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1

Accurate phylogenetic classification of DNA fragments based onsequence composition  

SciTech Connect

Metagenome studies have retrieved vast amounts of sequenceout of a variety of environments, leading to novel discoveries and greatinsights into the uncultured microbial world. Except for very simplecommunities, diversity makes sequence assembly and analysis a verychallenging problem. To understand the structure a 5 nd function ofmicrobial communities, a taxonomic characterization of the obtainedsequence fragments is highly desirable, yet currently limited mostly tothose sequences that contain phylogenetic marker genes. We show that forclades at the rank of domain down to genus, sequence composition allowsthe very accurate phylogenetic 10 characterization of genomic sequence.We developed a composition-based classifier, PhyloPythia, for de novophylogenetic sequence characterization and have trained it on adata setof 340 genomes. By extensive evaluation experiments we show that themethodis accurate across all taxonomic ranks considered, even forsequences that originate fromnovel organisms and are as short as 1kb.Application to two metagenome datasets 15 obtained from samples ofphosphorus-removing sludge showed that the method allows the accurateclassification at genus level of most sequence fragments from thedominant populations, while at the same time correctly characterizingeven larger parts of the samples at higher taxonomic levels.

McHardy, Alice C.; Garcia Martin, Hector; Tsirigos, Aristotelis; Hugenholtz, Philip; Rigoutsos, Isidore

2006-05-01

2

Discriminative features and classification methods for accurate classification  

Microsoft Academic Search

Automated classification and tracking approaches suffer from the high-dimensionality of the data and information space, which frequently rely upon both discriminative feature selection and efficient, accurate supervised classification strategies. Feature selection strategies have the benefit of representing the data in a modified reduced space to improve the efficacy of data mining, machine learning, and computer vision approaches. We have developed

Michael P. Dessauer; Sumeet Dua

2010-01-01

3

A higher-level phylogenetic classification of the Fungi  

Microsoft Academic Search

A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae,

David S. Hibbett; Manfred Binder; Joseph F. Bischoff; Meredith Blackwell; F. Cannon; Ove E. Eriksson; Sabine Huhndorf; Timothy James; Paul M. Kirk; Robert Lu Cking; H. Thorsten Lumbsch; François Lutzoni; P. Brandon Matheny; David J. McLaughlin; Martha J. Powell; Scott Redhead; Conrad L. Schoch; Joseph W. Spatafora; Joost A. Stalpers; Rytas Vilgalys; M. Catherine Aime; André Aptroot; Robert Bauer; Dominik Begerow; Gerald L. Benny; A Lisa; Pedro W. Crous; Yu-Cheng Dai; Walter Gams; David M. Geiser; Gareth W. Griffith; Cécile Gueidan; David L. Hawksworth; Geir Hestmark; Kentaro Hosaka; Richard A. Humber; Kevin D. Hyde; Joseph E. Ironside; Ko Ljalg; Cletus P. Kurtzman; Karl-Henrik Larsson; Robert Lichtwardt; Jolanta Mia Þ Dlikowska; Jolanta Mi?dlikowska; Andrew Miller; Jean-Marc Moncalvo; Sharon Mozley-Standridge; Franz Oberwinkler; Erast Parmasto; Valérie Reeb; Jack D. Rogers; Claude Roux; Leif Ryvarden; José Paulo Sampaio; Arthur Schüßler; Junta Sugiyama; R. Greg Thorn; Leif Tibell; Wendy A. Untereiner; Christopher Walker; Zheng Wang; Alex Weir; Michael Weiss; Merlin M. White; Katarina Winka; Yi-Jian Yao; Ning Zhang

2007-01-01

4

Discriminative features and classification methods for accurate classification  

NASA Astrophysics Data System (ADS)

Automated classification and tracking approaches suffer from the high-dimensionality of the data and information space, which frequently rely upon both discriminative feature selection and efficient, accurate supervised classification strategies. Feature selection strategies have the benefit of representing the data in a modified reduced space to improve the efficacy of data mining, machine learning, and computer vision approaches. We have developed feature-selection methods involving feature ranking and assimilation to discover reduced feature sets that produce accurate results in classification for automated classifiers with significant specificity and sensitivity. We have tested a wide range of spatial, texture, and wavelet-based feature sets for electro-optical (EO) aerial imagery and infrared (IR) land-based image sequences on several machine-learning algorithms for classification for performance evaluation and comparison. A detailed experimental evaluation is provided for the classification efficacy of the features and classifiers on the particular data sets, and is accompanied by a discussion of the particular success or failure. In the second section, we detail our novel feature set that combines moment and edge descriptors and produces high, robust accuracy when evaluated for classification. Our method leverages information previously calculated in the detection stage, which includes wavelet decomposition and texture statistics. We demonstrate the results of our feature set implementation and discuss methods for creating classifier decision rules to choose a particular classification algorithm dependent on certain operating conditions or data types adaptively.

