of trait evolution across an incomplete tree of life. We finally apply MECCA to an empirical example of body size evolution in carnivores, and show that there is no evidence for an elevated rate of body size evolution in the pinnipeds relative to terrestrial carnivores. ABC approaches can provide a useful alternative set of tools for future macroevolutionary studies where likelihood-dependent approaches are lacking. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Survival of oak root systems following frill girdle herbicide treatment for oak wilt control

Treesearch

Johann N. Bruhn; James J., Jr. Wetteroff; Linda Haugen

2003-01-01

Mechanical separation of root systems is widely used to prevent tree-to-tree vascular spread of oak wilt disease. A safe effective herbicide treatment would be valuable for this purpose in hilly, rocky, or urban settings. Three treatments were frill-girdle applied: 1) water, 2) undilutetd Garlon 3A (trichlopyr), or 3) half-strength aqueous Garlon 3A plus 24 ml per L...

Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference.

PubMed

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 flexibility. To determine whether biased reconstructions using optimization methods might affect inferences of functional properties, ancestral primate mitochondrial tRNA sequences were inferred and helix-forming propensities for conserved pairs were evaluated in silico. For ambiguously reconstructed nucleotides at sites with high base composition variability, ancestral tRNA sequences from Bayesian analyses were more compatible with canonical base pairing than were those inferred by other methods. Thus, nucleotide bias in reconstructed sequences apparently can lead to serious bias and inaccuracies in functional predictions.

A Clinical Decision Tree to Predict Whether a Bacteremic Patient Is Infected With an Extended-Spectrum β-Lactamase-Producing Organism.

PubMed

Goodman, Katherine E; Lessler, Justin; Cosgrove, Sara E; Harris, Anthony D; Lautenbach, Ebbing; Han, Jennifer H; Milstone, Aaron M; Massey, Colin J; Tamma, Pranita D

2016-10-01

Timely identification of extended-spectrum β-lactamase (ESBL) bacteremia can improve clinical outcomes while minimizing unnecessary use of broad-spectrum antibiotics, including carbapenems. However, most clinical microbiology laboratories currently require at least 24 additional hours from the time of microbial genus and species identification to confirm ESBL production. Our objective was to develop a user-friendly decision tree to predict which organisms are ESBL producing, to guide appropriate antibiotic therapy. We included patients ≥18 years of age with bacteremia due to Escherichia coli or Klebsiella species from October 2008 to March 2015 at Johns Hopkins Hospital. Isolates with ceftriaxone minimum inhibitory concentrations ≥2 µg/mL underwent ESBL confirmatory testing. Recursive partitioning was used to generate a decision tree to determine the likelihood that a bacteremic patient was infected with an ESBL producer. Discrimination of the original and cross-validated models was evaluated using receiver operating characteristic curves and by calculation of C-statistics. A total of 1288 patients with bacteremia met eligibility criteria. For 194 patients (15%), bacteremia was due to a confirmed ESBL producer. The final classification tree for predicting ESBL-positive bacteremia included 5 predictors: history of ESBL colonization/infection, chronic indwelling vascular hardware, age ≥43 years, recent hospitalization in an ESBL high-burden region, and ≥6 days of antibiotic exposure in the prior 6 months. The decision tree's positive and negative predictive values were 90.8% and 91.9%, respectively. Our findings suggest that a clinical decision tree can be used to estimate a bacteremic patient's likelihood of infection with ESBL-producing bacteria. Recursive partitioning offers a practical, user-friendly approach for addressing important diagnostic questions. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Toward a Model-Based Approach for Flight System Fault Protection

NASA Technical Reports Server (NTRS)

Day, John; Meakin, Peter; Murray, Alex

2012-01-01

Use SysML/UML to describe the physical structure of the system This part of the model would be shared with other teams - FS Systems Engineering, Planning & Execution, V&V, Operations, etc., in an integrated model-based engineering environment Use the UML Profile mechanism, defining Stereotypes to precisely express the concepts of the FP domain This extends the UML/SysML languages to contain our FP concepts Use UML/SysML, along with our profile, to capture FP concepts and relationships in the model Generate typical FP engineering products (the FMECA, Fault Tree, MRD, V&V Matrices)

The relationship between tree growth patterns and likelihood of mortality: A study of two tree species in the Sierra Nevada

USGS Publications Warehouse

Das, A.J.; Battles, J.J.; Stephenson, N.L.; van Mantgem, P.J.

2007-01-01

We examined mortality of Abies concolor (Gord. & Glend.) Lindl. (white fir) and Pinus lambertiana Dougl. (sugar pine) by developing logistic models using three growth indices obtained from tree rings: average growth, growth trend, and count of abrupt growth declines. For P. lambertiana, models with average growth, growth trend, and count of abrupt declines improved overall prediction (78.6% dead trees correctly classified, 83.7% live trees correctly classified) compared with a model with average recent growth alone (69.6% dead trees correctly classified, 67.3% live trees correctly classified). For A. concolor, counts of abrupt declines and longer time intervals improved overall classification (trees with DBH ???20 cm: 78.9% dead trees correctly classified and 76.7% live trees correctly classified vs. 64.9% dead trees correctly classified and 77.9% live trees correctly classified; trees with DBH <20 cm: 71.6% dead trees correctly classified and 71.0% live trees correctly classified vs. 67.2% dead trees correctly classified and 66.7% live trees correctly classified). In general, count of abrupt declines improved live-tree classification. External validation of A. concolor models showed that they functioned well at stands not used in model development, and the development of size-specific models demonstrated important differences in mortality risk between understory and canopy trees. Population-level mortality-risk models were developed for A. concolor and generated realistic mortality rates at two sites. Our results support the contention that a more comprehensive use of the growth record yields a more robust assessment of mortality risk. ?? 2007 NRC.

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

PubMed Central

Aberer, Andre J.; Krompass, Denis; Stamatakis, Alexandros

2013-01-01

Abstract The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive webservice implementing this algorithm. Compared with our previous method, the new algorithm is up to 4 orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world data sets, we show that our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116 334 taxa each. For simulated data sets, we show that when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum-likelihood trees that are topologically closer to the respective true trees. PMID:22962004

Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice.

PubMed

Aberer, Andre J; Krompass, Denis; Stamatakis, Alexandros

2013-01-01

The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive webservice implementing this algorithm. Compared with our previous method, the new algorithm is up to 4 orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world data sets, we show that our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116 334 taxa each. For simulated data sets, we show that when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum-likelihood trees that are topologically closer to the respective true trees.

On defining a unique phylogenetic tree with homoplastic characters.

PubMed

Goloboff, Pablo A; Wilkinson, Mark

2018-05-01

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

Local Influence and Robust Procedures for Mediation Analysis

ERIC Educational Resources Information Center

Zu, Jiyun; Yuan, Ke-Hai

2010-01-01

Existing studies of mediation models have been limited to normal-theory maximum likelihood (ML). Because real data in the social and behavioral sciences are seldom normally distributed and often contain outliers, classical methods generally lead to inefficient or biased parameter estimates. Consequently, the conclusions from a mediation analysis…

Tree-Based Global Model Tests for Polytomous Rasch Models

ERIC Educational Resources Information Center

Komboz, Basil; Strobl, Carolin; Zeileis, Achim

2018-01-01

Psychometric measurement models are only valid if measurement invariance holds between test takers of different groups. Global model tests, such as the well-established likelihood ratio (LR) test, are sensitive to violations of measurement invariance, such as differential item functioning and differential step functioning. However, these…

Acetone leaf extracts of some South African trees with high activity against Escherichia coli also have good antimycobacterial activity and selectivity index.

PubMed

Elisha, Ishaku L; Botha, Francien S; Madikizela, Balungile; McGaw, Lyndy J; Eloff, Jacobus N

2017-06-19

Tuberculosis is a world-wide problem affecting humans and animals. There is increasing development of resistance of the pathogens to current antimycobacterial agents. Many authors have investigated activities of extracts and isolated compounds from plants. The traditional uses of plants have frequently been the criterion to select plants investigated. In this contribution, we investigate whether plant extracts with very good activity against Escherichia coli may also be active against mycobacteria. The antimycobacterial activity of eight South African tree leaf extracts with high activity against Escherichia coli were determined in vitro against Mycobacterium smegmatis, M. fortuitum and M. aurum, using a serial microdilution method. The cellular cytotoxicity was also determined by the MTT assay using Vero monkey kidney cells. The selectivity index was determined by dividing the cytotoxicity of extracts by MIC. The antimycobacterial activity of the extracts ranged from 0.02 to 2.5 mg/ml. Mycobacterium smegmatis was more sensitive to the extracts (Average MIC = 0.96 mg/ml) and Mycobacterium aurum was comparatively resistant (Average MIC = 2.04 mg/ml). The extracts of Cremaspora triflora had strong antimycobacterial activity with a MIC of 0.05 mg/ml that compared reasonably well with that of streptomycin (0.01 mg/ml) and rifampicin (0.03 mg/ml), p > 0.05. Cremaspora triflora had the best selectivity index of 2.87 against Mycobacterium fortuitum. The high activity of C. triflora extracts against the fast-growing mycobacteria and good cellular safety is promising. It may be interesting to investigate extracts against pathogenic M. tuberculosis, M. bovis and M. avium cultures and to isolate active antimycobacterial compounds.

Object based technique for delineating and mapping 15 tree species using VHR WorldView-2 imagery

NASA Astrophysics Data System (ADS)

Mustafa, Yaseen T.; Habeeb, Hindav N.

2014-10-01

Monitoring and analyzing forests and trees are required task to manage and establish a good plan for the forest sustainability. To achieve such a task, information and data collection of the trees are requested. The fastest way and relatively low cost technique is by using satellite remote sensing. In this study, we proposed an approach to identify and map 15 tree species in the Mangish sub-district, Kurdistan Region-Iraq. Image-objects (IOs) were used as the tree species mapping unit. This is achieved using the shadow index, normalized difference vegetation index and texture measurements. Four classification methods (Maximum Likelihood, Mahalanobis Distance, Neural Network, and Spectral Angel Mapper) were used to classify IOs using selected IO features derived from WorldView-2 imagery. Results showed that overall accuracy was increased 5-8% using the Neural Network method compared with other methods with a Kappa coefficient of 69%. This technique gives reasonable results of various tree species classifications by means of applying the Neural Network method with IOs techniques on WorldView-2 imagery.

Tree planting in the south: what does the future hold.

Treesearch

Jeffrey D. Kline; Brett J. Butler; Ralph J. Alig

2002-01-01

Projected increasing demands for timber coupled with reduced harvests on public lands have led to concern among some forest policymakers regarding the adequacy of future U.S. timber supplies. One question concerns the likelihood that prevailing market incentives will induce industrial and nonindustrial private landowners to intensify forest management.

Likelihood of Timber Management on Nonindustrial Private Forests: Evidence From Research Studies

Treesearch

Ralph J. Alig; Karen J. Lee; Robert J. Moulton

1990-01-01

Research on timber management tendencies by nonindustrial private forest owners, while sometimes conflicting, provides useful information to support policy analyses of timber supply and investment behavior. Numerous research studies regarding tree planting, intermediate stand treatments, and timber harvesting are reviewed. Conclusive research findings include that: (1...

Indigenous Wildlife Rabies in Taiwan: Ferret Badgers, a Long Term Terrestrial Reservoir.

PubMed

Lan, Yu-Ching; Wen, Tzai-Hung; Chang, Chao-Chin; Liu, Hsin-Fu; Lee, Pei-Fen; Huang, Chung-Yuan; Chomel, Bruno B; Chen, Yi-Ming A

2017-01-01

The emerging disease of rabies was confirmed in Taiwan ferret badgers (FBs) and reported to the World Organization for Animal Health (OIE) on July 17, 2013. The spread of wildlife rabies can be related to neighborhood countries in Asia. The phylogenetic analysis was conducted by maximum likelihood (ML) methods and the Bayesian coalescent approach based on the glycoprotein (G) and nucleoprotein (N) genes. The phylogeographic and spatial temporal dynamics of viral transmission were determined by using SPREAD, QGIS. Therefore, the origin and the change with time of the viruses can be identified. Results showed the rabies virus of FB strains in Taiwan is a unique clade among other strains in Asia. According to the phylogeographic coalescent tree, three major genotypes of the FB rabies virus have circulated in three different geographical areas in Taiwan. Two genotypes have distributed into central and southern Taiwan between two ecological river barriers. The third genotype has been limited in southeastern Taiwan by the natural mountain barrier. The diversity of FB rabies viruses indicates that the biological profile of FBs could vary in different geographical areas in Taiwan. An enhanced surveillance system needs to be established near the currently identified natural barriers for early warnings of the rabies virus outbreak in Taiwan.

Indigenous Wildlife Rabies in Taiwan: Ferret Badgers, a Long Term Terrestrial Reservoir

PubMed Central

Wen, Tzai-Hung; Liu, Hsin-Fu; Lee, Pei-Fen; Chomel, Bruno B.

2017-01-01

The emerging disease of rabies was confirmed in Taiwan ferret badgers (FBs) and reported to the World Organization for Animal Health (OIE) on July 17, 2013. The spread of wildlife rabies can be related to neighborhood countries in Asia. The phylogenetic analysis was conducted by maximum likelihood (ML) methods and the Bayesian coalescent approach based on the glycoprotein (G) and nucleoprotein (N) genes. The phylogeographic and spatial temporal dynamics of viral transmission were determined by using SPREAD, QGIS. Therefore, the origin and the change with time of the viruses can be identified. Results showed the rabies virus of FB strains in Taiwan is a unique clade among other strains in Asia. According to the phylogeographic coalescent tree, three major genotypes of the FB rabies virus have circulated in three different geographical areas in Taiwan. Two genotypes have distributed into central and southern Taiwan between two ecological river barriers. The third genotype has been limited in southeastern Taiwan by the natural mountain barrier. The diversity of FB rabies viruses indicates that the biological profile of FBs could vary in different geographical areas in Taiwan. An enhanced surveillance system needs to be established near the currently identified natural barriers for early warnings of the rabies virus outbreak in Taiwan. PMID:28497055

What mediates tree mortality during drought in the southern Sierra Nevada?

USGS Publications Warehouse

Paz-Kagan, Tarin; Brodrick, Philip; Vaughn, Nicholas R.; Das, Adrian J.; Stephenson, Nathan L.; Nydick, Koren R.; Asner, Gregory P.

2017-01-01

Severe drought has the potential to cause selective mortality within a forest, thereby inducing shifts in forest species composition. The southern Sierra Nevada foothills and mountains of California have experienced extensive forest dieback due to drought stress and insect outbreak. We used high-fidelity imaging spectroscopy (HiFIS) and light detection and ranging (LiDAR) from the Carnegie Airborne Observatory (CAO) to estimate the effect of forest dieback on species composition in response to drought stress in Sequoia National Park. Our aims were: (1) to quantify site-specific conditions that mediate tree mortality along an elevation gradient in the southern Sierra Nevada Mountains; (2) to assess where mortality events have a greater probability of occurring; and (3) to estimate which tree species have a greater likelihood of mortality along the elevation gradient. A series of statistical models were generated to classify species composition and identify tree mortality, and the influences of different environmental factors were spatially quantified and analyzed to assess where mortality events have a greater likelihood of occurring. A higher probability of mortality was observed in the lower portion of the elevation gradient, on southwest and west-facing slopes, in areas with shallow soils, on shallower slopes, and at greater distances from water. All of these factors are related to site water balance throughout the landscape. Our results also suggest that mortality is species-specific along the elevation gradient, mainly affecting Pinus ponderosa and Pinus lambertiana at lower elevations. Selective mortality within the forest may drive long-term shifts in community composition along the elevation gradient.

What mediates tree mortality during drought in the southern Sierra Nevada?

PubMed

Paz-Kagan, Tarin; Brodrick, Philip G; Vaughn, Nicholas R; Das, Adrian J; Stephenson, Nathan L; Nydick, Koren R; Asner, Gregory P

2017-12-01

Severe drought has the potential to cause selective mortality within a forest, thereby inducing shifts in forest species composition. The southern Sierra Nevada foothills and mountains of California have experienced extensive forest dieback due to drought stress and insect outbreak. We used high-fidelity imaging spectroscopy (HiFIS) and light detection and ranging (LiDAR) from the Carnegie Airborne Observatory (CAO) to estimate the effect of forest dieback on species composition in response to drought stress in Sequoia National Park. Our aims were (1) to quantify site-specific conditions that mediate tree mortality along an elevation gradient in the southern Sierra Nevada Mountains, (2) to assess where mortality events have a greater probability of occurring, and (3) to estimate which tree species have a greater likelihood of mortality along the elevation gradient. A series of statistical models were generated to classify species composition and identify tree mortality, and the influences of different environmental factors were spatially quantified and analyzed to assess where mortality events have a greater likelihood of occurring. A higher probability of mortality was observed in the lower portion of the elevation gradient, on southwest- and west-facing slopes, in areas with shallow soils, on shallower slopes, and at greater distances from water. All of these factors are related to site water balance throughout the landscape. Our results also suggest that mortality is species-specific along the elevation gradient, mainly affecting Pinus ponderosa and Pinus lambertiana at lower elevations. Selective mortality within the forest may drive long-term shifts in community composition along the elevation gradient. © 2017 by the Ecological Society of America.

Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference

PubMed Central

Minh, Bui Quang; von Haeseler, Arndt

2015-01-01

Abstract In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original “full” terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference. PMID:26448206

Mapping grass communities based on multi-temporal Landsat TM imagery and environmental variables

NASA Astrophysics Data System (ADS)

Zeng, Yuandi; Liu, Yanfang; Liu, Yaolin; de Leeuw, Jan

2007-06-01

Information on the spatial distribution of grass communities in wetland is increasingly recognized as important for effective wetland management and biological conservation. Remote sensing techniques has been proved to be an effective alternative to intensive and costly ground surveys for mapping grass community. However, the mapping accuracy of grass communities in wetland is still not preferable. The aim of this paper is to develop an effective method to map grass communities in Poyang Lake Natural Reserve. Through statistic analysis, elevation is selected as an environmental variable for its high relationship with the distribution of grass communities; NDVI stacked from images of different months was used to generate Carex community map; the image in October was used to discriminate Miscanthus and Cynodon communities. Classifications were firstly performed with maximum likelihood classifier using single date satellite image with and without elevation; then layered classifications were performed using multi-temporal satellite imagery and elevation with maximum likelihood classifier, decision tree and artificial neural network separately. The results show that environmental variables can improve the mapping accuracy; and the classification with multitemporal imagery and elevation is significantly better than that with single date image and elevation (p=0.001). Besides, maximum likelihood (a=92.71%, k=0.90) and artificial neural network (a=94.79%, k=0.93) perform significantly better than decision tree (a=86.46%, k=0.83).

The Limits of Coding with Joint Constraints on Detected and Undetected Error Rates

NASA Technical Reports Server (NTRS)

Dolinar, Sam; Andrews, Kenneth; Pollara, Fabrizio; Divsalar, Dariush

2008-01-01

We develop a remarkably tight upper bound on the performance of a parameterized family of bounded angle maximum-likelihood (BA-ML) incomplete decoders. The new bound for this class of incomplete decoders is calculated from the code's weight enumerator, and is an extension of Poltyrev-type bounds developed for complete ML decoders. This bound can also be applied to bound the average performance of random code ensembles in terms of an ensemble average weight enumerator. We also formulate conditions defining a parameterized family of optimal incomplete decoders, defined to minimize both the total codeword error probability and the undetected error probability for any fixed capability of the decoder to detect errors. We illustrate the gap between optimal and BA-ML incomplete decoding via simulation of a small code.

Predicting Rotator Cuff Tears Using Data Mining and Bayesian Likelihood Ratios

PubMed Central

Lu, Hsueh-Yi; Huang, Chen-Yuan; Su, Chwen-Tzeng; Lin, Chen-Chiang

2014-01-01

Objectives Rotator cuff tear is a common cause of shoulder diseases. Correct diagnosis of rotator cuff tears can save patients from further invasive, costly and painful tests. This study used predictive data mining and Bayesian theory to improve the accuracy of diagnosing rotator cuff tears by clinical examination alone. Methods In this retrospective study, 169 patients who had a preliminary diagnosis of rotator cuff tear on the basis of clinical evaluation followed by confirmatory MRI between 2007 and 2011 were identified. MRI was used as a reference standard to classify rotator cuff tears. The predictor variable was the clinical assessment results, which consisted of 16 attributes. This study employed 2 data mining methods (ANN and the decision tree) and a statistical method (logistic regression) to classify the rotator cuff diagnosis into “tear” and “no tear” groups. Likelihood ratio and Bayesian theory were applied to estimate the probability of rotator cuff tears based on the results of the prediction models. Results Our proposed data mining procedures outperformed the classic statistical method. The correction rate, sensitivity, specificity and area under the ROC curve of predicting a rotator cuff tear were statistical better in the ANN and decision tree models compared to logistic regression. Based on likelihood ratios derived from our prediction models, Fagan's nomogram could be constructed to assess the probability of a patient who has a rotator cuff tear using a pretest probability and a prediction result (tear or no tear). Conclusions Our predictive data mining models, combined with likelihood ratios and Bayesian theory, appear to be good tools to classify rotator cuff tears as well as determine the probability of the presence of the disease to enhance diagnostic decision making for rotator cuff tears. PMID:24733553

A Test-Length Correction to the Estimation of Extreme Proficiency Levels

ERIC Educational Resources Information Center

Magis, David; Beland, Sebastien; Raiche, Gilles

2011-01-01

In this study, the estimation of extremely large or extremely small proficiency levels, given the item parameters of a logistic item response model, is investigated. On one hand, the estimation of proficiency levels by maximum likelihood (ML), despite being asymptotically unbiased, may yield infinite estimates. On the other hand, with an…

Weakly Informative Prior for Point Estimation of Covariance Matrices in Hierarchical Models

ERIC Educational Resources Information Center

Chung, Yeojin; Gelman, Andrew; Rabe-Hesketh, Sophia; Liu, Jingchen; Dorie, Vincent

2015-01-01

When fitting hierarchical regression models, maximum likelihood (ML) estimation has computational (and, for some users, philosophical) advantages compared to full Bayesian inference, but when the number of groups is small, estimates of the covariance matrix (S) of group-level varying coefficients are often degenerate. One can do better, even from…

Comparison of Radio Frequency Distinct Native Attribute and Matched Filtering Techniques for Device Discrimination and Operation Identification

DTIC Science & Technology

identification. URE from ten MSP430F5529 16-bit microcontrollers were analyzed using: 1) RF distinct native attributes (RF-DNA) fingerprints paired with multiple...discriminant analysis/maximum likelihood (MDA/ML) classification, 2) RF-DNA fingerprints paired with generalized relevance learning vector quantized

Phylogenetic analyses of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria

USDA-ARS?s Scientific Manuscript database

Fusarium (Hypocreales, Nectriaceae) is one of the most economically important and systematically challenging groups of mycotoxigenic phytopathogens and emergent human pathogens. We conducted maximum likelihood (ML), maximum parsimony (MP) and Bayesian (B) analyses on partial RNA polymerase largest (...

RECTAL-SPECIFIC MICROBICIDE APPLICATOR: EVALUATION AND COMPARISON WITH A VAGINAL APPLICATOR USED RECTALLY

PubMed Central

Carballo-Diéguez, Alex; Giguere, Rebecca; Dolezal, Curtis; Bauermeister, José; Leu, Cheng-Shiun; Valladares, Juan; Rohan, Lisa C.; Anton, Peter A.; Cranston, Ross D.; Febo, Irma; Mayer, Kenneth; McGowan, Ian

2014-01-01

An applicator designed for rectal delivery of microbicides was tested for acceptability by 95 young men who have sex with men, who self-administered 4mL of placebo gel prior to receptive anal intercourse over 90 days. Subsequently, 24 of the participants self-administered rectally 4mL of tenofovir or placebo gel over 7 days using a vaginal applicator, and compared both applicators on a Likert scale of 1–10, with 10 the highest rating. Participants reported high likelihood to use either applicator in the future (mean scores 9.3 and 8.8 respectively, p= ns). Those who tested both liked the vaginal applicator significantly more than the rectal applicator (7.8 vs. 5.2, p=0.003). Improvements in portability, conspicuousness, aesthetics, tip comfort, product assembly and packaging were suggested for both. This rectal-specific applicator was not superior to a vaginal applicator. While likelihood of future use is reportedly high, factors that decrease acceptability may erode product use over time in clinical trials. Further attention is needed to develop user-friendly, quick-acting rectal microbicide delivery systems. PMID:24858481

Quantifying the Strength of General Factors in Psychopathology: A Comparison of CFA with Maximum Likelihood Estimation, BSEM, and ESEM/EFA Bifactor Approaches.

PubMed

Murray, Aja Louise; Booth, Tom; Eisner, Manuel; Obsuth, Ingrid; Ribeaud, Denis

2018-05-22

Whether or not importance should be placed on an all-encompassing general factor of psychopathology (or p factor) in classifying, researching, diagnosing, and treating psychiatric disorders depends (among other issues) on the extent to which comorbidity is symptom-general rather than staying largely within the confines of narrower transdiagnostic factors such as internalizing and externalizing. In this study, we compared three methods of estimating p factor strength. We compared omega hierarchical and explained common variance calculated from confirmatory factor analysis (CFA) bifactor models with maximum likelihood (ML) estimation, from exploratory structural equation modeling/exploratory factor analysis models with a bifactor rotation, and from Bayesian structural equation modeling (BSEM) bifactor models. Our simulation results suggested that BSEM with small variance priors on secondary loadings might be the preferred option. However, CFA with ML also performed well provided secondary loadings were modeled. We provide two empirical examples of applying the three methodologies using a normative sample of youth (z-proso, n = 1,286) and a university counseling sample (n = 359).

Classification of Different Degrees of Disability Following Intracerebral Hemorrhage: A Decision Tree Analysis from VISTA-ICH Collaboration.

PubMed

Phan, Thanh G; Chen, Jian; Beare, Richard; Ma, Henry; Clissold, Benjamin; Van Ly, John; Srikanth, Velandai

2017-01-01

Prognostication following intracerebral hemorrhage (ICH) has focused on poor outcome at the expense of lumping together mild and moderate disability. We aimed to develop a novel approach at classifying a range of disability following ICH. The Virtual International Stroke Trial Archive collaboration database was searched for patients with ICH and known volume of ICH on baseline CT scans. Disability was partitioned into mild [modified Rankin Scale (mRS) at 90 days of 0-2], moderate (mRS = 3-4), and severe disabilities (mRS = 5-6). We used binary and trichotomy decision tree methodology. The data were randomly divided into training (2/3 of data) and validation (1/3 data) datasets. The area under the receiver operating characteristic curve (AUC) was used to calculate the accuracy of the decision tree model. We identified 957 patients, age 65.9 ± 12.3 years, 63.7% males, and ICH volume 22.6 ± 22.1 ml. The binary tree showed that lower ICH volume (<13.7 ml), age (<66.5 years), serum glucose (<8.95 mmol/l), and systolic blood pressure (<170 mm Hg) discriminate between mild versus moderate-to-severe disabilities with AUC of 0.79 (95% CI 0.73-0.85). Large ICH volume (>27.9 ml), older age (>69.5 years), and low Glasgow Coma Scale (<15) classify severe disability with AUC of 0.80 (95% CI 0.75-0.86). The trichotomy tree showed that ICH volume, age, and serum glucose can separate mild, moderate, and severe disability groups with AUC 0.79 (95% CI 0.71-0.87). Both the binary and trichotomy methods provide equivalent discrimination of disability outcome after ICH. The trichotomy method can classify three categories at once, whereas this action was not possible with the binary method. The trichotomy method may be of use to clinicians and trialists for classifying a range of disability in ICH.

Impact of D-Dimer for Prediction of Incident Occult Cancer in Patients with Unprovoked Venous Thromboembolism

PubMed Central

Han, Donghee; ó Hartaigh, Bríain; Lee, Ji Hyun; Cho, In-Jeong; Shim, Chi Young; Chang, Hyuk-Jae; Hong, Geu-Ru; Ha, Jong-Won; Chung, Namsik

2016-01-01

Background Unprovoked venous thromboembolism (VTE) is related to a higher incidence of occult cancer. D-dimer is clinically used for screening VTE, and has often been shown to be present in patients with malignancy. We explored the predictive value of D-dimer for detecting occult cancer in patients with unprovoked VTE. Methods We retrospectively examined data from 824 patients diagnosed with deep vein thrombosis or pulmonary thromboembolism. Of these, 169 (20.5%) patients diagnosed with unprovoked VTE were selected to participate in this study. D-dimer was categorized into three groups as: <2,000, 2,000–4,000, and >4,000 ng/ml. Cox regression analysis was employed to estimate the odds of occult cancer and metastatic state of cancer according to D-dimer categories. Results During a median 5.3 (interquartile range: 3.4–6.7) years of follow-up, 24 (14%) patients with unprovoked VTE were diagnosed with cancer. Of these patients, 16 (67%) were identified as having been diagnosed with metastatic cancer. Log transformed D-dimer levels were significantly higher in those with occult cancer as compared with patients without diagnosis of occult cancer (3.5±0.5 vs. 3.2±0.5, P-value = 0.009, respectively). D-dimer levels >4,000 ng/ml was independently associated with occult cancer (HR: 4.12, 95% CI: 1.54–11.04, P-value = 0.005) when compared with D-dimer levels <2,000 ng/ml, even after adjusting for age, gender, and type of VTE (e.g., deep vein thrombosis or pulmonary thromboembolism). D-dimer levels >4000 ng/ml were also associated with a higher likelihood of metastatic cancer (HR: 9.55, 95% CI: 2.46–37.17, P-value <0.001). Conclusion Elevated D-dimer concentrations >4000 ng/ml are independently associated with the likelihood of occult cancer among patients with unprovoked VTE. PMID:27073982

Impact of D-Dimer for Prediction of Incident Occult Cancer in Patients with Unprovoked Venous Thromboembolism.

PubMed

Han, Donghee; ó Hartaigh, Bríain; Lee, Ji Hyun; Cho, In-Jeong; Shim, Chi Young; Chang, Hyuk-Jae; Hong, Geu-Ru; Ha, Jong-Won; Chung, Namsik

2016-01-01

Unprovoked venous thromboembolism (VTE) is related to a higher incidence of occult cancer. D-dimer is clinically used for screening VTE, and has often been shown to be present in patients with malignancy. We explored the predictive value of D-dimer for detecting occult cancer in patients with unprovoked VTE. We retrospectively examined data from 824 patients diagnosed with deep vein thrombosis or pulmonary thromboembolism. Of these, 169 (20.5%) patients diagnosed with unprovoked VTE were selected to participate in this study. D-dimer was categorized into three groups as: <2,000, 2,000-4,000, and >4,000 ng/ml. Cox regression analysis was employed to estimate the odds of occult cancer and metastatic state of cancer according to D-dimer categories. During a median 5.3 (interquartile range: 3.4-6.7) years of follow-up, 24 (14%) patients with unprovoked VTE were diagnosed with cancer. Of these patients, 16 (67%) were identified as having been diagnosed with metastatic cancer. Log transformed D-dimer levels were significantly higher in those with occult cancer as compared with patients without diagnosis of occult cancer (3.5±0.5 vs. 3.2±0.5, P-value = 0.009, respectively). D-dimer levels >4,000 ng/ml was independently associated with occult cancer (HR: 4.12, 95% CI: 1.54-11.04, P-value = 0.005) when compared with D-dimer levels <2,000 ng/ml, even after adjusting for age, gender, and type of VTE (e.g., deep vein thrombosis or pulmonary thromboembolism). D-dimer levels >4000 ng/ml were also associated with a higher likelihood of metastatic cancer (HR: 9.55, 95% CI: 2.46-37.17, P-value <0.001). Elevated D-dimer concentrations >4000 ng/ml are independently associated with the likelihood of occult cancer among patients with unprovoked VTE.

Perceptual precision of passive body tilt is consistent with statistically optimal cue integration

PubMed Central

Karmali, Faisal; Nicoucar, Keyvan; Merfeld, Daniel M.

2017-01-01

When making perceptual decisions, humans have been shown to optimally integrate independent noisy multisensory information, matching maximum-likelihood (ML) limits. Such ML estimators provide a theoretic limit to perceptual precision (i.e., minimal thresholds). However, how the brain combines two interacting (i.e., not independent) sensory cues remains an open question. To study the precision achieved when combining interacting sensory signals, we measured perceptual roll tilt and roll rotation thresholds between 0 and 5 Hz in six normal human subjects. Primary results show that roll tilt thresholds between 0.2 and 0.5 Hz were significantly lower than predicted by a ML estimator that includes only vestibular contributions that do not interact. In this paper, we show how other cues (e.g., somatosensation) and an internal representation of sensory and body dynamics might independently contribute to the observed performance enhancement. In short, a Kalman filter was combined with an ML estimator to match human performance, whereas the potential contribution of nonvestibular cues was assessed using published bilateral loss patient data. Our results show that a Kalman filter model including previously proven canal-otolith interactions alone (without nonvestibular cues) can explain the observed performance enhancements as can a model that includes nonvestibular contributions. NEW & NOTEWORTHY We found that human whole body self-motion direction-recognition thresholds measured during dynamic roll tilts were significantly lower than those predicted by a conventional maximum-likelihood weighting of the roll angular velocity and quasistatic roll tilt cues. Here, we show that two models can each match this “apparent” better-than-optimal performance: 1) inclusion of a somatosensory contribution and 2) inclusion of a dynamic sensory interaction between canal and otolith cues via a Kalman filter model. PMID:28179477

Long-term success of stump sprout regeneration in baldcypress

Treesearch

Richard F. Keim; Jim L. Chambers; Melinda S. Hughes; Emile S. Gardiner; William H. Conner; John W. Day; Stephen P. Faulkner; Kenneth W. McLeod; Craig A. Miller; J. Andrew Nyman; Gary P. Shaffer; Luben D. Dimov

2006-01-01

Baldcypress [Taxodium distichum (L.) Rich.] is one of very few conifers that produces stump sprouts capable of becoming full-grown trees. Previous studies have addressed early survival of baldcypress stump sprouts but have not addressed the likelihood of sprouts becoming an important component of mature stands. We surveyed stands throughout south...

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

PubMed

Allende, Christian; Sohn, Erik; Little, Cedric

2015-12-29

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

Estimation of channel parameters and background irradiance for free-space optical link.

PubMed

Khatoon, Afsana; Cowley, William G; Letzepis, Nick; Giggenbach, Dirk

2013-05-10

Free-space optical communication can experience severe fading due to optical scintillation in long-range links. Channel estimation is also corrupted by background and electrical noise. Accurate estimation of channel parameters and scintillation index (SI) depends on perfect removal of background irradiance. In this paper, we propose three different methods, the minimum-value (MV), mean-power (MP), and maximum-likelihood (ML) based methods, to remove the background irradiance from channel samples. The MV and MP methods do not require knowledge of the scintillation distribution. While the ML-based method assumes gamma-gamma scintillation, it can be easily modified to accommodate other distributions. Each estimator's performance is compared using simulation data as well as experimental measurements. The estimators' performance are evaluated from low- to high-SI areas using simulation data as well as experimental trials. The MV and MP methods have much lower complexity than the ML-based method. However, the ML-based method shows better SI and background-irradiance estimation performance.

Mixture Factor Analysis for Approximating a Nonnormally Distributed Continuous Latent Factor with Continuous and Dichotomous Observed Variables

ERIC Educational Resources Information Center

Wall, Melanie M.; Guo, Jia; Amemiya, Yasuo

2012-01-01

Mixture factor analysis is examined as a means of flexibly estimating nonnormally distributed continuous latent factors in the presence of both continuous and dichotomous observed variables. A simulation study compares mixture factor analysis with normal maximum likelihood (ML) latent factor modeling. Different results emerge for continuous versus…

The Order-Restricted Association Model: Two Estimation Algorithms and Issues in Testing

ERIC Educational Resources Information Center

Galindo-Garre, Francisca; Vermunt, Jeroen K.

2004-01-01

This paper presents a row-column (RC) association model in which the estimated row and column scores are forced to be in agreement with a priori specified ordering. Two efficient algorithms for finding the order-restricted maximum likelihood (ML) estimates are proposed and their reliability under different degrees of association is investigated by…

Terrain Classification Using Multi-Wavelength Lidar Data

DTIC Science & Technology

2015-09-01

Figure 9. Pseudo- NDVI of three layers within the vertical structure of the forest. (Top) First return from the LiDAR instrument, including the ground...in NDVI throughout the vertical canopy. ........................................................17 Figure 10. Optech Titan operating wavelengths...and Ranging LMS LiDAR Mapping Suite ML Maximum Likelihood NIR Near Infrared N-D VIS n-Dimensional Visualizer NDVI Normalized Difference

Time-resolved speckle effects on the estimation of laser-pulse arrival times

NASA Technical Reports Server (NTRS)

Tsai, B.-M.; Gardner, C. S.

1985-01-01

A maximum-likelihood (ML) estimator of the pulse arrival in laser ranging and altimetry is derived for the case of a pulse distorted by shot noise and time-resolved speckle. The performance of the estimator is evaluated for pulse reflections from flat diffuse targets and compared with the performance of a suboptimal centroid estimator and a suboptimal Bar-David ML estimator derived under the assumption of no speckle. In the large-signal limit the accuracy of the estimator was found to improve as the width of the receiver observational interval increases. The timing performance of the estimator is expected to be highly sensitive to background noise when the received pulse energy is high and the receiver observational interval is large. Finally, in the speckle-limited regime the ML estimator performs considerably better than the suboptimal estimators.

A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0

PubMed Central

Bazinet, Adam L.; Zwickl, Derrick J.; Cummings, Michael P.

2014-01-01

We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum-likelihood phylogenetic analysis powered by grid computing. The gateway features a garli 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The garli web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic results. Although the garli web service has been used by the research community for over three years, here we formally announce the availability of the service, describe its capabilities, highlight new features and recent improvements, and provide details about how the grid system efficiently delivers high-quality phylogenetic results. [garli, gateway, grid computing, maximum likelihood, molecular evolution portal, phylogenetics, web service.] PMID:24789072

Mapping aerial metal deposition in metropolitan areas from tree bark: a case study in Sheffield, England.

PubMed

Schelle, E; Rawlins, B G; Lark, R M; Webster, R; Staton, I; McLeod, C W

2008-09-01

We investigated the use of metals accumulated on tree bark for mapping their deposition across metropolitan Sheffield by sampling 642 trees of three common species. Mean concentrations of metals were generally an order of magnitude greater than in samples from a remote uncontaminated site. We found trivially small differences among tree species with respect to metal concentrations on bark, and in subsequent statistical analyses did not discriminate between them. We mapped the concentrations of As, Cd and Ni by lognormal universal kriging using parameters estimated by residual maximum likelihood (REML). The concentrations of Ni and Cd were greatest close to a large steel works, their probable source, and declined markedly within 500 m of it and from there more gradually over several kilometres. Arsenic was much more evenly distributed, probably as a result of locally mined coal burned in domestic fires for many years. Tree bark seems to integrate airborne pollution over time, and our findings show that sampling and analysing it are cost-effective means of mapping and identifying sources.

bcgTree: automatized phylogenetic tree building from bacterial core genomes.

PubMed

Ankenbrand, Markus J; Keller, Alexander

2016-10-01

The need for multi-gene analyses in scientific fields such as phylogenetics and DNA barcoding has increased in recent years. In particular, these approaches are increasingly important for differentiating bacterial species, where reliance on the standard 16S rDNA marker can result in poor resolution. Additionally, the assembly of bacterial genomes has become a standard task due to advances in next-generation sequencing technologies. We created a bioinformatic pipeline, bcgTree, which uses assembled bacterial genomes either from databases or own sequencing results from the user to reconstruct their phylogenetic history. The pipeline automatically extracts 107 essential single-copy core genes, found in a majority of bacteria, using hidden Markov models and performs a partitioned maximum-likelihood analysis. Here, we describe the workflow of bcgTree and, as a proof-of-concept, its usefulness in resolving the phylogeny of 293 publically available bacterial strains of the genus Lactobacillus. We also evaluate its performance in both low- and high-level taxonomy test sets. The tool is freely available at github ( https://github.com/iimog/bcgTree ) and our institutional homepage ( http://www.dna-analytics.biozentrum.uni-wuerzburg.de ).

Birth-death models and coalescent point processes: the shape and probability of reconstructed phylogenies.

PubMed

Lambert, Amaury; Stadler, Tanja

2013-12-01

Forward-in-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees (i.e., phylogenies of extant species). Alternatively, reconstructed trees can be modelled by coalescent point processes (CPPs), where trees grow "horizontally" by the sequential addition of vertical edges. Each new edge starts at some random speciation time and ends at the present time; speciation times are drawn from the same distribution independently. CPPs lead to extremely fast computation of tree likelihoods and simulation of reconstructed trees. Their topology always follows the uniform distribution on ranked tree shapes (URT). We characterize which forward-in-time models lead to URT reconstructed trees and among these, which lead to CPP reconstructed trees. We show that for any "asymmetric" diversification model in which speciation rates only depend on time and extinction rates only depend on time and on a non-heritable trait (e.g., age), the reconstructed tree is CPP, even if extant species are incompletely sampled. If rates additionally depend on the number of species, the reconstructed tree is (only) URT (but not CPP). We characterize the common distribution of speciation times in the CPP description, and discuss incomplete species sampling as well as three special model cases in detail: (1) the extinction rate does not depend on a trait; (2) rates do not depend on time; (3) mass extinctions may happen additionally at certain points in the past. Copyright © 2013 Elsevier Inc. All rights reserved.