Dessauer, Michael P.; Dua, Sumeet

2010-04-01

5

Scaling up accurate phylogenetic reconstruction from gene-order data  

Microsoft Academic Search

Motivation: Phylogenetic reconstruction from gene-order data has attracted increasing attention from both biologists and computer scientists over the last few years. Methods used in reconstruction include distance-based methods (such as neighbor-joining), parsimony methods using sequence-based encodings, Bayesian approaches, and direct optimization. The latter, pioneered by Sankoff and extended by us with the software suite GRAPPA, is the most accurate approach,

Jijun Tang; Bernard M. E. Moret

2003-01-01

6

A Functional-Phylogenetic Classification System for Transmembrane Solute Transporters  

PubMed Central

A comprehensive classification system for transmembrane molecular transporters has been developed and recently approved by the transport panel of the nomenclature committee of the International Union of Biochemistry and Molecular Biology. This system is based on (i) transporter class and subclass (mode of transport and energy coupling mechanism), (ii) protein phylogenetic family and subfamily, and (iii) substrate specificity. Almost all of the more than 250 identified families of transporters include members that function exclusively in transport. Channels (115 families), secondary active transporters (uniporters, symporters, and antiporters) (78 families), primary active transporters (23 families), group translocators (6 families), and transport proteins of ill-defined function or of unknown mechanism (51 families) constitute distinct categories. Transport mode and energy coupling prove to be relatively immutable characteristics and therefore provide primary bases for classification. Phylogenetic grouping reflects structure, function, mechanism, and often substrate specificity and therefore provides a reliable secondary basis for classification. Substrate specificity and polarity of transport prove to be more readily altered during evolutionary history and therefore provide a tertiary basis for classification. With very few exceptions, a phylogenetic family of transporters includes members that function by a single transport mode and energy coupling mechanism, although a variety of substrates may be transported, sometimes with either inwardly or outwardly directed polarity. In this review, I provide cross-referencing of well-characterized constituent transporters according to (i) transport mode, (ii) energy coupling mechanism, (iii) phylogenetic grouping, and (iv) substrates transported. The structural features and distribution of recognized family members throughout the living world are also evaluated. The tabulations should facilitate familial and functional assignments of newly sequenced transport proteins that will result from future genome sequencing projects.

Saier, Milton H.

2000-01-01

7

Novel animal papillomavirus sequences and accurate phylogenetic placement.  

PubMed

All amniotes are probably infected by specific papillomaviruses (PVs), but knowledge about PV diversity remains sparse. An insufficient taxon sampling, and a focus on humans as hosts, may perturb phylogenetic analyses leading to wrong conclusions about PV evolution. We performed a systematic approach to explore the diversity of PVs combining rolling circle amplification with the use of "universal" primers to search for the presence of novel PV sequences in animal samples. We communicate 12 sequences putatively corresponding to novel PVs gained from 10 host species in eight mammal families: Bovidae, Canidae, Cervidae, Equidae, Hominidae, Phocoenidae, Procyonidae and Pteropodidae. The phylogenetic position of the new sequences was inferred with an evolutionary placement algorithm under a Maximum Likelihood framework using a pre-computed, well-resolved tree constructed with the E1-E2-L1 gene sequences as a backbone. The new sequences were phylogenetically diverse and could be respectively placed with confidence within all four PV crown groups. The prevailing presence of sequences from the crown groups Alpha+Omikron-PVs and Beta+Xi-PVs may correspond to an increased viral diversity in these taxa, or rather reflect a combination of anthropocentric bias and preferential amplification from commonly used "universal" primers. Our results combined with literature data support the view that the number and diversity of animal PVs is overwhelmingly large. PMID:22960206

Mengual-Chuliá, Beatriz; García-Pérez, Raquel; Gottschling, Marc; Nindl, Ingo; Bravo, Ignacio G

2012-12-01

8

Phylogenetic classification of Cordyceps and the clavicipitaceous fungi  

PubMed Central

Cordyceps, comprising over 400 species, was historically classified in the Clavicipitaceae, based on cylindrical asci, thickened ascus apices and filiform ascospores, which often disarticulate into part-spores. Cordyceps was characterized by the production of well-developed often stipitate stromata and an ecology as a pathogen of arthropods and Elaphomyces with infrageneric classifications emphasizing arrangement of perithecia, ascospore morphology and host affiliation. To refine the classification of Cordyceps and the Clavicipitaceae, the phylogenetic relationships of 162 taxa were estimated based on analyses consisting of five to seven loci, including the nuclear ribosomal small and large subunits (nrSSU and nrLSU), the elongation factor 1? (tef1), the largest and the second largest subunits of RNA polymerase II (rpb1 and rpb2), ?-tubulin (tub), and mitochondrial ATP6 (atp6). Our results strongly support the existence of three clavicipitaceous clades and reject the monophyly of both Cordyceps and Clavicipitaceae. Most diagnostic characters used in current classifications of Cordyceps (e.g., arrangement of perithecia, ascospore fragmentation, etc.) were not supported as being phylogenetically informative; the characters that were most consistent with the phylogeny were texture, pigmentation and morphology of stromata. Therefore, we revise the taxonomy of Cordyceps and the Clavicipitaceae to be consistent with the multi-gene phylogeny. The family Cordycipitaceae is validated based on the type of Cordyceps, C. militaris, and includes most Cordyceps species that possess brightly coloured, fleshy stromata. The new family Ophiocordycipitaceae is proposed based on Ophiocordyceps Petch, which we emend. The majority of species in this family produce darkly pigmented, tough to pliant stromata that often possess aperithecial apices. The new genus Elaphocordyceps is proposed for a subclade of the Ophiocordycipitaceae, which includes all species of Cordyceps that parasitize the fungal genus Elaphomyces and some closely related species that parasitize arthropods. The family Clavicipitaceae s. s. is emended and includes the core clade of grass symbionts (e.g., Balansia, Claviceps, Epichloë, etc.), and the entomopathogenic genus Hypocrella and relatives. In addition, the new genus Metacordyceps is proposed for Cordyceps species that are closely related to the grass symbionts in the Clavicipitaceae s. s. Metacordyceps includes teleomorphs linked to Metarhizium and other closely related anamorphs. Two new species are described, and lists of accepted names for species in Cordyceps, Elaphocordyceps, Metacordyceps and Ophiocordyceps are provided.

Sung, Gi-Ho; Hywel-Jones, Nigel L.; Sung, Jae-Mo; Luangsa-ard, J. Jennifer; Shrestha, Bhushan; Spatafora, Joseph W.

2007-01-01

9

Optimal selection of mother wavelet for accurate infant cry classification.  

PubMed

Wavelet theory is emerging as one of the prevalent tool in signal and image processing applications. However, the most suitable mother wavelet for these applications is still a relative question mark amongst researchers. Selection of best mother wavelet through parameterization leads to better findings for the analysis in comparison to random selection. The objective of this article is to compare the performance of the existing members of mother wavelets and to select the most suitable mother wavelet for accurate infant cry classification. Optimal wavelet is found using three different criteria namely the degree of similarity of mother wavelets, regularity of mother wavelets and accuracy of correct recognition during classification processes. Recorded normal and pathological infant cry signals are decomposed into five levels using wavelet packet transform. Energy and entropy features are extracted at different sub bands of cry signals and their effectiveness are tested with four supervised neural network architectures. Findings of this study expound that, the Finite impulse response based approximation of Meyer is the best wavelet candidate for accurate infant cry classification analysis. PMID:24691930

Saraswathy, J; Hariharan, M; Nadarajaw, Thiyagar; Khairunizam, Wan; Yaacob, Sazali

2014-06-01

10

Fast and accurate text classification via multiple linear discriminant projections  

Microsoft Academic Search

Support vector machines (SVMs) have shown superb\\u000a performance for text classification tasks. They are\\u000a accurate, robust, and quick to apply to test instances.\\u000a Their only potential drawback is their training time and\\u000a memory requirement. For n training instances held in\\u000a memory, the best-known SVM implementations take time\\u000a proportional to n a , where a is typically between 1.8 and\\u000a 2.1.

Soumen Chakrabarti; Shourya Roy; Mahesh V. Soundalgekar

2002-01-01

11

Phylogenetics, DNA, Classification And the Genus Hemerocallis1  

Microsoft Academic Search

The genus Hemerocallis has had various attempts at classification since the time of Stout. The primary approach has been via phenotypic methods and Erhart has recently proposed an alternative classification to Stout. With the introduction of various genetic methods for classifying the genus, a dendrogram has been proposed using the AFLP methods of genetic sampling. This paper reviews the various

Terrence P McGarty

12

Short Interspersed Elements (SINEs) in Plants: Origin, Classification, and Use as Phylogenetic Markers  

Microsoft Academic Search

Short interspersed elements (SINEs) are a class of dispersed mobile sequences that use RNA as an intermedi- ate in an amplification process called retroposition. The presence-absence of a SINE at a given locus has been used as a meaningful classification criterion to evaluate phylogenetic relations among species. We review here recent developments in the characterisation of plant SINEs and their

Jean-Marc Deragon; Xiaoyu Zhang

2006-01-01

13

Phylogenetic classification of peltigeralean fungi (Peltigerales, Ascomycota) based on ribosomal RNA small and large subunits  

Microsoft Academic Search

To provide a comprehensive molecular phylogeny for peltigeralean fungi and to establish a classification based on monophyly, phylogenetic analyses were carried out on sequences from the nuclear ribosomal large (LSU) and small (SSU) subunits obtained from 113 individuals that represent virtually all main lineages of ascomycetes. Analyses were also conducted on a subset of 77 individuals in which the ingroup