Maximum likelihood positioning and energy correction for scintillation detectors

NASA Astrophysics Data System (ADS)

Lerche, Christoph W.; Salomon, André; Goldschmidt, Benjamin; Lodomez, Sarah; Weissler, Björn; Solf, Torsten

2016-02-01

An algorithm for determining the crystal pixel and the gamma ray energy with scintillation detectors for PET is presented. The algorithm uses Likelihood Maximisation (ML) and therefore is inherently robust to missing data caused by defect or paralysed photo detector pixels. We tested the algorithm on a highly integrated MRI compatible small animal PET insert. The scintillation detector blocks of the PET gantry were built with the newly developed digital Silicon Photomultiplier (SiPM) technology from Philips Digital Photon Counting and LYSO pixel arrays with a pitch of 1 mm and length of 12 mm. Light sharing was used to readout the scintillation light from the 30× 30 scintillator pixel array with an 8× 8 SiPM array. For the performance evaluation of the proposed algorithm, we measured the scanner’s spatial resolution, energy resolution, singles and prompt count rate performance, and image noise. These values were compared to corresponding values obtained with Center of Gravity (CoG) based positioning methods for different scintillation light trigger thresholds and also for different energy windows. While all positioning algorithms showed similar spatial resolution, a clear advantage for the ML method was observed when comparing the PET scanner’s overall single and prompt detection efficiency, image noise, and energy resolution to the CoG based methods. Further, ML positioning reduces the dependence of image quality on scanner configuration parameters and was the only method that allowed achieving highest energy resolution, count rate performance and spatial resolution at the same time.

Robust multiperson detection and tracking for mobile service and social robots.

PubMed

Li, Liyuan; Yan, Shuicheng; Yu, Xinguo; Tan, Yeow Kee; Li, Haizhou

2012-10-01

This paper proposes an efficient system which integrates multiple vision models for robust multiperson detection and tracking for mobile service and social robots in public environments. The core technique is a novel maximum likelihood (ML)-based algorithm which combines the multimodel detections in mean-shift tracking. First, a likelihood probability which integrates detections and similarity to local appearance is defined. Then, an expectation-maximization (EM)-like mean-shift algorithm is derived under the ML framework. In each iteration, the E-step estimates the associations to the detections, and the M-step locates the new position according to the ML criterion. To be robust to the complex crowded scenarios for multiperson tracking, an improved sequential strategy to perform the mean-shift tracking is proposed. Under this strategy, human objects are tracked sequentially according to their priority order. To balance the efficiency and robustness for real-time performance, at each stage, the first two objects from the list of the priority order are tested, and the one with the higher score is selected. The proposed method has been successfully implemented on real-world service and social robots. The vision system integrates stereo-based and histograms-of-oriented-gradients-based human detections, occlusion reasoning, and sequential mean-shift tracking. Various examples to show the advantages and robustness of the proposed system for multiperson tracking from mobile robots are presented. Quantitative evaluations on the performance of multiperson tracking are also performed. Experimental results indicate that significant improvements have been achieved by using the proposed method.

DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.

PubMed

Kelly, Steven; Maini, Philip K

2013-01-01

The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.

Comparative height crown allometry and mechanical design in 22 tree species of Kuala Belalong rainforest, Brunei, Borneo.

PubMed

Osunkoya, Olusegun O; Omar-Ali, Kharunnisa; Amit, Norratna; Dayan, Juita; Daud, Dayanawati S; Sheng, Tan K

2007-12-01

In rainforests, trunk size, strength, crown position, and geometry of a tree affect light interception and the likelihood of mechanical failure. Allometric relationships of tree diameter, wood density, and crown architecture vs. height are described for a diverse range of rainforest trees in Brunei, northern Borneo. The understory species follow a geometric model in their diameter-height relationship (slope, β = 1.08), while the stress-elasticity models prevail (β = 1.27-1.61) for the midcanopy and canopy/emergent species. These relationships changed with ontogeny, especially for the understory species. Within species, the tree stability safety factor (SSF) and relative crown width decreased exponentially with increasing tree height. These trends failed to emerge in across-species comparisons and were reversed at a common (low) height. Across species, the relative crown depth decreased with maximum potential height and was indistinguishable at a common (low) height. Crown architectural traits influence SSF more than structural property of wood density. These findings emphasize the importance of applying a common reference size in comparative studies and suggest that forest trees (especially the understory group) may adapt to low light by having deeper rather than wider crowns due to an efficient distribution and geometry of their foliage.

Selectivity of Pinus sylvestris extract and essential oil to estrogen-insensitive breast cancer cells Pinus sylvestris against cancer cells.

PubMed

Hoai, Nguyen Thi; Duc, Ho Viet; Thao, Do Thi; Orav, Anne; Raal, Ain

2015-10-01

So far, the anticancer action of pine tree extracts has mainly been shown for the species distributed widely around the Asian countries. Therefore, this study was performed to examine the potential cytotoxicity of Scots pine (Pinus sylvestris L.) native also to the European region and growing widely in Estonia. The cytotoxic activity of methanol extract and essential oil of Scots pine needles was determined by sulforhodamine B assay in different human cancer cell lines. This needle extract was found to suppress the viability of several human cancer cell lines showing some selectivity to estrogen receptor negative breast cancer cells, MDA-MB-231(half maximal inhibitory concentration [IC50] 35 μg/ml) in comparison with estrogen receptor-positive breast cancer cells, MCF-7 (IC50 86 μg/ml). It is the strongest cytotoxic effect at all measured, thus far for the needles and leaves extracts derived from various pine species, and is also the first study comparing the anticancer effects of pine tree extracts on molecularly different human breast cancer cells. The essential oil showed the stronger cytotoxic effect to both negative and positive breast cancer cell lines (both IC50 29 μg/ml) than pine extract (IC50 42 and 80 μg/ml, respectively). The data from this report indicate that Scots pine needles extract and essential oil exhibits some potential as chemopreventive or chemotherapeutic agent for mammary tumors unresponsive to endocrine treatment.

Climate-FVS Version 2: Content, users guide, applications, and behavior

Treesearch

Nicholas L. Crookston

2014-01-01

Climate change in the 21st Century is projected to cause widespread changes in forest ecosystems. Climate-FVS is a modification to the Forest Vegetation Simulator designed to take climate change into account when predicting forest dynamics at decadal to century time scales. Individual tree climate viability scores measure the likelihood that the climate at a given...

Using Linguistic Knowledge in Statistical Machine Translation

DTIC Science & Technology

2010-09-01

on newswire test data . . . . . . . . . . . . . . . . . . . . . 65 3.4 Arabic to English MT results for Arabic morphological segmentation, measured on...web test data. . . . . . . . . . . . . . . . . . . . . . . . 65 3.5 Recombination Results. Percentage of sentences with mis-combined words...scores for syntactic reordering of the Spoken Language Domain. 90 5.1 Normalized likelihood of the test set alignments without decision trees, and then

Multiple Forensic Interviews during Investigations of Child Sexual Abuse: A Cost-Effectiveness Analysis

ERIC Educational Resources Information Center

Block, Stephanie D.; Foster, E. Michael; Pierce, Matthew W.; Berkoff, Molly C.; Runyan, Desmond K.

2013-01-01

In suspected child sexual abuse some professionals recommend multiple child interviews to increase the likelihood of disclosure or more details to improve decision-making and increase convictions. We modeled the yield of a policy of routinely conducting multiple child interviews and increased convictions. Our decision tree reflected the path of a…

Conversion from Tree to Graph Representation of Requirements

NASA Technical Reports Server (NTRS)

Mayank, Vimal; Everett, David Frank; Shmunis, Natalya; Austin, Mark

2009-01-01

A procedure and software to implement the procedure have been devised to enable conversion from a tree representation to a graph representation of the requirements governing the development and design of an engineering system. The need for this procedure and software and for other requirements-management tools arises as follows: In systems-engineering circles, it is well known that requirements- management capability improves the likelihood of success in the team-based development of complex systems involving multiple technological disciplines. It is especially desirable to be able to visualize (in order to identify and manage) requirements early in the system- design process, when errors can be corrected most easily and inexpensively.

Evidence of host-associated divergence from coral-eating snails (genus Coralliophila) in the Coral Triangle

NASA Astrophysics Data System (ADS)

Simmonds, Sara E.; Chou, Vincent; Cheng, Samantha H.; Rachmawati, Rita; Calumpong, Hilconida P.; Ngurah Mahardika, G.; Barber, Paul H.

2018-06-01

We studied how host-associations and geography shape the genetic structure of sister species of marine snails Coralliophila radula (A. Adams, 1853) and C. violacea (Kiener, 1836). These obligate ectoparasites prey upon corals and are sympatric throughout much of their ranges in coral reefs of the tropical and subtropical Indo-Pacific. We tested for population genetic structure of snails in relation to geography and their host corals using mtDNA (COI) sequences in minimum spanning trees and AMOVAs. We also examined the evolutionary relationships of their Porites host coral species using maximum likelihood trees of RAD-seq (restriction site-associated DNA sequencing) loci mapped to a reference transcriptome. A maximum likelihood tree of host corals revealed three distinct clades. Coralliophila radula showed a pronounced genetic break across the Sunda Shelf ( Φ CT = 0.735) but exhibited no genetic structure with respect to host. C. violacea exhibited significant geographic structure ( Φ CT = 0.427), with divergence among Hawaiian populations, the Coral Triangle and the Indian Ocean. Notably, C. violacea showed evidence of ecological divergence; two lineages were associated with different groups of host coral species, one widespread found at all sites, and the other restricted to the Coral Triangle. Sympatric populations of C. violacea found on different suites of coral species were highly divergent ( Φ CT = 0.561, d = 5.13%), suggesting that symbiotic relationships may contribute to lineage diversification in the Coral Triangle.

Phylogenetic relationships of the endangered Shenandoah salamander (Plethodon shenandoah) and other salamanders of the Plethodon cinereus group (Caudata : Plethodontidae)

USGS Publications Warehouse

Sites, J.W.; Morando, M.; Highton, R.; Huber, F.; Jung, R.E.

2004-01-01

The Shenandoah salamander (Plethodon shenandoah), known from isolated talus slopes on three of the highest mountains in Shenandoah National Park, is listed as state-endangered in Virginia and federally endangered under the U.S. Endangered Species Act. A 1999 paper by G. R. Thurow described P. shenandoah-like salamanders from three localities further south in the Blue Ridge Physiographic Province, which, if confirmed, would represent a range extension for P. shenandoah of approximately 90 km from its nearest known locality. Samples collected from two of these three localities were included in a molecular phylogenetic study of the known populations of P. shenandoah, and all other recognized species in the Plethodon cinereus group, using a 792 bp region of the mitochondrial cytochrome-b gene. Phylogenetic estimates were based on Bayesian, maximum likelihood, and maximum parsimony methods and topologies examined for placement of the new P. shenandoah-like samples relative to all others. All topologies recovered all haplotypes of the P. shenandoah-like animals nested within P. cinereus, and a statistical comparison of the best likelihood tree topology with one with an enforced (Thurow + Shenandoah P. shenandoah) clade revealed that the unconstrained tree had a significantly lower -In L score (P < 0.05, using the Shimodaira-Hasegawa test) than the constraint tree. This result and other anecdotal information give us no solid reason to consider the Thurow report valid. The current recovery program for P. shenandoah should remain focused on populations in Shenandoah National Park.

MIXED MODEL AND ESTIMATING EQUATION APPROACHES FOR ZERO INFLATION IN CLUSTERED BINARY RESPONSE DATA WITH APPLICATION TO A DATING VIOLENCE STUDY1

PubMed Central

Fulton, Kara A.; Liu, Danping; Haynie, Denise L.; Albert, Paul S.

2016-01-01

The NEXT Generation Health study investigates the dating violence of adolescents using a survey questionnaire. Each student is asked to affirm or deny multiple instances of violence in his/her dating relationship. There is, however, evidence suggesting that students not in a relationship responded to the survey, resulting in excessive zeros in the responses. This paper proposes likelihood-based and estimating equation approaches to analyze the zero-inflated clustered binary response data. We adopt a mixed model method to account for the cluster effect, and the model parameters are estimated using a maximum-likelihood (ML) approach that requires a Gaussian–Hermite quadrature (GHQ) approximation for implementation. Since an incorrect assumption on the random effects distribution may bias the results, we construct generalized estimating equations (GEE) that do not require the correct specification of within-cluster correlation. In a series of simulation studies, we examine the performance of ML and GEE methods in terms of their bias, efficiency and robustness. We illustrate the importance of properly accounting for this zero inflation by reanalyzing the NEXT data where this issue has previously been ignored. PMID:26937263

Maximum Likelihood Estimation of Spectra Information from Multiple Independent Astrophysics Data Sets

NASA Technical Reports Server (NTRS)

Howell, Leonard W., Jr.; Six, N. Frank (Technical Monitor)

2002-01-01

The Maximum Likelihood (ML) statistical theory required to estimate spectra information from an arbitrary number of astrophysics data sets produced by vastly different science instruments is developed in this paper. This theory and its successful implementation will facilitate the interpretation of spectral information from multiple astrophysics missions and thereby permit the derivation of superior spectral information based on the combination of data sets. The procedure is of significant value to both existing data sets and those to be produced by future astrophysics missions consisting of two or more detectors by allowing instrument developers to optimize each detector's design parameters through simulation studies in order to design and build complementary detectors that will maximize the precision with which the science objectives may be obtained. The benefits of this ML theory and its application is measured in terms of the reduction of the statistical errors (standard deviations) of the spectra information using the multiple data sets in concert as compared to the statistical errors of the spectra information when the data sets are considered separately, as well as any biases resulting from poor statistics in one or more of the individual data sets that might be reduced when the data sets are combined.

Scaled test statistics and robust standard errors for non-normal data in covariance structure analysis: a Monte Carlo study.

PubMed

Chou, C P; Bentler, P M; Satorra, A

1991-11-01

Research studying robustness of maximum likelihood (ML) statistics in covariance structure analysis has concluded that test statistics and standard errors are biased under severe non-normality. An estimation procedure known as asymptotic distribution free (ADF), making no distributional assumption, has been suggested to avoid these biases. Corrections to the normal theory statistics to yield more adequate performance have also been proposed. This study compares the performance of a scaled test statistic and robust standard errors for two models under several non-normal conditions and also compares these with the results from ML and ADF methods. Both ML and ADF test statistics performed rather well in one model and considerably worse in the other. In general, the scaled test statistic seemed to behave better than the ML test statistic and the ADF statistic performed the worst. The robust and ADF standard errors yielded more appropriate estimates of sampling variability than the ML standard errors, which were usually downward biased, in both models under most of the non-normal conditions. ML test statistics and standard errors were found to be quite robust to the violation of the normality assumption when data had either symmetric and platykurtic distributions, or non-symmetric and zero kurtotic distributions.

Validation of DNA-based identification software by computation of pedigree likelihood ratios.

PubMed

Slooten, K

2011-08-01

Disaster victim identification (DVI) can be aided by DNA-evidence, by comparing the DNA-profiles of unidentified individuals with those of surviving relatives. The DNA-evidence is used optimally when such a comparison is done by calculating the appropriate likelihood ratios. Though conceptually simple, the calculations can be quite involved, especially with large pedigrees, precise mutation models etc. In this article we describe a series of test cases designed to check if software designed to calculate such likelihood ratios computes them correctly. The cases include both simple and more complicated pedigrees, among which inbred ones. We show how to calculate the likelihood ratio numerically and algebraically, including a general mutation model and possibility of allelic dropout. In Appendix A we show how to derive such algebraic expressions mathematically. We have set up these cases to validate new software, called Bonaparte, which performs pedigree likelihood ratio calculations in a DVI context. Bonaparte has been developed by SNN Nijmegen (The Netherlands) for the Netherlands Forensic Institute (NFI). It is available free of charge for non-commercial purposes (see www.dnadvi.nl for details). Commercial licenses can also be obtained. The software uses Bayesian networks and the junction tree algorithm to perform its calculations. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Leak Detection and Location of Water Pipes Using Vibration Sensors and Modified ML Prefilter.

PubMed

Choi, Jihoon; Shin, Joonho; Song, Choonggeun; Han, Suyong; Park, Doo Il

2017-09-13

This paper proposes a new leak detection and location method based on vibration sensors and generalised cross-correlation techniques. Considering the estimation errors of the power spectral densities (PSDs) and the cross-spectral density (CSD), the proposed method employs a modified maximum-likelihood (ML) prefilter with a regularisation factor. We derive a theoretical variance of the time difference estimation error through summation in the discrete-frequency domain, and find the optimal regularisation factor that minimises the theoretical variance in practical water pipe channels. The proposed method is compared with conventional correlation-based techniques via numerical simulations using a water pipe channel model, and it is shown through field measurement that the proposed modified ML prefilter outperforms conventional prefilters for the generalised cross-correlation. In addition, we provide a formula to calculate the leak location using the time difference estimate when different types of pipes are connected.

Leak Detection and Location of Water Pipes Using Vibration Sensors and Modified ML Prefilter

PubMed Central

Shin, Joonho; Song, Choonggeun; Han, Suyong; Park, Doo Il

2017-01-01

This paper proposes a new leak detection and location method based on vibration sensors and generalised cross-correlation techniques. Considering the estimation errors of the power spectral densities (PSDs) and the cross-spectral density (CSD), the proposed method employs a modified maximum-likelihood (ML) prefilter with a regularisation factor. We derive a theoretical variance of the time difference estimation error through summation in the discrete-frequency domain, and find the optimal regularisation factor that minimises the theoretical variance in practical water pipe channels. The proposed method is compared with conventional correlation-based techniques via numerical simulations using a water pipe channel model, and it is shown through field measurement that the proposed modified ML prefilter outperforms conventional prefilters for the generalised cross-correlation. In addition, we provide a formula to calculate the leak location using the time difference estimate when different types of pipes are connected. PMID:28902154

Plane-dependent ML scatter scaling: 3D extension of the 2D simulated single scatter (SSS) estimate.

PubMed

Rezaei, Ahmadreza; Salvo, Koen; Vahle, Thomas; Panin, Vladimir; Casey, Michael; Boada, Fernando; Defrise, Michel; Nuyts, Johan

2017-07-24

Scatter correction is typically done using a simulation of the single scatter, which is then scaled to account for multiple scatters and other possible model mismatches. This scaling factor is determined by fitting the simulated scatter sinogram to the measured sinogram, using only counts measured along LORs that do not intersect the patient body, i.e. 'scatter-tails'. Extending previous work, we propose to scale the scatter with a plane dependent factor, which is determined as an additional unknown in the maximum likelihood (ML) reconstructions, using counts in the entire sinogram rather than only the 'scatter-tails'. The ML-scaled scatter estimates are validated using a Monte-Carlo simulation of a NEMA-like phantom, a phantom scan with typical contrast ratios of a 68 Ga-PSMA scan, and 23 whole-body 18 F-FDG patient scans. On average, we observe a 12.2% change in the total amount of tracer activity of the MLEM reconstructions of our whole-body patient database when the proposed ML scatter scales are used. Furthermore, reconstructions using the ML-scaled scatter estimates are found to eliminate the typical 'halo' artifacts that are often observed in the vicinity of high focal uptake regions.

Total Phenol Content and In Vitro Antioxidant Potential of Helicanthus elastica (Desr.) Danser-A Less-explored Indian Mango Mistletoe

PubMed Central

Sunil Kumar, Koppala Narayana; Saraswathy, Ariyamuthu; Amerjothy, Swaminathan; Susan, Thomas; Ravishankar, Basaviah

2014-01-01

Natural products are an important source of antioxidant molecules like tannins, phenolic compounds, flavonoids, etc., Helicanthus elastica (Desr.) Danser (Loranthaceae) is one such plant belonging to the category of mistletoe, and grows commonly on the mango trees in India. In the present study, an attempt has been made to assess the antioxidant properties of the plant. Ethanol extract of H. elastica growing on mango tree was studied using different in vitro models. Shade-dried whole plant material was extracted with ethanol by cold percolation. Fifty milligrams of the alcohol extract of H. elastica was weighed and dissolved in 10 ml of methanol. The resultant 5 mg/ml solution was suitably diluted to obtain different concentrations. Total phenol content, reducing power assay, and scavenging of free radicals like nitric oxide, hydroxyl, hydrogen peroxide, and 1,1-diphenyl-2-picrylhydrazyl were studied by standardized in vitro chemical methods using ascorbic acid as the standard. The total phenol content of the plant was found to be 1.89% w/w. The extract showed good reducing power as well as scavenging of free radicals (nitric oxide, hydroxyl, superoxide anion, and hydrogen peroxide) at concentrations ranging from 5 to 100 μg/ml. The study revealed the antioxidant potential of H. elastica. PMID:25379473

The potency of plant extracts as antimicrobials for the skin or hide preservation

NASA Astrophysics Data System (ADS)

Suparno, Ono; Afifah, Amalia; Panandita, Tania; Marimin, Purnawati, Rini

2017-03-01

Preservation of skin or hide uses antimicrobial that will be disposed in wastewater in the skin or hide processing resulting in the environmental pollution. Extracts of some types of plants contain some antimicrobial substances which are potential to be used as biocides for the preservation of skin or hide and are more environmentally friendly. The objectives of this study were to determine the phytochemical contents of moringa, cucumber tree or wuluh starfruit, cherry, and white leadtree or lamtoro leaves and to analyse the antibacterial activities of the plant extracts against microorganisms that cause spoilage of skin or hide. Phytochemical constituents of the dried plant leaves were extracted by 70% ethanol. The resulting extracts were analysed their phytochemical contents and antimicrobial activities against gram negative and gram positive bacteria (inhibition zone test) by well diffusion method, the minimum inhibitory concentration (MIC), and the minimum bactericidal concentration (MBC). Phytochemical test showed that the four leaf extracts contained alkaloids, saponins, tannins, flavonoids, steroids, and glycosides. The inhibition zones of the extracts against Escherichia coli were 5 mm for moringa leaf, 6 mm for cucumber tree leaf, 12 mm for cherry leaf, and 17 mm for white leadtree leaf. Inhibition zone of the extracts against Staphylococcus aureus were 2.5 mm for moringa leaf, 7 mm for cucumber tree leaf, 7.3 mm for cherry leaf, and 13 mm for white leadtree leaf. Inhibition zones of the extracts against Bacillus subtilis were 8 mm for moringa leaf, 9 mm for cucumber tree starfruit leaf, 14 mm for cherry leaf, and 15 mm for white leadtree leaf. The best MIC and MBC tests were demonstrated by white leadtree leaf extract against E. coli found at concentration of 1500 µg/ml, against S. aureus at concentration of 3000 µg/ml, and against B. subtilis at concentration of 3000 µg/ml. The ethanol extract of white leadtree leaf had the best antibacterial activity and antimicrobial potency compared to the extracts of moringa, cucumber tree starfruit, and cherry leaves. Therefore, the ethanol extract of white leadtree leaf had a potency as a preservative of animal skin or hide and might be able to substitute the biocides used in the skin or hide preservation.

Cloning and sequence analysis of chitin synthase gene fragments of Demodex mites.

PubMed

Zhao, Ya-e; Wang, Zheng-hang; Xu, Yang; Xu, Ji-ru; Liu, Wen-yan; Wei, Meng; Wang, Chu-ying

2012-10-01

To our knowledge, few reports on Demodex studied at the molecular level are available at present. In this study our group, for the first time, cloned, sequenced and analyzed the chitin synthase (CHS) gene fragments of Demodex folliculorum, Demodex brevis, and Demodex canis (three isolates from each species) from Xi'an China, by designing specific primers based on the only partial sequence of the CHS gene of D. canis from Japan, retrieved from GenBank. Results show that amplification was successful only in three D. canis isolates and one D. brevis isolate out of the nine Demodex isolates. The obtained fragments were sequenced to be 339 bp for D. canis and 338 bp for D. brevis. The CHS gene sequence similarities between the three Xi'an D. canis isolates and one Japanese D. canis isolate ranged from 99.7% to 100.0%, and those between four D. canis isolates and one D. brevis isolate were 99.1%-99.4%. Phylogenetic trees based on maximum parsimony (MP) and maximum likelihood (ML) methods shared the same clusters, according with the traditional classification. Two open reading frames (ORFs) were identified in each CHS gene sequenced, and their corresponding amino acid sequences were located at the catalytic domain. The relatively conserved sequences could be deduced to be a CHS class A gene, which is associated with chitin synthesis in the integument of Demodex mites.

Population genetics of Thamnaconus hypargyreus (Tetraodontiformes: Monacanthidae) in the South China Sea.

PubMed

Li, Yufang; Chen, Guobao; Yu, Jie; Wu, Shuiqing; Xiong, Dan; Li, Xia; Cui, Ke; Li, Yongzhen

2016-01-01

Knowledge of population structure is particularly important for long-term fisheries management and conservation. Lesser-spotted leatherjacket Thamnaconus hypargyreus is an economically important fish species in the South China Sea. Fish specimens (totally 158 individuals) used in this study were collected from five geographical locations in the north of the South China Sea and the southwestern Nansha Islands. The results were as follows: a total of 636 nucleotides of the mitochondrial DNA (mtDNA) control region (CR) of T. hypargyreus were amplified by polymerase chain reaction (PCR) technology. Both 103 mutations of nucleotide acids without inserting or deleting one and 91 haplotypes were found among the examined CR fragment. High haplotype diversity (0.9419 ± 0.0151) and nucleotide diversity (0.0095 ± 0.00506) relatively together with a recent and sudden population expansion which characterizes the genetic population structure of this species. Analysis of molecular variance (AMOVA) and the fixation indices (Fst) of five groups showed that the genetic variance mainly came from individuals within groups, and there was no genetic differentiation between groups. The phylogenetic trees including maximum likelihood (ML) and Bayesian inference (BI) proved no phylogeographic differentiation structure in five groups. The mtDNA marker suggested the five groups should be genetic homogeneity, which implied T. hypargyreus in the north and southwest continental shelf of the South China Sea belongs to one population.

Cloning and sequence analysis of chitin synthase gene fragments of Demodex mites*

PubMed Central

Zhao, Ya-e; Wang, Zheng-hang; Xu, Yang; Xu, Ji-ru; Liu, Wen-yan; Wei, Meng; Wang, Chu-ying

2012-01-01

To our knowledge, few reports on Demodex studied at the molecular level are available at present. In this study our group, for the first time, cloned, sequenced and analyzed the chitin synthase (CHS) gene fragments of Demodex folliculorum, Demodex brevis, and Demodex canis (three isolates from each species) from Xi’an China, by designing specific primers based on the only partial sequence of the CHS gene of D. canis from Japan, retrieved from GenBank. Results show that amplification was successful only in three D. canis isolates and one D. brevis isolate out of the nine Demodex isolates. The obtained fragments were sequenced to be 339 bp for D. canis and 338 bp for D. brevis. The CHS gene sequence similarities between the three Xi’an D. canis isolates and one Japanese D. canis isolate ranged from 99.7% to 100.0%, and those between four D. canis isolates and one D. brevis isolate were 99.1%–99.4%. Phylogenetic trees based on maximum parsimony (MP) and maximum likelihood (ML) methods shared the same clusters, according with the traditional classification. Two open reading frames (ORFs) were identified in each CHS gene sequenced, and their corresponding amino acid sequences were located at the catalytic domain. The relatively conserved sequences could be deduced to be a CHS class A gene, which is associated with chitin synthesis in the integument of Demodex mites. PMID:23024043

DNA barcoding of Clarias gariepinus, Coptodon zillii and Sarotherodon melanotheron from Southwestern Nigeria

PubMed Central

Falade, Mofolusho O.; Opene, Anthony J.; Benson, Otarigho

2016-01-01

DNA barcoding has been adopted as a gold standard rapid, precise and unifying identification system for animal species and provides a database of genetic sequences that can be used as a tool for universal species identification. In this study, we employed mitochondrial genes 16S rRNA (16S) and cytochrome oxidase subunit I (COI) for the identification of some Nigerian freshwater catfish and Tilapia species. Approximately 655 bp were amplified from the 5′ region of the mitochondrial cytochrome C oxidase subunit I (COI) gene whereas 570 bp were amplified for the 16S rRNA gene. Nucleotide divergences among sequences were estimated based on Kimura 2-parameter distances and the genetic relationships were assessed by constructing phylogenetic trees using the neighbour-joining (NJ) and maximum likelihood (ML) methods. Analyses of consensus barcode sequences for each species, and alignment of individual sequences from within a given species revealed highly consistent barcodes (99% similarity on average), which could be compared with deposited sequences in public databases. The nucleotide distance between species belonging to different genera based on COI ranged from 0.17% between Sarotherodon melanotheron and Coptodon zillii to 0.49% between Clarias gariepinus and C. zillii, indicating that S. melanotheron and C. zillii are closely related. Based on the data obtained, the utility of COI gene was confirmed in accurate identification of three fish species from Southwest Nigeria. PMID:27990256

Could machine learning improve the prediction of pelvic nodal status of prostate cancer patients? Preliminary results of a pilot study.

PubMed

De Bari, B; Vallati, M; Gatta, R; Simeone, C; Girelli, G; Ricardi, U; Meattini, I; Gabriele, P; Bellavita, R; Krengli, M; Cafaro, I; Cagna, E; Bunkheila, F; Borghesi, S; Signor, M; Di Marco, A; Bertoni, F; Stefanacci, M; Pasinetti, N; Buglione, M; Magrini, S M

2015-07-01

We tested and compared performances of Roach formula, Partin tables and of three Machine Learning (ML) based algorithms based on decision trees in identifying N+ prostate cancer (PC). 1,555 cN0 and 50 cN+ PC were analyzed. Results were also verified on an independent population of 204 operated cN0 patients, with a known pN status (187 pN0, 17 pN1 patients). ML performed better, also when tested on the surgical population, with accuracy, specificity, and sensitivity ranging between 48-86%, 35-91%, and 17-79%, respectively. ML potentially allows better prediction of the nodal status of PC, potentially allowing a better tailoring of pelvic irradiation.

Water-Tree Modelling and Detection for Underground Cables

NASA Astrophysics Data System (ADS)

Chen, Qi

In recent years, aging infrastructure has become a major concern for the power industry. Since its inception in early 20th century, the electrical system has been the cornerstone of an industrial society. Stable and uninterrupted delivery of electrical power is now a base necessity for the modern world. As the times march-on, however, the electrical infrastructure ages and there is the inevitable need to renew and replace the existing system. Unfortunately, due to time and financial constraints, many electrical systems today are forced to operate beyond their original design and power utilities must find ways to prolong the lifespan of older equipment. Thus, the concept of preventative maintenance arises. Preventative maintenance allows old equipment to operate longer and at better efficiency, but in order to implement preventative maintenance, the operators must know minute details of the electrical system, especially some of the harder to assess issues such water-tree. Water-tree induced insulation degradation is a problem typically associated with older cable systems. It is a very high impedance phenomenon and it is difficult to detect using traditional methods such as Tan-Delta or Partial Discharge. The proposed dissertation studies water-tree development in underground cables, potential methods to detect water-tree location and water-tree severity estimation. The dissertation begins by developing mathematical models of water-tree using finite element analysis. The method focuses on surface-originated vented tree, the most prominent type of water-tree fault in the field. Using the standard operation parameters of North American electrical systems, the water-tree boundary conditions are defined. By applying finite element analysis technique, the complex water-tree structure is broken down to homogeneous components. The result is a generalized representation of water-tree capacitance at different stages of development. The result from the finite element analysis is used to model water-tree in large system. Both empirical measurements and the mathematical model show that the impedance of early-stage water-tree is extremely large. As the result, traditional detection methods such Tan-Delta or Partial Discharge are not effective due to the excessively high accuracy requirement. A high-frequency pulse detection method is developed instead. The water-tree impedance is capacitive in nature and it can be reduced to manageable level by high-frequency inputs. The method is able to determine the location of early-stage water-tree in long-distance cables using economically feasible equipment. A pattern recognition method is developed to estimate the severity of water-tree using its pulse response from the high-frequency test method. The early-warning system for water-tree appearance is a tool developed to assist the practical implementation of the high-frequency pulse detection method. Although the equipment used by the detection method is economically feasible, it is still a specialized test and not designed for constant monitoring of the system. The test also place heavy stress on the cable and it is most effective when the cable is taken offline. As the result, utilities need a method to estimate the likelihood of water-tree presence before subjecting the cable to the specialized test. The early-warning system takes advantage of naturally occurring high-frequency events in the system and uses a deviation-comparison method to estimate the probability of water-tree presence on the cable. If the likelihood is high, then the utility can use the high-frequency pulse detection method to obtain accurate results. Specific pulse response patterns can be used to calculate the capacitance of water-tree. The calculated result, however, is subjected to margins of error due to limitations from the real system. There are both long-term and short-term methods to improve the accuracy. Computation algorithm improvement allows immediate improvement on accuracy of the capacitance estimation. The probability distribution of the calculation solution showed that improvements in waveform time-step measurement allow fundamental improves to the overall result.

Model-based estimation for dynamic cardiac studies using ECT.

PubMed

Chiao, P C; Rogers, W L; Clinthorne, N H; Fessler, J A; Hero, A O

1994-01-01

The authors develop a strategy for joint estimation of physiological parameters and myocardial boundaries using ECT (emission computed tomography). They construct an observation model to relate parameters of interest to the projection data and to account for limited ECT system resolution and measurement noise. The authors then use a maximum likelihood (ML) estimator to jointly estimate all the parameters directly from the projection data without reconstruction of intermediate images. They also simulate myocardial perfusion studies based on a simplified heart model to evaluate the performance of the model-based joint ML estimator and compare this performance to the Cramer-Rao lower bound. Finally, the authors discuss model assumptions and potential uses of the joint estimation strategy.

Association between split selection instability and predictive error in survival trees.

PubMed

Radespiel-Tröger, M; Gefeller, O; Rabenstein, T; Hothorn, T

2006-01-01

To evaluate split selection instability in six survival tree algorithms and its relationship with predictive error by means of a bootstrap study. We study the following algorithms: logrank statistic with multivariate p-value adjustment without pruning (LR), Kaplan-Meier distance of survival curves (KM), martingale residuals (MR), Poisson regression for censored data (PR), within-node impurity (WI), and exponential log-likelihood loss (XL). With the exception of LR, initial trees are pruned by using split-complexity, and final trees are selected by means of cross-validation. We employ a real dataset from a clinical study of patients with gallbladder stones. The predictive error is evaluated using the integrated Brier score for censored data. The relationship between split selection instability and predictive error is evaluated by means of box-percentile plots, covariate and cutpoint selection entropy, and cutpoint selection coefficients of variation, respectively, in the root node. We found a positive association between covariate selection instability and predictive error in the root node. LR yields the lowest predictive error, while KM and MR yield the highest predictive error. The predictive error of survival trees is related to split selection instability. Based on the low predictive error of LR, we recommend the use of this algorithm for the construction of survival trees. Unpruned survival trees with multivariate p-value adjustment can perform equally well compared to pruned trees. The analysis of split selection instability can be used to communicate the results of tree-based analyses to clinicians and to support the application of survival trees.

Modeling fuel treatment impacts on fire suppression cost savings: A review

Treesearch

Matthew P. Thompson; Nathaniel M. Anderson

2015-01-01

High up-front costs and uncertain return on investment make it difficult for land managers to economically justify large-scale fuel treatments, which remove trees and other vegetation to improve conditions for fire control, reduce the likelihood of ignition, or reduce potential damage from wildland fire if it occurs. In the short-term, revenue from harvested forest...

A New Lifetime Distribution with Bathtube and Unimodal Hazard Function

NASA Astrophysics Data System (ADS)

Barriga, Gladys D. C.; Louzada-Neto, Francisco; Cancho, Vicente G.

2008-11-01

In this paper we propose a new lifetime distribution which accommodate bathtub-shaped, unimodal, increasing and decreasing hazard function. Some special particular cases are derived, including the standard Weibull distribution. Maximum likelihood estimation is considered for estimate the tree parameters present in the model. The methodology is illustrated in a real data set on industrial devices on a lite test.

Fault and event tree analyses for process systems risk analysis: uncertainty handling formulations.

PubMed

Ferdous, Refaul; Khan, Faisal; Sadiq, Rehan; Amyotte, Paul; Veitch, Brian

2011-01-01

Quantitative risk analysis (QRA) is a systematic approach for evaluating likelihood, consequences, and risk of adverse events. QRA based on event (ETA) and fault tree analyses (FTA) employs two basic assumptions. The first assumption is related to likelihood values of input events, and the second assumption is regarding interdependence among the events (for ETA) or basic events (for FTA). Traditionally, FTA and ETA both use crisp probabilities; however, to deal with uncertainties, the probability distributions of input event likelihoods are assumed. These probability distributions are often hard to come by and even if available, they are subject to incompleteness (partial ignorance) and imprecision. Furthermore, both FTA and ETA assume that events (or basic events) are independent. In practice, these two assumptions are often unrealistic. This article focuses on handling uncertainty in a QRA framework of a process system. Fuzzy set theory and evidence theory are used to describe the uncertainties in the input event likelihoods. A method based on a dependency coefficient is used to express interdependencies of events (or basic events) in ETA and FTA. To demonstrate the approach, two case studies are discussed. © 2010 Society for Risk Analysis.

Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group.

PubMed

Tice, Alexander K; Shadwick, Lora L; Fiore-Donno, Anna Maria; Geisen, Stefan; Kang, Seungho; Schuler, Gabriel A; Spiegel, Frederick W; Wilkinson, Katherine A; Bonkowski, Michael; Dumack, Kenneth; Lahr, Daniel J G; Voelcker, Eckhard; Clauß, Steffen; Zhang, Junling; Brown, Matthew W

2016-12-28

Acanthamoebidae is a "family" level amoebozoan group composed of the genera Acanthamoeba, Protacanthamoeba, and very recently Luapeleamoeba. This clade of amoebozoans has received considerable attention from the broader scientific community as Acanthamoeba spp. represent both model organisms and human pathogens. While the classical composition of the group (Acanthamoeba + Protacanthamoeba) has been well accepted due to the morphological and ultrastructural similarities of its members, the Acanthamoebidae has never been highly statistically supported in single gene phylogenetic reconstructions of Amoebozoa either by maximum likelihood (ML) or Bayesian analyses. Here we show using a phylogenomic approach that the Acanthamoebidae is a fully supported monophyletic group within Amoebozoa with both ML and Bayesian analyses. We also expand the known range of morphological and life cycle diversity found in the Acanthamoebidae by demonstrating that the amoebozoans "Protostelium" arachisporum, Dracoamoeba jormungandri n. g. n. sp., and Vacuolamoeba acanthoformis n.g. n.sp., belong within the group. We also found that "Protostelium" pyriformis is clearly a species of Acanthamoeba making it the first reported sporocarpic member of the genus, that is, an amoeba that individually forms a walled, dormant propagule elevated by a non-cellular stalk. Our phylogenetic analyses recover a fully supported Acanthamoebidae composed of five genera. Two of these genera (Acanthamoeba and Luapeleameoba) have members that are sporocarpic. Our results provide high statistical support for an Acanthamoebidae that is composed of five distinct genera. This study increases the known morphological diversity of this group and shows that species of Acanthamoeba can include spore-bearing stages. This further illustrates the widespread nature of spore-bearing stages across the tree of Amoebozoa. This article was reviewed by Drs. Eugene Koonin, Purificacion Lopez-Garcia and Sandra Baldauf. Sandra Baldauf was nominated by Purificacion Lopez-Garcia, an Editorial Board member.

Molecular phylogeny of broken-back shrimps (genus Lysmata and allies): a test of the 'Tomlinson-Ghiselin' hypothesis explaining the evolution of hermaphroditism.

PubMed

Baeza, J Antonio

2013-10-01

The 'Tomlinson-Ghiselin' hypothesis (TGh) predicts that outcrossing simultaneous hermaphroditism (SH) is advantageous when population density is low because the probability of finding sexual partners is negligible. In shrimps from the family Lysmatidae, Bauer's historical contingency hypothesis (HCh) suggests that SH evolved in an ancestral tropical species that adopted a symbiotic lifestyle with, e.g., sea anemones and became a specialized fish-cleaner. Restricted mobility of shrimps due to their association with a host, and hence, reduced probability of encountering mating partners, would have favored SH. The HCh is a special case of the TGh. Herein, I examined within a phylogenetic framework whether the TGh/HCh explains the origin of SH in shrimps. A phylogeny of caridean broken-back shrimps in the families Lysmatidae, Barbouriidae, Merguiidae was first developed using nuclear and mitochondrial makers. Complete evidence phylogenetic analyses using maximum likelihood (ML) and Bayesian inference (BI) demonstrated that Lysmatidae+Barbouriidae are monophyletic. In turn, Merguiidae is sister to the Lysmatidae+Barbouriidae. ML and BI ancestral character-state reconstruction in the resulting phylogenetic trees indicated that the ancestral Lysmatidae was either gregarious or lived in small groups and was not symbiotic. Four different evolutionary transitions from a free-living to a symbiotic lifestyle occurred in shrimps. Therefore, the evolution of SH in shrimps cannot be explained by the TGh/HCh; reduced probability of encountering mating partners in an ancestral species due to its association with a sessile host did not favor SH in the Lysmatidae. It is proposed that two conditions acting together in the past; low male mating opportunities and brooding constraints, might have favored SH in the ancestral Lysmatidae+Barbouridae. Additional studies on the life history and phylogenetics of broken-back shrimps are needed to understand the evolution of SH in the ecologically diverse Caridea. Copyright © 2013 Elsevier Inc. All rights reserved.

Establishment of a standard reference material (SRM) herbal DNA barcode library of Vitex negundo L. (lagundi) for quality control measures.