JOLANTA MIADLIKOWSKA; F. Lutzoni

2004-01-01

14

Phylogenetics  

NSDL National Science Digital Library

This activity lets learners participate in the process of reconstructing a phylogenetic tree and introduces them to several core bioinformatics concepts, particularly in relation to evolution. Groups of learners (at least 10) repeat a secret message (five to seven similar-sounding words) like the game "Telephone". In this version of the game, however, learners write and then code what they hear, creating a model of a phylogenetic tree and using a species distance matrix. This resource includes background information about phylogenetic trees, maximum parsimony, and matrix theory (see page 6-7 of PDF).

Becker, Katrin; Becker, Jim; University, Truman S.

2005-01-01

15

Phylogenetics  

Microsoft Academic Search

The recent rapid expansion in the DNA and protein databases, arising from large-scale genomic and metagenomic sequence projects,\\u000a has forced significant development in the field of phylogenetics: the study of the evolutionary relatedness of the planet’s\\u000a inhabitants. Advances in phylogenetic analysis have greatly transformed our view of the landscape of evolutionary biology,\\u000a transcending the view of the tree of life

Roy D. Sleator

2011-01-01

16

Phylogeny and phylogenetic classification of the antbirds, ovenbirds, woodcreepers, and allies (Aves: Passeriformes: Infraorder Furnariides)  

USGS Publications Warehouse

The infraorder Furnariides is a diverse group of suboscine passerine birds comprising a substantial component of the Neotropical avifauna. The included species encompass a broad array of morphologies and behaviours, making them appealing for evolutionary studies, but the size of the group (ca. 600 species) has limited well-sampled higher-level phylogenetic studies. Using DNA sequence data from the nuclear RAG-1 and RAG-2 exons, we undertook a phylogenetic analysis of the Furnariides sampling 124 (more than 88%) of the genera. Basal relationships among family-level taxa differed depending on phylogenetic method, but all topologies had little nodal support, mirroring the results from earlier studies in which discerning relationships at the base of the radiation was also difficult. In contrast, branch support for family-rank taxa and for many relationships within those clades was generally high. Our results support the Melanopareidae and Grallariidae as distinct from the Rhinocryptidae and Formicariidae, respectively. Within the Furnariides our data contradict some recent phylogenetic hypotheses and suggest that further study is needed to resolve these discrepancies. Of the few genera represented by multiple species, several were not monophyletic, indicating that additional systematic work remains within furnariine families and must include dense taxon sampling. We use this study as a basis for proposing a new phylogenetic classification for the group and in the process erect new family-group names for clades having high branch support across methods. ?? 2009 The Willi Hennig Society.

Moyle, R. G.; Chesser, R. T.; Brumfield, R. T.; Tello, J. G.; Marchese, D. J.; Cracraft, J.

2009-01-01

17

Phylogenetic Analysis and Classification of the Fungal bHLH Domain  

PubMed Central

The basic Helix-Loop-Helix (bHLH) domain is an essential highly conserved DNA-binding domain found in many transcription factors in all eukaryotic organisms. The bHLH domain has been well studied in the Animal and Plant Kingdoms but has yet to be characterized within Fungi. Herein, we obtained and evaluated the phylogenetic relationship of 490 fungal-specific bHLH containing proteins from 55 whole genome projects composed of 49 Ascomycota and 6 Basidiomycota organisms. We identified 12 major groupings within Fungi (F1–F12); identifying conserved motifs and functions specific to each group. Several classification models were built to distinguish the 12 groups and elucidate the most discerning sites in the domain. Performance testing on these models, for correct group classification, resulted in a maximum sensitivity and specificity of 98.5% and 99.8%, respectively. We identified 12 highly discerning sites and incorporated those into a set of rules (simplified model) to classify sequences into the correct group. Conservation of amino acid sites and phylogenetic analyses established that like plant bHLH proteins, fungal bHLH–containing proteins are most closely related to animal Group B. The models used in these analyses were incorporated into a software package, the source code for which is available at www.fungalgenomics.ncsu.edu.

Sailsbery, Joshua K.; Atchley, William R.; Dean, Ralph A.