PubMed

Olivar, Jay Edneil C; Alaba, Joanner Paulus Erik P; Atienza, Jose Francisco M; Tan, Jerick Jeffrey S; Umali, Maximo T; Alejandro, Grecebio Jonathan D

2016-05-01

The majority of the population in the Philippines relies on herbal products as their primary source for their healthcare needs. After the recognition of Vitex negundo L. (lagundi) as an important and effective alternative medicine for cough, sore throat, asthma and fever by the Philippine Department of Health (DOH), there was an increase in the production of lagundi-based herbal products in the form of teas, capsules and syrups. The efficiency of these products is greatly reliant on the use of authentic plant material, and to this day no standard protocol has been established to authenticate plant materials. DNA barcoding offers a quick and reliable species authentication tool, but its application to plant material has been less successful due to (1) lack of a standard DNA barcoding loci in plants and (2) poor DNA yield from powderised plant products. This study reports the successful application of DNA barcoding in the authentication of five V. negundo herbal products sold in the Philippines. Also, the first standard reference material (SRM) herbal library for the recognition of authentic V. negundo samples was established using 42 gene accessions of ITS, psbA-trnH and matK barcoding loci. Authentication of the herbal products utilised the SRM following the BLASTn and maximum-likelihood (ML) tree construction criterion. Barcode sequences were retrieved for ITS and psbA-trnH of all products tested and the results of the study revealed that only one out of five herbal products satisfied both BLASTn and ML criterion and was considered to contain authentic V. negundo. The results prompt the urgent need to utilise DNA barcoding in authenticating herbal products available in the Philippine market. Authentication of these products will secure consumer health by preventing the negative effects of adulteration, substitution and contamination.

The performance of monotonic and new non-monotonic gradient ascent reconstruction algorithms for high-resolution neuroreceptor PET imaging.

PubMed

Angelis, G I; Reader, A J; Kotasidis, F A; Lionheart, W R; Matthews, J C

2011-07-07

Iterative expectation maximization (EM) techniques have been extensively used to solve maximum likelihood (ML) problems in positron emission tomography (PET) image reconstruction. Although EM methods offer a robust approach to solving ML problems, they usually suffer from slow convergence rates. The ordered subsets EM (OSEM) algorithm provides significant improvements in the convergence rate, but it can cycle between estimates converging towards the ML solution of each subset. In contrast, gradient-based methods, such as the recently proposed non-monotonic maximum likelihood (NMML) and the more established preconditioned conjugate gradient (PCG), offer a globally convergent, yet equally fast, alternative to OSEM. Reported results showed that NMML provides faster convergence compared to OSEM; however, it has never been compared to other fast gradient-based methods, like PCG. Therefore, in this work we evaluate the performance of two gradient-based methods (NMML and PCG) and investigate their potential as an alternative to the fast and widely used OSEM. All algorithms were evaluated using 2D simulations, as well as a single [(11)C]DASB clinical brain dataset. Results on simulated 2D data show that both PCG and NMML achieve orders of magnitude faster convergence to the ML solution compared to MLEM and exhibit comparable performance to OSEM. Equally fast performance is observed between OSEM and PCG for clinical 3D data, but NMML seems to perform poorly. However, with the addition of a preconditioner term to the gradient direction, the convergence behaviour of NMML can be substantially improved. Although PCG is a fast convergent algorithm, the use of a (bent) line search increases the complexity of the implementation, as well as the computational time involved per iteration. Contrary to previous reports, NMML offers no clear advantage over OSEM or PCG, for noisy PET data. Therefore, we conclude that there is little evidence to replace OSEM as the algorithm of choice for many applications, especially given that in practice convergence is often not desired for algorithms seeking ML estimates.

A greener Greenland? Climatic potential and long-term constraints on future expansions of trees and shrubs

PubMed Central

Normand, Signe; Randin, Christophe; Ohlemüller, Ralf; Bay, Christian; Høye, Toke T.; Kjær, Erik D.; Körner, Christian; Lischke, Heike; Maiorano, Luigi; Paulsen, Jens; Pearman, Peter B.; Psomas, Achilleas; Treier, Urs A.; Zimmermann, Niklaus E.; Svenning, Jens-Christian

2013-01-01

Warming-induced expansion of trees and shrubs into tundra vegetation will strongly impact Arctic ecosystems. Today, a small subset of the boreal woody flora found during certain Plio-Pleistocene warm periods inhabits Greenland. Whether the twenty-first century warming will induce a re-colonization of a rich woody flora depends on the roles of climate and migration limitations in shaping species ranges. Using potential treeline and climatic niche modelling, we project shifts in areas climatically suitable for tree growth and 56 Greenlandic, North American and European tree and shrub species from the Last Glacial Maximum through the present and into the future. In combination with observed tree plantings, our modelling highlights that a majority of the non-native species find climatically suitable conditions in certain parts of Greenland today, even in areas harbouring no native trees. Analyses of analogous climates indicate that these conditions are widespread outside Greenland, thus increasing the likelihood of woody invasions. Nonetheless, we find a substantial migration lag for Greenland's current and future woody flora. In conclusion, the projected climatic scope for future expansions is strongly limited by dispersal, soil development and other disequilibrium dynamics, with plantings and unintentional seed dispersal by humans having potentially large impacts on spread rates. PMID:23836785

A greener Greenland? Climatic potential and long-term constraints on future expansions of trees and shrubs.

PubMed

Normand, Signe; Randin, Christophe; Ohlemüller, Ralf; Bay, Christian; Høye, Toke T; Kjær, Erik D; Körner, Christian; Lischke, Heike; Maiorano, Luigi; Paulsen, Jens; Pearman, Peter B; Psomas, Achilleas; Treier, Urs A; Zimmermann, Niklaus E; Svenning, Jens-Christian

2013-08-19

Warming-induced expansion of trees and shrubs into tundra vegetation will strongly impact Arctic ecosystems. Today, a small subset of the boreal woody flora found during certain Plio-Pleistocene warm periods inhabits Greenland. Whether the twenty-first century warming will induce a re-colonization of a rich woody flora depends on the roles of climate and migration limitations in shaping species ranges. Using potential treeline and climatic niche modelling, we project shifts in areas climatically suitable for tree growth and 56 Greenlandic, North American and European tree and shrub species from the Last Glacial Maximum through the present and into the future. In combination with observed tree plantings, our modelling highlights that a majority of the non-native species find climatically suitable conditions in certain parts of Greenland today, even in areas harbouring no native trees. Analyses of analogous climates indicate that these conditions are widespread outside Greenland, thus increasing the likelihood of woody invasions. Nonetheless, we find a substantial migration lag for Greenland's current and future woody flora. In conclusion, the projected climatic scope for future expansions is strongly limited by dispersal, soil development and other disequilibrium dynamics, with plantings and unintentional seed dispersal by humans having potentially large impacts on spread rates.

The relationships within the Chaitophorinae and Drepanosiphinae (Hemiptera, Aphididae) inferred from molecular-based phylogeny and comprehensive morphological data

PubMed Central

Wieczorek, Karina; Lachowska-Cierlik, Dorota; Kajtoch, Łukasz; Kanturski, Mariusz

2017-01-01

The Chaitophorinae is a bionomically diverse Holarctic subfamily of Aphididae. The current classification includes two tribes: the Chaitophorini associated with deciduous trees and shrubs, and Siphini that feed on monocotyledonous plants. We present the first phylogenetic hypothesis for the subfamily, based on molecular and morphological datasets. Molecular analyses were based on the mitochondrial gene cytochrome oxidase subunit I (COI) and the nuclear gene elongation factor-1α (EF-1α). Phylogenetic inferences were obtained individually on each of genes and joined alignments using Bayesian inference (BI) and Maximum likelihood (ML). In phylogenetic trees reconstructed on the basis of nuclear and mitochondrial genes as well as a morphological dataset, the monophyly of Siphini and the genus Chaitophorus was supported. Periphyllus forms independent lineages from Chaitophorus and Siphini. Within this genus two clades comprising European and Asiatic species, respectively, were indicated. Concerning relationships within the subfamily, EF-1α and joined COI and EF-1α genes analysis strongly supports the hypothesis that Chaitophorini do not form a monophyletic clade. Periphyllus is a sister group to a clade containing Chaitophorus and Siphini. The Asiatic unit of Periphyllus also includes Trichaitophorus koyaensis. The analysis of morphological dataset under equally weighted parsimony also supports the view that Chaitophorini is an artificial taxon, as Lambersaphis pruinosae and Pseudopterocomma hughi, both traditionally included in the Chaitophorini, formed independent lineages. COI analyses support consistent groups within the subfamily, but relationships between groups are poorly resolved. These analyses were extended to include the species of closely related and phylogenetically unstudied subfamily Drepanosiphinae, which produced congruent results. Genera Drepanosiphum and Depanaphis are monophyletic and sister. The position of Yamatocallis tokyoensis differs in the molecular and morphological analyses, i.e. it is either an independent lineage (EF-1α, COI, joined COI and EF-1α genes) or is nested inside this unit (morphology). Our data also support separation of Chaitophorinae from Drepanosiphinae. PMID:28288166

Method and apparatus for detecting a desired behavior in digital image data

DOEpatents

Kegelmeyer, Jr., W. Philip

1997-01-01

A method for detecting stellate lesions in digitized mammographic image data includes the steps of prestoring a plurality of reference images, calculating a plurality of features for each of the pixels of the reference images, and creating a binary decision tree from features of randomly sampled pixels from each of the reference images. Once the binary decision tree has been created, a plurality of features, preferably including an ALOE feature (analysis of local oriented edges), are calculated for each of the pixels of the digitized mammographic data. Each of these plurality of features of each pixel are input into the binary decision tree and a probability is determined, for each of the pixels, corresponding to the likelihood of the presence of a stellate lesion, to create a probability image. Finally, the probability image is spatially filtered to enforce local consensus among neighboring pixels and the spatially filtered image is output.

Method and apparatus for detecting a desired behavior in digital image data

DOEpatents

Kegelmeyer, Jr., W. Philip

1997-01-01

A method for detecting stellate lesions in digitized mammographic image data includes the steps of prestoring a plurality of reference images, calculating a plurality of features for each of the pixels of the reference images, and creating a binary decision tree from features of randomly sampled pixels from each of the reference images. Once the binary decision tree has been created, a plurality of features, preferably including an ALOE feature (analysis of local oriented edges), are calculated for each of the pixels of the digitized mammographic data. Each of these plurality of features of each pixel are input into the binary decision tree and a probability is determined, for each of the pixels, corresponding to the likelihood of the presence of a stellate lesion, to create a probability image. Finally, the probability image is spacially filtered to enforce local consensus among neighboring pixels and the spacially filtered image is output.

Use of multi-frequency, multi-polarization, multi-angle airborne radars for class discrimination in a southern temperature forest

NASA Technical Reports Server (NTRS)

Mehta, N. C.

1984-01-01

The utility of radar scatterometers for discrimination and characterization of natural vegetation was investigated. Backscatter measurements were acquired with airborne multi-frequency, multi-polarization, multi-angle radar scatterometers over a test site in a southern temperate forest. Separability between ground cover classes was studied using a two-class separability measure. Very good separability is achieved between most classes. Longer wavelength is useful in separating trees from non-tree classes, while shorter wavelength and cross polarization are helpful for discrimination among tree classes. Using the maximum likelihood classifier, 50% overall classification accuracy is achieved using a single, short-wavelength scatterometer channel. Addition of multiple incidence angles and another radar band improves classification accuracy by 20% and 50%, respectively, over the single channel accuracy. Incorporation of a third radar band seems redundant for vegetation classification. Vertical transmit polarization is critically important for all classes.

DNA barcoding and phylogeny of Calidris and Tringa (Aves: Scolopacidae).

PubMed

Huang, Zuhao; Tu, Feiyun

2017-07-01

The avian genera Calidris and Tringa are the largest of the widespread family of Scolopacidae. The phylogeny of members of the two genera is still a matter of controversial. Mitochondrial cytochrome c oxidase subunit I (COI) can serve as a fast and accurate marker for the identification and phylogeny of animal species. In this study, we analyzed the COI barcodes of thirty-one species of the two genera. All the species had distinct COI sequences. Two hundred and twenty-one variable sites were identified. Kimura two-parameter distances were calculated between barcodes. Neighbor-joining and maximum likelihood methods were used to construct phylogenetic trees. All the species could be discriminated by their distinct clades in the phylogenetic trees. The phylogenetic trees grouped all the species of Calidris and Tringa into different monophyletic clade, respectively. COI data showed a well-supported phylogeny for Calidris and Tringa species.

Adaptive early detection ML/PDA estimator for LO targets with EO sensors

NASA Astrophysics Data System (ADS)

Chummun, Muhammad R.; Kirubarajan, Thiagalingam; Bar-Shalom, Yaakov

2000-07-01

The batch Maximum Likelihood Estimator, combined with Probabilistic Data (ML-PDA), has been shown to be effective in acquiring low observable (LO) - low SNR - non-maneuvering targets in the presence of heavy clutter. The use of signal strength or amplitude information (AI) in the ML-PDA estimator with AI in a sliding-window fashion, to detect high- speed targets in heavy clutter using electro-optical (EO) sensors. The initial time and the length of the sliding-window are adjusted adaptively according to the information content of the received measurements. A track validation scheme via hypothesis testing is developed to confirm the estimated track, that is, the presence of a target, in each window. The sliding-window ML-PDA approach, together with track validation, enables early detection by rejecting noninformative scans, target reacquisition in case of temporary target disappearance and the handling of targets with speeds evolving over time. The proposed algorithm is shown to detect the target, which is hidden in as many as 600 false alarms per scan, 10 frames earlier than the Multiple Hypothesis Tracking (MHT) algorithm.

One normal void and residual following MUS surgery is all that is necessary in most patients.

PubMed

Ballard, Paul; Shawer, Sami; Anderson, Colette; Khunda, Aethele

2018-04-01

There is considerable variation worldwide on how the assessment of voiding function is performed following midurethral sling (MUS) surgery. There is potentially a financial cost, and reduction in efficiency when patient discharge is delayed. Using our current practice of two normal void and residual (V&R) readings before discharge, the aim of this retrospective study was to evaluate the likelihood of an abnormal second V&R test if the first V&R test was normal in order to determine if a policy of discharge after only one satisfactory V&R test is reasonable. Data from 400 patients who had had MUS surgery with or without other procedures were collected. Our unit protocol included two consecutive voids of greater than 200 ml with residuals less than 150 ml before discharge. The patients were divided into the following groups: MUS only, MUS plus anterior colporrhaphy (AR) plus any other procedures (MUS/AR), and MUS with any non-AR procedures (MUS+). Complete datasets were available for 335 patients. Once inadequate tests (low volume voids <200 ml) had been excluded (28% overall), the likelihood of an abnormal second V&R test if the first test was normal was 7.1% overall, but 3.6% for MUS, 11.5% for MUS/AR and 8.6% for MUS+. The findings in the MUS-only group indicate that it is probably safe to discharge patients after one satisfactory V&R test, as long as safety measures such as 'open access' are available so that patients have unhindered readmission if problems arise.

Selectivity of Pinus sylvestris extract and essential oil to estrogen-insensitive breast cancer cells Pinus sylvestris against cancer cells

PubMed Central

Hoai, Nguyen Thi; Duc, Ho Viet; Thao, Do Thi; Orav, Anne; Raal, Ain

2015-01-01

Background: So far, the anticancer action of pine tree extracts has mainly been shown for the species distributed widely around the Asian countries. Objective: Therefore, this study was performed to examine the potential cytotoxicity of Scots pine (Pinus sylvestris L.) native also to the European region and growing widely in Estonia. Materials and Methods: The cytotoxic activity of methanol extract and essential oil of Scots pine needles was determined by sulforhodamine B assay in different human cancer cell lines. Results: This needle extract was found to suppress the viability of several human cancer cell lines showing some selectivity to estrogen receptor negative breast cancer cells, MDA-MB-231(half maximal inhibitory concentration [IC50] 35 μg/ml) in comparison with estrogen receptor-positive breast cancer cells, MCF-7 (IC50 86 μg/ml). It is the strongest cytotoxic effect at all measured, thus far for the needles and leaves extracts derived from various pine species, and is also the first study comparing the anticancer effects of pine tree extracts on molecularly different human breast cancer cells. The essential oil showed the stronger cytotoxic effect to both negative and positive breast cancer cell lines (both IC50 29 μg/ml) than pine extract (IC50 42 and 80 μg/ml, respectively). Conclusion: The data from this report indicate that Scots pine needles extract and essential oil exhibits some potential as chemopreventive or chemotherapeutic agent for mammary tumors unresponsive to endocrine treatment. PMID:26664017

When Can Categorical Variables Be Treated as Continuous? A Comparison of Robust Continuous and Categorical SEM Estimation Methods under Suboptimal Conditions

ERIC Educational Resources Information Center

Rhemtulla, Mijke; Brosseau-Liard, Patricia E.; Savalei, Victoria

2012-01-01

A simulation study compared the performance of robust normal theory maximum likelihood (ML) and robust categorical least squares (cat-LS) methodology for estimating confirmatory factor analysis models with ordinal variables. Data were generated from 2 models with 2-7 categories, 4 sample sizes, 2 latent distributions, and 5 patterns of category…

Automatic Modulation Classification of Common Communication and Pulse Compression Radar Waveforms using Cyclic Features

DTIC Science & Technology

2013-03-01

intermediate frequency LFM linear frequency modulation MAP maximum a posteriori MATLAB® matrix laboratory ML maximun likelihood OFDM orthogonal frequency...spectrum, frequency hopping, and orthogonal frequency division multiplexing ( OFDM ) modulations. Feature analysis would be a good research thrust to...determine feature relevance and decide if removing any features improves performance. Also, extending the system for simulations using a MIMO receiver or

Pseudo-coherent demodulation for mobile satellite systems

NASA Technical Reports Server (NTRS)

Divsalar, Dariush; Simon, Marvin K.

1993-01-01

This paper proposes three so-called pseudo-coherent demodulation schemes for use in land mobile satellite channels. The schemes are derived based on maximum likelihood (ML) estimation and detection of an N-symbol observation of the received signal. Simulation results for all three demodulators are presented to allow comparison with the performance of differential PSK (DPSK) and ideal coherent demodulation for various system parameter sets of practical interest.

Ensemble Learning Method for Hidden Markov Models

DTIC Science & Technology

2014-12-01

Ensemble HMM landmine detector Mine signatures vary according to the mine type, mine size , and burial depth. Similarly, clutter signatures vary with soil ...approaches for the di erent K groups depending on their size and homogeneity. In particular, we investigate the maximum likelihood (ML), the minimum...propose using and optimizing various training approaches for the different K groups depending on their size and homogeneity. In particular, we

An efficient algorithm to compute marginal posterior genotype probabilities for every member of a pedigree with loops

PubMed Central

2009-01-01

Background Marginal posterior genotype probabilities need to be computed for genetic analyses such as geneticcounseling in humans and selective breeding in animal and plant species. Methods In this paper, we describe a peeling based, deterministic, exact algorithm to compute efficiently genotype probabilities for every member of a pedigree with loops without recourse to junction-tree methods from graph theory. The efficiency in computing the likelihood by peeling comes from storing intermediate results in multidimensional tables called cutsets. Computing marginal genotype probabilities for individual i requires recomputing the likelihood for each of the possible genotypes of individual i. This can be done efficiently by storing intermediate results in two types of cutsets called anterior and posterior cutsets and reusing these intermediate results to compute the likelihood. Examples A small example is used to illustrate the theoretical concepts discussed in this paper, and marginal genotype probabilities are computed at a monogenic disease locus for every member in a real cattle pedigree. PMID:19958551

Maximum likelihood estimation for predicting the probability of obtaining variable shortleaf pine regeneration densities

Treesearch

Thomas B. Lynch; Jean Nkouka; Michael M. Huebschmann; James M. Guldin

2003-01-01

A logistic equation is the basis for a model that predicts the probability of obtaining regeneration at specified densities. The density of regeneration (trees/ha) for which an estimate of probability is desired can be specified by means of independent variables in the model. When estimating parameters, the dependent variable is set to 1 if the regeneration density (...

Integrating regeneration, genetic resistance, and timing of intervention for the long-term sustainability of ecosystems challenged by non-native pests - a novel proactive approach

Treesearch

A. W Schoettle; J. G. Klutsch; R. A. Sniezko

2012-01-01

Global trade increases the likelihood of introduction of non-native, invasive species which can threaten native species and their associated ecosystems. This has led to significant impacts to forested landscapes, including extensive tree mortality, shifts in ecosystem composition, and vulnerabilities to other stresses. With the increased appreciation of the importance...

Approximate, computationally efficient online learning in Bayesian spiking neurons.

PubMed

Kuhlmann, Levin; Hauser-Raspe, Michael; Manton, Jonathan H; Grayden, David B; Tapson, Jonathan; van Schaik, André

2014-03-01

Bayesian spiking neurons (BSNs) provide a probabilistic interpretation of how neurons perform inference and learning. Online learning in BSNs typically involves parameter estimation based on maximum-likelihood expectation-maximization (ML-EM) which is computationally slow and limits the potential of studying networks of BSNs. An online learning algorithm, fast learning (FL), is presented that is more computationally efficient than the benchmark ML-EM for a fixed number of time steps as the number of inputs to a BSN increases (e.g., 16.5 times faster run times for 20 inputs). Although ML-EM appears to converge 2.0 to 3.6 times faster than FL, the computational cost of ML-EM means that ML-EM takes longer to simulate to convergence than FL. FL also provides reasonable convergence performance that is robust to initialization of parameter estimates that are far from the true parameter values. However, parameter estimation depends on the range of true parameter values. Nevertheless, for a physiologically meaningful range of parameter values, FL gives very good average estimation accuracy, despite its approximate nature. The FL algorithm therefore provides an efficient tool, complementary to ML-EM, for exploring BSN networks in more detail in order to better understand their biological relevance. Moreover, the simplicity of the FL algorithm means it can be easily implemented in neuromorphic VLSI such that one can take advantage of the energy-efficient spike coding of BSNs.

Dynamical analysis of contrastive divergence learning: Restricted Boltzmann machines with Gaussian visible units.

PubMed

Karakida, Ryo; Okada, Masato; Amari, Shun-Ichi

2016-07-01

The restricted Boltzmann machine (RBM) is an essential constituent of deep learning, but it is hard to train by using maximum likelihood (ML) learning, which minimizes the Kullback-Leibler (KL) divergence. Instead, contrastive divergence (CD) learning has been developed as an approximation of ML learning and widely used in practice. To clarify the performance of CD learning, in this paper, we analytically derive the fixed points where ML and CDn learning rules converge in two types of RBMs: one with Gaussian visible and Gaussian hidden units and the other with Gaussian visible and Bernoulli hidden units. In addition, we analyze the stability of the fixed points. As a result, we find that the stable points of CDn learning rule coincide with those of ML learning rule in a Gaussian-Gaussian RBM. We also reveal that larger principal components of the input data are extracted at the stable points. Moreover, in a Gaussian-Bernoulli RBM, we find that both ML and CDn learning can extract independent components at one of stable points. Our analysis demonstrates that the same feature components as those extracted by ML learning are extracted simply by performing CD1 learning. Expanding this study should elucidate the specific solutions obtained by CD learning in other types of RBMs or in deep networks. Copyright © 2016 Elsevier Ltd. All rights reserved.

MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics.

PubMed

Helaers, Raphaël; Milinkovitch, Michel C

2010-07-15

The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences. Still, the choice of a phylogeny inference software is often dictated by a combination of parameters not related to the raw performance of the implemented algorithm(s) but rather by practical issues such as ergonomics and/or the availability of specific functionalities. Here, we present MetaPIGA v2.0, a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood), including a Simulated Annealing algorithm, a classical Genetic Algorithm, and the Metapopulation Genetic Algorithm (metaGA) together with complex substitution models, discrete Gamma rate heterogeneity, and the possibility to partition data. MetaPIGA v2.0 also implements the Likelihood Ratio Test, the Akaike Information Criterion, and the Bayesian Information Criterion for automated selection of substitution models that best fit the data. Heuristics and substitution models are highly customizable through manual batch files and command line processing. However, MetaPIGA v2.0 also offers an extensive graphical user interface for parameters setting, generating and running batch files, following run progress, and manipulating result trees. MetaPIGA v2.0 uses standard formats for data sets and trees, is platform independent, runs in 32 and 64-bits systems, and takes advantage of multiprocessor and multicore computers. The metaGA resolves the major problem inherent to classical Genetic Algorithms by maintaining high inter-population variation even under strong intra-population selection. Implementation of the metaGA together with additional stochastic heuristics into a single software will allow rigorous optimization of each heuristic as well as a meaningful comparison of performances among these algorithms. MetaPIGA v2.0 gives access both to high customization for the phylogeneticist, as well as to an ergonomic interface and functionalities assisting the non-specialist for sound inference of large phylogenetic trees using nucleotide sequences. MetaPIGA v2.0 and its extensive user-manual are freely available to academics at http://www.metapiga.org.

MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics

PubMed Central

2010-01-01

Background The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences. Still, the choice of a phylogeny inference software is often dictated by a combination of parameters not related to the raw performance of the implemented algorithm(s) but rather by practical issues such as ergonomics and/or the availability of specific functionalities. Results Here, we present MetaPIGA v2.0, a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood), including a Simulated Annealing algorithm, a classical Genetic Algorithm, and the Metapopulation Genetic Algorithm (metaGA) together with complex substitution models, discrete Gamma rate heterogeneity, and the possibility to partition data. MetaPIGA v2.0 also implements the Likelihood Ratio Test, the Akaike Information Criterion, and the Bayesian Information Criterion for automated selection of substitution models that best fit the data. Heuristics and substitution models are highly customizable through manual batch files and command line processing. However, MetaPIGA v2.0 also offers an extensive graphical user interface for parameters setting, generating and running batch files, following run progress, and manipulating result trees. MetaPIGA v2.0 uses standard formats for data sets and trees, is platform independent, runs in 32 and 64-bits systems, and takes advantage of multiprocessor and multicore computers. Conclusions The metaGA resolves the major problem inherent to classical Genetic Algorithms by maintaining high inter-population variation even under strong intra-population selection. Implementation of the metaGA together with additional stochastic heuristics into a single software will allow rigorous optimization of each heuristic as well as a meaningful comparison of performances among these algorithms. MetaPIGA v2.0 gives access both to high customization for the phylogeneticist, as well as to an ergonomic interface and functionalities assisting the non-specialist for sound inference of large phylogenetic trees using nucleotide sequences. MetaPIGA v2.0 and its extensive user-manual are freely available to academics at http://www.metapiga.org. PMID:20633263

Species history and divergence times of viviparous and oviparous Chinese toad-headed sand lizards (Phrynocephalus) on the Qinghai-Tibetan Plateau.

PubMed

Jin, Y-T; Brown, R P

2013-08-01

The Qinghai-Tibetan Plateau (QTP) is an important biogeographical area and has recently become a focus for biodiversity studies. Phyrnocephalus lizards form a widespread Eurasian group with oviparous and viviparous reproductive modes, but two previous mtDNA studies of species from around the QTP have provided different phylogenetic hypotheses. We analysed three loci (mtDNA, RAG-1, AME) from all recognised Chinese Phrynocephalus species to reconstruct the speciation history of the group and to estimate species divergence times. The effects of mtDNA partitioning strategy on phylogenetic inference were examined. Bayes factor comparisons of marginal likelihoods (mLs) estimated using stepping-stone sampling revealed that partitioning strategy had a major impact on mL. Nevertheless, it had a negligible effect on the inferred tree topology. The impact of hard-bound uniform or equivalent soft-bound gamma speciation time calibration priors as well as the use of a fixed topology (as opposed to integration over all possible species histories) on divergence time estimation were also assessed, and found to have little impact on posterior estimates. All three gene trees and the species tree supported the hypothesis that the Chinese species form oviparous and viviparous sister clades. This was in agreement with an early mtDNA study but differed from a subsequent reanalysis of the mtDNA data. Inclusion of mtDNA from more widely distributed Phrynocephalus (from previous studies) indicates that the oviparous P. interscapularis from Central Asia lies outside the clade of Chinese viviparous and oviparous species, but that other Asian oviparous species lie within the Chinese oviparous clade. The median of the posterior on the divergence time of Chinese oviparous and viviparous species was 9.7 Ma ago (95% interval: 7.2-13.0 Ma ago), which coincides with major uplifting of the QTP and indicates that viviparity evolved when this clade became restricted to regions of high elevation. We also found that cladogenesis within the viviparous clade began around 5 Ma ago whereas those in the oviparous clade began around 8.6 Ma ago. We establish more robust estimates of divergence times and relationships within this important group and so provide improved insights into the origins of Phrynocephalus diversity across the QTP. Copyright © 2013 Elsevier Inc. All rights reserved.

[Cytotoxicity of the secondary metabolites of Marine Mangrove Fungus Paecilomyces sp. tree 1-7 on human hepatoma cell line HepG2].

PubMed

Cai, Xiao-Ling; Gao, Jun-Ping; Li, Qing; Wen, Lu; She, Zhi-Gang; Lin, Yong-Cheng

2008-06-01

To study the cytotoxicity of the secondary metabolites of Marine Mangrove Fungus Paecilomyces sp. Tree 1-7 on human hepatoma cell line HepG2 cultured in vitro. Three groups were divided: compounds group, 5-Fu group and control group. The cytotoxicity was measured by MTT method when HepG2 cells were treated by different concentration of the secondary metabolites of Paecilomyces sp. Tree 1-7. Secalonic acid A, tenellic acid A and alternin inhibited the growth of human hepatoma cell line HepG2, the IC50 separately were 2.0, 62.1 and 7.0 microg/ml. Secalonic acid A and alternin have strong cytotoxicity on HepG2 cultured in vitro.

Model-based estimation for dynamic cardiac studies using ECT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chiao, P.C.; Rogers, W.L.; Clinthorne, N.H.

1994-06-01

In this paper, the authors develop a strategy for joint estimation of physiological parameters and myocardial boundaries using ECT (Emission Computed Tomography). The authors construct an observation model to relate parameters of interest to the projection data and to account for limited ECT system resolution and measurement noise. The authors then use a maximum likelihood (ML) estimator to jointly estimate all the parameters directly from the projection data without reconstruction of intermediate images. The authors also simulate myocardial perfusion studies based on a simplified heart model to evaluate the performance of the model-based joint ML estimator and compare this performancemore » to the Cramer-Rao lower bound. Finally, model assumptions and potential uses of the joint estimation strategy are discussed.« less

Estimating the arrival times of photon-limited laser pulses in the presence of shot and speckle noise

NASA Technical Reports Server (NTRS)

Abshire, James B.; Mcgarry, Jan F.

1987-01-01

Maximum-likelihood (ML) receivers are frequently used to optimize the timing performance of laser-ranging and laser-altimetry systems in the presence of shot and speckle noise. Monte Carlo method was used to examine ML-receiver performance with return signals in the 10-5000-photoelectron (pe) range. The simulations were performed for shot noise only and for shot and speckle noise. The results agree with previous theory for signal strengths greater than about 100 pe's but show that the theory can significantly underestimate timing errors for weaker received signals. Sharp high-bandwidth features in the detected signals are shown to improve timing performance only if their signal levels are greater than 4-5 pe's.

[Clinical examination and the Valsalva maneuver in heart failure].

PubMed

Liniado, Guillermo E; Beck, Martín A; Gimeno, Graciela M; González, Ana L; Cianciulli, Tomás F; Castiello, Gustavo G; Gagliardi, Juan A

2018-01-01

Congestion in heart failure patients with reduced ejection fraction (HFrEF) is relevant and closely linked to the clinical course. Bedside blood pressure measurement during the Valsalva maneuver (Val) added to clinical examination may improve the assessment of congestion when compared to NT-proBNP levels and left atrial pressure (LAP) estimation by Doppler echocardiography, as surrogate markers of congestion in HFrEF. A clinical examination, LAP and blood tests were performed in 69 HFrEF ambulatory patients with left ventricular ejection fraction ≤ 40% and sinus rhythm. Framingham Heart Failure Score (HFS) was used to evaluate clinical congestion; Val was classified as normal or abnormal, NT-proBNP was classified as low (< 1000 pg/ml) or high (≥ 1000 pg/ml) and the ratio between Doppler early mitral inflow and tissue diastolic velocity was used to estimate LAP and was classified as low (E/e'< 15) or high (E/e' ≥ 15). A total of 69 patients with HFrEF were included; 27 had a HFS ≥ 2 and 13 of them had high NT-proBNP. HFS ≥ 2 had a 62% sensitivity, 70% specificity and a positive likelihood ratio of 2.08 (p=0.01) to detect congestion. When Val was added to clinical examination, the presence of a HFS ≥ 2 and abnormal Val showed a 100% sensitivity, 64% specificity and a positive likelihood ratio of 2.8 (p = 0.0004). Compared with LAP, the presence of HFS = 2 and abnormal Val had 86% sensitivity, 54% specificity and a positive likelihood ratio of 1.86 (p = 0.03). In conclusion, an integrated clinical examination with the addition Valsalva maneuver may improve the assessment of congestion in patients with HFrEF.

Plane-dependent ML scatter scaling: 3D extension of the 2D simulated single scatter (SSS) estimate

NASA Astrophysics Data System (ADS)

Rezaei, Ahmadreza; Salvo, Koen; Vahle, Thomas; Panin, Vladimir; Casey, Michael; Boada, Fernando; Defrise, Michel; Nuyts, Johan

2017-08-01

Scatter correction is typically done using a simulation of the single scatter, which is then scaled to account for multiple scatters and other possible model mismatches. This scaling factor is determined by fitting the simulated scatter sinogram to the measured sinogram, using only counts measured along LORs that do not intersect the patient body, i.e. ‘scatter-tails’. Extending previous work, we propose to scale the scatter with a plane dependent factor, which is determined as an additional unknown in the maximum likelihood (ML) reconstructions, using counts in the entire sinogram rather than only the ‘scatter-tails’. The ML-scaled scatter estimates are validated using a Monte-Carlo simulation of a NEMA-like phantom, a phantom scan with typical contrast ratios of a 68Ga-PSMA scan, and 23 whole-body 18F-FDG patient scans. On average, we observe a 12.2% change in the total amount of tracer activity of the MLEM reconstructions of our whole-body patient database when the proposed ML scatter scales are used. Furthermore, reconstructions using the ML-scaled scatter estimates are found to eliminate the typical ‘halo’ artifacts that are often observed in the vicinity of high focal uptake regions.

Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times.

PubMed

dos Reis, Mario; Yang, Ziheng

2011-07-01

The molecular clock provides a powerful way to estimate species divergence times. If information on some species divergence times is available from the fossil or geological record, it can be used to calibrate a phylogeny and estimate divergence times for all nodes in the tree. The Bayesian method provides a natural framework to incorporate different sources of information concerning divergence times, such as information in the fossil and molecular data. Current models of sequence evolution are intractable in a Bayesian setting, and Markov chain Monte Carlo (MCMC) is used to generate the posterior distribution of divergence times and evolutionary rates. This method is computationally expensive, as it involves the repeated calculation of the likelihood function. Here, we explore the use of Taylor expansion to approximate the likelihood during MCMC iteration. The approximation is much faster than conventional likelihood calculation. However, the approximation is expected to be poor when the proposed parameters are far from the likelihood peak. We explore the use of parameter transforms (square root, logarithm, and arcsine) to improve the approximation to the likelihood curve. We found that the new methods, particularly the arcsine-based transform, provided very good approximations under relaxed clock models and also under the global clock model when the global clock is not seriously violated. The approximation is poorer for analysis under the global clock when the global clock is seriously wrong and should thus not be used. The results suggest that the approximate method may be useful for Bayesian dating analysis using large data sets.

Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased.

PubMed

Xi, Zhenxiang; Liu, Liang; Davis, Charles C

2015-11-01

The development and application of coalescent methods are undergoing rapid changes. One little explored area that bears on the application of gene-tree-based coalescent methods to species tree estimation is gene informativeness. Here, we investigate the accuracy of these coalescent methods when genes have minimal phylogenetic information, including the implementation of the multilocus bootstrap approach. Using simulated DNA sequences, we demonstrate that genes with minimal phylogenetic information can produce unreliable gene trees (i.e., high error in gene tree estimation), which may in turn reduce the accuracy of species tree estimation using gene-tree-based coalescent methods. We demonstrate that this problem can be alleviated by sampling more genes, as is commonly done in large-scale phylogenomic analyses. This applies even when these genes are minimally informative. If gene tree estimation is biased, however, gene-tree-based coalescent analyses will produce inconsistent results, which cannot be remedied by increasing the number of genes. In this case, it is not the gene-tree-based coalescent methods that are flawed, but rather the input data (i.e., estimated gene trees). Along these lines, the commonly used program PhyML has a tendency to infer one particular bifurcating topology even though it is best represented as a polytomy. We additionally corroborate these findings by analyzing the 183-locus mammal data set assembled by McCormack et al. (2012) using ultra-conserved elements (UCEs) and flanking DNA. Lastly, we demonstrate that when employing the multilocus bootstrap approach on this 183-locus data set, there is no strong conflict between species trees estimated from concatenation and gene-tree-based coalescent analyses, as has been previously suggested by Gatesy and Springer (2014). Copyright © 2015 Elsevier Inc. All rights reserved.

Novel information theory-based measures for quantifying incongruence among phylogenetic trees.

PubMed

Salichos, Leonidas; Stamatakis, Alexandros; Rokas, Antonis

2014-05-01

Phylogenies inferred from different data matrices often conflict with each other necessitating the development of measures that quantify this incongruence. Here, we introduce novel measures that use information theory to quantify the degree of conflict or incongruence among all nontrivial bipartitions present in a set of trees. The first measure, internode certainty (IC), calculates the degree of certainty for a given internode by considering the frequency of the bipartition defined by the internode (internal branch) in a given set of trees jointly with that of the most prevalent conflicting bipartition in the same tree set. The second measure, IC All (ICA), calculates the degree of certainty for a given internode by considering the frequency of the bipartition defined by the internode in a given set of trees in conjunction with that of all conflicting bipartitions in the same underlying tree set. Finally, the tree certainty (TC) and TC All (TCA) measures are the sum of IC and ICA values across all internodes of a phylogeny, respectively. IC, ICA, TC, and TCA can be calculated from different types of data that contain nontrivial bipartitions, including from bootstrap replicate trees to gene trees or individual characters. Given a set of phylogenetic trees, the IC and ICA values of a given internode reflect its specific degree of incongruence, and the TC and TCA values describe the global degree of incongruence between trees in the set. All four measures are implemented and freely available in version 8.0.0 and subsequent versions of the widely used program RAxML.

Joint amalgamation of most parsimonious reconciled gene trees

PubMed Central

Scornavacca, Celine; Jacox, Edwin; Szöllősi, Gergely J.

2015-01-01

Motivation: Traditionally, gene phylogenies have been reconstructed solely on the basis of molecular sequences; this, however, often does not provide enough information to distinguish between statistically equivalent relationships. To address this problem, several recent methods have incorporated information on the species phylogeny in gene tree reconstruction, leading to dramatic improvements in accuracy. Although probabilistic methods are able to estimate all model parameters but are computationally expensive, parsimony methods—generally computationally more efficient—require a prior estimate of parameters and of the statistical support. Results: Here, we present the Tree Estimation using Reconciliation (TERA) algorithm, a parsimony based, species tree aware method for gene tree reconstruction based on a scoring scheme combining duplication, transfer and loss costs with an estimate of the sequence likelihood. TERA explores all reconciled gene trees that can be amalgamated from a sample of gene trees. Using a large scale simulated dataset, we demonstrate that TERA achieves the same accuracy as the corresponding probabilistic method while being faster, and outperforms other parsimony-based methods in both accuracy and speed. Running TERA on a set of 1099 homologous gene families from complete cyanobacterial genomes, we find that incorporating knowledge of the species tree results in a two thirds reduction in the number of apparent transfer events. Availability and implementation: The algorithm is implemented in our program TERA, which is freely available from http://mbb.univ-montp2.fr/MBB/download_sources/16__TERA. Contact: celine.scornavacca@univ-montp2.fr, ssolo@angel.elte.hu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25380957

Evaluation of selective control information detection scheme in orthogonal frequency division multiplexing-based radio-over-fiber and visible light communication links

NASA Astrophysics Data System (ADS)

Dalarmelina, Carlos A.; Adegbite, Saheed A.; Pereira, Esequiel da V.; Nunes, Reginaldo B.; Rocha, Helder R. O.; Segatto, Marcelo E. V.; Silva, Jair A. L.

2017-05-01

Block-level detection is required to decode what may be classified as selective control information (SCI) such as control format indicator in 4G-long-term evolution systems. Using optical orthogonal frequency division multiplexing over radio-over-fiber (RoF) links, we report the experimental evaluation of an SCI detection scheme based on a time-domain correlation (TDC) technique in comparison with the conventional maximum likelihood (ML) approach. When compared with the ML method, it is shown that the TDC method improves detection performance over both 20 and 40 km of standard single mode fiber (SSMF) links. We also report a performance analysis of the TDC scheme in noisy visible light communication channel models after propagation through 40 km of SSMF. Experimental and simulation results confirm that the TDC method is attractive for practical orthogonal frequency division multiplexing-based RoF and fiber-wireless systems. Unlike the ML method, another key benefit of the TDC is that it requires no channel estimation.