2012-01-01

18

Rapid phylogenetic and functional classification of short genomic fragments with signature peptides  

PubMed Central

Background Classification is difficult for shotgun metagenomics data from environments such as soils, where the diversity of sequences is high and where reference sequences from close relatives may not exist. Approaches based on sequence-similarity scores must deal with the confounding effects that inheritance and functional pressures exert on the relation between scores and phylogenetic distance, while approaches based on sequence alignment and tree-building are typically limited to a small fraction of gene families. We describe an approach based on finding one or more exact matches between a read and a precomputed set of peptide 10-mers. Results At even the largest phylogenetic distances, thousands of 10-mer peptide exact matches can be found between pairs of bacterial genomes. Genes that share one or more peptide 10-mers typically have high reciprocal BLAST scores. Among a set of 403 representative bacterial genomes, some 20 million 10-mer peptides were found to be shared. We assign each of these peptides as a signature of a particular node in a phylogenetic reference tree based on the RNA polymerase genes. We classify the phylogeny of a genomic fragment (e.g., read) at the most specific node on the reference tree that is consistent with the phylogeny of observed signature peptides it contains. Using both synthetic data from four newly-sequenced soil-bacterium genomes and ten real soil metagenomics data sets, we demonstrate a sensitivity and specificity comparable to that of the MEGAN metagenomics analysis package using BLASTX against the NR database. Phylogenetic and functional similarity metrics applied to real metagenomics data indicates a signal-to-noise ratio of approximately 400 for distinguishing among environments. Our method assigns ~6.6 Gbp/hr on a single CPU, compared with 25 kbp/hr for methods based on BLASTX against the NR database. Conclusions Classification by exact matching against a precomputed list of signature peptides provides comparable results to existing techniques for reads longer than about 300 bp and does not degrade severely with shorter reads. Orders of magnitude faster than existing methods, the approach is suitable now for inclusion in analysis pipelines and appears to be extensible in several different directions.

2012-01-01

19

How Accurate and Robust Are the Phylogenetic Estimates of Austronesian Language Relationships?  

PubMed Central

We recently used computational phylogenetic methods on lexical data to test between two scenarios for the peopling of the Pacific. Our analyses of lexical data supported a pulse-pause scenario of Pacific settlement in which the Austronesian speakers originated in Taiwan around 5,200 years ago and rapidly spread through the Pacific in a series of expansion pulses and settlement pauses. We claimed that there was high congruence between traditional language subgroups and those observed in the language phylogenies, and that the estimated age of the Austronesian expansion at 5,200 years ago was consistent with the archaeological evidence. However, the congruence between the language phylogenies and the evidence from historical linguistics was not quantitatively assessed using tree comparison metrics. The robustness of the divergence time estimates to different calibration points was also not investigated exhaustively. Here we address these limitations by using a systematic tree comparison metric to calculate the similarity between the Bayesian phylogenetic trees and the subgroups proposed by historical linguistics, and by re-estimating the age of the Austronesian expansion using only the most robust calibrations. The results show that the Austronesian language phylogenies are highly congruent with the traditional subgroupings, and the date estimates are robust even when calculated using a restricted set of historical calibrations.

Greenhill, Simon J.; Drummond, Alexei J.; Gray, Russell D.

2010-01-01

20

[An accurate approach to hyperspectral mineral identification based on naive bayesian classification model].  

PubMed

The spectral absorption features are very similar between some minerals, especially hydrothermal alteration minerals related to mineralization, and they are also influenced by other factors such as spectral mixture. As a result, many of the spectral identification approaches for the minerals with similar spectral absorption features are prone to confusion and misjudgment. Therefore, to solve the phenomenon of "same mineral has different spectrums, and same spectrum belongs to different minerals", this paper proposes an accurate approach to hyperspectral mineral identification based on naive bayesian classification model. By testing and analyzing muscovite and kaolinite, the two typical alteration minerals, and comparing this approach with spectral angle matching, binary encoding and spectral feature fitting, the three popular spectral identification approaches, the results show that this approach can make more obvious differences among different minerals having similar spectrums, and has higher classification accuracy, since it is based on the position of absorption feature, absorption depth and the slope of continuum. PMID:24822429

He, Jin-Xin; Chen, Sheng-Bo; Wang, Yang; Wu, Yan-Fan

2014-02-01

21

Determining suitable image resolutions for accurate supervised crop classification using remote sensing data  

NASA Astrophysics Data System (ADS)

Mapping the spatial distribution of crops has become a fundamental input for agricultural production monitoring using remote sensing. However, the multi-temporality that is often necessary to accurately identify crops and to monitor crop growth generally comes at the expense of coarser observation supports, and can lead to increasingly erroneous class allocations caused by mixed pixels. For a given application like crop classification, the spatial resolution requirement (e.g. in terms of a maximum tolerable pixel size) differs considerably over different landscapes. To analyse the spatial resolution requirements for accurate crop identification via image classification, this study builds upon and extends a conceptual framework established in a previous work1. This framework allows defining quantitatively the spatial resolution requirements for crop monitoring based on simulating how agricultural landscapes, and more specifically the fields covered by a crop of interest, are seen by instruments with increasingly coarser resolving power. The concept of crop specific pixel purity, defined as the degree of homogeneity of the signal encoded in a pixel with respect to the target crop type, is used to analyse how mixed the pixels can be (as they become coarser), without undermining their capacity to describe the desired surface properties. In this case, this framework has been steered towards answering the question: "What is the spatial resolution requirement for crop identification via supervised image classification, in particular minimum and coarsest acceptable pixel sizes, and how do these requirements change over different landscapes?" The framework is applied over four contrasting agro-ecological landscapes in Middle Asia. Inputs to the experiment were eight multi-temporal images from the RapidEye sensor, the simulated pixel sizes range from 6.5 m to 396.5 m. Constraining parameters for crop identification were defined by setting thresholds for classification accuracy and uncertainty. Different types of crops display marked individuality regarding the pixel size requirements, depending on the spatial structures and cropping pattern in the sites. The coarsest acceptable pixel sizes and corresponding purities for the same type of crop were found to vary from site to site, and some crops could not be identified using pixels coarser than 200 m.

Löw, Fabian; Duveiller, Grégory

2013-10-01

22

A Novel Method of Amplification of FFPET-Derived RNA Enables Accurate Disease Classification with Microarrays  

PubMed Central

A new method for amplification and labeling of RNA is assessed that permits gene expression microarray analysis of formalin-fixed paraffin-embedded tissue (FFPET) samples. Valid biological data were obtained using gene expression microarrays of diffuse large B-cell lymphoma (DLBCL) FFPET samples. We examined 59 matched DLBCL patient samples, FFPET, and fresh/frozen. The samples contained both prognostic subgroups of DLBCL: germinal center B-cell (GCB) and activated B-cell (ABC). Fresh/frozen (FF) samples were amplified by both the traditional Eberwine oligo-dT method and a new method described herein. The matching FFPET samples were also amplified using the new method. Here we detail the comparison of results from all three datasets of matched samples. An established classification model built from previous data accurately classified these new samples. This new method provides a useful technology advance for microarray analysis of FFPET archival samples.

Williams, P. Mickey; Li, Rui; Johnson, Nathalie A.; Wright, George; Heath, Joe-Don; Gascoyne, Randy D.

2010-01-01

23

Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator  

NASA Astrophysics Data System (ADS)

The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequences of these rearrangements. However, even simple models lead to NP-hard problems, particularly in the area of phylogenetic analysis. Current approaches are limited to small collections of genomes and low-resolution data (typically a few hundred syntenic blocks). Moreover, whereas phylogenetic analyses from sequence data are deemed incomplete unless bootstrapping scores (a measure of confidence) are given for each tree edge, no equivalent to bootstrapping exists for rearrangement-based phylogenetic analysis.

Lin, Yu; Rajan, Vaibhav; Moret, Bernard M. E.

24

Identification, phylogenetic analysis and classification of porcine group C rotavirus VP7 sequences from the United States and Canada.  

PubMed

Rotavirus C (RVC) is a major cause of gastroenteritis in swine. Between December 2009 and October 2011, 7520 porcine samples were analyzed from herds in the US and Canada. RVC RNA was detected in 46% of the tested samples. In very young pigs (?3 days old) and young piglets (4-20 days old), 78% and 65%, respectively, RVC positive samples were negative for RVA and RVB. RVC RNA was also detected in 10% of tested lung tissues. Additionally, we investigated the porcine RVC molecular diversity by sequencing the VP7 gene segment of 65 specimens, yielding 70 VP7 gene sequences. Based on pairwise identity frequency profiles and phylogenetic analyses, an 85% nucleotide classification cut-off value was calculated using the novel sequence data generated in this study (n=70) and previously published RVC VP7 sequences (n=82), which resulted in the identification of 9 VP7 RVC genotypes, G1 to G9. PMID:24074581

Marthaler, Douglas; Rossow, Kurt; Culhane, Marie; Collins, James; Goyal, Sagar; Ciarlet, Max; Matthijnssens, Jelle

2013-11-01

25

Archaeal--Eubacterial Mergers in the Origin of Eukarya: Phylogenetic Classification of Life  

Microsoft Academic Search

A symbiosis-based phylogeny leads to a consistent, useful classification system for all life. ``Kingdoms'' and ``Domains'' are replaced by biological names for the most inclusive taxa: Prokarya (bacteria) and Eukarya (symbiosis-derived nucleated organisms). The earliest Eukarya, anaerobic mastigotes, hypothetically originated from permanent whole-cell fusion between members of Archaea (e.g., Thermoplasma-like organisms) and of Eubacteria (e.g., Spirochaeta-like organisms). Molecular biology, life-history,

Lynn Margulis

1996-01-01

26

Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life.  