Joint Symbol Timing and CFO Estimation for OFDM/OQAM Systems in Multipath Channels

NASA Astrophysics Data System (ADS)

Fusco, Tilde; Petrella, Angelo; Tanda, Mario

2009-12-01

The problem of data-aided synchronization for orthogonal frequency division multiplexing (OFDM) systems based on offset quadrature amplitude modulation (OQAM) in multipath channels is considered. In particular, the joint maximum-likelihood (ML) estimator for carrier-frequency offset (CFO), amplitudes, phases, and delays, exploiting a short known preamble, is derived. The ML estimators for phases and amplitudes are in closed form. Moreover, under the assumption that the CFO is sufficiently small, a closed form approximate ML (AML) CFO estimator is obtained. By exploiting the obtained closed form solutions a cost function whose peaks provide an estimate of the delays is derived. In particular, the symbol timing (i.e., the delay of the first multipath component) is obtained by considering the smallest estimated delay. The performance of the proposed joint AML estimator is assessed via computer simulations and compared with that achieved by the joint AML estimator designed for AWGN channel and that achieved by a previously derived joint estimator for OFDM systems.

ML Frame Synchronization for OFDM Systems Using a Known Pilot and Cyclic Prefixes

NASA Astrophysics Data System (ADS)

Huh, Heon

Orthogonal frequency-division multiplexing (OFDM) is a popular air interface technology that is adopted as a standard modulation scheme for 4G communication systems owing to its excellent spectral efficiency. For OFDM systems, synchronization problems have received much attention along with peak-to-average power ratio (PAPR) reduction. In addition to frequency offset estimation, frame synchronization is a challenging problem that must be solved to achieve optimal system performance. In this paper, we present a maximum likelihood (ML) frame synchronizer for OFDM systems. The synchronizer exploits a synchronization word and cyclic prefixes together to improve the synchronization performance. Numerical results show that the performance of the proposed frame synchronizer is better than that of conventional schemes. The proposed synchronizer can be used as a reference for evaluating the performance of other suboptimal frame synchronizers. We also modify the proposed frame synchronizer to reduce the implementation complexity and propose a near-ML synchronizer for time-varying fading channels.

The effects of wood dusts on the redox status and cell death in mouse macrophages (RAW 264.7) and human leukocytes in vitro.

PubMed

Naarala, J; Kasanen, J-P; Pasanen, P; Pasanen, A-L; Liimatainen, A; Pennanen, S; Liesivuori, J

2003-07-11

Wood dusts are classified as carcinogenic to humans and also produce other toxic, allergic, and acute effects in woodworkers. However, little is known about causative agents in wood dusts and their mechanisms of action. The effects of different tree species and particle size for biological activity were studied. The differences in the production of reactive oxygen species (ROS) and cell death (necrotic and apoptotic) between mouse macrophage (RAW 264.7) cells and human polymorphonuclear leukocytes (PMNL) for pine, birch, and beech dust exposures were investigated in vitro. The pine and birch dust exposure (1-100 microg/ml) produced concentration-dependent ROS production in both the cells, which was one order of magnitude higher with pine dust. The ROS production was faster in human PNML than murine RAW cells. The higher concentrations (500 and/or 1000 microg/ml) decreased ROS formation. With pine and birch dust exposure, this was probably due to the necrotic cell death. The pine dust concentrations of 500 and 1000 microg/ml were cytotoxic to human PMNL. The beech dust exposure activated the ROS production and decreased the cell viability only at the highest concentrations, being least potent of the three dusts. A sign of the apoptotic cell death in the murine RAW cells was observed at the pine dust concentration of 100 microg/ml. The exposure to the birch and beech dusts with a smaller particle size (<5 microm) produced greater ROS production than exposure to the corresponding dust with a wide range of particle sizes. However, changing the particle size did not affect the cell viability. The results indicate that the type of wood dust (tree species and possibly particle size) has a significant impact on the function and viability of phagocytic cells.

GASP: Gapped Ancestral Sequence Prediction for proteins

PubMed Central

Edwards, Richard J; Shields, Denis C

2004-01-01

Background The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a simple procedure and relies on accurate alignments and phylogenies. Several algorithms exist based on Maximum Parsimony or Maximum Likelihood methods but many current implementations are unable to process residues with gaps, which may represent insertion/deletion (indel) events or sequence fragments. Results Here we present a new algorithm, GASP (Gapped Ancestral Sequence Prediction), for predicting ancestral sequences from phylogenetic trees and the corresponding multiple sequence alignments. Alignments may be of any size and contain gaps. GASP first assigns the positions of gaps in the phylogeny before using a likelihood-based approach centred on amino acid substitution matrices to assign ancestral amino acids. Important outgroup information is used by first working down from the tips of the tree to the root, using descendant data only to assign probabilities, and then working back up from the root to the tips using descendant and outgroup data to make predictions. GASP was tested on a number of simulated datasets based on real phylogenies. Prediction accuracy for ungapped data was similar to three alternative algorithms tested, with GASP performing better in some cases and worse in others. Adding simple insertions and deletions to the simulated data did not have a detrimental effect on GASP accuracy. Conclusions GASP (Gapped Ancestral Sequence Prediction) will predict ancestral sequences from multiple protein alignments of any size. Although not as accurate in all cases as some of the more sophisticated maximum likelihood approaches, it can process a wide range of input phylogenies and will predict ancestral sequences for gapped and ungapped residues alike. PMID:15350199

Using artificial intelligence to predict the risk for posterior capsule opacification after phacoemulsification.

PubMed

Mohammadi, Seyed-Farzad; Sabbaghi, Mostafa; Z-Mehrjardi, Hadi; Hashemi, Hassan; Alizadeh, Somayeh; Majdi, Mercede; Taee, Farough

2012-03-01

To apply artificial intelligence models to predict the occurrence of posterior capsule opacification (PCO) after phacoemulsification. Farabi Eye Hospital, Tehran, Iran. Clinical-based cross-sectional study. The posterior capsule status of eyes operated on for age-related cataract and the need for laser capsulotomy were determined. After a literature review, data polishing, and expert consultation, 10 input variables were selected. The QUEST algorithm was used to develop a decision tree. Three back-propagation artificial neural networks were constructed with 4, 20, and 40 neurons in 2 hidden layers and trained with the same transfer functions (log-sigmoid and linear transfer) and training protocol with randomly selected eyes. They were then tested on the remaining eyes and the networks compared for their performance. Performance indices were used to compare resultant models with the results of logistic regression analysis. The models were trained using 282 randomly selected eyes and then tested using 70 eyes. Laser capsulotomy for clinically significant PCO was indicated or had been performed 2 years postoperatively in 40 eyes. A sample decision tree was produced with accuracy of 50% (likelihood ratio 0.8). The best artificial neural network, which showed 87% accuracy and a positive likelihood ratio of 8, was achieved with 40 neurons. The area under the receiver-operating-characteristic curve was 0.71. In comparison, logistic regression reached accuracy of 80%; however, the likelihood ratio was not measurable because the sensitivity was zero. A prototype artificial neural network was developed that predicted posterior capsule status (requiring capsulotomy) with reasonable accuracy. No author has a financial or proprietary interest in any material or method mentioned. Copyright © 2012 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

An Algorithm for Efficient Maximum Likelihood Estimation and Confidence Interval Determination in Nonlinear Estimation Problems

NASA Technical Reports Server (NTRS)

Murphy, Patrick Charles

1985-01-01

An algorithm for maximum likelihood (ML) estimation is developed with an efficient method for approximating the sensitivities. The algorithm was developed for airplane parameter estimation problems but is well suited for most nonlinear, multivariable, dynamic systems. The ML algorithm relies on a new optimization method referred to as a modified Newton-Raphson with estimated sensitivities (MNRES). MNRES determines sensitivities by using slope information from local surface approximations of each output variable in parameter space. The fitted surface allows sensitivity information to be updated at each iteration with a significant reduction in computational effort. MNRES determines the sensitivities with less computational effort than using either a finite-difference method or integrating the analytically determined sensitivity equations. MNRES eliminates the need to derive sensitivity equations for each new model, thus eliminating algorithm reformulation with each new model and providing flexibility to use model equations in any format that is convenient. A random search technique for determining the confidence limits of ML parameter estimates is applied to nonlinear estimation problems for airplanes. The confidence intervals obtained by the search are compared with Cramer-Rao (CR) bounds at the same confidence level. It is observed that the degree of nonlinearity in the estimation problem is an important factor in the relationship between CR bounds and the error bounds determined by the search technique. The CR bounds were found to be close to the bounds determined by the search when the degree of nonlinearity was small. Beale's measure of nonlinearity is developed in this study for airplane identification problems; it is used to empirically correct confidence levels for the parameter confidence limits. The primary utility of the measure, however, was found to be in predicting the degree of agreement between Cramer-Rao bounds and search estimates.

The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods.

PubMed

Nagy, László G; Urban, Alexander; Orstadius, Leif; Papp, Tamás; Larsson, Ellen; Vágvölgyi, Csaba

2010-12-01

Recently developed comparative phylogenetic methods offer a wide spectrum of applications in evolutionary biology, although it is generally accepted that their statistical properties are incompletely known. Here, we examine and compare the statistical power of the ML and Bayesian methods with regard to selection of best-fit models of fruiting-body evolution and hypothesis testing of ancestral states on a real-life data set of a physiological trait (autodigestion) in the family Psathyrellaceae. Our phylogenies are based on the first multigene data set generated for the family. Two different coding regimes (binary and multistate) and two data sets differing in taxon sampling density are examined. The Bayesian method outperformed Maximum Likelihood with regard to statistical power in all analyses. This is particularly evident if the signal in the data is weak, i.e. in cases when the ML approach does not provide support to choose among competing hypotheses. Results based on binary and multistate coding differed only modestly, although it was evident that multistate analyses were less conclusive in all cases. It seems that increased taxon sampling density has favourable effects on inference of ancestral states, while model parameters are influenced to a smaller extent. The model best fitting our data implies that the rate of losses of deliquescence equals zero, although model selection in ML does not provide proper support to reject three of the four candidate models. The results also support the hypothesis that non-deliquescence (lack of autodigestion) has been ancestral in Psathyrellaceae, and that deliquescent fruiting bodies represent the preferred state, having evolved independently several times during evolution. Copyright © 2010 Elsevier Inc. All rights reserved.

Statistical Properties of Maximum Likelihood Estimators of Power Law Spectra Information

NASA Technical Reports Server (NTRS)

Howell, L. W., Jr.

2003-01-01

A simple power law model consisting of a single spectral index, sigma(sub 2), is believed to be an adequate description of the galactic cosmic-ray (GCR) proton flux at energies below 10(exp 13) eV, with a transition at the knee energy, E(sub k), to a steeper spectral index sigma(sub 2) greater than sigma(sub 1) above E(sub k). The maximum likelihood (ML) procedure was developed for estimating the single parameter sigma(sub 1) of a simple power law energy spectrum and generalized to estimate the three spectral parameters of the broken power law energy spectrum from simulated detector responses and real cosmic-ray data. The statistical properties of the ML estimator were investigated and shown to have the three desirable properties: (Pl) consistency (asymptotically unbiased), (P2) efficiency (asymptotically attains the Cramer-Rao minimum variance bound), and (P3) asymptotically normally distributed, under a wide range of potential detector response functions. Attainment of these properties necessarily implies that the ML estimation procedure provides the best unbiased estimator possible. While simulation studies can easily determine if a given estimation procedure provides an unbiased estimate of the spectra information, and whether or not the estimator is approximately normally distributed, attainment of the Cramer-Rao bound (CRB) can only be ascertained by calculating the CRB for an assumed energy spectrum- detector response function combination, which can be quite formidable in practice. However, the effort in calculating the CRB is very worthwhile because it provides the necessary means to compare the efficiency of competing estimation techniques and, furthermore, provides a stopping rule in the search for the best unbiased estimator. Consequently, the CRB for both the simple and broken power law energy spectra are derived herein and the conditions under which they are stained in practice are investigated.

The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

Treesearch

C.L. Schoch; G.-H. Sung; F. Lopez-Giraldez

2009-01-01

We present a six-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the fungi are resolved for...

Spermatogenic and Phylo-molecular Characterizations of Isolated Fasciola Spp. From Cattle, North West Iran.

PubMed

Rouhani, Soheila; Raeghi, Saber; Spotin, Adel

2017-01-01

Fascioliasis is economically important to the livestock industry that caused with Fasciola hepatica and Fasciola gigantica. The objective of this study was to identify these two species F. hepatica and F. gigantica by using nuclear and mitochondrial markers (ITS1, ND1 and CO1) and have been employed to analyze intraspecific phylogenetic relations of Fasciola spp. Approximately 150 Fasciola specimens were collected, then stained with haematoxylin-carmine dye and observed under an optical microscope to examine for the existence of sperm. The ITS1 marker was used to identify different Fasciola and phylogenetic analysis based on ND1 and CO1 sequence data were conducted by maximum likelihood algorithm. Fasciola samples were separated into 2 groups. Almost all specimens had many sperms in the seminal vesicle (spermic fluke) and one fluke did not contain any sperm in the seminal vesicle. The aspermic sample had F. gigantica RFLP pattern with ITS1 gene. Phylogenetic analysis based on NDI and COI sequence data were conducted by maximum likelihood showed a similar topology of the trees obtained particularly for F. hepatica and F. gigantica. This study demonstrated that aspermic Fasciola found in this region of Iran has same genetic structures through the spermic F. gigantica populations in accordance to phylogenetic tree.

Multi-gene phylogeny of jacks and pompanos (Carangidae), including placement of monotypic vadigo Campogramma glaycos.

PubMed

Damerau, M; Freese, M; Hanel, R

2018-01-01

In this study, the phylogenetic trees of jacks and pompanos (Carangidae), an ecologically and morphologically diverse, globally distributed fish family, are inferred from a complete, concatenated data set of two mitochondrial (cytochrome c oxidase I, cytochrome b) loci and one nuclear (myosin heavy chain 6) locus. Maximum likelihood and Bayesian inferences are largely congruent and show a clear separation of Carangidae into the four subfamilies: Scomberoidinae, Trachinotinae, Naucratinae and Caranginae. The inclusion of the carangid sister lineages Coryphaenidae (dolphinfishes) and Rachycentridae (cobia), however, render Carangidae paraphyletic. The phylogenetic trees also show with high statistical support that the monotypic vadigo Campogramma glaycos is the sister to all other species within the Naucratinae. © 2017 The Fisheries Society of the British Isles.

Triamcinolone Acetonide Selectively Inhibits Angiogenesis in Small Blood Vessels and Decreases Vessel Diameter within the Vascular Tree

NASA Technical Reports Server (NTRS)

McKay, Terri L.; Gredeon, Dan J.; Vickerman, Mary B.; Hylton, alan G.; Ribita, Daniela; Olar, Harry H.; Kaiser, Peter K.; Parsons-Wingerter, Patricia

2007-01-01

The steroid triamcinolone acetonide (TA) is a potent anti-angiogenesis drug used to treat retinal vascular diseases that include diabetic retinopathy, vascular occlusions and choroidal neovascularization. To quantify the effects of TA on branching morphology within the angiogenic microvascular tree of the chorioallantoic membrane (CAM) of quail embryos. Increasing concentrations of TA (0-16 ng/ml) were applied topically on embryonic day 7 (E7) to the chorioallantoic membrane (CAM) of quail embryos cultured in Petri dishes, and incubated for an additional 24 or 48 hours until fixation. Binary (black/white) microscopic images of arterial end points were quantified by VESGEN software (for Generational Analysis of Vessel Branching) to obtain major vascular parameters that include vessel diameter (Dv), fractal dimension (Df), tortuosity (Tv) and densities of vessel area, length, number and branch point (Av, Lv, Nv and Brv). For assessment of specific changes in vascular morphology induced by TA, the VESGEN software automatically segmented the vascular tree into branching generations (G1...G10) according to changes in vessel diameter and branching. Vessel density decreased significantly up to 34% as the function of increasing concentration of TA according to Av, Lv, Brv, Nv and Df. TA selectively inhibited the growth of new, small vessels, because Lv decreased from 13.14plus or minus 0.61 cm/cm2 for controls to 8.012 plus or minus 0.82 cm/cm2 at 16 ng TA/ml in smaller branching generations (G7-G10), and for Nv from 473.83 plus or minus 29.85 cm(-)2 to 302.32 plus or minus 33.09 cm-()2. In contrast, vessel diameter (Dv) decreased throughout the vascular tree (G1-G10).

Water absorption and method improvement concerning electrical conductivity testing Acacia mangium (Fabaceae) seeds.

PubMed

de Oliveira, Daniel Luiz; Smiderle, Oscar Jose; Paulino, Pollyana Priscila Schuertz; Souza, Aline das Graças

2016-12-01

Acacia is an important forest species of rapid growth whose seeds have tegument dormancy. In this work it was intended to characterize water absorption pattern after seed dormancy break, and to determine the amount of water, container size and the need of breaking the tegument dormancy, as to perform electrical conductivity test in small and large seeds of Acacia mangium (Fabaceae). The seeds were collected from 10, 8 and 6 years old trees established in poor yielding-capacity soils on savannah areas of Roraima, Brazil; seeds were classified in six lots concerning to seed size and tree age. Germination tests (50 seeds and four replications per lot) were carried out on germitest® paper maintained on gerbox at 25 °C. Imbibition was verified by seed weighing at different times (0, 2, 5, 8, 12, 16, 24, 36, 48, 60, 72, 84, 96 and 120 hours). The electrical conductivity test consisted of three experiments, distinguished by the amount of water used and by the container size in which seeds were immersed. Seeds of A. mangium coming from 10 years old trees presented increased germination percent and germination speed than seeds of six-year old trees. Small seeds presented increased in electrical conductivity and water absorption until 120 hours when compared to large seeds. The immersion of seeds of A. mangium in 40 mL of distilled water into 180 mL plastic containers, after dormancy break, it is indicated for the determination of electrical conductivity test. The ratio of electrolytes by seed mass, after 24 hours of immersion in water, turns electrical conductivity test more accurate concerning A. mangium seeds.

Root susceptibility and inoculum production from roots of eastern oak species to Phytophthora ramorum

USDA-ARS?s Scientific Manuscript database

Little is known about root susceptibility of eastern tree species to Phytophthora ramorum. In this study, we examined root susceptibility and inoculum production from roots. Oak radicles of several eastern oak species were exposed to zoospore suspensions of 1, 10, 100, or 1000 zoospores per ml at ...

ccML, a new mark-up language to improve ISO/EN 13606-based electronic health record extracts practical edition.

PubMed

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Cáceres, Jesús; Somolinos, Roberto; Pascual, Mario; Martínez, Ignacio; Salvador, Carlos H; Monteagudo, José Luis

2013-01-01

The objective of this paper is to introduce a new language called ccML, designed to provide convenient pragmatic information to applications using the ISO/EN13606 reference model (RM), such as electronic health record (EHR) extracts editors. EHR extracts are presently built using the syntactic and semantic information provided in the RM and constrained by archetypes. The ccML extra information enables the automation of the medico-legal context information edition, which is over 70% of the total in an extract, without modifying the RM information. ccML is defined using a W3C XML schema file. Valid ccML files complement the RM with additional pragmatics information. The ccML language grammar is defined using formal language theory as a single-type tree grammar. The new language is tested using an EHR extracts editor application as proof-of-concept system. Seven ccML PVCodes (predefined value codes) are introduced in this grammar to cope with different realistic EHR edition situations. These seven PVCodes have different interpretation strategies, from direct look up in the ccML file itself, to more complex searches in archetypes or system precomputation. The possibility to declare generic types in ccML gives rise to ambiguity during interpretation. The criterion used to overcome ambiguity is that specificity should prevail over generality. The opposite would make the individual specific element declarations useless. A new mark-up language ccML is introduced that opens up the possibility of providing applications using the ISO/EN13606 RM with the necessary pragmatics information to be practical and realistic.

Effects of Tree-crop Farming on Land-cover Transitions in a Mosaic Landscape in the Eastern Region of Ghana.

PubMed

Asubonteng, Kwabena; Pfeffer, Karin; Ros-Tonen, Mirjam; Verbesselt, Jan; Baud, Isa

2018-05-11

Tree crops such as cocoa and oil palm are important to smallholders' livelihoods and national economies of tropical producer countries. Governments seek to expand tree-crop acreages and improve yields. Existing literature has analyzed socioeconomic and environmental effects of tree-crop expansion, but its spatial effects on the landscape are yet to be explored. This study aims to assess the effects of tree-crop farming on the composition and the extent of land-cover transitions in a mixed cocoa/oil palm landscape in Ghana. Land-cover maps of 1986 and 2015 produced through ISODATA, and maximum likelihood classification were validated with field reference, Google Earth data, and key respondent interviews. Post-classification change detection was conducted and the transition matrix analyzed using intensity analysis. Cocoa and oil palm areas have increased in extent by 8.9% and 11.2%, respectively, mainly at the expense of food-crop land and forest. The intensity of forest loss to both tree crops is at a lower intensity than the loss of food-crop land. There were transitions between cocoa and oil palm, but the gains in oil palm outweigh those of cocoa. Cocoa and oil palm have increased in area and dominance. The main cover types converted to tree-crop areas are food-crop land and off-reserve forest. This is beginning to have serious implications for food security and livelihood options that depend on ecosystem services provided by the mosaic landscape. Tree-crop policies should take account of the geographical distribution of tree-commodity production at landscape level and its implications for food production and ecosystems services.

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances.

PubMed

Gil, Manuel

2014-01-01

Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances

PubMed Central

2014-01-01

Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error. PMID:25279263

Generating Scenarios When Data Are Missing

NASA Technical Reports Server (NTRS)

Mackey, Ryan

2007-01-01

The Hypothetical Scenario Generator (HSG) is being developed in conjunction with other components of artificial-intelligence systems for automated diagnosis and prognosis of faults in spacecraft, aircraft, and other complex engineering systems. The HSG accepts, as input, possibly incomplete data on the current state of a system (see figure). The HSG models a potential fault scenario as an ordered disjunctive tree of conjunctive consequences, wherein the ordering is based upon the likelihood that a particular conjunctive path will be taken for the given set of inputs. The computation of likelihood is based partly on a numerical ranking of the degree of completeness of data with respect to satisfaction of the antecedent conditions of prognostic rules. The results from the HSG are then used by a model-based artificial- intelligence subsystem to predict realistic scenarios and states.

Restoration of a single superresolution image from several blurred, noisy, and undersampled measured images.

PubMed

Elad, M; Feuer, A

1997-01-01

The three main tools in the single image restoration theory are the maximum likelihood (ML) estimator, the maximum a posteriori probability (MAP) estimator, and the set theoretic approach using projection onto convex sets (POCS). This paper utilizes the above known tools to propose a unified methodology toward the more complicated problem of superresolution restoration. In the superresolution restoration problem, an improved resolution image is restored from several geometrically warped, blurred, noisy and downsampled measured images. The superresolution restoration problem is modeled and analyzed from the ML, the MAP, and POCS points of view, yielding a generalization of the known superresolution restoration methods. The proposed restoration approach is general but assumes explicit knowledge of the linear space- and time-variant blur, the (additive Gaussian) noise, the different measured resolutions, and the (smooth) motion characteristics. A hybrid method combining the simplicity of the ML and the incorporation of nonellipsoid constraints is presented, giving improved restoration performance, compared with the ML and the POCS approaches. The hybrid method is shown to converge to the unique optimal solution of a new definition of the optimization problem. Superresolution restoration from motionless measurements is also discussed. Simulations demonstrate the power of the proposed methodology.

Modeling abundance effects in distance sampling

USGS Publications Warehouse

Royle, J. Andrew; Dawson, D.K.; Bates, S.

2004-01-01

Distance-sampling methods are commonly used in studies of animal populations to estimate population density. A common objective of such studies is to evaluate the relationship between abundance or density and covariates that describe animal habitat or other environmental influences. However, little attention has been focused on methods of modeling abundance covariate effects in conventional distance-sampling models. In this paper we propose a distance-sampling model that accommodates covariate effects on abundance. The model is based on specification of the distance-sampling likelihood at the level of the sample unit in terms of local abundance (for each sampling unit). This model is augmented with a Poisson regression model for local abundance that is parameterized in terms of available covariates. Maximum-likelihood estimation of detection and density parameters is based on the integrated likelihood, wherein local abundance is removed from the likelihood by integration. We provide an example using avian point-transect data of Ovenbirds (Seiurus aurocapillus) collected using a distance-sampling protocol and two measures of habitat structure (understory cover and basal area of overstory trees). The model yields a sensible description (positive effect of understory cover, negative effect on basal area) of the relationship between habitat and Ovenbird density that can be used to evaluate the effects of habitat management on Ovenbird populations.

Morphological and molecular differentiation of Parastrigea (Trematoda: Strigeidae) from Mexico, with the description of a new species.

PubMed

Hernández-Mena, David Iván; García-Prieto, Luís; García-Varela, Martín

2014-04-01

Parastrigea plataleae n. sp. (Digenea: Strigeidae) is described from the intestine of the roseate spoonbill Platalea ajaja (Threskiornithidae) from four localities on the Pacific coast of Mexico. The new species is mainly distinguished from the other 18 described species of Parastrigea based on the ratio of its hindbody length to forebody length. A principal component analysis (PCA) of 16 morphometric traits for 15 specimens of P. plataleae n. sp., five of Parastrigea cincta and 11 of Parastrigea diovadena previously recorded in Mexico, clearly shows three clusters, which correspond to the three species. DNA sequences of the internal transcribed spacers (ITSs) of ribosomal DNA and the mitochondrial gene cytochrome c oxidase subunit I (cox 1) were used to corroborate this morphological distinction. The genetic divergence estimated among P. plataleae n. sp., P. cincta and P. diovadena ranged from 0.5 to 1.48% for ITSs and from 9.31 to 11.47% for cox 1. Maximum parsimony (MP) and maximum likelihood (ML) analyses were performed on the combined datasets (ITSs+cox 1) and on each dataset alone. All of the phylogenetic analyses indicated that the specimens from the roseate spoonbill represent a clade with strong bootstrap support. The morphological evidence and the genetic divergence in combination with the reciprocal monophyly in all of the phylogenetic trees support the hypothesis that the digeneans found in the intestines of roseate spoonbills represent a new species. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

A molecular phylogeny of rose chafers (Coleoptera: Scarabaeidae: Cetoniinae) reveals a complex and concerted morphological evolution related to their flight mode.

PubMed

Šípek, Petr; Fabrizi, Silvia; Eberle, Jonas; Ahrens, Dirk

2016-08-01

Rose chafers (Cetoniinae) are a large group of flower visitors within the pleurostict Scarabaeidae that are characterized by their distinctive flight mode with nearly closed forewings. Despite their popularity, this is the first study to use molecular data to infer their phylogenetic relationships. We used partial gene sequences for 28S rRNA, cytochrome oxidase I (cox1) and 16S rRNA (rrnL) for 299 species, representing most recognized subfamilies of Scarabaeidae, including 125 species of Cetoniinae. Combined analyses using maximum parsimony, maximum likelihood and Bayesian inferences recovered Cetoniinae as monophyletic in all analyses, with the sister clade composed of Rutelinae and Dynastinae. Rutelinae was always recovered as paraphyletic with respect to Dynastinae. Trichiini sensu lato (s.l.) was recovered as a polyphyletic clade, while Cetoniini s.l. was recovered as paraphyletic. The inferred topologies were also supported by site bootstrapping of the ML trees. With the exception of Cremastochelini, most tribes of Cetoniinae were poly- or paraphyletic, indicating the critical need for a careful revision of rose chafer classification. Analysis of elytral base structure (including 11 scored characters) in the context of phylogeny, revealed a complex, concerted and rapid transformation of the single trait elements linked to a modified flight mode with closed elytra. This appears to be unlinked to the lateral sinuation of the elytra, which originated independently several times at later stages in the evolution of the group. Copyright © 2016 Elsevier Inc. All rights reserved.

Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mueller, Rachel Lockridge; Macey, J. Robert; Jaekel, Martin

2004-08-01

The evolutionary history of the largest salamander family (Plethodontidae) is characterized by extreme morphological homoplasy. Analysis of the mechanisms generating such homoplasy requires an independent, molecular phylogeny. To this end, we sequenced 24 complete mitochondrial genomes (22 plethodontids and two outgroup taxa), added data for three species from GenBank, and performed partitioned and unpartitioned Bayesian, ML, and MP phylogenetic analyses. We explored four dataset partitioning strategies to account for evolutionary process heterogeneity among genes and codon positions, all of which yielded increased model likelihoods and decreased numbers of supported nodes in the topologies (PP > 0.95) relative to the unpartitionedmore » analysis. Our phylogenetic analyses yielded congruent trees that contrast with the traditional morphology-based taxonomy; the monophyly of three out of four major groups is rejected. Reanalysis of current hypotheses in light of these new evolutionary relationships suggests that (1) a larval life history stage re-evolved from a direct-developing ancestor multiple times, (2) there is no phylogenetic support for the ''Out of Appalachia'' hypothesis of plethodontid origins, and (3) novel scenarios must be reconstructed for the convergent evolution of projectile tongues, reduction in toe number, and specialization for defensive tail loss. Some of these novel scenarios imply morphological transformation series that proceed in the opposite direction than was previously thought. In addition, they suggest surprising evolutionary lability in traits previously interpreted to be conservative.« less

The phylogenetic relationships of known mosquito (Diptera: Culicidae) mitogenomes.

PubMed

Chu, Hongliang; Li, Chunxiao; Guo, Xiaoxia; Zhang, Hengduan; Luo, Peng; Wu, Zhonghua; Wang, Gang; Zhao, Tongyan

2018-01-01

The known mosquito mitogenomes, containing a total of 34 species, which belong to five genera, were collected from GenBank, and the practicality and effectiveness of the variation in the complete mitochondrial DNA genome and portions of mitochondrial COI gene were assessed to reconstruct the phylogeny of mosquitoes. Phylogenetic trees were reconstructed on the basis of parsimony, maximum likelihood, and Bayesian (BI) methods. It is concluded that: (1) Both mitogenomes and COI gene support the monophly of following taxa: Subgenus Nyssorhynchus, Subgenus Cellia, Anopheles albitarsis complex, Anopheles gambiae complex, and Anopheles punctulatus group; (2) Genus Aedes is not monophyletic relative to Ochlerotatus vigilax; (3) The mitogenome results indicate a close relationship between Anopheles epiroticus and Anopheles gambiae complex, Anopheles dirus complex and Anopheles punctulatus group, respectively; (4) The Bayesian posterior probability (BPP) within phylogenetic tree reconstructed by mitogenomes is higher than COI tree. The results show that phylogenetic relationships reconstructed using the mitogenomes were more similar to those based on morphological data.

The applicability of ordinary least squares to consistently short distances between taxa in phylogenetic tree construction and the normal distribution test consequences.

PubMed

Roux, C Z

2009-05-01

Short phylogenetic distances between taxa occur, for example, in studies on ribosomal RNA-genes with slow substitution rates. For consistently short distances, it is proved that in the completely singular limit of the covariance matrix ordinary least squares (OLS) estimates are minimum variance or best linear unbiased (BLU) estimates of phylogenetic tree branch lengths. Although OLS estimates are in this situation equal to generalized least squares (GLS) estimates, the GLS chi-square likelihood ratio test will be inapplicable as it is associated with zero degrees of freedom. Consequently, an OLS normal distribution test or an analogous bootstrap approach will provide optimal branch length tests of significance for consistently short phylogenetic distances. As the asymptotic covariances between branch lengths will be equal to zero, it follows that the product rule can be used in tree evaluation to calculate an approximate simultaneous confidence probability that all interior branches are positive.

A review of all Recent species in the genus Novocrania (Craniata, Brachiopoda).

PubMed

Robinson, Jeffrey H

2017-10-10

The Recent species in the craniid genus Novocrania are reviewed, based on the examination of actual specimens wherever possible, especially for species named from one or a few specimens. The fourteen Recent species currently in the literature are reduced to eight; five species names are synonymized. One species name was given to a specimen that is not a craniid. The wide morphological ranges of the remaining Novocrania species are described and figured and the extended geographical ranges illustrated. Diagnoses of the remaining species are provided. The long-standing debate whether Novocrania anomala and N. turbinata are separate species or synonyms is resolved; they are separate species. New molecular analyses and a relative time-tree are provided by Cohen et al. (Appendix 1), the time-tree is calibrated herein and the results of Cohen et al. (2014; Appendix 1) and the time tree are discussed. The likelihood of craniid long-distance migration based on their geographical ranges is discussed.

Temporal and spatial diversification of Pteroglossus araçaris (AVES: Ramphastidae) in the neotropics: constant rate of diversification does not support an increase in radiation during the Pleistocene.

PubMed

Patel, Swati; Weckstein, Jason D; Patané, José S L; Bates, John M; Aleixo, Alexandre

2011-01-01

We use the small-bodied toucan genus Pteroglossus to test hypotheses about diversification in the lowland Neotropics. We sequenced three mitochondrial genes and one nuclear intron from all Pteroglossus species and used these data to reconstruct phylogenetic trees based on maximum parsimony, maximum likelihood, and Bayesian analyses. These phylogenetic trees were used to make inferences regarding both the pattern and timing of diversification for the group. We used the uplift of the Talamanca highlands of Costa Rica and western Panama as a geologic calibration for estimating divergence times on the Pteroglossus tree and compared these results with a standard molecular clock calibration. Then, we used likelihood methods to model the rate of diversification. Based on our analyses, the onset of the Pteroglossus radiation predates the Pleistocene, which has been predicted to have played a pivotal role in diversification in the Amazon rainforest biota. We found a constant rate of diversification in Pteroglossus evolutionary history, and thus no support that events during the Pleistocene caused an increase in diversification. We compare our data to other avian phylogenies to better understand major biogeographic events in the Neotropics. These comparisons support recurring forest connections between the Amazonian and Atlantic forests, and the splitting of cis/trans Andean species after the final uplift of the Andes. At the subspecies level, there is evidence for reciprocal monophyly and groups are often separated by major rivers, demonstrating the important role of rivers in causing or maintaining divergence. Because some of the results presented here conflict with current taxonomy of Pteroglossus, new taxonomic arrangements are suggested. Copyright © 2010 Elsevier Inc. All rights reserved.

The complete mitochondrial genome structure of the jaguar (Panthera onca).

PubMed

Caragiulo, Anthony; Dougherty, Eric; Soto, Sofia; Rabinowitz, Salisa; Amato, George

2016-01-01

The jaguar (Panthera onca) is the largest felid in the Western hemisphere, and the only member of the Panthera genus in the New World. The jaguar inhabits most countries within Central and South America, and is considered near threatened by the International Union for the Conservation of Nature. This study represents the first sequence of the entire jaguar mitogenome, which was the only Panthera mitogenome that had not been sequenced. The jaguar mitogenome is 17,049 bases and possesses the same molecular structure as other felid mitogenomes. Bayesian inference (BI) and maximum likelihood (ML) were used to determine the phylogenetic placement of the jaguar within the Panthera genus. Both BI and ML analyses revealed the jaguar to be sister to the tiger/leopard/snow leopard clade.

Improvement of range spatial resolution of medical ultrasound imaging by element-domain signal processing

NASA Astrophysics Data System (ADS)

Hasegawa, Hideyuki

2017-07-01

The range spatial resolution is an important factor determining the image quality in ultrasonic imaging. The range spatial resolution in ultrasonic imaging depends on the ultrasonic pulse length, which is determined by the mechanical response of the piezoelectric element in an ultrasonic probe. To improve the range spatial resolution without replacing the transducer element, in the present study, methods based on maximum likelihood (ML) estimation and multiple signal classification (MUSIC) were proposed. The proposed methods were applied to echo signals received by individual transducer elements in an ultrasonic probe. The basic experimental results showed that the axial half maximum of the echo from a string phantom was improved from 0.21 mm (conventional method) to 0.086 mm (ML) and 0.094 mm (MUSIC).

The Role of Cis-Lunar Space in Future Global Space Exploration

NASA Technical Reports Server (NTRS)

Bobskill, Marianne R.; Lupisella, Mark L.

2012-01-01

Cis-lunar space offers affordable near-term opportunities to help pave the way for future global human exploration of deep space, acting as a bridge between present missions and future deep space missions. While missions in cis-lunar space have value unto themselves, they can also play an important role in enabling and reducing risk for future human missions to the Moon, Near-Earth Asteroids (NEAs), Mars, and other deep space destinations. The Cis-Lunar Destination Team of NASA's Human Spaceflight Architecture Team (HAT) has been analyzing cis-lunar destination activities and developing notional missions (or "destination Design Reference Missions" [DRMs]) for cis-lunar locations to inform roadmap and architecture development, transportation and destination elements definition, operations, and strategic knowledge gaps. The cis-lunar domain is defined as that area of deep space under the gravitational influence of the earth-moon system. This includes a set of earth-centered orbital locations in low earth orbit (LEO), geosynchronous earth orbit (GEO), highly elliptical and high earth orbits (HEO), earth-moon libration or "Lagrange" points (E-ML1 through E-ML5, and in particular, E-ML1 and E-ML2), and low lunar orbit (LLO). To help explore this large possibility space, we developed a set of high level cis-lunar mission concepts in the form of a large mission tree, defined primarily by mission duration, pre-deployment, type of mission, and location. The mission tree has provided an overall analytical context and has helped in developing more detailed design reference missions that are then intended to inform capabilities, operations, and architectures. With the mission tree as context, we will describe two destination DRMs to LEO and GEO, based on present human space exploration architectural considerations, as well as our recent work on defining mission activities that could be conducted with an EML1 or EML2 facility, the latter of which will be an emphasis of this paper, motivated in part by recent interest expressed at the Global Exploration Roadmap Stakeholder meeting. This paper will also explore the links between this HAT Cis-Lunar Destination Team analysis and the recently released ISECG Global Exploration Roadmap and other potential international considerations, such as preventing harmful interference to radio astronomy observations in the shielded zone of the moon.

Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Asplenium ferns.

PubMed

Shepherd, Lara D; Holland, Barbara R; Perrie, Leon R

2008-07-01

A previous study of the relationships amongst three subgroups of the Austral Asplenium ferns found conflicting signal between the two chloroplast loci investigated. Because organelle genomes like those of chloroplasts and mitochondria are thought to be non-recombining, with a single evolutionary history, we sequenced four additional chloroplast loci with the expectation that this would resolve these relationships. Instead, the conflict was only magnified. Although tree-building analyses favoured one of the three possible trees, one of the alternative trees actually had one more supporting site (six versus five) and received greater support in spectral and neighbor-net analyses. Simulations suggested that chance alone was unlikely to produce strong support for two of the possible trees and none for the third. Likelihood permutation tests indicated that the concatenated chloroplast sequence data appeared to have experienced recombination. However, recombination between the chloroplast genomes of different species would be highly atypical, and corollary supporting observations, like chloroplast heteroplasmy, are lacking. Wider taxon sampling clarified the composition of the Austral group, but the conflicting signal meant analyses (e.g., morphological evolution, biogeographic) conditional on a well-supported phylogeny could not be performed.

Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition.

PubMed

Penny, D; Hasegawa, M; Waddell, P J; Hendy, M D

1999-03-01

We explore the tree of mammalian mtDNA sequences, using particularly the LogDet transform on amino acid sequences, the distance Hadamard transform, and the Closest Tree selection criterion. The amino acid composition of different species show significant differences, even within mammals. After compensating for these differences, nearest-neighbor bootstrap results suggest that the tree is locally stable, though a few groups show slightly greater rearrangements when a large proportion of the constant sites are removed. Many parts of the trees we obtain agree with those on published protein ML trees. Interesting results include a preference for rodent monophyly. The detection of a few alternative signals to those on the optimal tree were obtained using the distance Hadamard transform (with results expressed as a Lento plot). One rearrangement suggested was the interchange of the position of primates and rodents on the optimal tree. The basic stability of the tree, combined with two calibration points (whale/cow and horse/rhinoceros), together with a distant secondary calibration from the mammal/bird divergence, allows inferences of the times of divergence of putative clades. Allowing for sampling variances due to finite sequence length, most major divergences amongst lineages leading to modern orders, appear to occur well before the Cretaceous/Tertiary (K/T) boundary. Implications arising from these early divergences are discussed, particularly the possibility of competition between the small dinosaurs and the new mammal clades.

Phylogenomic analyses data of the avian phylogenomics project.

PubMed

Jarvis, Erich D; Mirarab, Siavash; Aberer, Andre J; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon Y W; Faircloth, Brant C; Nabholz, Benoit; Howard, Jason T; Suh, Alexander; Weber, Claudia C; da Fonseca, Rute R; Alfaro-Núñez, Alonzo; Narula, Nitish; Liu, Liang; Burt, Dave; Ellegren, Hans; Edwards, Scott V; Stamatakis, Alexandros; Mindell, David P; Cracraft, Joel; Braun, Edward L; Warnow, Tandy; Jun, Wang; Gilbert, M Thomas Pius; Zhang, Guojie

2015-01-01

Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses. Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence. The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.

Effectiveness of differing trap types for the detection of emerald ash borer (Coleoptera: Buprestidae).

PubMed

Marshall, Jordan M; Storer, Andrew J; Fraser, Ivich; Beachy, Jessica A; Mastro, Victor C

2009-08-01

The early detection of populations of a forest pest is important to begin initial control efforts, minimizing the risk of further spread and impact. Emerald ash borer (Agrilus planipennis Fairmaire) is an introduced pestiferous insect of ash (Fraxinus spp. L.) in North America. The effectiveness of trapping techniques, including girdled trap trees with sticky bands and purple prism traps, was tested in areas with low- and high-density populations of emerald ash borer. At both densities, large girdled trap trees (>30 cm diameter at breast height [dbh], 1.37 m in height) captured a higher rate of adult beetles per day than smaller trees. However, the odds of detecting emerald ash borer increased as the dbh of the tree increased by 1 cm for trap trees 15-25 cm dbh. Ash species used for the traps differed in the number of larvae per cubic centimeter of phloem. Emerald ash borer larvae were more likely to be detected below, compared with above, the crown base of the trap tree. While larval densities within a trap tree were related to the species of ash, adult capture rates were not. These results provide support for focusing state and regional detection programs on the detection of emerald ash borer adults. If bark peeling for larvae is incorporated into these programs, peeling efforts focused below the crown base may increase likelihood of identifying new infestations while reducing labor costs. Associating traps with larger trees ( approximately 25 cm dbh) may increase the odds of detecting low-density populations of emerald ash borer, possibly reducing the time between infestation establishment and implementing management strategies.

Ecological disequilibrium drives insect pest and pathogen accumulation in non-native trees

PubMed Central

Burgess, Treena I.; Le Roux, Johannes J.; Richardson, David M.; Slippers, Bernard; Wingfield, Michael J.

2017-01-01

Abstract Non-native trees have become dominant components of many landscapes, including urban ecosystems, commercial forestry plantations, fruit orchards and as invasives in natural ecosystems. Often, these trees have been separated from their natural enemies (i.e. insects and pathogens) leading to ecological disequilibrium, that is, the immediate breakdown of historically co-evolved interactions once introduced into novel environments. Long-established, non-native tree plantations provide useful experiments to explore the dimensions of such ecological disequilibria. We quantify the status quo of non-native insect pests and pathogens catching up with their tree hosts (planted Acacia, Eucalyptus and Pinus species) in South Africa, and examine which native South African enemy species utilize these trees as hosts. Interestingly, pines, with no confamilial relatives in South Africa and the longest residence time (almost two centuries), have acquired only one highly polyphagous native pathogen. This is in contrast to acacias and eucalypts, both with many native and confamilial relatives in South Africa that have acquired more native pathogens. These patterns support the known role of phylogenetic relatedness of non-native and native floras in influencing the likelihood of pathogen shifts between them. This relationship, however, does not seem to hold for native insects. Native insects appear far more likely to expand their feeding habits onto non-native tree hosts than are native pathogens, although they are generally less damaging. The ecological disequilibrium conditions of non-native trees are deeply rooted in the eco-evolutionary experience of the host plant, co-evolved natural enemies and native organisms from the introduced range. We should expect considerable spatial and temporal variation in ecological disequilibrium conditions among non-native taxa, which can be significantly influenced by biosecurity and management practices. PMID:28013250

Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees

PubMed Central

Kenah, Eben; Britton, Tom; Halloran, M. Elizabeth; Longini, Ira M.

2016-01-01

Recent work has attempted to use whole-genome sequence data from pathogens to reconstruct the transmission trees linking infectors and infectees in outbreaks. However, transmission trees from one outbreak do not generalize to future outbreaks. Reconstruction of transmission trees is most useful to public health if it leads to generalizable scientific insights about disease transmission. In a survival analysis framework, estimation of transmission parameters is based on sums or averages over the possible transmission trees. A phylogeny can increase the precision of these estimates by providing partial information about who infected whom. The leaves of the phylogeny represent sampled pathogens, which have known hosts. The interior nodes represent common ancestors of sampled pathogens, which have unknown hosts. Starting from assumptions about disease biology and epidemiologic study design, we prove that there is a one-to-one correspondence between the possible assignments of interior node hosts and the transmission trees simultaneously consistent with the phylogeny and the epidemiologic data on person, place, and time. We develop algorithms to enumerate these transmission trees and show these can be used to calculate likelihoods that incorporate both epidemiologic data and a phylogeny. A simulation study confirms that this leads to more efficient estimates of hazard ratios for infectiousness and baseline hazards of infectious contact, and we use these methods to analyze data from a foot-and-mouth disease virus outbreak in the United Kingdom in 2001. These results demonstrate the importance of data on individuals who escape infection, which is often overlooked. The combination of survival analysis and algorithms linking phylogenies to transmission trees is a rigorous but flexible statistical foundation for molecular infectious disease epidemiology. PMID:27070316

ccML, a new mark-up language to improve ISO/EN 13606-based electronic health record extracts practical edition

PubMed Central

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Cáceres, Jesús; Somolinos, Roberto; Pascual, Mario; Martínez, Ignacio; Salvador, Carlos H; Monteagudo, José Luis

2013-01-01

Objective The objective of this paper is to introduce a new language called ccML, designed to provide convenient pragmatic information to applications using the ISO/EN13606 reference model (RM), such as electronic health record (EHR) extracts editors. EHR extracts are presently built using the syntactic and semantic information provided in the RM and constrained by archetypes. The ccML extra information enables the automation of the medico-legal context information edition, which is over 70% of the total in an extract, without modifying the RM information. Materials and Methods ccML is defined using a W3C XML schema file. Valid ccML files complement the RM with additional pragmatics information. The ccML language grammar is defined using formal language theory as a single-type tree grammar. The new language is tested using an EHR extracts editor application as proof-of-concept system. Results Seven ccML PVCodes (predefined value codes) are introduced in this grammar to cope with different realistic EHR edition situations. These seven PVCodes have different interpretation strategies, from direct look up in the ccML file itself, to more complex searches in archetypes or system precomputation. Discussion The possibility to declare generic types in ccML gives rise to ambiguity during interpretation. The criterion used to overcome ambiguity is that specificity should prevail over generality. The opposite would make the individual specific element declarations useless. Conclusion A new mark-up language ccML is introduced that opens up the possibility of providing applications using the ISO/EN13606 RM with the necessary pragmatics information to be practical and realistic. PMID:23019241

Modeling Off-Nominal Behavior in SysML

NASA Technical Reports Server (NTRS)

Day, John C.; Donahue, Kenneth; Ingham, Michel; Kadesch, Alex; Kennedy, Andrew K.; Post, Ethan

2012-01-01

Specification and development of fault management functionality in systems is performed in an ad hoc way - more of an art than a science. Improvements to system reliability, availability, safety and resilience will be limited without infusion of additional formality into the practice of fault management. Key to the formalization of fault management is a precise representation of off-nominal behavior. Using the upcoming Soil Moisture Active-Passive (SMAP) mission for source material, we have modeled the off-nominal behavior of the SMAP system during its initial spin-up activity, using the System Modeling Language (SysML). In the course of developing these models, we have developed generic patterns for capturing off-nominal behavior in SysML. We show how these patterns provide useful ways of reasoning about the system (e.g., checking for completeness and effectiveness) and allow the automatic generation of typical artifacts (e.g., success trees and FMECAs) used in system analyses.

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

PubMed Central

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

2016-01-01

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

Determinants of farmers' tree planting investment decision as a degraded landscape management strategy in the central highlands of Ethiopia

NASA Astrophysics Data System (ADS)

Gessesse, B.; Bewket, W.; Bräuning, A.

2015-11-01

Land degradation due to lack of sustainable land management practices are one of the critical challenges in many developing countries including Ethiopia. This study explores the major determinants of farm level tree planting decision as a land management strategy in a typical framing and degraded landscape of the Modjo watershed, Ethiopia. The main data were generated from household surveys and analysed using descriptive statistics and binary logistic regression model. The model significantly predicted farmers' tree planting decision (Chi-square = 37.29, df = 15, P<0.001). Besides, the computed significant value of the model suggests that all the considered predictor variables jointly influenced the farmers' decision to plant trees as a land management strategy. In this regard, the finding of the study show that local land-users' willingness to adopt tree growing decision is a function of a wide range of biophysical, institutional, socioeconomic and household level factors, however, the likelihood of household size, productive labour force availability, the disparity of schooling age, level of perception of the process of deforestation and the current land tenure system have positively and significantly influence on tree growing investment decisions in the study watershed. Eventually, the processes of land use conversion and land degradation are serious which in turn have had adverse effects on agricultural productivity, local food security and poverty trap nexus. Hence, devising sustainable and integrated land management policy options and implementing them would enhance ecological restoration and livelihood sustainability in the study watershed.

Determinants of farmers' tree-planting investment decisions as a degraded landscape management strategy in the central highlands of Ethiopia

NASA Astrophysics Data System (ADS)

Gessesse, Berhan; Bewket, Woldeamlak; Bräuning, Achim

2016-04-01

Land degradation due to lack of sustainable land management practices is one of the critical challenges in many developing countries including Ethiopia. This study explored the major determinants of farm-level tree-planting decisions as a land management strategy in a typical farming and degraded landscape of the Modjo watershed, Ethiopia. The main data were generated from household surveys and analysed using descriptive statistics and a binary logistic regression model. The model significantly predicted farmers' tree-planting decisions (χ2 = 37.29, df = 15, P < 0.001). Besides, the computed significant value of the model revealed that all the considered predictor variables jointly influenced the farmers' decisions to plant trees as a land management strategy. The findings of the study demonstrated that the adoption of tree-growing decisions by local land users was a function of a wide range of biophysical, institutional, socioeconomic and household-level factors. In this regard, the likelihood of household size, productive labour force availability, the disparity of schooling age, level of perception of the process of deforestation and the current land tenure system had a critical influence on tree-growing investment decisions in the study watershed. Eventually, the processes of land-use conversion and land degradation were serious, which in turn have had adverse effects on agricultural productivity, local food security and poverty trap nexus. Hence, the study recommended that devising and implementing sustainable land management policy options would enhance ecological restoration and livelihood sustainability in the study watershed.

Analysis of occlusal variables, dental attrition, and age for distinguishing healthy controls from female patients with intracapsular temporomandibular disorders.

PubMed

Seligman, D A; Pullinger, A G

2000-01-01

Confusion about the relationship of occlusion to temporomandibular disorders (TMD) persists. This study attempted to identify occlusal and attrition factors plus age that would characterize asymptomatic normal female subjects. A total of 124 female patients with intracapsular TMD were compared with 47 asymptomatic female controls for associations to 9 occlusal factors, 3 attrition severity measures, and age using classification tree, multiple stepwise logistic regression, and univariate analyses. Models were tested for accuracy (sensitivity and specificity) and total contribution to the variance. The classification tree model had 4 terminal nodes that used only anterior attrition and age. "Normals" were mainly characterized by low attrition levels, whereas patients had higher attrition and tended to be younger. The tree model was only moderately useful (sensitivity 63%, specificity 94%) in predicting normals. The logistic regression model incorporated unilateral posterior crossbite and mediotrusive attrition severity in addition to the 2 factors in the tree, but was slightly less accurate than the tree (sensitivity 51%, specificity 90%). When only occlusal factors were considered in the analysis, normals were additionally characterized by a lack of anterior open bite, smaller overjet, and smaller RCP-ICP slides. The log likelihood accounted for was similar for both the tree (pseudo R(2) = 29.38%; mean deviance = 0.95) and the multiple logistic regression (Cox Snell R(2) = 30.3%, mean deviance = 0.84) models. The occlusal and attrition factors studied were only moderately useful in differentiating normals from TMD patients.

The critical amplifying role of increasing atmospheric moisture demand on tree mortality and associated regional die-off

DOE PAGES

Breshears, David D.; Adams, Henry D.; Eamus, Derek; ...

2013-08-02

Drought-induced tree mortality, including large-scale die-off events and increases in background rates of mortality, is a global phenomenon (Allen et al., 2010) that can directly impact numerous earth system properties and ecosystem goods and services (Adams et al., 2010; Breshears et al., 2011; Anderegg et al., 2013). Tree mortality is particularly of concern because of the likelihood that it will increase in frequency and extent with climate change (McDowell et al., 2008, 2011; Adams et al., 2009; McDowell, 2011; Williams et al., 2013). Recent plant science advances related to drought have focused on understanding the physiological mechanisms that not onlymore » affect plant growth and associated carbon metabolism, but also the more challenging issue of predicting plant mortality thresholds (McDowell et al., 2013). Although some advances related to mechanisms of mortality have been made and have increased emphasis on interrelationships between carbon metabolism and plant hydraulics (McDowell et al., 2011), notably few studies have specifically evaluated effects of increasing atmospheric demand for moisture (i.e., vapour pressure deficit; VPD) on rates of tree death. In this opinion article we highlight the importance of considering the key risks of future large-scale tree die-off and other mortality events arising from increased VPD. Here we focus on mortality of trees, but our point about the importance of VPD is also relevant to other vascular plants.« less

Receiver design for SPAD-based VLC systems under Poisson-Gaussian mixed noise model.

PubMed

Mao, Tianqi; Wang, Zhaocheng; Wang, Qi

2017-01-23

Single-photon avalanche diode (SPAD) is a promising photosensor because of its high sensitivity to optical signals in weak illuminance environment. Recently, it has drawn much attention from researchers in visible light communications (VLC). However, existing literature only deals with the simplified channel model, which only considers the effects of Poisson noise introduced by SPAD, but neglects other noise sources. Specifically, when an analog SPAD detector is applied, there exists Gaussian thermal noise generated by the transimpedance amplifier (TIA) and the digital-to-analog converter (D/A). Therefore, in this paper, we propose an SPAD-based VLC system with pulse-amplitude-modulation (PAM) under Poisson-Gaussian mixed noise model, where Gaussian-distributed thermal noise at the receiver is also investigated. The closed-form conditional likelihood of received signals is derived using the Laplace transform and the saddle-point approximation method, and the corresponding quasi-maximum-likelihood (quasi-ML) detector is proposed. Furthermore, the Poisson-Gaussian-distributed signals are converted to Gaussian variables with the aid of the generalized Anscombe transform (GAT), leading to an equivalent additive white Gaussian noise (AWGN) channel, and a hard-decision-based detector is invoked. Simulation results demonstrate that, the proposed GAT-based detector can reduce the computational complexity with marginal performance loss compared with the proposed quasi-ML detector, and both detectors are capable of accurately demodulating the SPAD-based PAM signals.

Diagnostic Accuracy of Tests for Polyuria in Lithium-Treated Patients.

PubMed

Kinahan, James Conor; NiChorcorain, Aoife; Cunningham, Sean; Freyne, Aideen; Cooney, Colm; Barry, Siobhan; Kelly, Brendan D

2015-08-01

In lithium-treated patients, polyuria increases the risk of dehydration and lithium toxicity. If detected early, it is reversible. Despite its prevalence and associated morbidity in clinical practice, it remains underrecognized and therefore undertreated. The 24-hour urine collection is limited by its convenience and practicality. This study explores the diagnostic accuracy of alternative tests such as questionnaires on subjective polyuria, polydipsia, nocturia (dichotomous and ordinal responses), early morning urine sample osmolality (EMUO), and fluid intake record (FIR). This is a cross-sectional study of 179 lithium-treated patients attending a general adult and an old age psychiatry service. Participants completed the tests after completing an accurate 24-hour urine collection. The diagnostic accuracy of the individual tests was explored using the appropriate statistical techniques. Seventy-nine participants completed all of the tests. Polydipsia severity, EMUO, and FIR significantly differentiated the participants with polyuria (area under the receiver operating characteristic curve of 0.646, 0.760, and 0.846, respectively). Of the tests investigated, the FIR made the largest significant change in the probability that a patient experiences polyuria (<2000 mL/24 hours; interval likelihood ratio, 0.18 and >3500 mL/24 hours; interval likelihood ratio, 14). Symptomatic questioning, EMUO, and an FIR could be used in clinical practice to inform the prescriber of the probability that a lithium-treated patient is experiencing polyuria.

Multistage classification of multispectral Earth observational data: The design approach

NASA Technical Reports Server (NTRS)

Bauer, M. E. (Principal Investigator); Muasher, M. J.; Landgrebe, D. A.

1981-01-01

An algorithm is proposed which predicts the optimal features at every node in a binary tree procedure. The algorithm estimates the probability of error by approximating the area under the likelihood ratio function for two classes and taking into account the number of training samples used in estimating each of these two classes. Some results on feature selection techniques, particularly in the presence of a very limited set of training samples, are presented. Results comparing probabilities of error predicted by the proposed algorithm as a function of dimensionality as compared to experimental observations are shown for aircraft and LANDSAT data. Results are obtained for both real and simulated data. Finally, two binary tree examples which use the algorithm are presented to illustrate the usefulness of the procedure.

Branch length estimation and divergence dating: estimates of error in Bayesian and maximum likelihood frameworks.

PubMed

Schwartz, Rachel S; Mueller, Rachel L

2010-01-11

Estimates of divergence dates between species improve our understanding of processes ranging from nucleotide substitution to speciation. Such estimates are frequently based on molecular genetic differences between species; therefore, they rely on accurate estimates of the number of such differences (i.e. substitutions per site, measured as branch length on phylogenies). We used simulations to determine the effects of dataset size, branch length heterogeneity, branch depth, and analytical framework on branch length estimation across a range of branch lengths. We then reanalyzed an empirical dataset for plethodontid salamanders to determine how inaccurate branch length estimation can affect estimates of divergence dates. The accuracy of branch length estimation varied with branch length, dataset size (both number of taxa and sites), branch length heterogeneity, branch depth, dataset complexity, and analytical framework. For simple phylogenies analyzed in a Bayesian framework, branches were increasingly underestimated as branch length increased; in a maximum likelihood framework, longer branch lengths were somewhat overestimated. Longer datasets improved estimates in both frameworks; however, when the number of taxa was increased, estimation accuracy for deeper branches was less than for tip branches. Increasing the complexity of the dataset produced more misestimated branches in a Bayesian framework; however, in an ML framework, more branches were estimated more accurately. Using ML branch length estimates to re-estimate plethodontid salamander divergence dates generally resulted in an increase in the estimated age of older nodes and a decrease in the estimated age of younger nodes. Branch lengths are misestimated in both statistical frameworks for simulations of simple datasets. However, for complex datasets, length estimates are quite accurate in ML (even for short datasets), whereas few branches are estimated accurately in a Bayesian framework. Our reanalysis of empirical data demonstrates the magnitude of effects of Bayesian branch length misestimation on divergence date estimates. Because the length of branches for empirical datasets can be estimated most reliably in an ML framework when branches are <1 substitution/site and datasets are > or =1 kb, we suggest that divergence date estimates using datasets, branch lengths, and/or analytical techniques that fall outside of these parameters should be interpreted with caution.

Statistical Properties of Maximum Likelihood Estimators of Power Law Spectra Information

NASA Technical Reports Server (NTRS)

Howell, L. W.

2002-01-01

A simple power law model consisting of a single spectral index, a is believed to be an adequate description of the galactic cosmic-ray (GCR) proton flux at energies below 10(exp 13) eV, with a transition at the knee energy, E(sub k), to a steeper spectral index alpha(sub 2) greater than alpha(sub 1) above E(sub k). The Maximum likelihood (ML) procedure was developed for estimating the single parameter alpha(sub 1) of a simple power law energy spectrum and generalized to estimate the three spectral parameters of the broken power law energy spectrum from simulated detector responses and real cosmic-ray data. The statistical properties of the ML estimator were investigated and shown to have the three desirable properties: (P1) consistency (asymptotically unbiased). (P2) efficiency asymptotically attains the Cramer-Rao minimum variance bound), and (P3) asymptotically normally distributed, under a wide range of potential detector response functions. Attainment of these properties necessarily implies that the ML estimation procedure provides the best unbiased estimator possible. While simulation studies can easily determine if a given estimation procedure provides an unbiased estimate of the spectra information, and whether or not the estimator is approximately normally distributed, attainment of the Cramer-Rao bound (CRB) can only he ascertained by calculating the CRB for an assumed energy spectrum-detector response function combination, which can be quite formidable in practice. However. the effort in calculating the CRB is very worthwhile because it provides the necessary means to compare the efficiency of competing estimation techniques and, furthermore, provides a stopping rule in the search for the best unbiased estimator. Consequently, the CRB for both the simple and broken power law energy spectra are derived herein and the conditions under which they are attained in practice are investigated. The ML technique is then extended to estimate spectra information from an arbitrary number of astrophysics data sets produced by vastly different science instruments. This theory and its successful implementation will facilitate the interpretation of spectral information from multiple astrophysics missions and thereby permit the derivation of superior spectral parameter estimates based on the combination of data sets.

The prevalence of terraced treescapes in analyses of phylogenetic data sets.

PubMed

Dobrin, Barbara H; Zwickl, Derrick J; Sanderson, Michael J

2018-04-04

The pattern of data availability in a phylogenetic data set may lead to the formation of terraces, collections of equally optimal trees. Terraces can arise in tree space if trees are scored with parsimony or with partitioned, edge-unlinked maximum likelihood. Theory predicts that terraces can be large, but their prevalence in contemporary data sets has never been surveyed. We selected 26 data sets and phylogenetic trees reported in recent literature and investigated the terraces to which the trees would belong, under a common set of inference assumptions. We examined terrace size as a function of the sampling properties of the data sets, including taxon coverage density (the proportion of taxon-by-gene positions with any data present) and a measure of gene sampling "sufficiency". We evaluated each data set in relation to the theoretical minimum gene sampling depth needed to reduce terrace size to a single tree, and explored the impact of the terraces found in replicate trees in bootstrap methods. Terraces were identified in nearly all data sets with taxon coverage densities < 0.90. They were not found, however, in high-coverage-density (i.e., ≥ 0.94) transcriptomic and genomic data sets. The terraces could be very large, and size varied inversely with taxon coverage density and with gene sampling sufficiency. Few data sets achieved a theoretical minimum gene sampling depth needed to reduce terrace size to a single tree. Terraces found during bootstrap resampling reduced overall support. If certain inference assumptions apply, trees estimated from empirical data sets often belong to large terraces of equally optimal trees. Terrace size correlates to data set sampling properties. Data sets seldom include enough genes to reduce terrace size to one tree. When bootstrap replicate trees lie on a terrace, statistical support for phylogenetic hypotheses may be reduced. Although some of the published analyses surveyed were conducted with edge-linked inference models (which do not induce terraces), unlinked models have been used and advocated. The present study describes the potential impact of that inference assumption on phylogenetic inference in the context of the kinds of multigene data sets now widely assembled for large-scale tree construction.

Use of Bayesian event trees in semi-quantitative volcano eruption forecasting and hazard analysis

NASA Astrophysics Data System (ADS)

Wright, Heather; Pallister, John; Newhall, Chris

2015-04-01

Use of Bayesian event trees to forecast eruptive activity during volcano crises is an increasingly common practice for the USGS-USAID Volcano Disaster Assistance Program (VDAP) in collaboration with foreign counterparts. This semi-quantitative approach combines conceptual models of volcanic processes with current monitoring data and patterns of occurrence to reach consensus probabilities. This approach allows a response team to draw upon global datasets, local observations, and expert judgment, where the relative influence of these data depends upon the availability and quality of monitoring data and the degree to which the volcanic history is known. The construction of such event trees additionally relies upon existence and use of relevant global databases and documented past periods of unrest. Because relevant global databases may be underpopulated or nonexistent, uncertainty in probability estimations may be large. Our 'hybrid' approach of combining local and global monitoring data and expert judgment facilitates discussion and constructive debate between disciplines: including seismology, gas geochemistry, geodesy, petrology, physical volcanology and technology/engineering, where difference in opinion between response team members contributes to definition of the uncertainty in the probability estimations. In collaboration with foreign colleagues, we have created event trees for numerous areas experiencing volcanic unrest. Event trees are created for a specified time frame and are updated, revised, or replaced as the crisis proceeds. Creation of an initial tree is often prompted by a change in monitoring data, such that rapid assessment of probability is needed. These trees are intended as a vehicle for discussion and a way to document relevant data and models, where the target audience is the scientists themselves. However, the probabilities derived through the event-tree analysis can also be used to help inform communications with emergency managers and the public. VDAP trees evaluate probabilities of: magmatic intrusion, likelihood of eruption, magnitude of eruption, and types of associated hazardous events and their extents. In a few cases, trees have been extended to also assess and communicate vulnerability and relative risk.

Is BAMM Flawed? Theoretical and Practical Concerns in the Analysis of Multi-Rate Diversification Models

PubMed Central

Mitchell, Jonathan S.; Chang, Jonathan

2017-01-01

Bayesian analysis of macroevolutionary mixtures (BAMM) is a statistical framework that uses reversible jump Markov chain Monte Carlo to infer complex macroevolutionary dynamics of diversification and phenotypic evolution on phylogenetic trees. A recent article by Moore et al. (MEA) reported a number of theoretical and practical concerns with BAMM. Major claims from MEA are that (i) BAMM’s likelihood function is incorrect, because it does not account for unobserved rate shifts; (ii) the posterior distribution on the number of rate shifts is overly sensitive to the prior; and (iii) diversification rate estimates from BAMM are unreliable. Here, we show that these and other conclusions from MEA are generally incorrect or unjustified. We first demonstrate that MEA’s numerical assessment of the BAMM likelihood is compromised by their use of an invalid likelihood function. We then show that “unobserved rate shifts” appear to be irrelevant for biologically plausible parameterizations of the diversification process. We find that the purportedly extreme prior sensitivity reported by MEA cannot be replicated with standard usage of BAMM v2.5, or with any other version when conventional Bayesian model selection is performed. Finally, we demonstrate that BAMM performs very well at estimating diversification rate variation across the \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}${\\sim}$\\end{document}20% of simulated trees in MEA’s data set for which it is theoretically possible to infer rate shifts with confidence. Due to ascertainment bias, the remaining 80% of their purportedly variable-rate phylogenies are statistically indistinguishable from those produced by a constant-rate birth–death process and were thus poorly suited for the summary statistics used in their performance assessment. We demonstrate that inferences about diversification rates have been accurate and consistent across all major previous releases of the BAMM software. We recognize an acute need to address the theoretical foundations of rate-shift models for phylogenetic trees, and we expect BAMM and other modeling frameworks to improve in response to mathematical and computational innovations. However, we remain optimistic that that the imperfect tools currently available to comparative biologists have provided and will continue to provide important insights into the diversification of life on Earth. PMID:28334223

Is BAMM Flawed? Theoretical and Practical Concerns in the Analysis of Multi-Rate Diversification Models.

PubMed

Rabosky, Daniel L; Mitchell, Jonathan S; Chang, Jonathan

2017-07-01

Bayesian analysis of macroevolutionary mixtures (BAMM) is a statistical framework that uses reversible jump Markov chain Monte Carlo to infer complex macroevolutionary dynamics of diversification and phenotypic evolution on phylogenetic trees. A recent article by Moore et al. (MEA) reported a number of theoretical and practical concerns with BAMM. Major claims from MEA are that (i) BAMM's likelihood function is incorrect, because it does not account for unobserved rate shifts; (ii) the posterior distribution on the number of rate shifts is overly sensitive to the prior; and (iii) diversification rate estimates from BAMM are unreliable. Here, we show that these and other conclusions from MEA are generally incorrect or unjustified. We first demonstrate that MEA's numerical assessment of the BAMM likelihood is compromised by their use of an invalid likelihood function. We then show that "unobserved rate shifts" appear to be irrelevant for biologically plausible parameterizations of the diversification process. We find that the purportedly extreme prior sensitivity reported by MEA cannot be replicated with standard usage of BAMM v2.5, or with any other version when conventional Bayesian model selection is performed. Finally, we demonstrate that BAMM performs very well at estimating diversification rate variation across the ${\\sim}$20% of simulated trees in MEA's data set for which it is theoretically possible to infer rate shifts with confidence. Due to ascertainment bias, the remaining 80% of their purportedly variable-rate phylogenies are statistically indistinguishable from those produced by a constant-rate birth-death process and were thus poorly suited for the summary statistics used in their performance assessment. We demonstrate that inferences about diversification rates have been accurate and consistent across all major previous releases of the BAMM software. We recognize an acute need to address the theoretical foundations of rate-shift models for phylogenetic trees, and we expect BAMM and other modeling frameworks to improve in response to mathematical and computational innovations. However, we remain optimistic that that the imperfect tools currently available to comparative biologists have provided and will continue to provide important insights into the diversification of life on Earth. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

ANTIPROLIFERATIVE EFFECT ON BREAST CANCER (MCF7) OF MORINGA OLEIFERA SEED EXTRACTS.

PubMed

Adebayo, Ismail Abiola; Arsad, Hasni; Samian, Mohd Razip

2017-01-01

Moringa oleifera belongs to plant family, Moringaceae and popularly called "wonderful tree", for it is used traditionally to cure many diseases including cancer in Africa and Asia, however, there is limited knowledge on cytotoxic activity of Moringa oleifera seeds on MCF7 breast cancer cell. The present study evaluated antiproliferative effect on MCF7 of the seed. Seeds of Moringa oleifera were grinded to powder and its phytochemicals were extracted using water and 80% ethanol solvents, part of the ethanolic extract were sequentially partitioned to fractions with four solvents (hexane, dichloromethane, chloroform, and n-butanol). Antiproliferative effects on MCF7 of the samples were determined. Finally, potent samples that significantly inhibited MCF7 growth were tested on MCF 10A. Crude water extract, hexane and dichloromethane fractions of the seeds inhibited the proliferation of MCF7 with the following IC 50 values 280 μg/ml, 130 μg/ml and 26 μg/ml respectively, however, of the 3 samples, only hexane fraction had minimal cytotoxic effect on MCF 10A (IC 50 > 400μg/ml). Moringa oleifera seed has antiproliferative effect on MCF7.

Bayesian Weibull tree models for survival analysis of clinico-genomic data

PubMed Central

Clarke, Jennifer; West, Mike

2008-01-01

An important goal of research involving gene expression data for outcome prediction is to establish the ability of genomic data to define clinically relevant risk factors. Recent studies have demonstrated that microarray data can successfully cluster patients into low- and high-risk categories. However, the need exists for models which examine how genomic predictors interact with existing clinical factors and provide personalized outcome predictions. We have developed clinico-genomic tree models for survival outcomes which use recursive partitioning to subdivide the current data set into homogeneous subgroups of patients, each with a specific Weibull survival distribution. These trees can provide personalized predictive distributions of the probability of survival for individuals of interest. Our strategy is to fit multiple models; within each model we adopt a prior on the Weibull scale parameter and update this prior via Empirical Bayes whenever the sample is split at a given node. The decision to split is based on a Bayes factor criterion. The resulting trees are weighted according to their relative likelihood values and predictions are made by averaging over models. In a pilot study of survival in advanced stage ovarian cancer we demonstrate that clinical and genomic data are complementary sources of information relevant to survival, and we use the exploratory nature of the trees to identify potential genomic biomarkers worthy of further study. PMID:18618012

The Impacts of Climate-Induced Drought on Biogeochemical Cycles

NASA Astrophysics Data System (ADS)

Peng, C.

2014-12-01

Terrestrial ecosystems and, in particular, forests exert strong controls on the global biogeochemical cycles and influence regional hydrology and climatology directly through water and surface energy budgets. Recent studies indicated that forest mortality caused by rising temperature and drought from around the world have unexpectedly increased in the past decade and they collectively illustrate the vulnerability of many forested ecosystems to rapid increases in tree mortality due to warmer temperatures and more severe drought. Persistent changes in tree mortality rates can alter forest structure, composition, and ecosystem services (such as albedo and carbon sequestration). Quantifying potential impacts of tree mortality on ecosystem processes requires research into mortality effects on carbon, energy, and water budgets at both site and regional levels. Despite recent progress, the uncertainty around mortality responses still limits our ability to predict the likelihood and anticipate the impacts of tree die-off. Studies are needed that explore tree death physiology for a wide variety of functional types, connect patterns of mortality with climate events, and quantify the impacts on carbon, energy, and water flux. In this presentation, I will highlight recent research progress, and identify key research needs and future challenges to predict the consequence and impacts of drought-induced large-scale forest mortality on biogeochemical cycles. I will focus on three main forest ecosystems (tropic rainforest in Amazon, temperate forest in Western USA, and boreal forest in Canada) as detailed case studies.

RY-Coding and Non-Homogeneous Models Can Ameliorate the Maximum-Likelihood Inferences From Nucleotide Sequence Data with Parallel Compositional Heterogeneity.

PubMed

Ishikawa, Sohta A; Inagaki, Yuji; Hashimoto, Tetsuo

2012-01-01

In phylogenetic analyses of nucleotide sequences, 'homogeneous' substitution models, which assume the stationarity of base composition across a tree, are widely used, albeit individual sequences may bear distinctive base frequencies. In the worst-case scenario, a homogeneous model-based analysis can yield an artifactual union of two distantly related sequences that achieved similar base frequencies in parallel. Such potential difficulty can be countered by two approaches, 'RY-coding' and 'non-homogeneous' models. The former approach converts four bases into purine and pyrimidine to normalize base frequencies across a tree, while the heterogeneity in base frequency is explicitly incorporated in the latter approach. The two approaches have been applied to real-world sequence data; however, their basic properties have not been fully examined by pioneering simulation studies. Here, we assessed the performances of the maximum-likelihood analyses incorporating RY-coding and a non-homogeneous model (RY-coding and non-homogeneous analyses) on simulated data with parallel convergence to similar base composition. Both RY-coding and non-homogeneous analyses showed superior performances compared with homogeneous model-based analyses. Curiously, the performance of RY-coding analysis appeared to be significantly affected by a setting of the substitution process for sequence simulation relative to that of non-homogeneous analysis. The performance of a non-homogeneous analysis was also validated by analyzing a real-world sequence data set with significant base heterogeneity.

A Parameter Estimation Scheme for Multiscale Kalman Smoother (MKS) Algorithm Used in Precipitation Data Fusion

NASA Technical Reports Server (NTRS)

Wang, Shugong; Liang, Xu

2013-01-01

A new approach is presented in this paper to effectively obtain parameter estimations for the Multiscale Kalman Smoother (MKS) algorithm. This new approach has demonstrated promising potentials in deriving better data products based on data of different spatial scales and precisions. Our new approach employs a multi-objective (MO) parameter estimation scheme (called MO scheme hereafter), rather than using the conventional maximum likelihood scheme (called ML scheme) to estimate the MKS parameters. Unlike the ML scheme, the MO scheme is not simply built on strict statistical assumptions related to prediction errors and observation errors, rather, it directly associates the fused data of multiple scales with multiple objective functions in searching best parameter estimations for MKS through optimization. In the MO scheme, objective functions are defined to facilitate consistency among the fused data at multiscales and the input data at their original scales in terms of spatial patterns and magnitudes. The new approach is evaluated through a Monte Carlo experiment and a series of comparison analyses using synthetic precipitation data. Our results show that the MKS fused precipitation performs better using the MO scheme than that using the ML scheme. Particularly, improvements are significant compared to that using the ML scheme for the fused precipitation associated with fine spatial resolutions. This is mainly due to having more criteria and constraints involved in the MO scheme than those included in the ML scheme. The weakness of the original ML scheme that blindly puts more weights onto the data associated with finer resolutions is overcome in our new approach.

[Interspecific allelopathic effect of different organs' aqueous extracts of Betula platyphylla and Larix olgensis on their seed germination and seedling growth].

PubMed

Liu, Zhong-Ling; Wang, Qing-Cheng; Hao, Long-Fei

2011-12-01

In this paper, the Betula platyphylla root-, branch-, and foliage aqueous extracts and Larix olgensis root-, branch-, foliage-, and bark aqueous extracts over a range of concentrations 5.0, 12.5, 25.0, 50.0, and 100.0 mg x mL(-1) were used to study their interspecific allelopathic effect on the seed germination and seedling growth of the two tree species. All the L. olgensis organs' extracts, except its root extracts at concentration 5.0 mg x mL(-1), had inhibition effect on B. platyphylla seed germination rate, which was 54%, 58%, 59%, and 66% under the effects of L. olgensis foliage-, branch-, bark-, and root extracts, respectively, as compared with the control. With increasing concentration, the inhibition effect of L. olgensis root- and branch extracts increased while that of L. olgensis foliage- and bark extracts decreased. The L. olgensis organs' extracts, especially the foliage extracts at concentration 100.0 mg x mL(-1), had strong inhibition effect on B. platyphylla seed radicle- and hypocotyl length growth, with a decrement of 38% and 55% (P < 0.05), respectively. L. olgensis branch- and foliage extracts promoted, but root- and bark extracts inhibited B. platyphylla seedling growth and biomass production. B. platyphylla organs' extracts promoted L. olgensis seed germination, root- and branch extracts promoted hypocotyl length growth, but foliage extracts at 50.0 and 100.0 mg x mL(-1) decreased the hypocotyl length growth by 27% and 28% (P < 0.05), respectively. B. platyphylla organs' extracts mainly promoted L. olgensis seedling growth, with the height- and collar diameter growth and biomass accumulation at B. platyphylla foliage extracts concentration 5.0 mg x mL(-1) increased by 54%, 60%, and 100% (P < 0.05), respectively. Our results suggested that there existed obvious allelopathic effect between B. platyphylla and L. olgensis, and thus, mixed planting B. platyphylla and L. olgensis could have promotion effects on the growth of the two tree species.

[Anti-fungi activity of organic extracts from the tree Fagara monophylla (Rutaceae) in Venezuela].

PubMed

Gómez, Yrma; Gil, Katiuska; González, Elba; Farías, Luz Marina

2007-01-01

The tree Fagara monophylla ranges throughout Tropical America. The genus Fagara has a diversity of alkaloid compounds with antibiotic properties; nevertheless, there are few reports antifungal activity of its organic compounds. Organic extracts from Venezuelan F. monophylla were tested for antimicrobial activity against Aspergillus terreus, A. flavus, Penicillium digitatum, P. funiculosum, P. citrinum, Paecilomyces and Candida albicans. Minimal Inhibitory Concentration (MIC) was determined. The susceptibility trials of organic fractions (Hex., CH2Cl2 and MeOH) showed that the highest inhibition was presented by MeOH against A. flavus (55 mm), P. digitatum (60 mm), P. funiculosum (56 mm) and C. albicans (26 mm). The activities of MeOH/EtOAc fractions 1 and 2 suggest a combined effect against A. flavus, P. digitatum and P. funiculosum. The MIC of 1 MeOH/ EtOAc subfraction activity was lower against C. albicans (32 microg/ml) and moderate (128 microg/ml) against P. digitatum. This organic extract has a great antifungal potential. The phytochemical proves and TLC testing on the organic extract, and the MeOH/EtOAc subfraction, respectively, indicated the presence of alkaloid compounds.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wahl, Daniel E.; Yocky, David A.; Jakowatz, Jr., Charles V.

In previous research, two-pass repeat-geometry synthetic aperture radar (SAR) coherent change detection (CCD) predominantly utilized the sample degree of coherence as a measure of the temporal change occurring between two complex-valued image collects. Previous coherence-based CCD approaches tend to show temporal change when there is none in areas of the image that have a low clutter-to-noise power ratio. Instead of employing the sample coherence magnitude as a change metric, in this paper, we derive a new maximum-likelihood (ML) temporal change estimate—the complex reflectance change detection (CRCD) metric to be used for SAR coherent temporal change detection. The new CRCD estimatormore » is a surprisingly simple expression, easy to implement, and optimal in the ML sense. As a result, this new estimate produces improved results in the coherent pair collects that we have tested.« less

Phytochemicals and antidiabetic activity of Eusideroxylon zwageri stem bark collected from East Kalimantan, Indonesia

NASA Astrophysics Data System (ADS)

Kusuma, I. W.; Rahmini; Ramadhan, R.; Rahmawati, N.; Suwasono, R. A.; Sari, NM

2018-04-01

Eusideroxylon zwagery (Lauraceae), a tropical tree species known as ulin or borneo iron wood and traditionally used for the treatment of diabetes in the Ethnic of Kutai. Plant extract was prepared by maceration using ethanol. The plant extract was evaluated its DPPH and superoxide radicals scavenging activity, the inhibition on α-glucosidase and α-amylase activity as antidiabetic potential and the analysis of the total phenolic, total flavonoids and proanthocyanidin contents. The ethanolic extract of the stem bark was 8.62% on the dry weight basis. The IC50 values of antioxidant activity of the extract in DPPH and superoxide radical scavenging mechanisms were 44.90 µg/ml and 30.47 µg/ml. In antidiabetic assay, the E. zwageri stem bark extract showed IC50 value 58.45µg/ml in ɑ-glucosidase inhibition, and 9.04 µg/ml in ɑ-amylase inhibition. Quercetin, an antidiabetic activity-having flavonoid, displayed IC50 values 2.00 µg/ml and 4.04 µg/ml in ɑ-glucosidase and ɑ-amylase inhibitory assays. In phytochemical assay, the extract had 31.28 GAE/g extract (mg), 30.48 CE/g extract (mg) and 183.3 PE/g extract (mg) for the total phenolic, total flavonoid and total proanthocyanidin contents. The limited reports of E. zwageri indicated the needs to search the active compounds from plant as potential antidiabetic agents by considering plant conservation status.

Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms.

PubMed

Ruhlman, Tracey; Lee, Seung-Bum; Jansen, Robert K; Hostetler, Jessica B; Tallon, Luke J; Town, Christopher D; Daniell, Henry

2006-08-31

Carrot (Daucus carota) is a major food crop in the US and worldwide. Its capacity for storage and its lifecycle as a biennial make it an attractive species for the introduction of foreign genes, especially for oral delivery of vaccines and other therapeutic proteins. Until recently efforts to express recombinant proteins in carrot have had limited success in terms of protein accumulation in the edible tap roots. Plastid genetic engineering offers the potential to overcome this limitation, as demonstrated by the accumulation of BADH in chromoplasts of carrot taproots to confer exceedingly high levels of salt resistance. The complete plastid genome of carrot provides essential information required for genetic engineering. Additionally, the sequence data add to the rapidly growing database of plastid genomes for assessing phylogenetic relationships among angiosperms. The complete carrot plastid genome is 155,911 bp in length, with 115 unique genes and 21 duplicated genes within the IR. There are four ribosomal RNAs, 30 distinct tRNA genes and 18 intron-containing genes. Repeat analysis reveals 12 direct and 2 inverted repeats > or = 30 bp with a sequence identity > or = 90%. Phylogenetic analysis of nucleotide sequences for 61 protein-coding genes using both maximum parsimony (MP) and maximum likelihood (ML) were performed for 29 angiosperms. Phylogenies from both methods provide strong support for the monophyly of several major angiosperm clades, including monocots, eudicots, rosids, asterids, eurosids II, euasterids I, and euasterids II. The carrot plastid genome contains a number of dispersed direct and inverted repeats scattered throughout coding and non-coding regions. This is the first sequenced plastid genome of the family Apiaceae and only the second published genome sequence of the species-rich euasterid II clade. Both MP and ML trees provide very strong support (100% bootstrap) for the sister relationship of Daucus with Panax in the euasterid II clade. These results provide the best taxon sampling of complete chloroplast genomes and the strongest support yet for the sister relationship of Caryophyllales to the asterids. The availability of the complete plastid genome sequence should facilitate improved transformation efficiency and foreign gene expression in carrot through utilization of endogenous flanking sequences and regulatory elements.