PubMed Central

A symbiosis-based phylogeny leads to a consistent, useful classification system for all life. "Kingdoms" and "Domains" are replaced by biological names for the most inclusive taxa: Prokarya (bacteria) and Eukarya (symbiosis-derived nucleated organisms). The earliest Eukarya, anaerobic mastigotes, hypothetically originated from permanent whole-cell fusion between members of Archaea (e.g., Thermoplasma-like organisms) and of Eubacteria (e.g., Spirochaeta-like organisms). Molecular biology, life-history, and fossil record evidence support the reunification of bacteria as Prokarya while subdividing Eukarya into uniquely defined subtaxa: Protoctista, Animalia, Fungi, and Plantae. Images Fig. 1

Margulis, L

1996-01-01

27

Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life  

NASA Technical Reports Server (NTRS)

A symbiosis-based phylogeny leads to a consistent, useful classification system for all life. "Kingdoms" and "Domains" are replaced by biological names for the most inclusive taxa: Prokarya (bacteria) and Eukarya (symbiosis-derived nucleated organisms). The earliest Eukarya, anaerobic mastigotes, hypothetically originated from permanent whole-cell fusion between members of Archaea (e.g., Thermoplasma-like organisms) and of Eubacteria (e.g., Spirochaeta-like organisms). Molecular biology, life-history, and fossil record evidence support the reunification of bacteria as Prokarya while subdividing Eukarya into uniquely defined subtaxa: Protoctista, Animalia, Fungi, and Plantae.

Margulis, L.

1996-01-01

28

Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles  

PubMed Central

Identification and characterization of functional elements in the noncoding regions of genomes is an elusive and time-consuming activity whose output does not keep up with the pace of genome sequencing. Hundreds of bacterial genomes lay unexploited in terms of noncoding sequence analysis, although they may conceal a wide diversity of novel RNA genes, riboswitches, or other regulatory elements. We describe a strategy that exploits the entirety of available bacterial genomes to classify all noncoding elements of a selected reference species in a single pass. This method clusters noncoding elements based on their profile of presence among species. Most noncoding RNAs (ncRNAs) display specific signatures that enable their grouping in distinct clusters, away from sequence conservation noise and other elements such as promoters. We submitted 24 ncRNA candidates from Staphylococcus aureus to experimental validation and confirmed the presence of seven novel small RNAs or riboswitches. Besides offering a powerful method for de novo ncRNA identification, the analysis of phylogenetic profiles opens a new path toward the identification of functional relationships between co-evolving coding and noncoding elements.

Marchais, Antonin; Naville, Magali; Bohn, Chantal; Bouloc, Philippe; Gautheret, Daniel

2009-01-01

29

TWARIT: an extremely rapid and efficient approach for phylogenetic classification of metagenomic sequences.  

PubMed

Phylogenetic assignment of individual sequence reads to their respective taxa, referred to as 'taxonomic binning', constitutes a key step of metagenomic analysis. Existing binning methods have limitations either with respect to time or accuracy/specificity of binning. Given these limitations, development of a method that can bin vast amounts of metagenomic sequence data in a rapid, efficient and computationally inexpensive manner can profoundly influence metagenomic analysis in computational resource poor settings. We introduce TWARIT, a hybrid binning algorithm, that employs a combination of short-read alignment and composition-based signature sorting approaches to achieve rapid binning rates without compromising on binning accuracy and specificity. TWARIT is validated with simulated and real-world metagenomes and the results demonstrate significantly lower overall binning times compared to that of existing methods. Furthermore, the binning accuracy and specificity of TWARIT are observed to be comparable/superior to them. A web server implementing TWARIT algorithm is available at http://metagenomics.atc.tcs.com/Twarit/ PMID:22710135

Reddy, Rachamalla Maheedhar; Mohammed, Monzoorul Haque; Mande, Sharmila S

2012-09-01

30

Highly Accurate Real-Time Classification of Channel-Captured DNA Termini  

NASA Astrophysics Data System (ADS)

A computational method is briefly described for classification of individual DNA molecules measured by an ?-hemolysin channel detector. Classification is performed with better than 99% accuracy for DNA hairpin molecules that differ only in their terminal Watson-Crick base pairs. Signal classification was initially done on synthetic data streams, where sampling on real mixtures of hairpins was modeled in order to establish performance metrics (i.e., where train and test data were of known type, via single-species data files). Signal classification was then performed on observations from real mixtures of DNA hairpins. Hidden Markov Models (HMMs) were used with Expectation/Maximization for de-noising and for associating a feature vector with the ionic current blockade of the DNA molecule. Support Vector Machines (SVMs) were used as discriminators, and were the focus of off-line training. A multi-class SVM architecture was designed to place less discriminatory load on weaker discriminators, and novel SVM kernels were used to boost discrimination strength. The tuning on HMMs and SVMs enabled biophysical analysis of the captured molecule states and state-transitions structure revealed in the biophysical analysis was used for better feature selection. This analysis is presented in more detail, but with less discussion, in Winters-Hilt et al. 2003.