Evidence of new species for malaria vector Anopheles nuneztovari sensu lato in the Brazilian Amazon region.

PubMed

Scarpassa, Vera Margarete; Cunha-Machado, Antonio Saulo; Saraiva, José Ferreira

2016-04-12

Anopheles nuneztovari sensu lato comprises cryptic species in northern South America, and the Brazilian populations encompass distinct genetic lineages within the Brazilian Amazon region. This study investigated, based on two molecular markers, whether these lineages might actually deserve species status. Specimens were collected in five localities of the Brazilian Amazon, including Manaus, Careiro Castanho and Autazes, in the State of Amazonas; Tucuruí, in the State of Pará; and Abacate da Pedreira, in the State of Amapá, and analysed for the COI gene (Barcode region) and 12 microsatellite loci. Phylogenetic analyses were performed using the maximum likelihood (ML) approach. Intra and inter samples genetic diversity were estimated using population genetics analyses, and the genetic groups were identified by means of the ML, Bayesian and factorial correspondence analyses and the Bayesian analysis of population structure. The Barcode region dataset (N = 103) generated 27 haplotypes. The haplotype network suggested three lineages. The ML tree retrieved five monophyletic groups. Group I clustered all specimens from Manaus and Careiro Castanho, the majority of Autazes and a few from Abacate da Pedreira. Group II clustered most of the specimens from Abacate da Pedreira and a few from Autazes and Tucuruí. Group III clustered only specimens from Tucuruí (lineage III), strongly supported (97 %). Groups IV and V clustered specimens of A. nuneztovari s.s. and A. dunhami, strongly (98 %) and weakly (70 %) supported, respectively. In the second phylogenetic analysis, the sequences from GenBank, identified as A. goeldii, clustered to groups I and II, but not to group III. Genetic distances (Kimura-2 parameters) among the groups ranged from 1.60 % (between I and II) to 2.32 % (between I and III). Microsatellite data revealed very high intra-population genetic variability. Genetic distances showed the highest and significant values (P = 0.005) between Tucuruí and all the other samples, and between Abacate da Pedreira and all the other samples. Genetic distances, Bayesian (Structure and BAPS) analyses and FCA suggested three distinct biological groups, supporting the barcode region results. The two markers revealed three genetic lineages for A. nuneztovari s.l. in the Brazilian Amazon region. Lineages I and II may represent genetically distinct groups or species within A. goeldii. Lineage III may represent a new species, distinct from the A. goeldii group, and may be the most ancestral in the Brazilian Amazon. They may have differences in Plasmodium susceptibility and should therefore be investigated further.

Rapid allopolyploid radiation of moonwort ferns (Botrychium; Ophioglossaceae) revealed by PacBio sequencing of homologous and homeologous nuclear regions.

PubMed

Dauphin, Benjamin; Grant, Jason R; Farrar, Donald R; Rothfels, Carl J

2018-03-01

Polyploidy is a major speciation process in vascular plants, and is postulated to be particularly important in shaping the diversity of extant ferns. However, limitations in the availability of bi-parental markers for ferns have greatly limited phylogenetic investigation of polyploidy in this group. With a large number of allopolyploid species, the genus Botrychium is a classic example in ferns where recurrent polyploidy is postulated to have driven frequent speciation events. Here, we use PacBio sequencing and the PURC bioinformatics pipeline to capture all homeologous or allelic copies of four long (∼1 kb) low-copy nuclear regions from a sample of 45 specimens (25 diploids and 20 polyploids) representing 37 Botrychium taxa, and three outgroups. This sample includes most currently recognized Botrychium species in Europe and North America, and the majority of our specimens were genotyped with co-dominant nuclear allozymes to ensure species identification. We analyzed the sequence data using maximum likelihood (ML) and Bayesian inference (BI) concatenated-data ("gene tree") approaches to explore the relationships among Botrychium species. Finally, we estimated divergence times among Botrychium lineages and inferred the multi-labeled polyploid species tree showing the origins of the polyploid taxa, and their relationships to each other and to their diploid progenitors. We found strong support for the monophyly of the major lineages within Botrychium and identified most of the parental donors of the polyploids; these results largely corroborate earlier morphological and allozyme-based investigations. Each polyploid had at least two distinct homeologs, indicating that all sampled polyploids are likely allopolyploids (rather than autopolyploids). Our divergence-time analyses revealed that these allopolyploid lineages originated recently-within the last two million years-and thus that the genus has undergone a recent radiation, correlated with multiple independent allopolyploidizations across the phylogeny. Also, we found strong parental biases in the formation of allopolyploids, with individual diploid species participating multiple times as either the maternal or paternal donor (but not both). Finally, we discuss the role of polyploidy in the evolutionary history of Botrychium and the interspecific reproductive barriers possibly involved in these parental biases. Copyright © 2017 Elsevier Inc. All rights reserved.

Normal Theory Two-Stage ML Estimator When Data Are Missing at the Item Level

PubMed Central

Savalei, Victoria; Rhemtulla, Mijke

2017-01-01

In many modeling contexts, the variables in the model are linear composites of the raw items measured for each participant; for instance, regression and path analysis models rely on scale scores, and structural equation models often use parcels as indicators of latent constructs. Currently, no analytic estimation method exists to appropriately handle missing data at the item level. Item-level multiple imputation (MI), however, can handle such missing data straightforwardly. In this article, we develop an analytic approach for dealing with item-level missing data—that is, one that obtains a unique set of parameter estimates directly from the incomplete data set and does not require imputations. The proposed approach is a variant of the two-stage maximum likelihood (TSML) methodology, and it is the analytic equivalent of item-level MI. We compare the new TSML approach to three existing alternatives for handling item-level missing data: scale-level full information maximum likelihood, available-case maximum likelihood, and item-level MI. We find that the TSML approach is the best analytic approach, and its performance is similar to item-level MI. We recommend its implementation in popular software and its further study. PMID:29276371

Normal Theory Two-Stage ML Estimator When Data Are Missing at the Item Level.

PubMed

Savalei, Victoria; Rhemtulla, Mijke

2017-08-01

In many modeling contexts, the variables in the model are linear composites of the raw items measured for each participant; for instance, regression and path analysis models rely on scale scores, and structural equation models often use parcels as indicators of latent constructs. Currently, no analytic estimation method exists to appropriately handle missing data at the item level. Item-level multiple imputation (MI), however, can handle such missing data straightforwardly. In this article, we develop an analytic approach for dealing with item-level missing data-that is, one that obtains a unique set of parameter estimates directly from the incomplete data set and does not require imputations. The proposed approach is a variant of the two-stage maximum likelihood (TSML) methodology, and it is the analytic equivalent of item-level MI. We compare the new TSML approach to three existing alternatives for handling item-level missing data: scale-level full information maximum likelihood, available-case maximum likelihood, and item-level MI. We find that the TSML approach is the best analytic approach, and its performance is similar to item-level MI. We recommend its implementation in popular software and its further study.

Plant DNA barcodes and assessment of phylogenetic community structure of a tropical mixed dipterocarp forest in Brunei Darussalam (Borneo)

PubMed Central

Abu Salim, Kamariah; Chase, Mark W.; Dexter, Kyle G.; Pennington, R. Toby; Tan, Sylvester; Kaye, Maria Ellen; Samuel, Rosabelle

2017-01-01

DNA barcoding is a fast and reliable tool to assess and monitor biodiversity and, via community phylogenetics, to investigate ecological and evolutionary processes that may be responsible for the community structure of forests. In this study, DNA barcodes for the two widely used plastid coding regions rbcL and matK are used to contribute to identification of morphologically undetermined individuals, as well as to investigate phylogenetic structure of tree communities in 70 subplots (10 × 10m) of a 25-ha forest-dynamics plot in Brunei (Borneo, Southeast Asia). The combined matrix (rbcL + matK) comprised 555 haplotypes (from ≥154 genera, 68 families and 25 orders sensu APG, Angiosperm Phylogeny Group, 2016), making a substantial contribution to tree barcode sequences from Southeast Asia. Barcode sequences were used to reconstruct phylogenetic relationships using maximum likelihood, both with and without constraining the topology of taxonomic orders to match that proposed by the Angiosperm Phylogeny Group. A third phylogenetic tree was reconstructed using the program Phylomatic to investigate the influence of phylogenetic resolution on results. Detection of non-random patterns of community assembly was determined by net relatedness index (NRI) and nearest taxon index (NTI). In most cases, community assembly was either random or phylogenetically clustered, which likely indicates the importance to community structure of habitat filtering based on phylogenetically correlated traits in determining community structure. Different phylogenetic trees gave similar overall results, but the Phylomatic tree produced greater variation across plots for NRI and NTI values, presumably due to noise introduced by using an unresolved phylogenetic tree. Our results suggest that using a DNA barcode tree has benefits over the traditionally used Phylomatic approach by increasing precision and accuracy and allowing the incorporation of taxonomically unidentified individuals into analyses. PMID:29049301

Lethal Trap Trees and Semiochemical Repellents as Area Host Protection Strategies for Spruce Beetle (Coleoptera: Curculionidae, Scolytinae) in Utah.

PubMed

Matthew Hansen, E; Steven Munson, A; Blackford, Darren C; Wakarchuk, David; Scott Baggett, L

2016-10-01

We tested lethal trap trees and repellent semiochemicals as area treatments to protect host trees from spruce beetle (Dendroctonus rufipennis Kirby) attacks. Lethal trap tree treatments ("spray treatment") combined a spruce beetle bait with carbaryl treatment of the baited spruce. Repellent treatments ("spray-repellent") combined a baited lethal trap tree within a 16-m grid of MCH (3-methylcyclohex-2-en-1-one) and two novel spruce beetle repellents. After beetle flight, we surveyed all trees within 50 m of plot center, stratified by 10-m radius subplots, and compared attack rates to those from baited and unbaited control plots. Compared to the baited controls, spruce in the spray treatment had significantly reduced likelihood of a more severe attack classification (e.g., mass-attacked over strip-attacked or unsuccessful-attacked over unattacked). Because spruce in the spray treatment also had significantly heightened probability of more severe attack classification than those in the unbaited controls, however, we do not recommend lethal trap trees as a stand-alone beetle suppression strategy for epidemic beetle populations. Spruce in the spray-repellent treatment were slightly more likely to be classified as more severely attacked within 30 m of plot center compared to unbaited controls but, overall, had reduced probabilities of beetle attack over the entire 50-m radius plots. The semiochemical repellents deployed in this study were effective at reducing attacks on spruce within treated plots despite the presence of a centrally located spruce beetle bait. Further testing will be required to clarify operational protocols such as dose, elution rate, and release device spacing. Published by Oxford University Press on behalf of Entomological Society of America 2016. This work is written by US Government employees and is in the public domain in the US.

Effect of growth substrate, method of fermentation, and nitrogen source on lignocellulose-degrading enzymes production by white-rot basidiomycetes.

PubMed

Elisashvili, Vladimir; Kachlishvili, Eva; Penninckx, Michel

2008-11-01

The exploration of seven physiologically different white rot fungi potential to produce cellulase, xylanase, laccase, and manganese peroxidase (MnP) showed that the enzyme yield and their ratio in enzyme preparations significantly depends on the fungus species, lignocellulosic growth substrate, and cultivation method. The fruit residues were appropriate growth substrates for the production of hydrolytic enzymes and laccase. The highest endoglucanase (111 U ml(-1)) and xylanase (135 U ml(-1)) activities were revealed in submerged fermentation (SF) of banana peels by Pycnoporus coccineus. In the same cultivation conditions Cerrena maxima accumulated the highest level of laccase activity (7,620 U l(-1)). The lignified materials (wheat straw and tree leaves) appeared to be appropriate for the MnP secretion by majority basidiomycetes. With few exceptions, SF favored to hydrolases and laccase production by fungi tested whereas SSF was appropriate for the MnP accumulation. Thus, the Coriolopsis polyzona hydrolases activity increased more than threefold, while laccase yield increased 15-fold when tree leaves were undergone to SF instead SSF. The supplementation of nitrogen to the control medium seemed to have a negative effect on all enzyme production in SSF of wheat straw and tree leaves by Pleurotus ostreatus. In SF peptone and ammonium containing salts significantly increased C. polyzona and Trametes versicolor hydrolases and laccase yields. However, in most cases the supplementation of media with additional nitrogen lowered the fungi specific enzyme activities. Especially strong repression of T. versicolor MnP production was revealed.

Anacardium occidentale (cashew) pollen allergy in patients with allergic bronchial asthma.

PubMed

Fernandes, L; Mesquita, A M

1995-02-01

The cashew tree grows in abundance in the hills and plains of Goa, India. Because of the financial yield, more and more trees are being planted each year. The cashew tree flowers once a year between January and March, but pollination is mostly entomophilous. For the first time, a study was conducted to establish the possible role of the cashew pollen in triggering allergic asthma. A stock solution of pollen extract was prepared with the standard weight/volume method for intradermal skin tests and a bronchial provocation tests (BPTs). The protein content of the antigen, estimated with the use of Folin phenol reagent and a spectrophotometer, was 28.72 mg/ml. Ten healthy volunteers and 65 subjects with allergic asthma, as documented by previous positive skin test reactions to various pollens, were studied. Of the 65 patients, 26 (40%) had positive skin test reactions in various grades. BPTs were performed in 22 of the 26 patients after their baseline peak expiratory flow volume was assessed. Twenty (90.9%) patients had a positive BPT result, and the majority of patients had grade III and grade IV reactions. None of the control subjects (n = 10) had positive responses to either intradermal tests or the BPT. Serum IgE levels, estimated by ELISA, were high in patients with positive skin test responses and showed a linear correlation with cutaneous sensitivity. Control subjects showed normal levels of IgE (39.0 +/- 7.87 IU/ml). This study provided us with knowledge of an additional pollen, Anacardium occidentale, which could trigger an asthmatic response in allergic individuals.

A machine-learning approach reveals that alignment properties alone can accurately predict inference of lateral gene transfer from discordant phylogenies.

PubMed

Roettger, Mayo; Martin, William; Dagan, Tal

2009-09-01

Among the methods currently used in phylogenomic practice to detect the presence of lateral gene transfer (LGT), one of the most frequently employed is the comparison of gene tree topologies for different genes. In cases where the phylogenies for different genes are incompatible, or discordant, for well-supported branches there are three simple interpretations for the result: 1) gene duplications (paralogy) followed by many independent gene losses have occurred, 2) LGT has occurred, or 3) the phylogeny is well supported but for reasons unknown is nonetheless incorrect. Here, we focus on the third possibility by examining the properties of 22,437 published multiple sequence alignments, the Bayesian maximum likelihood trees for which either do or do not suggest the occurrence of LGT by the criterion of discordant branches. The alignments that produce discordant phylogenies differ significantly in several salient alignment properties from those that do not. Using a support vector machine, we were able to predict the inference of discordant tree topologies with up to 80% accuracy from alignment properties alone.

Multi-locus phylogeny and divergence time estimates of Enallagma damselflies (Odonata: Coenagrionidae).

PubMed

Callahan, Melissa S; McPeek, Mark A

2016-01-01

Reconstructing evolutionary patterns of species and populations provides a framework for asking questions about the impacts of climate change. Here we use a multilocus dataset to estimate gene trees under maximum likelihood and Bayesian models to obtain a robust estimate of relationships for a genus of North American damselflies, Enallagma. Using a relaxed molecular clock, we estimate the divergence times for this group. Furthermore, to account for the fact that gene tree analyses can overestimate ages of population divergences, we use a multi-population coalescent model to gain a more accurate estimate of divergence times. We also infer diversification rates using a method that allows for variation in diversification rate through time and among lineages. Our results reveal a complex evolutionary history of Enallagma, in which divergence events both predate and occur during Pleistocene climate fluctuations. There is also evidence of diversification rate heterogeneity across the tree. These divergence time estimates provide a foundation for addressing the relative significance of historical climatic events in the diversification of this genus. Copyright © 2015 Elsevier Inc. All rights reserved.

Testing the impact of morphological rate heterogeneity on ancestral state reconstruction of five floral traits in angiosperms.

PubMed

Reyes, Elisabeth; Nadot, Sophie; von Balthazar, Maria; Schönenberger, Jürg; Sauquet, Hervé

2018-06-21

Ancestral state reconstruction is an important tool to study morphological evolution and often involves estimating transition rates among character states. However, various factors, including taxonomic scale and sampling density, may impact transition rate estimation and indirectly also the probability of the state at a given node. Here, we test the influence of rate heterogeneity using maximum likelihood methods on five binary perianth characters, optimized on a phylogenetic tree of angiosperms including 1230 species sampled from all families. We compare the states reconstructed by an equal-rate (Mk1) and a two-rate model (Mk2) fitted either with a single set of rates for the whole tree or as a partitioned model, allowing for different rates on five partitions of the tree. We find strong signal for rate heterogeneity among the five subdivisions for all five characters, but little overall impact of the choice of model on reconstructed ancestral states, which indicates that most of our inferred ancestral states are the same whether heterogeneity is accounted for or not.

A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0.

PubMed

Bazinet, Adam L; Zwickl, Derrick J; Cummings, Michael P

2014-09-01

We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum-likelihood phylogenetic analysis powered by grid computing. The gateway features a garli 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The garli web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic results. Although the garli web service has been used by the research community for over three years, here we formally announce the availability of the service, describe its capabilities, highlight new features and recent improvements, and provide details about how the grid system efficiently delivers high-quality phylogenetic results. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Estimating the influence of population density and dispersal behavior on the ability to detect and monitor Agrilus planipennis (Coleoptera: Buprestidae) populations.

PubMed

Mercader, R J; Siegert, N W; McCullough, D G

2012-02-01

Emerald ash borer, Agrilus planipennis Fairmaire (Coleoptera: Buprestidae), a phloem-feeding pest of ash (Fraxinus spp.) trees native to Asia, was first discovered in North America in 2002. Since then, A. planipennis has been found in 15 states and two Canadian provinces and has killed tens of millions of ash trees. Understanding the probability of detecting and accurately delineating low density populations of A. planipennis is a key component of effective management strategies. Here we approach this issue by 1) quantifying the efficiency of sampling nongirdled ash trees to detect new infestations of A. planipennis under varying population densities and 2) evaluating the likelihood of accurately determining the localized spread of discrete A. planipennis infestations. To estimate the probability a sampled tree would be detected as infested across a gradient of A. planipennis densities, we used A. planipennis larval density estimates collected during intensive surveys conducted in three recently infested sites with known origins. Results indicated the probability of detecting low density populations by sampling nongirdled trees was very low, even when detection tools were assumed to have three-fold higher detection probabilities than nongirdled trees. Using these results and an A. planipennis spread model, we explored the expected accuracy with which the spatial extent of an A. planipennis population could be determined. Model simulations indicated a poor ability to delineate the extent of the distribution of localized A. planipennis populations, particularly when a small proportion of the population was assumed to have a higher propensity for dispersal.

Shallow microearthquakes near Chongqing, China triggered by the Rayleigh waves of the 2015 M7.8 Gorkha, Nepal earthquake

NASA Astrophysics Data System (ADS)

Han, Libo; Peng, Zhigang; Johnson, Christopher W.; Pollitz, Fred F.; Li, Lu; Wang, Baoshan; Wu, Jing; Li, Qiang; Wei, Hongmei

2017-12-01

We present a case of remotely triggered seismicity in Southwest China by the 2015/04/25 M7.8 Gorkha, Nepal earthquake. A local magnitude ML3.8 event occurred near the Qijiang district south of Chongqing city approximately 12 min after the Gorkha mainshock. Within 30 km of this ML3.8 event there are 62 earthquakes since 2009 and only 7 ML > 3 events, which corresponds to a likelihood of 0.3% for a ML > 3 on any given day by a random chance. This observation motivates us to investigate the relationship between the ML3.8 event and the Gorkha mainshock. The ML3.8 event was listed in the China Earthquake National Center (CENC) catalog and occurred at shallow depth (∼3 km). By examining high-frequency waveforms, we identify a smaller local event (∼ML 2.5) ∼ 15 s before the ML3.8 event. Both events occurred during the first two cycles of the Rayleigh waves from the Gorkha mainshock. We perform seismic event detection based on envelope function and waveform matching by using the two events as templates. Both analyses found a statistically significant rate change during the mainshock, suggesting that they were indeed dynamically triggered by the Rayleigh waves. Both events occurred during the peak normal and dilatational stress changes (∼10-30 kPa), consistent with observations of dynamic triggering in other geothermal/volcanic regions. Although other recent events (i.e., the 2011 M9.1 Tohoku-Oki earthquake) produced similar peak ground velocities, the 2015 Gorkha mainshock was the only event that produced clear dynamic triggering in this region. The triggering site is close to hydraulic fracturing wells that began production in 2013-2014. Hence we suspect that fluid injections may increase the region's susceptibility to remote dynamic triggering.

Shallow microearthquakes near Chongqing, China triggered by the Rayleigh waves of the 2015 M7.8 Gorkha, Nepal earthquake

USGS Publications Warehouse

Han, Libo; Peng, Zhigang; Johnson, Christopher W.; Pollitz, Fred; Li, Lu; Wang, Baoshan; Wu, Jing; Li, Qiang; Wei, Hongmei

2017-01-01

We present a case of remotely triggered seismicity in Southwest China by the 2015/04/25 M7.8 Gorkha, Nepal earthquake. A local magnitude ML3.8 event occurred near the Qijiang district south of Chongqing city approximately 12 min after the Gorkha mainshock. Within 30km of this ML3.8 event there are 62 earthquakes since 2009 and only 7 ML>3events, which corresponds to a likelihood of 0.3% for a ML>3on any given day by a random chance. This observation motivates us to investigate the relationship between the ML3.8 event and the Gorkha mainshock. The ML3.8 event is listed in the China Earthquake National Center (CENC) catalog and occurred at shallow depth (∼3km). By examining high-frequency waveforms, we identify a smaller local event (∼ML2.5) ∼15s before the ML3.8 event. Both events occurred during the first two cycles of the Rayleigh waves from the Gorkha mainshock. We perform seismic event detection based on envelope function and waveform matching by using the two events as templates. Both analyses found a statistically significant rate change during the mainshock, suggesting that they were indeed dynamically triggered by the Rayleigh waves. Both events occurred during the peak normal and dilatational stress changes (∼10–30 kPa), consistent with observations of dynamic triggering in other geothermal/volcanic regions. Although other recent events (i.e., the 2011 M9.1 Tohoku-Oki earthquake) produced similar peak ground velocities, the 2015 Gorkha mainshock was the only event that produced clear dynamic triggering in this region. The triggering site is close to hydraulic fracturing wells that began production in 2013–2014. Hence we suspect that fluid injections may increase the region’s susceptibility to remote dynamic triggering.

Length variation and sequence divergence in mitochondrial control region of Schizothoracine (Teleostei: Cyperinidae) species.

PubMed

Syed, Mudasir Ahmad; Bhat, Farooz Ahmad; Balkhi, Masood-ul Hassan; Bhat, Bilal Ahmad

2016-01-01

Schizothoracine fish commonly called snow trouts inhibit the entire network of snow and spring fed cool waters of Kashmir, India. Over 10 species reported earlier, only five species have been found, these include Schizothorax niger, Schizothorax esocinus, Schizothorax plagiostomus, Schizothorax curvifrons and Schizothorax labiatus. The relationship between these species is contradicting. To understand the evolutionary relation of these species, we examined the sequence information of mitochondrial D-loop of 25 individuals representing five species. Sequence alignment showed D-loop region highly variable and length variation was observed in di-nucleotide (TA)n microsatellite between and within species. Interestingly, all these species have (TA)n microsatellite not associated with longer tandem repeats at the 3' end of the mitochondrial control region and do not show heteroplasmy. Our analysis also indicates the presence of four conserved sequence blocks (CSB), CSB-D, CSB-1, CSB-II and CSB-III, four (Termination Associated Sequence) TAS motifs and 15bp pyrimidine block within the mitochondrial control region, that are highly conserved within genus Schizothorax when compared with other species. The phylogenetic analysis carried by Maximum likelihood (ML), Neighbor Joining (NJ) and Bayesian inference (BI) generated almost identical results. The resultant BI tree showed a close genetic relationship of all the five species and supports two distinct grouping of S. esocinus species. Besides the species relation, the presence of length variation in tandem repeats is attributed to differences in predicting the stability of secondary structures. The role of CSBs and TASs, reported so far as main regulatory signals, would explain the conservation of these elements in evolution.

Diagnostic value of survivin for malignant pleural effusion: a clinical study and meta-analysis.

PubMed

Tian, Panwen; Shen, Yongchun; Wan, Chun; Yang, Ting; An, Jing; Yi, Qun; Chen, Lei; Wang, Tao; Wang, Ye; Wen, Fuqiang

2014-01-01

To investigate the diagnostic accuracy of survivin for malignant pleural effusion (MPE). Pleural effusion samples were collected from 40 MPE patients and 45 non-MPE patients. Pleural levels of survivin were measured by ELISA. Literature search was performed in Pubmed and Embase to identify studies regarding the usefulness of survivin to diagnose MPE. Data were retrieved and the pooled sensitivity, specificity and other diagnostic indexes were calculated. The summary receiver operating characteristics (SROC) curve was used to determine the overall diagnostic accuracy. The pleural levels of survivin were higher in MPE patients than non-MPE patients (844.17 ± 358.30 vs. 508.08 ± 169.58 pg/ml, P < 0.05), at a cut-off value of 683.2 pg/ml, the sensitivity and specificity were 57.50% and 88.89%, respectively. A total of six studies were included in present meta-analysis, the overall diagnostic estimates were: sensitivity 0.74 (95% CI: 0.59-0.85); specificity, 0.85 (95% CI: 0.79-0.89); positive likelihood ratio, 4.79 (95% CI: 3.48-6.61); negative likelihood ratio, 0.31 (95% CI: 0.19-0.50), and diagnostic odds ratio, 15.59 (95% CI: 7.69-31.61). The area under SROC curve was 0.86 (95% CI: 0.82-0.89). Our study confirms that the pleural survivin plays a role in the diagnosis of MPE. More studies at a large scale should be performed to validate our findings.

Maximum likelihood estimation of protein kinetic parameters under weak assumptions from unfolding force spectroscopy experiments

NASA Astrophysics Data System (ADS)

Aioanei, Daniel; Samorì, Bruno; Brucale, Marco

2009-12-01

Single molecule force spectroscopy (SMFS) is extensively used to characterize the mechanical unfolding behavior of individual protein domains under applied force by pulling chimeric polyproteins consisting of identical tandem repeats. Constant velocity unfolding SMFS data can be employed to reconstruct the protein unfolding energy landscape and kinetics. The methods applied so far require the specification of a single stretching force increase function, either theoretically derived or experimentally inferred, which must then be assumed to accurately describe the entirety of the experimental data. The very existence of a suitable optimal force model, even in the context of a single experimental data set, is still questioned. Herein, we propose a maximum likelihood (ML) framework for the estimation of protein kinetic parameters which can accommodate all the established theoretical force increase models. Our framework does not presuppose the existence of a single force characteristic function. Rather, it can be used with a heterogeneous set of functions, each describing the protein behavior in the stretching time range leading to one rupture event. We propose a simple way of constructing such a set of functions via piecewise linear approximation of the SMFS force vs time data and we prove the suitability of the approach both with synthetic data and experimentally. Additionally, when the spontaneous unfolding rate is the only unknown parameter, we find a correction factor that eliminates the bias of the ML estimator while also reducing its variance. Finally, we investigate which of several time-constrained experiment designs leads to better estimators.

Experimental investigation of extended Kalman Filter combined with carrier phase recovery for 16-QAM system

NASA Astrophysics Data System (ADS)

Shu, Tong; Li, Yan; Yu, Miao; Zhang, Yifan; Zhou, Honghang; Qiu, Jifang; Guo, Hongxiang; Hong, Xiaobin; Wu, Jian

2018-02-01

Performance of Extended Kalman Filter combined with the Viterbi-Viterbi phase estimation (VVPE-EKF) for joint phase noise mitigation and amplitude noise equalization is experimental demonstrated. Experimental results show that, for 11.2 Gbaud SP-16-QAM, the proposed VVPE-EKF achieves 0.9 dB required OSNR reduction at bit error ratio (BER) of 3.8e-3 compared to the VVPE. The result of maximum likelihood combined with VVPE (VVPE-ML) is only 0.3 dB. For 28 GBaud SP-16-QAM signal, VVPE-EKF achieves 3 dB required OSNR reduction at BER=3.8e-3 (7% HD-FEC threshold) compared to VVPE. And VVPE-ML can reduce the required OSNR for 1.7 dB compared to the VVPE. VVPE-EKF outperforms DD-EKF 3.7 dB and 0.7 dB for 11.2 GBaud and 28 GBaud system, respectively.

Five-year lung function observations and associations with a smoking ban among healthy miners at high altitude (4000 m).

PubMed

Vinnikov, Denis; Blanc, Paul D; Brimkulov, Nurlan; Redding-Jones, Rupert

2013-12-01

To assess the annual lung function decline associated with the reduction of secondhand smoke exposure in a high-altitude industrial workforce. We performed pulmonary function tests annually among 109 high-altitude gold-mine workers over 5 years of follow-up. The first 3 years included greater likelihood of exposure to secondhand smoke exposure before the initiation of extensive smoking restrictions that came into force in the last 2 years of observation. In repeated measures modeling, taking into account the time elapsed in relation to the smoking ban, there was a 115 ± 9 (standard error) mL per annum decline in lung function before the ban, but a 178 ± 20 (standard error) mL per annum increase afterward (P < 0.001, both slopes). Institution of a workplace smoking ban at high altitude may be beneficial in terms of lung function decline.

Iterative Code-Aided ML Phase Estimation and Phase Ambiguity Resolution

NASA Astrophysics Data System (ADS)

Wymeersch, Henk; Moeneclaey, Marc

2005-12-01

As many coded systems operate at very low signal-to-noise ratios, synchronization becomes a very difficult task. In many cases, conventional algorithms will either require long training sequences or result in large BER degradations. By exploiting code properties, these problems can be avoided. In this contribution, we present several iterative maximum-likelihood (ML) algorithms for joint carrier phase estimation and ambiguity resolution. These algorithms operate on coded signals by accepting soft information from the MAP decoder. Issues of convergence and initialization are addressed in detail. Simulation results are presented for turbo codes, and are compared to performance results of conventional algorithms. Performance comparisons are carried out in terms of BER performance and mean square estimation error (MSEE). We show that the proposed algorithm reduces the MSEE and, more importantly, the BER degradation. Additionally, phase ambiguity resolution can be performed without resorting to a pilot sequence, thus improving the spectral efficiency.

Channel Training for Analog FDD Repeaters: Optimal Estimators and Cramér-Rao Bounds

NASA Astrophysics Data System (ADS)

Wesemann, Stefan; Marzetta, Thomas L.

2017-12-01

For frequency division duplex channels, a simple pilot loop-back procedure has been proposed that allows the estimation of the UL & DL channels at an antenna array without relying on any digital signal processing at the terminal side. For this scheme, we derive the maximum likelihood (ML) estimators for the UL & DL channel subspaces, formulate the corresponding Cram\\'er-Rao bounds and show the asymptotic efficiency of both (SVD-based) estimators by means of Monte Carlo simulations. In addition, we illustrate how to compute the underlying (rank-1) SVD with quadratic time complexity by employing the power iteration method. To enable power control for the data transmission, knowledge of the channel gains is needed. Assuming that the UL & DL channels have on average the same gain, we formulate the ML estimator for the channel norm, and illustrate its robustness against strong noise by means of simulations.

A family of chaotic pure analog coding schemes based on baker's map function

NASA Astrophysics Data System (ADS)

Liu, Yang; Li, Jing; Lu, Xuanxuan; Yuen, Chau; Wu, Jun

2015-12-01

This paper considers a family of pure analog coding schemes constructed from dynamic systems which are governed by chaotic functions—baker's map function and its variants. Various decoding methods, including maximum likelihood (ML), minimum mean square error (MMSE), and mixed ML-MMSE decoding algorithms, have been developed for these novel encoding schemes. The proposed mirrored baker's and single-input baker's analog codes perform a balanced protection against the fold error (large distortion) and weak distortion and outperform the classical chaotic analog coding and analog joint source-channel coding schemes in literature. Compared to the conventional digital communication system, where quantization and digital error correction codes are used, the proposed analog coding system has graceful performance evolution, low decoding latency, and no quantization noise. Numerical results show that under the same bandwidth expansion, the proposed analog system outperforms the digital ones over a wide signal-to-noise (SNR) range.

An evaluation of portion size estimation aids: precision, ease of use and likelihood of future use.

PubMed

Faulkner, Gemma P; Livingstone, M Barbara E; Pourshahidi, L Kirsty; Spence, Michelle; Dean, Moira; O'Brien, Sinead; Gibney, Eileen R; Wallace, Julie Mw; McCaffrey, Tracy A; Kerr, Maeve A

2016-09-01

The present study aimed to evaluate the precision, ease of use and likelihood of future use of portion size estimation aids (PSEA). A range of PSEA were used to estimate the serving sizes of a range of commonly eaten foods and rated for ease of use and likelihood of future usage. For each food, participants selected their preferred PSEA from a range of options including: quantities and measures; reference objects; measuring; and indicators on food packets. These PSEA were used to serve out various foods (e.g. liquid, amorphous, and composite dishes). Ease of use and likelihood of future use were noted. The foods were weighed to determine the precision of each PSEA. Males and females aged 18-64 years (n 120). The quantities and measures were the most precise PSEA (lowest range of weights for estimated portion sizes). However, participants preferred household measures (e.g. 200 ml disposable cup) - deemed easy to use (median rating of 5), likely to use again in future (all scored either 4 or 5 on a scale from 1='not very likely' to 5='very likely to use again') and precise (narrow range of weights for estimated portion sizes). The majority indicated they would most likely use the PSEA preparing a meal (94 %), particularly dinner (86 %) in the home (89 %; all P<0·001) for amorphous grain foods. Household measures may be precise, easy to use and acceptable aids for estimating the appropriate portion size of amorphous grain foods.

The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae)

PubMed Central

McCann, Jamie; 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. PMID:27611687

The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae).

PubMed

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.

Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics.

PubMed

Lambert, Amaury; Alexander, Helen K; Stadler, Tanja

2014-07-07

The reconstruction of phylogenetic trees based on viral genetic sequence data sequentially sampled from an epidemic provides estimates of the past transmission dynamics, by fitting epidemiological models to these trees. To our knowledge, none of the epidemiological models currently used in phylogenetics can account for recovery rates and sampling rates dependent on the time elapsed since transmission, i.e. age of infection. Here we introduce an epidemiological model where infectives leave the epidemic, by either recovery or sampling, after some random time which may follow an arbitrary distribution. We derive an expression for the likelihood of the phylogenetic tree of sampled infectives under our general epidemiological model. The analytic concept developed in this paper will facilitate inference of past epidemiological dynamics and provide an analytical framework for performing very efficient simulations of phylogenetic trees under our model. The main idea of our analytic study is that the non-Markovian epidemiological model giving rise to phylogenetic trees growing vertically as time goes by can be represented by a Markovian "coalescent point process" growing horizontally by the sequential addition of pairs of coalescence and sampling times. As examples, we discuss two special cases of our general model, described in terms of influenza and HIV epidemics. Though phrased in epidemiological terms, our framework can also be used for instance to fit macroevolutionary models to phylogenies of extant and extinct species, accounting for general species lifetime distributions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Factors Associated with Young Adults’ Pregnancy Likelihood

PubMed Central

Kitsantas, Panagiota; Lindley, Lisa L.; Wu, Huichuan

2014-01-01

OBJECTIVES While progress has been made to reduce adolescent pregnancies in the United States, rates of unplanned pregnancy among young adults (18–29 years) remain high. In this study, we assessed factors associated with perceived likelihood of pregnancy (likelihood of getting pregnant/getting partner pregnant in the next year) among sexually experienced young adults who were not trying to get pregnant and had ever used contraceptives. METHODS We conducted a secondary analysis of 660 young adults, 18–29 years old in the United States, from the cross-sectional National Survey of Reproductive and Contraceptive Knowledge. Logistic regression and classification tree analyses were conducted to generate profiles of young adults most likely to report anticipating a pregnancy in the next year. RESULTS Nearly one-third (32%) of young adults indicated they believed they had at least some likelihood of becoming pregnant in the next year. Young adults who believed that avoiding pregnancy was not very important were most likely to report pregnancy likelihood (odds ratio [OR], 5.21; 95% CI, 2.80–9.69), as were young adults for whom avoiding a pregnancy was important but not satisfied with their current contraceptive method (OR, 3.93; 95% CI, 1.67–9.24), attended religious services frequently (OR, 3.0; 95% CI, 1.52–5.94), were uninsured (OR, 2.63; 95% CI, 1.31–5.26), and were likely to have unprotected sex in the next three months (OR, 1.77; 95% CI, 1.04–3.01). DISCUSSION These results may help guide future research and the development of pregnancy prevention interventions targeting sexually experienced young adults. PMID:25782849

Effects of oxamyl on the citrus nematode, Tylenchulus semipenetrans, and on infection of sweet orange.

PubMed

Baines, R C; Small, R H

1976-04-01

Foliar sprays of 4 microg/ml oxamyl on sweet orange trees in a greenhouse slightly depressed the number of Tylenchulus semipenetrans larvae obtained from roots and soil, but similar treatments were not effective in two orchards. Soil drench treatments decreased the number of citrus nematode larvae obtained from roots or soil of citrus plants grown itt a greenhouse and in orchards. Exposure to 5-10 microg/ml of oxamyl in water was lethal to only a few second-stage larvae treated 10 days, and many second-stage larvae in 2.0 microg/ml oxamyl recovered motility when transferred to fresh water. Aqueous solutions of 50 and 100 microg/ml of oxamyl were toxic to citrus nematode larvae. Additional observations indicate that oxamyl interfered with hatch of citrus nematode larvae and was nematistatic and/or protected sweet orange roots from infection. Oxamyl degraded at different rates in two soils. The number of citrus nematode larvae that infected and developed on sweet orange roots was increased by an undetermined product of the degradation of oxamyl in soil, water, and possibly within plants. This product apparently was translocated in roots.

Mapping urban forest tree species using IKONOS imagery: preliminary results.

PubMed

Pu, Ruiliang

2011-01-01

A stepwise masking system with high-resolution IKONOS imagery was developed to identify and map urban forest tree species/groups in the City of Tampa, Florida, USA. The eight species/groups consist of sand live oak (Quercus geminata), laurel oak (Quercus laurifolia), live oak (Quercus virginiana), magnolia (Magnolia grandiflora), pine (species group), palm (species group), camphor (Cinnamomum camphora), and red maple (Acer rubrum). The system was implemented with soil-adjusted vegetation index (SAVI) threshold, textural information after running a low-pass filter, and brightness threshold of NIR band to separate tree canopies from non-vegetated areas from other vegetation types (e.g., grass/lawn) and to separate the tree canopies into sunlit and shadow areas. A maximum likelihood classifier was used to identify and map forest type and species. After IKONOS imagery was preprocessed, a total of nine spectral features were generated, including four spectral bands, three hue-intensity-saturation indices, one SAVI, and one texture image. The identified and mapped results were examined with independent ground survey data. The experimental results indicate that when classifying all the eight tree species/ groups with the high-resolution IKONOS image data, the identifying accuracy was very low and could not satisfy a practical application level, and when merging the eight species/groups into four major species/groups, the average accuracy is still low (average accuracy = 73%, overall accuracy = 86%, and κ = 0.76 with sunlit test samples). Such a low accuracy of identifying and mapping the urban tree species/groups is attributable to low spatial resolution IKONOS image data relative to tree crown size, to complex and variable background spectrum impact on crown spectra, and to shadow/shaded impact. The preliminary results imply that to improve the tree species identification accuracy and achieve a practical application level in urban area, multi-temporal (multi-seasonal) or hyperspectral data image data should be considered for use in the future.

The transmission process: A combinatorial stochastic process for the evolution of transmission trees over networks.

PubMed

Sainudiin, Raazesh; Welch, David

2016-12-07

We derive a combinatorial stochastic process for the evolution of the transmission tree over the infected vertices of a host contact network in a susceptible-infected (SI) model of an epidemic. Models of transmission trees are crucial to understanding the evolution of pathogen populations. We provide an explicit description of the transmission process on the product state space of (rooted planar ranked labelled) binary transmission trees and labelled host contact networks with SI-tags as a discrete-state continuous-time Markov chain. We give the exact probability of any transmission tree when the host contact network is a complete, star or path network - three illustrative examples. We then develop a biparametric Beta-splitting model that directly generates transmission trees with exact probabilities as a function of the model parameters, but without explicitly modelling the underlying contact network, and show that for specific values of the parameters we can recover the exact probabilities for our three example networks through the Markov chain construction that explicitly models the underlying contact network. We use the maximum likelihood estimator (MLE) to consistently infer the two parameters driving the transmission process based on observations of the transmission trees and use the exact MLE to characterize equivalence classes over the space of contact networks with a single initial infection. An exploratory simulation study of the MLEs from transmission trees sampled from three other deterministic and four random families of classical contact networks is conducted to shed light on the relation between the MLEs of these families with some implications for statistical inference along with pointers to further extensions of our models. The insights developed here are also applicable to the simplest models of "meme" evolution in online social media networks through transmission events that can be distilled from observable actions such as "likes", "mentions", "retweets" and "+1s" along with any concomitant comments. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Remote Detection and Modeling of Abrupt and Gradual Tree Mortality in the Southwestern USA

NASA Astrophysics Data System (ADS)

Muss, J. D.; Xu, C.; McDowell, N. G.

2014-12-01

Current climate models predict a warming and drying trend that has a high probability of increasing the frequency and spatial extent of tree mortality events. Field surveys can be used to identify, date, and attribute a cause of mortality to specific trees, but monetary and time constraints prevent broad-scale surveys, which are necessary to establish regional or global trends in tree mortality. This is significant because widespread forest mortality will likely lead to radical changes in evapotranspiration and surface albedo, which could compound climate change. While understanding the causes and mechanisms of tree mortality events is crucial, it is equally important to be able to detect and monitor mortality and subsequent changes to the ecosystem at broad spatial- and temporal-scales. Over the past five years our ability to remotely detect abrupt forest mortality events has improved greatly, but gradual events—such as those caused by drought or certain types of insects—are still difficult to identify. Moreover, it is virtually impossible to quantify the amount of mortality that has occurred within a mixed pixel. We have developed a system that fuses climate and satellite-derived spectral data to identify both the date and the agent of forest mortality events. This system has been used with Landsat time series data to detect both abrupt and general trends in tree loss that have occurred during the past quarter-century in northern New Mexico. It has also been used with MODIS data to identify pixels with a high likelihood of drought-caused tree mortality in the Southwestern US. These candidate pixels were then fed to ED-FRT, a coupled forest dynamics-radiative transfer model, to generate estimates of drought-induced. We demonstrate a multi-scale approach that can produce results that will be instrumental in advancing our understanding of tree mortality-climate feedbacks, and improve our ability to predict what forests could look like in the future.

Likelihood inference of non-constant diversification rates with incomplete taxon sampling.

PubMed

Höhna, Sebastian

2014-01-01

Large-scale phylogenies provide a valuable source to study background diversification rates and investigate if the rates have changed over time. Unfortunately most large-scale, dated phylogenies are sparsely sampled (fewer than 5% of the described species) and taxon sampling is not uniform. Instead, taxa are frequently sampled to obtain at least one representative per subgroup (e.g. family) and thus to maximize diversity (diversified sampling). So far, such complications have been ignored, potentially biasing the conclusions that have been reached. In this study I derive the likelihood of a birth-death process with non-constant (time-dependent) diversification rates and diversified taxon sampling. Using simulations I test if the true parameters and the sampling method can be recovered when the trees are small or medium sized (fewer than 200 taxa). The results show that the diversification rates can be inferred and the estimates are unbiased for large trees but are biased for small trees (fewer than 50 taxa). Furthermore, model selection by means of Akaike's Information Criterion favors the true model if the true rates differ sufficiently from alternative models (e.g. the birth-death model is recovered if the extinction rate is large and compared to a pure-birth model). Finally, I applied six different diversification rate models--ranging from a constant-rate pure birth process to a decreasing speciation rate birth-death process but excluding any rate shift models--on three large-scale empirical phylogenies (ants, mammals and snakes with respectively 149, 164 and 41 sampled species). All three phylogenies were constructed by diversified taxon sampling, as stated by the authors. However only the snake phylogeny supported diversified taxon sampling. Moreover, a parametric bootstrap test revealed that none of the tested models provided a good fit to the observed data. The model assumptions, such as homogeneous rates across species or no rate shifts, appear to be violated.

Phylogenetic relationships in Epidendroideae (Orchidaceae), one of the great flowering plant radiations: progressive specialization and diversification.

PubMed

Freudenstein, John V; Chase, Mark W

2015-03-01

The largest subfamily of orchids, Epidendroideae, represents one of the most significant diversifications among flowering plants in terms of pollination strategy, vegetative adaptation and number of species. Although many groups in the subfamily have been resolved, significant relationships in the tree remain unclear, limiting conclusions about diversification and creating uncertainty in the classification. This study brings together DNA sequences from nuclear, plastid and mitochrondrial genomes in order to clarify relationships, to test associations of key characters with diversification and to improve the classification. Sequences from seven loci were concatenated in a supermatrix analysis for 312 genera representing most of epidendroid diversity. Maximum-likelihood and parsimony analyses were performed on this matrix and on subsets of the data to generate trees and to investigate the effect of missing values. Statistical character-associated diversification analyses were performed. Likelihood and parsimony analyses yielded highly resolved trees that are in strong agreement and show significant support for many key clades. Many previously proposed relationships among tribes and subtribes are supported, and some new relationships are revealed. Analyses of subsets of the data suggest that the relatively high number of missing data for the full analysis is not problematic. Diversification analyses show that epiphytism is most strongly associated with diversification among epidendroids, followed by expansion into the New World and anther characters that are involved with pollinator specificity, namely early anther inflexion, cellular pollinium stalks and the superposed pollinium arrangement. All tested characters show significant association with speciation in Epidendroideae, suggesting that no single character accounts for the success of this group. Rather, it appears that a succession of key features appeared that have contributed to diversification, sometimes in parallel. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Dynamically heterogenous partitions and phylogenetic inference: an evaluation of analytical strategies with cytochrome b and ND6 gene sequences in cranes.

PubMed

Krajewski, C; Fain, M G; Buckley, L; King, D G

1999-11-01

ki ctes over whether molecular sequence data should be partitioned for phylogenetic analysis often confound two types of heterogeneity among partitions. We distinguish historical heterogeneity (i.e., different partitions have different evolutionary relationships) from dynamic heterogeneity (i.e., different partitions show different patterns of sequence evolution) and explore the impact of the latter on phylogenetic accuracy and precision with a two-gene, mitochondrial data set for cranes. The well-established phylogeny of cranes allows us to contrast tree-based estimates of relevant parameter values with estimates based on pairwise comparisons and to ascertain the effects of incorporating different amounts of process information into phylogenetic estimates. We show that codon positions in the cytochrome b and NADH dehydrogenase subunit 6 genes are dynamically heterogenous under both Poisson and invariable-sites + gamma-rates versions of the F84 model and that heterogeneity includes variation in base composition and transition bias as well as substitution rate. Estimates of transition-bias and relative-rate parameters from pairwise sequence comparisons were comparable to those obtained as tree-based maximum likelihood estimates. Neither rate-category nor mixed-model partitioning strategies resulted in a loss of phylogenetic precision relative to unpartitioned analyses. We suggest that weighted-average distances provide a computationally feasible alternative to direct maximum likelihood estimates of phylogeny for mixed-model analyses of large, dynamically heterogenous data sets. Copyright 1999 Academic Press.

Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants.

PubMed

Nickrent, D L; Parkinson, C L; Palmer, J D; Duff, R J

2000-12-01

A widely held view of land plant relationships places liverworts as the first branch of the land plant tree, whereas some molecular analyses and a cladistic study of morphological characters indicate that hornworts are the earliest land plants. To help resolve this conflict, we used parsimony and likelihood methods to analyze a 6, 095-character data set composed of four genes (chloroplast rbcL and small-subunit rDNA from all three plant genomes) from all major land plant lineages. In all analyses, significant support was obtained for the monophyly of vascular plants, lycophytes, ferns (including PSILOTUM: and EQUISETUM:), seed plants, and angiosperms. Relationships among the three bryophyte lineages were unresolved in parsimony analyses in which all positions were included and weighted equally. However, in parsimony and likelihood analyses in which rbcL third-codon-position transitions were either excluded or downweighted (due to apparent saturation), hornworts were placed as sister to all other land plants, with mosses and liverworts jointly forming the second deepest lineage. Decay analyses and Kishino-Hasegawa tests of the third-position-excluded data set showed significant support for the hornwort-basal topology over several alternative topologies, including the commonly cited liverwort-basal topology. Among the four genes used, mitochondrial small-subunit rDNA showed the lowest homoplasy and alone recovered essentially the same topology as the multigene tree. This molecular phylogeny presents new opportunities to assess paleontological evidence and morphological innovations that occurred during the early evolution of terrestrial plants.

Comparison of solid-phase cytometry and the plate count method for the evaluation of the survival of bacteria in pharmaceutical oils.

PubMed

De Prijck, K; Peeters, E; Nelis, H J

2008-12-01

To compare the survival of four bacterial strains (Escherichia coli, Proteus mirabilis, Staphylococcus aureus, Pseudomonas aeruginosa) in pharmaceutical oils, including jojoba oil/tea tree oil, carbol oil, jojoba oil and sesame oil. Oils were spiked with the test bacteria in a concentration of 10(4) CFU ml(-1). Bacteria were extracted from oils with phosphate-buffered saline containing 0.5% Tween 20. Aliquots of the pooled water layers were analysed by solid-phase cytometry and plate counting. Plate counts dropped to zero for all test strains exposed for 24 h to three of the four oils. In contrast, significant numbers of viable cells were still detected by SPC, except in the jojoba oil/tea tree oil mixture and partly in sesame oil. Exposure of bacteria for 24 h to the two oils containing an antimicrobial led to a loss of their culturability but not necessarily of their viability. The antibacterial activity of the jojoba oil/tea tree oil mixture supersedes that of carbol oil. These in vitro data suggest that the jojoba oil/tea tree oil mixture more than carbol oil inhibits bacterial proliferation when used for intermittent self-catherization.

Fluorescein angiography versus optical coherence tomography for diagnosis of uveitic macular edema.

PubMed

Kempen, John H; Sugar, Elizabeth A; Jaffe, Glenn J; Acharya, Nisha R; Dunn, James P; Elner, Susan G; Lightman, Susan L; Thorne, Jennifer E; Vitale, Albert T; Altaweel, Michael M

2013-09-01

To evaluate agreement between fluorescein angiography (FA) and optical coherence tomography (OCT) results for diagnosis of macular edema in patients with uveitis. Multicenter cross-sectional study. Four hundred seventy-nine eyes with uveitis from 255 patients. The macular status of dilated eyes with intermediate uveitis, posterior uveitis, or panuveitis was assessed via Stratus-3 OCT and FA. To evaluate agreement between the diagnostic approaches, κ statistics were used. Macular thickening (MT; center point thickness, ≥ 240 μm per reading center grading of OCT images) and macular leakage (ML; central subfield fluorescein leakage, ≥ 0.44 disc areas per reading center grading of FA images), and agreement between these outcomes in diagnosing macular edema. Optical coherence tomography (90.4%) more frequently returned usable information regarding macular edema than FA (77%) or biomicroscopy (76%). Agreement in diagnosis of MT and ML (κ = 0.44) was moderate. Macular leakage was present in 40% of cases free of MT, whereas MT was present in 34% of cases without ML. Biomicroscopic evaluation for macular edema failed to detect 40% and 45% of cases of MT and ML, respectively, and diagnosed 17% and 17% of cases with macular edema that did not have MT or ML, respectively; these results may underestimate biomicroscopic errors (ophthalmologists were not explicitly masked to OCT and FA results). Among eyes free of ML, phakic eyes without cataract rarely (4%) had MT. No factors were found that effectively ruled out ML when MT was absent. Optical coherence tomography and FA offered only moderate agreement regarding macular edema status in uveitis cases, probably because what they measure (MT and ML) are related but nonidentical macular pathologic characteristics. Given its lower cost, greater safety, and greater likelihood of obtaining usable information, OCT may be the best initial test for evaluation of suspected macular edema. However, given that ML cannot be ruled out if MT is absent and vice versa, obtaining the second test after negative results on the first seems justified when detection of ML or MT would alter management. Given that biomicroscopic evaluation for macular edema erred frequently, ancillary testing for macular edema seems indicated when knowledge of ML or MT status would affect management. Proprietary or commercial disclosure may be found after the references. Copyright © 2013 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Fluorescein angiography vs. optical coherence tomography for diagnosis of uveitic macular edema

PubMed Central

Kempen, John H.; Sugar, Elizabeth A.; Jaffe, Glenn J.; Acharya, Nisha R.; Dunn, James P.; Elner, Susan G.; Lightman, Susan L.; Thorne, Jennifer E.; Vitale, Albert T.; Altaweel, Michael M.

2013-01-01

Objective To evaluate agreement between fluorescein angiography (FA) and optical coherence tomography (OCT) for diagnosis of macular edema in patients with uveitis. Design Multicenter cross-sectional study Participants Four hundred seventy-nine eyes with uveitis of 255 patients Methods The macular status of dilated eyes with intermediate, posterior or panuveitis was assessed via Stratus-3 OCT and FA. Kappa statistics evaluated agreement between the diagnostic approaches. Main Outcome Measures Macular thickening (center point thickness ≥240 μm per reading center grading of OCT images-“MT”) and macular leakage (central subfield fluorescein leakage ≥0.44 disk areas per reading center grading of FA images-“ML”); agreement amongst these outcomes in diagnosing “macular edema.” Results OCT (90.4%) more frequently returned usable information regarding macular edema than FA (77%) and biomicroscopy (76%). Agreement in diagnosis of MT and ML (κ=0.44) was moderate. ML was present in 40% of cases free of MT, whereas MT was present in 34% of cases without ML. Biomicroscopic evaluation for macular edema failed to detect 40% and 45% of cases of MT and ML respectively and diagnosed 17% and 17% of cases with macular edema which did not have MT or ML respectively; these results may underestimate biomicroscopic errors (ophthalmologists were not explicitly masked to OCT and FA results). Among eyes free of ML, phakic eyes without cataract rarely (4%) had MT. No factors were found that effectively ruled out ML when MT was absent. Conclusion OCT and FA offered only moderate agreement regarding macular edema status in uveitis cases, probably because what they measure (MT and ML) are related but non-identical macular pathologies. Given its lower cost, greater safety, and greater likelihood of obtaining usable information, OCT may be the best initial test for evaluation of suspected macular edema. However, given that ML cannot be ruled out if MT is absent and vice versa, obtaining the second test after a negative result on the first seems justified when detection of ML or MT would alter management. Given that biomicroscopic evaluation for macular edema frequently erred, ancillary testing for macular edema seems indicated when knowledge of ML or MT status would affect management. PMID:23706700

Inhibition of protein glycation by essential oils of branchlets and fruits of Juniperus communis subsp. hemisphaerica

PubMed Central

Asgary, S.; Naderi, G.A.; Shams Ardekani, M.R.; Sahebkar, A.; Airin, A.; Aslani, S.; Kasher, T.; Emami, S.A.

2014-01-01

Oxidative stress and protein glycation play pivotal roles in the pathophysiology of diabetes mellitus and its vascular complications. The present study aimed to investigate the anti-glycation properties of essential oils obtained from different parts of Juniperus communis subsp. hemisphaerica. The branchlets of male tree (BMT) and branchlets of female (BFT) tree, and fruits of J. communis subsp. hemisphaerica were extracted using steam distillation method. The oils were phytochemically analyzed using gas chromatography-mass spectrometry. Anti-glycation properties were evaluated using hemoglobin and insulin glycation assays. Overall, 18 volatile components were identified in the J. communis subsp. hemisphaerica oils, amounting to 82.1%, 100.0% and 96.4% of the BMT, BFT and fruit oils, respectively. Promising inhibitory activity was observed from all concentrations of the tested oils in the hemoglobin and insulin glycation assays. The inhibitory activities peaked to 89.9% (BFT oil; 200 μg mL-1) and 81.0% (BFT oil; 600 μg mL-1) in the hemoglobin and insulin glycation assays, respectively. The evidence from this study suggests that essential oils obtained from the fruits and branchlets of J. communis subsp. hemisphaerica possess anti-glycation properties. These activities may find implication for the prevention and treatment of diabetic complications. PMID:25657787

Inhibition of protein glycation by essential oils of branchlets and fruits of Juniperus communis subsp. hemisphaerica.

PubMed

Asgary, S; Naderi, G A; Shams Ardekani, M R; Sahebkar, A; Airin, A; Aslani, S; Kasher, T; Emami, S A

2014-01-01

Oxidative stress and protein glycation play pivotal roles in the pathophysiology of diabetes mellitus and its vascular complications. The present study aimed to investigate the anti-glycation properties of essential oils obtained from different parts of Juniperus communis subsp. hemisphaerica. The branchlets of male tree (BMT) and branchlets of female (BFT) tree, and fruits of J. communis subsp. hemisphaerica were extracted using steam distillation method. The oils were phytochemically analyzed using gas chromatography-mass spectrometry. Anti-glycation properties were evaluated using hemoglobin and insulin glycation assays. Overall, 18 volatile components were identified in the J. communis subsp. hemisphaerica oils, amounting to 82.1%, 100.0% and 96.4% of the BMT, BFT and fruit oils, respectively. Promising inhibitory activity was observed from all concentrations of the tested oils in the hemoglobin and insulin glycation assays. The inhibitory activities peaked to 89.9% (BFT oil; 200 μg mL(-1)) and 81.0% (BFT oil; 600 μg mL(-1)) in the hemoglobin and insulin glycation assays, respectively. The evidence from this study suggests that essential oils obtained from the fruits and branchlets of J. communis subsp. hemisphaerica possess anti-glycation properties. These activities may find implication for the prevention and treatment of diabetic complications.

Identification and quantitation of asparagine and citrulline using high-performance liquid chromatography (HPLC).

PubMed

Bai, Cheng; Reilly, Charles C; Wood, Bruce W

2007-03-28

High-performance liquid chromatography (HPLC) analysis was used for identification of two problematic ureides, asparagine and citrulline. We report here a technique that takes advantage of the predictable delay in retention time of the co-asparagine/citrulline peak to enable both qualitative and quantitative analysis of asparagine and citrulline using the Platinum EPS reverse-phase C18 column (Alltech Associates). Asparagine alone is eluted earlier than citrulline alone, but when both of them are present in biological samples they may co-elute. HPLC retention times for asparagine and citrulline were influenced by other ureides in the mixture. We found that at various asparagines and citrulline ratios [= 3:1, 1:1, and 1:3; corresponding to 75:25, 50:50, and 25:75 (microMol ml(-1)/microMol ml(-1))], the resulting peak exhibited different retention times. Adjustment of ureide ratios as internal standards enables peak identification and quantification. Both chemicals were quantified in xylem sap samples of pecan [Carya illinoinensis (Wangenh.) K. Koch] trees. Analysis revealed that tree nickel nutrition status affects relative concentrations of Urea Cycle intermediates, asparagine and citrulline, present in sap. Consequently, we concluded that the HPLC methods are presented to enable qualitative and quantitative analysis of these metabolically important ureides.

The effects of raking on sugar pine mortality following prescribed fire in Sequoia and Kings Canyon National Parks, California, USA

USGS Publications Warehouse

Nesmith, Jonathan C. B.; O'Hara, Kevin L.; van Mantgem, Phillip J.; de Valpine, Perry

2010-01-01

Prescribed fire is an important tool for fuel reduction, the control of competing vegetation, and forest restoration. The accumulated fuels associated with historical fire exclusion can cause undesirably high tree mortality rates following prescribed fires and wildfires. This is especially true for sugar pine (Pinus lambertiana Douglas), which is already negatively affected by the introduced pathogen white pine blister rust (Cronartium ribicola J.C. Fisch. ex Rabenh). We tested the efficacy of raking away fuels around the base of sugar pine to reduce mortality following prescribed fire in Sequoia and Kings Canyon national parks, California, USA. This study was conducted in three prescribed fires and included 457 trees, half of which had the fuels around their bases raked away to mineral soil to 0.5 m away from the stem. Fire effects were assessed and tree mortality was recorded for three years after prescribed fires. Overall, raking had no detectable effect on mortality: raked trees averaged 30% mortality compared to 36% for unraked trees. There was a significant effect, however, between the interaction of raking and average pre-treatment forest floor fuel depth: the predicted probability of survival of a 50 cm dbh tree was 0.94 vs. 0.96 when average pre-treatment fuel depth was 0 cm for a raked and unraked tree, respectively. When average pre-treatment forest floor fuel depth was 30 cm, the predicted probability of survival for a raked 50 cm dbh tree was 0.60 compared to only 0.07 for an unraked tree. Raking did not affect mortality when fire intensity, measured as percent crown volume scorched, was very low (0% scorch) or very high (>80% scorch), but the raking treatment significantly increased the proportion of trees that survived by 9.6% for trees that burned under moderate fire intensity (1% to 80% scorch). Raking significantly reduced the likelihood of bole charring and bark beetle activity three years post fire. Fuel depth and anticipated fire intensity need to be accounted for to maximize the effectiveness of the treatments. Raking is an important management option to reduce tree mortality from prescribed fire, but is most effective under specific fuel and burning conditions.

An object-oriented approach to risk and reliability analysis : methodology and aviation safety applications.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dandini, Vincent John; Duran, Felicia Angelica; Wyss, Gregory Dane

2003-09-01

This article describes how features of event tree analysis and Monte Carlo-based discrete event simulation can be combined with concepts from object-oriented analysis to develop a new risk assessment methodology, with some of the best features of each. The resultant object-based event scenario tree (OBEST) methodology enables an analyst to rapidly construct realistic models for scenarios for which an a priori discovery of event ordering is either cumbersome or impossible. Each scenario produced by OBEST is automatically associated with a likelihood estimate because probabilistic branching is integral to the object model definition. The OBEST methodology is then applied to anmore » aviation safety problem that considers mechanisms by which an aircraft might become involved in a runway incursion incident. The resulting OBEST model demonstrates how a close link between human reliability analysis and probabilistic risk assessment methods can provide important insights into aviation safety phenomenology.« less

An Illustration of Generalised Arma (garma) Time Series Modeling of Forest Area in Malaysia

NASA Astrophysics Data System (ADS)

Pillai, Thulasyammal Ramiah; Shitan, Mahendran

Forestry is the art and science of managing forests, tree plantations, and related natural resources. The main goal of forestry is to create and implement systems that allow forests to continue a sustainable provision of environmental supplies and services. Forest area is land under natural or planted stands of trees, whether productive or not. Forest area of Malaysia has been observed over the years and it can be modeled using time series models. A new class of GARMA models have been introduced in the time series literature to reveal some hidden features in time series data. For these models to be used widely in practice, we illustrate the fitting of GARMA (1, 1; 1, δ) model to the Annual Forest Area data of Malaysia which has been observed from 1987 to 2008. The estimation of the model was done using Hannan-Rissanen Algorithm, Whittle's Estimation and Maximum Likelihood Estimation.

Automatic Centerline Extraction of Coverd Roads by Surrounding Objects from High Resolution Satellite Images

NASA Astrophysics Data System (ADS)

Kamangir, H.; Momeni, M.; Satari, M.

2017-09-01

This paper presents an automatic method to extract road centerline networks from high and very high resolution satellite images. The present paper addresses the automated extraction roads covered with multiple natural and artificial objects such as trees, vehicles and either shadows of buildings or trees. In order to have a precise road extraction, this method implements three stages including: classification of images based on maximum likelihood algorithm to categorize images into interested classes, modification process on classified images by connected component and morphological operators to extract pixels of desired objects by removing undesirable pixels of each class, and finally line extraction based on RANSAC algorithm. In order to evaluate performance of the proposed method, the generated results are compared with ground truth road map as a reference. The evaluation performance of the proposed method using representative test images show completeness values ranging between 77% and 93%.

Rearrangement moves on rooted phylogenetic networks

PubMed Central

Gambette, Philippe; van Iersel, Leo; Jones, Mark; Scornavacca, Celine

2017-01-01

Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based principles, and in a Bayesian context. Their basic components are rearrangement moves that specify all possible ways of generating alternative phylogenies from a given one, and whose fundamental property is to be able to transform, by repeated application, any phylogeny into any other phylogeny. Despite their long tradition in tree-based phylogenetics, very little research has gone into studying similar rearrangement operations for phylogenetic network—that is, phylogenies explicitly representing scenarios that include reticulate events such as hybridization, horizontal gene transfer, population admixture, and recombination. To fill this gap, we propose “horizontal” moves that ensure that every network of a certain complexity can be reached from any other network of the same complexity, and “vertical” moves that ensure reachability between networks of different complexities. When applied to phylogenetic trees, our horizontal moves—named rNNI and rSPR—reduce to the best-known moves on rooted phylogenetic trees, nearest-neighbor interchange and rooted subtree pruning and regrafting. Besides a number of reachability results—separating the contributions of horizontal and vertical moves—we prove that rNNI moves are local versions of rSPR moves, and provide bounds on the sizes of the rNNI neighborhoods. The paper focuses on the most biologically meaningful versions of phylogenetic networks, where edges are oriented and reticulation events clearly identified. Moreover, our rearrangement moves are robust to the fact that networks with higher complexity usually allow a better fit with the data. Our goal is to provide a solid basis for practical phylogenetic network reconstruction. PMID:28763439

Probabilistic Risk Assessment of Hydraulic Fracturing in Unconventional Reservoirs by Means of Fault Tree Analysis: An Initial Discussion

NASA Astrophysics Data System (ADS)

Rodak, C. M.; McHugh, R.; Wei, X.

2016-12-01

The development and combination of horizontal drilling and hydraulic fracturing has unlocked unconventional hydrocarbon reserves around the globe. These advances have triggered a number of concerns regarding aquifer contamination and over-exploitation, leading to scientific studies investigating potential risks posed by directional hydraulic fracturing activities. These studies, balanced with potential economic benefits of energy production, are a crucial source of information for communities considering the development of unconventional reservoirs. However, probabilistic quantification of the overall risk posed by hydraulic fracturing at the system level are rare. Here we present the concept of fault tree analysis to determine the overall probability of groundwater contamination or over-exploitation, broadly referred to as the probability of failure. The potential utility of fault tree analysis for the quantification and communication of risks is approached with a general application. However, the fault tree design is robust and can handle various combinations of regional-specific data pertaining to relevant spatial scales, geological conditions, and industry practices where available. All available data are grouped into quantity and quality-based impacts and sub-divided based on the stage of the hydraulic fracturing process in which the data is relevant as described by the USEPA. Each stage is broken down into the unique basic events required for failure; for example, to quantify the risk of an on-site spill we must consider the likelihood, magnitude, composition, and subsurface transport of the spill. The structure of the fault tree described above can be used to render a highly complex system of variables into a straightforward equation for risk calculation based on Boolean logic. This project shows the utility of fault tree analysis for the visual communication of the potential risks of hydraulic fracturing activities on groundwater resources.

Interspecific variation in growth responses to climate and competition of five eastern tree species.

PubMed

Rollinson, Christine R; Kaye, Margot W; Canham, Charles D

2016-04-01

Climate and competition are often presented from two opposing views of the dominant driver of individual tree growth and species distribution in temperate forests, such as those in the eastern United States. Previous studies have provided abundant evidence indicating that both factors influence tree growth, and we argue that these effects are not independent of one another and rather that interactions between climate, competition, and size best describe tree growth. To illustrate this point, we describe the growth responses of five common eastern tree species to interacting effects of temperature, precipitation, competition, and individual size using maximum likelihood estimation. Models that explicitly include interactions among these four factors explained over half of the variance in annual growth for four out of five species using annual climate. Expanding temperature and precipitation analyses to include seasonal interactions resulted in slightly improved models with a mean R2 of 0.61 (SD 0.10). Growth responses to individual factors as well their interactions varied greatly among species. For example, growth sensitivity to temperature for Quercus rubra increased with maximum annual precipitation, but other species showed no change in sensitivity or slightly reduced annual growth. Our results also indicate that three-way interactions among individual stem size, competition, and temperature may determine which of the five co-occurring species in our study could have the highest growth rate in a given year. Continued consideration and quantification of interactions among climate, competition, and individual-based characteristics are likely to increase understanding of key biological processes such as tree growth. Greater parameterization of interactions between traditionally segregated factors such as climate and competition may also help build a framework to reconcile drivers of individual-based processes such as growth with larger-scale patterns of species distribution.

In vitro and ex vivo activity of Melaleuca alternifolia against protoscoleces of Echinococcus ortleppi.

PubMed

Monteiro, Danieli Urach; Azevedo, Maria Isabel; Weiblen, Carla; DE Avila Botton, Sônia; Funk, Nadine Lysyk; DE Bona DA Silva, Cristiane; Zanette, Régis Adriel; Schwanz, Thiago Guilherme; DE LA Rue, Mário Luiz

2017-02-01

Cystic echinococcosis is a zoonotic disease of difficult diagnosis and treatment. The use of protoscolicidal agents in procedures is of utmost importance for treatment success. This study was aimed at analysing the in vitro and ex vivo activity of Melaleuca alternifolia oil (tea tree oil - TTO), its nanoemulsion formulation (NE-TTO) and its major component (terpinen-4-ol) against Echinococcus ortleppi protoscoleces obtained from cattle. Concentrations of 2·5, 5 and 10 mg mL-1 of TTO, 10 mg mL-1 of NE-TTO and 1, 1·5 and 2 mg mL-1 of terpinen-4-ol were evaluated in vitro against protoscoleces at 5, 10, 15 and 30 min. TTO was also injected directly into hydatid cysts (ex vivo analysis, n = 20) and the viability of protoscoleces was evaluated at 5, 15 and 30 min. The results indicated protoscolicidal effect at all tested formulations and concentrations. Terpinen-4-ol (2 mg mL-1) activity was superior when compared with the highest concentration of TTO. NE-TTO reached a gradual protoscolicidal effect. TTO at 20 mg mL-1 showed 90% protoscolicidal action in hydatid cysts at 5 min. The results showed that TTO affects the viability of E. ortleppi protoscoleces, suggesting a new protoscolicidal option to the treatment of cystic equinococcosis.

14-3-3η Autoantibodies: Diagnostic Use in Early Rheumatoid Arthritis.

PubMed

Maksymowych, Walter P; Boire, Gilles; van Schaardenburg, Dirkjan; Wichuk, Stephanie; Turk, Samina; Boers, Maarten; Siminovitch, Katherine A; Bykerk, Vivian; Keystone, Ed; Tak, Paul Peter; van Kuijk, Arno W; Landewé, Robert; van der Heijde, Desiree; Murphy, Mairead; Marotta, Anthony

2015-09-01

To describe the expression and diagnostic use of 14-3-3η autoantibodies in early rheumatoid arthritis (RA). 14-3-3η autoantibody levels were measured using an electrochemiluminescent multiplexed assay in 500 subjects (114 disease-modifying antirheumatic drug-naive patients with early RA, 135 with established RA, 55 healthy, 70 autoimmune, and 126 other non-RA arthropathy controls). 14-3-3η protein levels were determined in an earlier analysis. Two-tailed Student t tests and Mann-Whitney U tests compared differences among groups. Receiver-operator characteristic (ROC) curves were generated and diagnostic performance was estimated by area under the curve (AUC), as well as specificity, sensitivity, and likelihood ratios (LR) for optimal cutoffs. Median serum 14-3-3η autoantibody concentrations were significantly higher (p < 0.0001) in patients with early RA (525 U/ml) when compared with healthy controls (235 U/ml), disease controls (274 U/ml), autoimmune disease controls (274 U/ml), patients with osteoarthritis (259 U/ml), and all controls (265 U/ml). ROC curve analysis comparing early RA with healthy controls demonstrated a significant (p < 0.0001) AUC of 0.90 (95% CI 0.85-0.95). At an optimal cutoff of ≥ 380 U/ml, the ROC curve yielded a sensitivity of 73%, a specificity of 91%, and a positive LR of 8.0. Adding 14-3-3η autoantibodies to 14-3-3η protein positivity enhanced the identification of patients with early RA from 59% to 90%; addition of 14-3-3η autoantibodies to anticitrullinated protein antibodies (ACPA) and/or rheumatoid factor (RF) increased identification from 72% to 92%. Seventy-two percent of RF- and ACPA-seronegative patients were positive for 14-3-3η autoantibodies. 14-3-3η autoantibodies, alone and in combination with the 14-3-3η protein, RF, and/or ACPA identified most patients with early RA.

Inhibition effect of tea tree oil on Listeria monocytogenes growth and exotoxin proteins listeriolysin O and p60 secretion.

PubMed

Liu, Z; Meng, R; Zhao, X; Shi, C; Zhang, X; Zhang, Y; Guo, N

2016-12-01

Listeria monocytogenes (L. monocytogenes) is a Gram-positive bacterium that causes infections in humans. In this study, the effects of tea tree oil (TTO) at subinhibitory concentrations on L. monocytogenes growth and two important exotoxin proteins secreted by L. monocytogenes were researched. Treatment with half of minimal inhibitory concentration of TTO demonstrated very little or no reduction in numbers of viable ATCC 19115 cells. Listeriolysin O (LLO) and p60, were investigated. A listeriolysin assay was used to investigate the hemolytic activities of L. monocytogenes exposed to TTO, and the secretion of LLO and p60 was detected by immunoblot analysis. Additionally, real-time RT-PCR was used to analyse the influence of TTO on the transcription of LLO and p60 encoded genes hly and iap respectively. According to our experimental results, we propose that TTO could be used as a promising natural compound against L. monocytogenes and its virulence factors. This is the first report on the influence of subinhibitory concentrations of tea tree oil (TTO) on the secretion of listeriolysin O (LLO) and p60, the critical virulence factors involved in Listeria pathogenesis. The results showed that TTO at 0·25 mg ml -1 reduced the secretion of LLO and p60 to 10 and 34·9% respectively, in addtion, the transcription of hly and iap was reduced to 10 and 4·3% at 0·5 mg ml -1 respectively. We propose that TTO could be used as a promising antimicrobial compound and virulence inhibitor against L. monocytogenes. © 2016 The Society for Applied Microbiology.

Chemical Composition and Allelopathic Potential of Essential Oils from Citharexylum spinosum L. Grown in Tunisia.

PubMed

El Ayeb-Zakhama, Asma; Sakka-Rouis, Lamia; Flamini, Guido; Ben Jannet, Hichem; Harzallah-Skhiri, Fethia

2017-04-01

Citharexylum spinosum L. (Verbenaceae) also known as Citharexylum quadrangulare Jacq. or Citharexylum fruticosum L. is an exotic tree introduced many years ago in Tunisia, specially used as a street and park ornamental tree. Essential oils (EOs) were obtained by hydrodistillation of the different parts (roots, stems, leaves, flowers and fruits; drupes) collected from trees grown in the area of Monastir (Tunisia). In total, 84 compounds, representing 90.1 - 98.4% of the whole oil composition, were identified by GC-FID and GC/MS analyses. The root EO was distinguished by its high content in monoterpene hydrocarbons (α-phellandrene; 30.8%) whereas that obtained from stems was dominated by sesquiterpene hydrocarbons (cuparene; 16.4%). The leaf oil was rich in an apocarotenoid derivative (hexahydrofarnesylacetone; 26%) and an aliphatic hydrocarbon (nonadecane; 14.5%). Flowers oil was rich in esters (2-phenylethyl benzoate; 33.5%). Finally, drupes oil was rich in oxygenated sesquiterpenes (β-eudesmol; 33.1%). Flowers oil showed a significant phytotoxic effect against lettuce seeds germination, it induces a total inhibition when tested at 1 mg/ml. Root and shoot elongation seemed to be more affected than germination. The inhibition of the shoot length varied from 3.6% to 100% and that of the root from 16.1% to 100%. The highest inhibition of 100% was detected for flower oil tested at 1 mg/ml. Our in vitro studies suggest a possible and new alternative use of C. spinosum EOs in herbicidal formulations, further experiments involving field conditions are necessary to confirm its herbicidal potential. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

Empirical best linear unbiased prediction method for small areas with restricted maximum likelihood and bootstrap procedure to estimate the average of household expenditure per capita in Banjar Regency

NASA Astrophysics Data System (ADS)

Aminah, Agustin Siti; Pawitan, Gandhi; Tantular, Bertho

2017-03-01

So far, most of the data published by Statistics Indonesia (BPS) as data providers for national statistics are still limited to the district level. Less sufficient sample size for smaller area levels to make the measurement of poverty indicators with direct estimation produced high standard error. Therefore, the analysis based on it is unreliable. To solve this problem, the estimation method which can provide a better accuracy by combining survey data and other auxiliary data is required. One method often used for the estimation is the Small Area Estimation (SAE). There are many methods used in SAE, one of them is Empirical Best Linear Unbiased Prediction (EBLUP). EBLUP method of maximum likelihood (ML) procedures does not consider the loss of degrees of freedom due to estimating β with β ^. This drawback motivates the use of the restricted maximum likelihood (REML) procedure. This paper proposed EBLUP with REML procedure for estimating poverty indicators by modeling the average of household expenditures per capita and implemented bootstrap procedure to calculate MSE (Mean Square Error) to compare the accuracy EBLUP method with the direct estimation method. Results show that EBLUP method reduced MSE in small area estimation.

Empirically Derived Dehydration Scoring and Decision Tree Models for Children With Diarrhea: Assessment and Internal Validation in a Prospective Cohort Study in Dhaka, Bangladesh

PubMed Central

Glavis-Bloom, Justin; Modi, Payal; Nasrin, Sabiha; Rege, Soham; Chu, Chieh; Schmid, Christopher H; Alam, Nur H

2015-01-01

Introduction: Diarrhea remains one of the most common and most deadly conditions affecting children worldwide. Accurately assessing dehydration status is critical to determining treatment course, yet no clinical diagnostic models for dehydration have been empirically derived and validated for use in resource-limited settings. Methods: In the Dehydration: Assessing Kids Accurately (DHAKA) prospective cohort study, a random sample of children under 5 with acute diarrhea was enrolled between February and June 2014 in Bangladesh. Local nurses assessed children for clinical signs of dehydration on arrival, and then serial weights were obtained as subjects were rehydrated. For each child, the percent weight change with rehydration was used to classify subjects with severe dehydration (>9% weight change), some dehydration (3–9%), or no dehydration (<3%). Clinical variables were then entered into logistic regression and recursive partitioning models to develop the DHAKA Dehydration Score and DHAKA Dehydration Tree, respectively. Models were assessed for their accuracy using the area under their receiver operating characteristic curve (AUC) and for their reliability through repeat clinical exams. Bootstrapping was used to internally validate the models. Results: A total of 850 children were enrolled, with 771 included in the final analysis. Of the 771 children included in the analysis, 11% were classified with severe dehydration, 45% with some dehydration, and 44% with no dehydration. Both the DHAKA Dehydration Score and DHAKA Dehydration Tree had significant AUCs of 0.79 (95% CI = 0.74, 0.84) and 0.76 (95% CI = 0.71, 0.80), respectively, for the diagnosis of severe dehydration. Additionally, the DHAKA Dehydration Score and DHAKA Dehydration Tree had significant positive likelihood ratios of 2.0 (95% CI = 1.8, 2.3) and 2.5 (95% CI = 2.1, 2.8), respectively, and significant negative likelihood ratios of 0.23 (95% CI = 0.13, 0.40) and 0.28 (95% CI = 0.18, 0.44), respectively, for the diagnosis of severe dehydration. Both models demonstrated 90% agreement between independent raters and good reproducibility using bootstrapping. Conclusion: This study is the first to empirically derive and internally validate accurate and reliable clinical diagnostic models for dehydration in a resource-limited setting. After external validation, frontline providers may use these new tools to better manage acute diarrhea in children. PMID:26374802

Empirically Derived Dehydration Scoring and Decision Tree Models for Children With Diarrhea: Assessment and Internal Validation in a Prospective Cohort Study in Dhaka, Bangladesh.

PubMed

Levine, Adam C; Glavis-Bloom, Justin; Modi, Payal; Nasrin, Sabiha; Rege, Soham; Chu, Chieh; Schmid, Christopher H; Alam, Nur H

2015-08-18

Diarrhea remains one of the most common and most deadly conditions affecting children worldwide. Accurately assessing dehydration status is critical to determining treatment course, yet no clinical diagnostic models for dehydration have been empirically derived and validated for use in resource-limited settings. In the Dehydration: Assessing Kids Accurately (DHAKA) prospective cohort study, a random sample of children under 5 with acute diarrhea was enrolled between February and June 2014 in Bangladesh. Local nurses assessed children for clinical signs of dehydration on arrival, and then serial weights were obtained as subjects were rehydrated. For each child, the percent weight change with rehydration was used to classify subjects with severe dehydration (>9% weight change), some dehydration (3-9%), or no dehydration (<3%). Clinical variables were then entered into logistic regression and recursive partitioning models to develop the DHAKA Dehydration Score and DHAKA Dehydration Tree, respectively. Models were assessed for their accuracy using the area under their receiver operating characteristic curve (AUC) and for their reliability through repeat clinical exams. Bootstrapping was used to internally validate the models. A total of 850 children were enrolled, with 771 included in the final analysis. Of the 771 children included in the analysis, 11% were classified with severe dehydration, 45% with some dehydration, and 44% with no dehydration. Both the DHAKA Dehydration Score and DHAKA Dehydration Tree had significant AUCs of 0.79 (95% CI = 0.74, 0.84) and 0.76 (95% CI = 0.71, 0.80), respectively, for the diagnosis of severe dehydration. Additionally, the DHAKA Dehydration Score and DHAKA Dehydration Tree had significant positive likelihood ratios of 2.0 (95% CI = 1.8, 2.3) and 2.5 (95% CI = 2.1, 2.8), respectively, and significant negative likelihood ratios of 0.23 (95% CI = 0.13, 0.40) and 0.28 (95% CI = 0.18, 0.44), respectively, for the diagnosis of severe dehydration. Both models demonstrated 90% agreement between independent raters and good reproducibility using bootstrapping. This study is the first to empirically derive and internally validate accurate and reliable clinical diagnostic models for dehydration in a resource-limited setting. After external validation, frontline providers may use these new tools to better manage acute diarrhea in children. © Levine et al.

Testing Multivariate Adaptive Regression Splines (MARS) as a Method of Land Cover Classification of TERRA-ASTER Satellite Images.

PubMed

Quirós, Elia; Felicísimo, Angel M; Cuartero, Aurora

2009-01-01

This work proposes a new method to classify multi-spectral satellite images based on multivariate adaptive regression splines (MARS) and compares this classification system with the more common parallelepiped and maximum likelihood (ML) methods. We apply the classification methods to the land cover classification of a test zone located in southwestern Spain. The basis of the MARS method and its associated procedures are explained in detail, and the area under the ROC curve (AUC) is compared for the three methods. The results show that the MARS method provides better results than the parallelepiped method in all cases, and it provides better results than the maximum likelihood method in 13 cases out of 17. These results demonstrate that the MARS method can be used in isolation or in combination with other methods to improve the accuracy of soil cover classification. The improvement is statistically significant according to the Wilcoxon signed rank test.

Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset

PubMed Central

2011-01-01

Background The avian family Cettiidae, including the genera Cettia, Urosphena, Tesia, Abroscopus and Tickellia and Orthotomus cucullatus, has recently been proposed based on analysis of a small number of loci and species. The close relationship of most of these taxa was unexpected, and called for a comprehensive study based on multiple loci and dense taxon sampling. In the present study, we infer the relationships of all except one of the species in this family using one mitochondrial and three nuclear loci. We use traditional gene tree methods (Bayesian inference, maximum likelihood bootstrapping, parsimony bootstrapping), as well as a recently developed Bayesian species tree approach (*BEAST) that accounts for lineage sorting processes that might produce discordance between gene trees. We also analyse mitochondrial DNA for a larger sample, comprising multiple individuals and a large number of subspecies of polytypic species. Results There are many topological incongruences among the single-locus trees, although none of these is strongly supported. The multi-locus tree inferred using concatenated sequences and the species tree agree well with each other, and are overall well resolved and well supported by the data. The main discrepancy between these trees concerns the most basal split. Both methods infer the genus Cettia to be highly non-monophyletic, as it is scattered across the entire family tree. Deep intraspecific divergences are revealed, and one or two species and one subspecies are inferred to be non-monophyletic (differences between methods). Conclusions The molecular phylogeny presented here is strongly inconsistent with the traditional, morphology-based classification. The remarkably high degree of non-monophyly in the genus Cettia is likely to be one of the most extraordinary examples of misconceived relationships in an avian genus. The phylogeny suggests instances of parallel evolution, as well as highly unequal rates of morphological divergence in different lineages. This complex morphological evolution apparently misled earlier taxonomists. These results underscore the well-known but still often neglected problem of basing classifications on overall morphological similarity. Based on the molecular data, a revised taxonomy is proposed. Although the traditional and species tree methods inferred much the same tree in the present study, the assumption by species tree methods that all species are monophyletic is a limitation in these methods, as some currently recognized species might have more complex histories. PMID:22142197

A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments.

PubMed

Rajan, Vaibhav

2013-03-01

Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common practice in phylogenetic analysis. Although masking is often done manually, automated methods are necessary to handle the much larger data sets being prepared today. In this study, we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns-similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological data sets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood-based analyses. Software available upon request from the author.

A Distance Measure for Genome Phylogenetic Analysis

NASA Astrophysics Data System (ADS)

Cao, Minh Duc; Allison, Lloyd; Dix, Trevor

Phylogenetic analyses of species based on single genes or parts of the genomes are often inconsistent because of factors such as variable rates of evolution and horizontal gene transfer. The availability of more and more sequenced genomes allows phylogeny construction from complete genomes that is less sensitive to such inconsistency. For such long sequences, construction methods like maximum parsimony and maximum likelihood are often not possible due to their intensive computational requirement. Another class of tree construction methods, namely distance-based methods, require a measure of distances between any two genomes. Some measures such as evolutionary edit distance of gene order and gene content are computational expensive or do not perform well when the gene content of the organisms are similar. This study presents an information theoretic measure of genetic distances between genomes based on the biological compression algorithm expert model. We demonstrate that our distance measure can be applied to reconstruct the consensus phylogenetic tree of a number of Plasmodium parasites from their genomes, the statistical bias of which would mislead conventional analysis methods. Our approach is also used to successfully construct a plausible evolutionary tree for the γ-Proteobacteria group whose genomes are known to contain many horizontally transferred genes.

Bayesian inference on multiscale models for poisson intensity estimation: applications to photon-limited image denoising.

PubMed

Lefkimmiatis, Stamatios; Maragos, Petros; Papandreou, George

2009-08-01

We present an improved statistical model for analyzing Poisson processes, with applications to photon-limited imaging. We build on previous work, adopting a multiscale representation of the Poisson process in which the ratios of the underlying Poisson intensities (rates) in adjacent scales are modeled as mixtures of conjugate parametric distributions. Our main contributions include: 1) a rigorous and robust regularized expectation-maximization (EM) algorithm for maximum-likelihood estimation of the rate-ratio density parameters directly from the noisy observed Poisson data (counts); 2) extension of the method to work under a multiscale hidden Markov tree model (HMT) which couples the mixture label assignments in consecutive scales, thus modeling interscale coefficient dependencies in the vicinity of image edges; 3) exploration of a 2-D recursive quad-tree image representation, involving Dirichlet-mixture rate-ratio densities, instead of the conventional separable binary-tree image representation involving beta-mixture rate-ratio densities; and 4) a novel multiscale image representation, which we term Poisson-Haar decomposition, that better models the image edge structure, thus yielding improved performance. Experimental results on standard images with artificially simulated Poisson noise and on real photon-limited images demonstrate the effectiveness of the proposed techniques.

Autumnal resorption and accretion of trace metals in gallery forest tree. [Quercus macrocarpa, Quercus muehlenbergii, Fraxinus pennsylvanica, Celtis occidentalis, and Ulmus rubra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Killingbeck, K.T.

1985-02-01

Autumnal resorption and accretion of copper (Cu), iron (Fe), zinc (Zn), and manganese (Mn) were measured in the foliage of five gallery forest trees species on the Konza Prairie Research Natural Area. Presenescence and postabscission leaves from five trees each of Quercus macrocarpa, Q. muehlenbergii, Fraxinus pennsylvanica, Celtis occidentalis, and Ulmus rubra, were sampled. Three species resorbed 19, 25, and 26%, respectively, of their presenescence foliar Zn, and one species resorbed 35% of its presenescence foliar Fe. This validates the prediction made by others that Zn and Fe are withdrawn from the senescing foliage of at least some deciduous species.more » Net accretions of Cu (43, 44, 69%), Fe (36, 40%), and Mn (19, 57%) occurred during the same period. The two oak species were responsible for most of the resorption, while the three non-oak species accounted for all of the significant accretions. Such well-defined differences in element conservation may influence interspecific competition by accentuating, or compensating for, species differences in element uptake ability and element use efficiency. Demand:availability ratios proved useful in predicting the likelihood that a given element would be conserved through resorption.« less

Tongues on the EDGE: language preservation priorities based on threat and lexical distinctiveness

PubMed Central

Davies, T. Jonathan

2017-01-01

Languages are being lost at rates exceeding the global loss of biodiversity. With the extinction of a language we lose irreplaceable dimensions of culture and the insight it provides on human history and the evolution of linguistic diversity. When setting conservation goals, biologists give higher priority to species likely to go extinct. Recent methods now integrate information on species evolutionary relationships to prioritize the conservation of those with a few close relatives. Advances in the construction of language trees allow us to use these methods to develop language preservation priorities that minimize loss of linguistic diversity. The evolutionarily distinct and globally endangered (EDGE) metric, used in conservation biology, accounts for a species’ originality (evolutionary distinctiveness—ED) and its likelihood of extinction (global endangerment—GE). Here, we use a similar framework to inform priorities for language preservation by generating rankings for 350 Austronesian languages. Kavalan, Tanibili, Waropen and Sengseng obtained the highest EDGE scores, while Xârâcùù (Canala), Nengone and Palauan are among the most linguistically distinct, but are not currently threatened. We further provide a way of dealing with incomplete trees, a common issue for both species and language trees. PMID:29308253

Growing trees in child brains: graph theoretical analysis of electroencephalography-derived minimum spanning tree in 5- and 7-year-old children reflects brain maturation.

PubMed

Boersma, Maria; Smit, Dirk J A; Boomsma, Dorret I; De Geus, Eco J C; Delemarre-van de Waal, Henriette A; Stam, Cornelis J

2013-01-01

The child brain is a small-world network, which is hypothesized to change toward more ordered configurations with development. In graph theoretical studies, comparing network topologies under different conditions remains a critical point. Constructing a minimum spanning tree (MST) might present a solution, since it does not require setting a threshold and uses a fixed number of nodes and edges. In this study, the MST method is introduced to examine developmental changes in functional brain network topology in young children. Resting-state electroencephalography was recorded from 227 children twice at 5 and 7 years of age. Synchronization likelihood (SL) weighted matrices were calculated in three different frequency bands from which MSTs were constructed, which represent constructs of the most important routes for information flow in a network. From these trees, several parameters were calculated to characterize developmental change in network organization. The MST diameter and eccentricity significantly increased, while the leaf number and hierarchy significantly decreased in the alpha band with development. Boys showed significant higher leaf number, betweenness, degree and hierarchy and significant lower SL, diameter, and eccentricity than girls in the theta band. The developmental changes indicate a shift toward more decentralized line-like trees, which supports the previously hypothesized increase toward regularity of brain networks with development. Additionally, girls showed more line-like decentralized configurations, which is consistent with the view that girls are ahead of boys in brain development. MST provides an elegant method sensitive to capture subtle developmental changes in network organization without the bias of network comparison.

Diagnostic accuracy of second-generation dual-source computed tomography coronary angiography with iterative reconstructions: a real-world experience.

PubMed

Maffei, E; Martini, C; Rossi, A; Mollet, N; Lario, C; Castiglione Morelli, M; Clemente, A; Gentile, G; Arcadi, T; Seitun, S; Catalano, O; Aldrovandi, A; Cademartiri, F

2012-08-01

The authors evaluated the diagnostic accuracy of second-generation dual-source (DSCT) computed tomography coronary angiography (CTCA) with iterative reconstructions for detecting obstructive coronary artery disease (CAD). Between June 2010 and February 2011, we enrolled 160 patients (85 men; mean age 61.2±11.6 years) with suspected CAD. All patients underwent CTCA and conventional coronary angiography (CCA). For the CTCA scan (Definition Flash, Siemens), we use prospective tube current modulation and 70-100 ml of iodinated contrast material (Iomeprol 400 mgI/ ml, Bracco). Data sets were reconstructed with iterative reconstruction algorithm (IRIS, Siemens). CTCA and CCA reports were used to evaluate accuracy using the threshold for significant stenosis at ≥50% and ≥70%, respectively. No patient was excluded from the analysis. Heart rate was 64.3±11.9 bpm and radiation dose was 7.2±2.1 mSv. Disease prevalence was 30% (48/160). Sensitivity, specificity and positive and negative predictive values of CTCA in detecting significant stenosis were 90.1%, 93.3%, 53.2% and 99.1% (per segment), 97.5%, 91.2%, 61.4% and 99.6% (per vessel) and 100%, 83%, 71.6% and 100% (per patient), respectively. Positive and negative likelihood ratios at the per-patient level were 5.89 and 0.0, respectively. CTCA with second-generation DSCT in the real clinical world shows a diagnostic performance comparable with previously reported validation studies. The excellent negative predictive value and likelihood ratio make CTCA a first-line noninvasive method for diagnosing obstructive CAD.

Empirical projection-based basis-component decomposition method

NASA Astrophysics Data System (ADS)

Brendel, Bernhard; Roessl, Ewald; Schlomka, Jens-Peter; Proksa, Roland

2009-02-01

Advances in the development of semiconductor based, photon-counting x-ray detectors stimulate research in the domain of energy-resolving pre-clinical and clinical computed tomography (CT). For counting detectors acquiring x-ray attenuation in at least three different energy windows, an extended basis component decomposition can be performed in which in addition to the conventional approach of Alvarez and Macovski a third basis component is introduced, e.g., a gadolinium based CT contrast material. After the decomposition of the measured projection data into the basis component projections, conventional filtered-backprojection reconstruction is performed to obtain the basis-component images. In recent work, this basis component decomposition was obtained by maximizing the likelihood-function of the measurements. This procedure is time consuming and often unstable for excessively noisy data or low intrinsic energy resolution of the detector. Therefore, alternative procedures are of interest. Here, we introduce a generalization of the idea of empirical dual-energy processing published by Stenner et al. to multi-energy, photon-counting CT raw data. Instead of working in the image-domain, we use prior spectral knowledge about the acquisition system (tube spectra, bin sensitivities) to parameterize the line-integrals of the basis component decomposition directly in the projection domain. We compare this empirical approach with the maximum-likelihood (ML) approach considering image noise and image bias (artifacts) and see that only moderate noise increase is to be expected for small bias in the empirical approach. Given the drastic reduction of pre-processing time, the empirical approach is considered a viable alternative to the ML approach.

Sedative load and salivary secretion and xerostomia in community-dwelling older people.

PubMed

Tiisanoja, Antti; Syrjälä, Anna-Maija; Komulainen, Kaija; Hartikainen, Sirpa; Taipale, Heidi; Knuuttila, Matti; Ylöstalo, Pekka

2016-06-01

The aim was to investigate how sedative load and the total number of drugs used are related to hyposalivation and xerostomia among 75-year-old or older dentate, non-smoking, community-dwelling people. The study population consisted of 152 older people from the Oral Health GeMS study. The data were collected by interviews and clinical examinations during 2004-2005. Sedative load, which measures the cumulative effect of taking multiple drugs with sedative properties, was calculated using the Sedative Load Model. The results showed that participants with a sedative load of either 1-2 or ≥3 had an increased likelihood of having low stimulated salivary flow (<0.7 ml/min; OR: 2.4; CI: 0.6-8.6 and OR: 11; CI: 2.2-59; respectively) and low unstimulated salivary flow (<0.1 ml/min; OR: 2.7, CI: 1.0-7.4 and OR: 4.5, CI: 1.0-20, respectively) compared with participants without a sedative load. Participants with a sedative load ≥3 had an increased likelihood of having xerostomia (OR: 2.5, CI: 0.5-12) compared with participants without a sedative load. The results showed that the association between the total number of drugs and hyposalivation was weaker than the association between sedative load and hyposalivation. Sedative load is strongly related to hyposalivation and to a lesser extent with xerostomia. The adverse effects of drugs on saliva secretion are specifically related to drugs with sedative properties. © 2014 John Wiley & Sons A/S and The Gerodontology Association. Published by John Wiley & Sons Ltd.

Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

PubMed Central

Tang, Cuong Q; Humphreys, Aelys M; Fontaneto, Diego; Barraclough, Timothy G; Paradis, Emmanuel

2014-01-01

Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses. PMID:25821577

Thinning, tree-growth, and resistance to multi-year drought in a mixed-conifer forest of northern California

USGS Publications Warehouse

Vernon, Michael J.; Sherriff, Rosemary L.; van Mantgem, Phillip; Kane, Jeffrey M.

2018-01-01

Drought is an important stressor in forest ecosystems that can influence tree vigor and survival. In the U.S., forest managers use two primary management techniques to promote resistance and resilience to drought: prescribed fire and mechanical thinning. Generally applied to reduce fuels and fire hazard, treatments may also reduce competition for resources that may improve tree-growth and reduce mortality during drought. A recent severe and prolonged drought in California provided a natural experiment to investigate tree-growth responses to fuel treatments and climatic stress. We assessed tree-growth from 299 ponderosa pine (Pinus ponderosa) and Douglas-fir (Pseudotsuga menziesii) in treated and untreated stands during severe drought from 2012 to 2015 in the mixed-conifer forests of Whiskeytown National Recreation Area (WNRA) in northern California. The treatment implemented at WNRA removed 34% of live basal area through mechanical thinning with a subsequent pile burning of residual fuels. Tree-growth was positively associated with crown ratio and negatively associated with competition and a 1-year lag of climate water deficit, an index of drought. Douglas-fir generally had higher annual growth than ponderosa pine, although factors affecting growth were the same for both species. Drought resistance, expressed as the ratio between mean growth during drought and mean growth pre-drought, was higher in treated stands compared to untreated stands during both years of severe drought (2014 and 2015) for ponderosa pine but only one year (2014) for Douglas-fir. Thinning improved drought resistance, but tree size, competition and species influenced this response. On-going thinning treatments focused on fuels and fire hazard reduction are likely to be effective at promoting growth and greater drought resistance in dry mixed-conifer forests. Given the likelihood of future droughts, land managers may choose to implement similar treatments to reduce potential impacts.

Indocyanine Green Guided Pelvic Lymph Node Dissection: An Efficient Technique to Classify the Lymph Node Status of Patients with Prostate Cancer Who Underwent Radical Prostatectomy.

PubMed

Ramírez-Backhaus, Miguel; Mira Moreno, Alejandra; Gómez Ferrer, Alvaro; Calatrava Fons, Ana; Casanova, Juan; Solsona Narbón, Eduardo; Ortiz Rodríguez, Isabel María; Rubio Briones, José

2016-11-01

We evaluated the effectiveness of indocyanine green guided pelvic lymph node dissection for the optimal staging of prostate cancer and analyzed whether the technique could replace extended pelvic lymph node dissection. A solution of 25 mg indocyanine green in 5 ml sterile water was transperineally injected. Pelvic lymph node dissection was started with the indocyanine green stained nodes followed by extended pelvic lymph node dissection. Primary outcome measures were sensitivity, specificity, predictive value and likelihood ratio of a negative test of indocyanine green guided pelvic lymph node dissection. A total of 84 patients with a median age of 63.55 years and a median prostate specific antigen of 8.48 ng/ml were included in the study. Of these patients 60.7% had intermediate risk disease and 25% had high or very high risk disease. A median of 7 indocyanine green stained nodes per patient was detected (range 2 to 18) with a median of 22 nodes excised during extended pelvic lymph node dissection. Lymph node metastasis was identified in 25 patients, 23 of whom had disease properly classified by indocyanine green guided pelvic lymph node dissection. The most frequent location of indocyanine green stained nodes was the proximal internal iliac artery followed by the fossa of Marcille. The negative predictive value was 96.7% and the likelihood ratio of a negative test was 8%. Overall 1,856 nodes were removed and 603 were stained indocyanine green. Pathological examination revealed 82 metastatic nodes, of which 60% were indocyanine green stained. The negative predictive value was 97.4% but the likelihood ratio of a negative test was 58.5%. Indocyanine green guided pelvic lymph node dissection correctly staged 97% of cases. However, according to our data it cannot replace extended pelvic lymph node dissection. Nevertheless, its high negative predictive value could allow us to avoid extended pelvic lymph node dissection if we had an accurate intraoperative lymph fluorescent analysis. Copyright © 2016 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Towards a brief definition of burnout syndrome by subtypes: Development of the "Burnout Clinical Subtypes Questionnaire" (BCSQ-12)

PubMed Central

2011-01-01

Background Burnout has traditionally been described by means of the dimensions of exhaustion, cynicism and lack of eficacy from the "Maslach Burnout Inventory-General Survey" (MBI-GS). The "Burnout Clinical Subtype Questionnaire" (BCSQ-12), comprising the dimensions of overload, lack of development and neglect, is proposed as a brief means of identifying the different ways this disorder is manifested. The aim of the study is to test the construct and criterial validity of the BCSQ-12. Method A cross-sectional design was used on a multi-occupational sample of randomly selected university employees (n = 826). An exploratory factor analysis (EFA) was performed on half of the sample using the maximum likelihood (ML) method with varimax orthogonal rotation, while confirmatory factor analysis (CFA) was performed on the other half by means of the ML method. ROC curve analysis was preformed in order to assess the discriminatory capacity of BCSQ-12 when compared to MBI-GS. Cut-off points were proposed for the BCSQ-12 that optimized sensitivity and specificity. Multivariate binary logistic regression models were used to estimate effect size as an odds ratio (OR) adjusted for sociodemographic and occupational variables. Contrasts for sex and occupation were made using Mann-Whitney U and Kruskall-Wallis tests on the dimensions of both models. Results EFA offered a solution containing 3 factors with eigenvalues > 1, explaining 73.22% of variance. CFA presented the following indices: χ2 = 112.04 (p < 0.001), χ2/gl = 2.44, GFI = 0.958, AGFI = 0.929, RMSEA = 0.059, SRMR = 0.057, NFI = 0.958, NNFI = 0.963, IFI = 0.975, CFI = 0.974. The area under the ROC curve for 'overload' with respect to the 'exhaustion' was = 0.75 (95% CI = 0.71-0.79); it was = 0.80 (95% CI = 0.76-0.86) for 'lack of development' with respect to 'cynicism' and = 0.74 (95% CI = 0.70-0.78) for 'neglect' with respect to 'inefficacy'. The presence of 'overload' increased the likelihood of suffering from 'exhaustion' (OR = 5.25; 95% IC = 3.62-7.60); 'lack of development' increased the likelihood from 'cynicism' (OR = 6.77; 95% CI = 4.79-9.57); 'neglect' increased the likelihood from 'inefficacy' (OR = 5.21; 95% CI = 3.57-7.60). No differences were found with regard to sex, but there were differences depending on occupation. Conclusions Our results support the validity of the definition of burnout proposed in the BSCQ-12 through the brief differentiation of clinical subtypes. PMID:21933381

Training in cortical control of neuroprosthetic devices improves signal extraction from small neuronal ensembles.

PubMed

Helms Tillery, S I; Taylor, D M; Schwartz, A B

2003-01-01

We have recently developed a closed-loop environment in which we can test the ability of primates to control the motion of a virtual device using ensembles of simultaneously recorded neurons /29/. Here we use a maximum likelihood method to assess the information about task performance contained in the neuronal ensemble. We trained two animals to control the motion of a computer cursor in three dimensions. Initially the animals controlled cursor motion using arm movements, but eventually they learned to drive the cursor directly from cortical activity. Using a population vector (PV) based upon the relation between cortical activity and arm motion, the animals were able to control the cursor directly from the brain in a closed-loop environment, but with difficulty. We added a supervised learning method that modified the parameters of the PV according to task performance (adaptive PV), and found that animals were able to exert much finer control over the cursor motion from brain signals. Here we describe a maximum likelihood method (ML) to assess the information about target contained in neuronal ensemble activity. Using this method, we compared the information about target contained in the ensemble during arm control, during brain control early in the adaptive PV, and during brain control after the adaptive PV had settled and the animal could drive the cursor reliably and with fine gradations. During the arm-control task, the ML was able to determine the target of the movement in as few as 10% of the trials, and as many as 75% of the trials, with an average of 65%. This average dropped when the animals used a population vector to control motion of the cursor. On average we could determine the target in around 35% of the trials. This low percentage was also reflected in poor control of the cursor, so that the animal was unable to reach the target in a large percentage of trials. Supervised adjustment of the population vector parameters produced new weighting coefficients and directional tuning parameters for many neurons. This produced a much better performance of the brain-controlled cursor motion. It was also reflected in the maximum likelihood measure of cell activity, producing the correct target based only on neuronal activity in over 80% of the trials on average. The changes in maximum likelihood estimates of target location based on ensemble firing show that an animal's ability to regulate the motion of a cortically controlled device is not crucially dependent on the experimenter's ability to estimate intention from neuronal activity.

Ensemble candidate classification for the LOTAAS pulsar survey

NASA Astrophysics Data System (ADS)

Tan, C. M.; Lyon, R. J.; Stappers, B. W.; Cooper, S.; Hessels, J. W. T.; Kondratiev, V. I.; Michilli, D.; Sanidas, S.

2018-03-01

One of the biggest challenges arising from modern large-scale pulsar surveys is the number of candidates generated. Here, we implemented several improvements to the machine learning (ML) classifier previously used by the LOFAR Tied-Array All-Sky Survey (LOTAAS) to look for new pulsars via filtering the candidates obtained during periodicity searches. To assist the ML algorithm, we have introduced new features which capture the frequency and time evolution of the signal and improved the signal-to-noise calculation accounting for broad profiles. We enhanced the ML classifier by including a third class characterizing RFI instances, allowing candidates arising from RFI to be isolated, reducing the false positive return rate. We also introduced a new training data set used by the ML algorithm that includes a large sample of pulsars misclassified by the previous classifier. Lastly, we developed an ensemble classifier comprised of five different Decision Trees. Taken together these updates improve the pulsar recall rate by 2.5 per cent, while also improving the ability to identify pulsars with wide pulse profiles, often misclassified by the previous classifier. The new ensemble classifier is also able to reduce the percentage of false positive candidates identified from each LOTAAS pointing from 2.5 per cent (˜500 candidates) to 1.1 per cent (˜220 candidates).

GPSit: An automated method for evolutionary analysis of nonculturable ciliated microeukaryotes.

PubMed

Chen, Xiao; Wang, Yurui; Sheng, Yalan; Warren, Alan; Gao, Shan

2018-05-01

Microeukaryotes are among the most important components of the microbial food web in almost all aquatic and terrestrial ecosystems worldwide. In order to gain a better understanding their roles and functions in ecosystems, sequencing coupled with phylogenomic analyses of entire genomes or transcriptomes is increasingly used to reconstruct the evolutionary history and classification of these microeukaryotes and thus provide a more robust framework for determining their systematics and diversity. More importantly, phylogenomic research usually requires high levels of hands-on bioinformatics experience. Here, we propose an efficient automated method, "Guided Phylogenomic Search in trees" (GPSit), which starts from predicted protein sequences of newly sequenced species and a well-defined customized orthologous database. Compared with previous protocols, our method streamlines the entire workflow by integrating all essential and other optional operations. In so doing, the manual operation time for reconstructing phylogenetic relationships is reduced from days to several hours, compared to other methods. Furthermore, GPSit supports user-defined parameters in most steps and thus allows users to adapt it to their studies. The effectiveness of GPSit is demonstrated by incorporating available online data and new single-cell data of three nonculturable marine ciliates (Anteholosticha monilata, Deviata sp. and Diophrys scutum) under moderate sequencing coverage (~5×). Our results indicate that the former could reconstruct robust "deep" phylogenetic relationships while the latter reveals the presence of intermediate taxa in shallow relationships. Based on empirical phylogenomic data, we also used GPSit to evaluate the impact of different levels of missing data on two commonly used methods of phylogenetic analyses, maximum likelihood (ML) and Bayesian inference (BI) methods. We found that BI is less sensitive to missing data when fast-evolving sites are removed. © 2018 John Wiley & Sons Ltd.

Microevolutionary analyses of Pythium insidiosum isolates of Brazil and Thailand based on exo-1,3-β-glucanase gene.

PubMed

Ribeiro, Tatiana Corrêa; Weiblen, Carla; de Azevedo, Maria Isabel; de Avila Botton, Sônia; Robe, Lizandra Jaqueline; Pereira, Daniela Isabel Brayer; Monteiro, Danieli Urach; Lorensetti, Douglas Miotto; Santurio, Janio Morais

2017-03-01

Pythium insidiosum is an important oomycete due to its ability to infect humans and animals. It causes pythiosis, a disease of difficult treatment that occurs more frequently in humans in Thailand and in horses in Brazil. Since cell-wall components are frequently related to host shifts, we decided here to use sequences from the exo-1,3-β-glucanase gene (exo1), which encodes an immunodominant protein putatively involved in cell wall remodeling, to investigate the microevolutionary relationships of Brazilian and Thai isolates of P. insidiosum. After neutrality ratification, the phylogenetic analyses performed through Maximum parsimony (MP), Neighbor-joining (NJ), Maximum likelihood (ML), and Bayesian analysis (BA) strongly supported Thai isolates being paraphyletic in relation to those from Brazil. The structure recovered by these analyses, as well as by Spatial Analysis of Molecular Variance (SAMOVA), suggests the subdivision of P. insidiosum into three clades or population groups, which are able to explain almost 81% of the variation encountered for exo1. Moreover, the two identified Thai clades were almost as strongly differentiated between each other, as they were from the Brazilian clade, suggesting an ancient Asian subdivision. The derived positioning in the phylogenetic tree, linked to the lower diversity values and the recent expansion signs detected for the Brazilian clade, further support this clade as derived in relation to the Asian populations. Thus, although some patterns presented here are compatible with those recovered with different molecular markers, exo1 was revealed to be a good marker for studying evolution in Pythium, providing robust and strongly supported results with regard to the patterns of origin and diversification of P. insidiosum. Copyright © 2016 Elsevier B.V. All rights reserved.

Revisiting the phylogeny of Bombacoideae (Malvaceae): Novel relationships, morphologically cohesive clades, and a new tribal classification based on multilocus phylogenetic analyses.

PubMed

Carvalho-Sobrinho, Jefferson G; Alverson, William S; Alcantara, Suzana; Queiroz, Luciano P; Mota, Aline C; Baum, David A

2016-08-01

Bombacoideae (Malvaceae) is a clade of deciduous trees with a marked dominance in many forests, especially in the Neotropics. The historical lack of a well-resolved phylogenetic framework for Bombacoideae hinders studies in this ecologically important group. We reexamined phylogenetic relationships in this clade based on a matrix of 6465 nuclear (ETS, ITS) and plastid (matK, trnL-trnF, trnS-trnG) DNA characters. We used maximum parsimony, maximum likelihood, and Bayesian inference to infer relationships among 108 species (∼70% of the total number of known species). We analyzed the evolution of selected morphological traits: trunk or branch prickles, calyx shape, endocarp type, seed shape, and seed number per fruit, using ML reconstructions of their ancestral states to identify possible synapomorphies for major clades. Novel phylogenetic relationships emerged from our analyses, including three major lineages marked by fruit or seed traits: the winged-seed clade (Bernoullia, Gyranthera, and Huberodendron), the spongy endocarp clade (Adansonia, Aguiaria, Catostemma, Cavanillesia, and Scleronema), and the Kapok clade (Bombax, Ceiba, Eriotheca, Neobuchia, Pachira, Pseudobombax, Rhodognaphalon, and Spirotheca). The Kapok clade, the most diverse lineage of the subfamily, includes sister relationships (i) between Pseudobombax and "Pochota fendleri" a historically incertae sedis taxon, and (ii) between the Paleotropical genera Bombax and Rhodognaphalon, implying just two bombacoid dispersals to the Old World, the other one involving Adansonia. This new phylogenetic framework offers new insights and a promising avenue for further evolutionary studies. In view of this information, we present a new tribal classification of the subfamily, accompanied by an identification key. Copyright © 2016 Elsevier Inc. All rights reserved.

A novel mitochondrial genome of Arborophila and new insight into Arborophila evolutionary history.

PubMed

Yan, Chaochao; Mou, Biqin; Meng, Yang; Tu, Feiyun; Fan, Zhenxin; Price, Megan; Yue, Bisong; Zhang, Xiuyue

2017-01-01

The lineage of the Bar-backed Partridge (Arborophila brunneopectus) was investigated to determine the phylogenetic relationships within Arborophila as the species is centrally distributed within an area covered by the distributions of 22 South-east Asian hill partridge species. The complete mitochondrial genome (mitogenome) of A. brunneopectus was determined and compared with four other hill partridge species mitogenomes. NADH subunit genes are radical in hill partridge mitogenomes and contain the most potential positive selective sites around where variable sites are abundant. Together with 44 other mitogenomes of closely related species, we reconstructed highly resolved phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) analyses and calculated the divergence and dispersal history of Arborophila using combined datasets composed of their 13-protein coding sequences. Arborophila is reportedly be the oldest group in Phasianidae whose ancestors probably originated in Asia. A. rufipectus shares a closer relationship with A. ardens and A. brunneopectus compared to A. gingica and A. rufogularis, and such relationships were supported and profiled by NADH dehydrogenase subunit 5 (ND5). The intragenus divergence of all five Arborophila species occurred in the Miocene (16.84~5.69 Mya) when there were periods of climate cooling. We propose that these cooling events in the Miocene forced hill partridges from higher to lower altitudes, which led to geographic isolation and speciation. We demonstrated that the apparently deleterious +1 frameshift mutation in NADH dehydrogenase subunit 3 (ND3) found in all Arborophila is an ancient trait that has been eliminated in some younger lineages, such as Passeriformes. It is unclear of the biological advantages of this elimination for the relevant taxa and this requires further investigation.

Novel joint cupping clinical maneuver for ultrasonographic detection of knee joint effusions.

PubMed

Uryasev, Oleg; Joseph, Oliver C; McNamara, John P; Dallas, Apostolos P

2013-11-01

Knee effusions occur due to traumatic and atraumatic causes. Clinical diagnosis currently relies on several provocative techniques to demonstrate knee joint effusions. Portable bedside ultrasonography (US) is becoming an adjunct to diagnosis of effusions. We hypothesized that a US approach with a clinical joint cupping maneuver increases sensitivity in identifying effusions as compared to US alone. Using unembalmed cadaver knees, we injected fluid to create effusions up to 10 mL. Each effusion volume was measured in a lateral transverse location with respect to the patella. For each effusion we applied a joint cupping maneuver from an inferior approach, and re-measured the effusion. With increased volume of saline infusion, the mean depth of effusion on ultrasound imaging increased as well. Using a 2-mm cutoff, we visualized an effusion without the joint cupping maneuver at 2.5 mL and with the joint cupping technique at 1 mL. Mean effusion diameter increased on average 0.26 cm for the joint cupping maneuver as compared to without the maneuver. The effusion depth was statistically different at 2.5 and 7.5 mL (P < .05). Utilizing a joint cupping technique in combination with US is a valuable tool in assessing knee effusions, especially those of subclinical levels. Effusion measurements are complicated by uneven distribution of effusion fluid. A clinical joint cupping maneuver concentrates the fluid in one recess of the joint, increasing the likelihood of fluid detection using US. © 2013 Elsevier Inc. All rights reserved.

Water: an essential but overlooked nutrient.

PubMed

Kleiner, S M

1999-02-01

Water is an essential nutrient required for life. To be well hydrated, the average sedentary adult man must consume at least 2,900 mL (12 c) fluid per day, and the average sedentary adult woman at least 2,200 mL (9 c) fluid per day, in the form of noncaffeinated, nonalcoholic beverages, soups, and foods. Solid foods contribute approximately 1,000 mL (4 c) water, with an additional 250 mL (1 c) coming from the water of oxidation. The Nationwide Food Consumption Surveys indicate that a portion of the population may be chronically mildly dehydrated. Several factors may increase the likelihood of chronic, mild dehydration, including a poor thirst mechanism, dissatisfaction with the taste of water, common consumption of the natural diuretics caffeine and alcohol, participation in exercise, and environmental conditions. Dehydration of as little as 2% loss of body weight results in impaired physiological and performance responses. New research indicates that fluid consumption in general and water consumption in particular can have an effect on the risk of urinary stone disease; cancers of the breast, colon, and urinary tract; childhood and adolescent obesity; mitral valve prolapse; salivary gland function; and overall health in the elderly. Dietitians should be encouraged to promote and monitor fluid and water intake among all of their clients and patients through education and to help them design a fluid intake plan. The influence of chronic mild dehydration on health and disease merits further research.

Direct Position Determination of Unknown Signals in the Presence of Multipath Propagation

PubMed Central

Yu, Hongyi

2018-01-01

A novel geolocation architecture, termed “Multiple Transponders and Multiple Receivers for Multiple Emitters Positioning System (MTRE)” is proposed in this paper. Existing Direct Position Determination (DPD) methods take advantage of a rather simple channel assumption (line of sight channels with complex path attenuations) and a simplified MUltiple SIgnal Classification (MUSIC) algorithm cost function to avoid the high dimension searching. We point out that the simplified assumption and cost function reduce the positioning accuracy because of the singularity of the array manifold in a multi-path environment. We present a DPD model for unknown signals in the presence of Multi-path Propagation (MP-DPD) in this paper. MP-DPD adds non-negative real path attenuation constraints to avoid the mistake caused by the singularity of the array manifold. The Multi-path Propagation MUSIC (MP-MUSIC) method and the Active Set Algorithm (ASA) are designed to reduce the dimension of searching. A Multi-path Propagation Maximum Likelihood (MP-ML) method is proposed in addition to overcome the limitation of MP-MUSIC in the sense of a time-sensitive application. An iterative algorithm and an approach of initial value setting are given to make the MP-ML time consumption acceptable. Numerical results validate the performances improvement of MP-MUSIC and MP-ML. A closed form of the Cramér–Rao Lower Bound (CRLB) is derived as a benchmark to evaluate the performances of MP-MUSIC and MP-ML. PMID:29562601

Direct Position Determination of Unknown Signals in the Presence of Multipath Propagation.

PubMed

Du, Jianping; Wang, Ding; Yu, Wanting; Yu, Hongyi

2018-03-17

A novel geolocation architecture, termed "Multiple Transponders and Multiple Receivers for Multiple Emitters Positioning System (MTRE)" is proposed in this paper. Existing Direct Position Determination (DPD) methods take advantage of a rather simple channel assumption (line of sight channels with complex path attenuations) and a simplified MUltiple SIgnal Classification (MUSIC) algorithm cost function to avoid the high dimension searching. We point out that the simplified assumption and cost function reduce the positioning accuracy because of the singularity of the array manifold in a multi-path environment. We present a DPD model for unknown signals in the presence of Multi-path Propagation (MP-DPD) in this paper. MP-DPD adds non-negative real path attenuation constraints to avoid the mistake caused by the singularity of the array manifold. The Multi-path Propagation MUSIC (MP-MUSIC) method and the Active Set Algorithm (ASA) are designed to reduce the dimension of searching. A Multi-path Propagation Maximum Likelihood (MP-ML) method is proposed in addition to overcome the limitation of MP-MUSIC in the sense of a time-sensitive application. An iterative algorithm and an approach of initial value setting are given to make the MP-ML time consumption acceptable. Numerical results validate the performances improvement of MP-MUSIC and MP-ML. A closed form of the Cramér-Rao Lower Bound (CRLB) is derived as a benchmark to evaluate the performances of MP-MUSIC and MP-ML.

Moringa oleifera leaf extracts inhibit 6beta-hydroxylation of testosterone by CYP3A4.

PubMed

Monera, Tsitsi G; Wolfe, Alan R; Maponga, Charles C; Benet, Leslie Z; Guglielmo, Joseph

2008-10-01

Moringa oleifera is a tropical tree often used as a herbal medicine, including by people who test positive for HIV. Since herbal constituents may interact with drugs via inhibition of metabolizing enzymes, we investigated the effects of extracts of M. oleifera on the CYP3A4-mediated 6beta-hydroxylation of testosterone. Methanolic and aqueous leaf and root of extracts of M. oleifera with concentrations between 0.01 and 10 mg/ml were incubated with testosterone and mixed-sex human liver microsomes in the presence of NADPH. Metabolite concentrations were determined by HPLC. The cytotoxicity of the extracts was tested with HepG2 cells using the MTT formazan assay. Significant CYP3A4 inhibitory effects were found, with IC50 values of 0.5 and 2.5 mg/ml for leaf-methanol and leaf-water extracts, respectively. Root extracts were less active. Cytotoxicity was observed only with the leaf-water extract (IC50 = 6 mg/ml). Further investigation is warranted to elucidate the potential of M. oleifera for clinically significant interactions with antiretroviral and other drugs.

Evaluation of the antimicrobial properties of different parts of Citrus aurantifolia (lime fruit) as used locally.

PubMed

Aibinu, Ibukun; Adenipekun, Tayo; Adelowotan, Toyin; Ogunsanya, Tolu; Odugbemi, Tolu

2006-11-13

We investigated the potency of Citrus aurantifolia (Lime fruit), against pathogens, in the different forms in which this fruit plant is used locally (juice of the fruit, burnt rind of the fruit commonly known as "epa-ijebu" in the Yoruba dialect) and the oil obtained from steam distillation of the fruit. The antimicrobial activity of "epa-ijebu" in different solvents was also compared. The solvents include palm-wine (a local alcoholic drink tapped from palm trees), Seaman's Schnapps 40% alcoholic drink, water, ethanol and fermented water from 3 days soaked milled maize known as "ekan-ogi" or "omidun" in the Yoruba dialect. Antimicrobial activity was carried out by the agar well diffusion. The clinical isolates used included Anaerobic facultative bacteria, namely: Staphylococcus aureus ATCC 25213, Staphylococcus aureus, Salmonella paratyphi, Shigella flexnerii, Streptococcus faecalis, Citrobacter spp, Serratia spp, Klebsiella pneumoniae, Pseudomonas aeruginosa, Escherichia coli ATCC 25922, and Escherichia coli; Fungi such as Aspergillus niger and Candida albicans; and Anaerobes which includes Bacteroides spp, Porphyromonas spp, and Clostridium spp. Crude extracts of all solvents used varied in zones of inhibition. The anaerobes and the gram-positive bacteria were susceptible to all the extracts with minimum inhibitory concentration (MIC) ranging from 32 mg/ml-128 g/ml. The activity against the fungi showed only the oil extract potent for A. niger, while Candida albicans was susceptible to all the extracts with MIC ranging from 256 mg/ml-512 mg/ml. The gram-negatives have MIC ranging from 64 mg/ml-512 mg/ml. Minimum bactericidal concentration (MBC) ranged between 32 mg/ml to 512 mg/ml depending on isolates and extracting solvent. The oil and palm-wine extract of "epa-ijebu" showed greater activity than the other extracts. The killing rate of the schnapps extract on S. aureus and E. coli was 1 and 3.5 hours respectively.