Winters-Hilt, Stephen

2003-05-01

31

Making an accurate classifier ensemble by voting on classifications from imputed learning sets  

Microsoft Academic Search

Ensemble methods often produce effective classifiers by learning a set of base classifiers from a diverse collection of the training sets. In this paper, we present a system, voting on classifications from imputed learning sets (VCI), that produces those diverse training sets by randomly removing a small percentage of attribute values from the original training set, and then using an

Xiaoyuan Su; Taghi M. Khoshgoftaar; Russell Greiner

2009-01-01

32

Assignment of Calibration Information to Deeper Phylogenetic Nodes is More Effective in Obtaining Precise and Accurate Divergence Time Estimates.  

PubMed

Divergence time estimation has become an essential tool for understanding macroevolutionary events. Molecular dating aims to obtain reliable inferences, which, within a statistical framework, means jointly increasing the accuracy and precision of estimates. Bayesian dating methods exhibit the propriety of a linear relationship between uncertainty and estimated divergence dates. This relationship occurs even if the number of sites approaches infinity and places a limit on the maximum precision of node ages. However, how the placement of calibration information may affect the precision of divergence time estimates remains an open question. In this study, relying on simulated and empirical data, we investigated how the location of calibration within a phylogeny affects the accuracy and precision of time estimates. We found that calibration priors set at median and deep phylogenetic nodes were associated with higher precision values compared to analyses involving calibration at the shallowest node. The results were independent of the tree symmetry. An empirical mammalian dataset produced results that were consistent with those generated by the simulated sequences. Assigning time information to the deeper nodes of a tree is crucial to guarantee the accuracy and precision of divergence times. This finding highlights the importance of the appropriate choice of outgroups in molecular dating. PMID:24855333

Mello, Beatriz; Schrago, Carlos G

2014-01-01

33

Assignment of Calibration Information to Deeper Phylogenetic Nodes is More Effective in Obtaining Precise and Accurate Divergence Time Estimates  

PubMed Central

Divergence time estimation has become an essential tool for understanding macroevolutionary events. Molecular dating aims to obtain reliable inferences, which, within a statistical framework, means jointly increasing the accuracy and precision of estimates. Bayesian dating methods exhibit the propriety of a linear relationship between uncertainty and estimated divergence dates. This relationship occurs even if the number of sites approaches infinity and places a limit on the maximum precision of node ages. However, how the placement of calibration information may affect the precision of divergence time estimates remains an open question. In this study, relying on simulated and empirical data, we investigated how the location of calibration within a phylogeny affects the accuracy and precision of time estimates. We found that calibration priors set at median and deep phylogenetic nodes were associated with higher precision values compared to analyses involving calibration at the shallowest node. The results were independent of the tree symmetry. An empirical mammalian dataset produced results that were consistent with those generated by the simulated sequences. Assigning time information to the deeper nodes of a tree is crucial to guarantee the accuracy and precision of divergence times. This finding highlights the importance of the appropriate choice of outgroups in molecular dating.

Mello, Beatriz; Schrago, Carlos G

2014-01-01

34

Expression analysis of LIM gene family in poplar, toward an updated phylogenetic classification  

PubMed Central

Background Plant LIM domain proteins may act as transcriptional activators of lignin biosynthesis and/or as actin binding and bundling proteins. Plant LIM genes have evolved in phylogenetic subgroups differing in their expression profiles: in the whole plant or specifically in pollen. However, several poplar PtLIM genes belong to uncharacterized monophyletic subgroups and the expression patterns of the LIM gene family in a woody plant have not been studied. Findings In this work, the expression pattern of the twelve duplicated poplar PtLIM genes has been investigated by semi quantitative RT-PCR in different vegetative and reproductive tissues. As in other plant species, poplar PtLIM genes were widely expressed in the tree or in particular tissues. Especially, PtXLIM1a, PtXLIM1b and PtWLIM1b genes were preferentially expressed in the secondary xylem, suggesting a specific function in wood formation. Moreover, the expression of these genes and of the PtPLIM2a gene was increased in tension wood. Western-blot analysis confirmed the preferential expression of PtXLIM1a protein during xylem differentiation and tension wood formation. Genes classified within the pollen specific PLIM2 and PLIM2-like subgroups were all strongly expressed in pollen but also in cottony hairs. Interestingly, pairs of duplicated PtLIM genes exhibited different expression patterns indicating subfunctionalisations in specific tissues. Conclusions The strong expression of several LIM genes in cottony hairs and germinating pollen, as well as in xylem fibers suggests an involvement of plant LIM domain proteins in the control of cell expansion. Comparisons of expression profiles of poplar LIM genes with the published functions of closely related plant LIM genes suggest conserved functions in the areas of lignin biosynthesis, pollen tube growth and mechanical stress response. Based on these results, we propose a novel nomenclature of poplar LIM domain proteins.

2012-01-01

35

Time series shapelets: a novel technique that allows accurate, interpretable and fast classification  

Microsoft Academic Search

Classification of time series has been attracting great interest over the past decade. While dozens of techniques have been\\u000a introduced, recent empirical evidence has strongly suggested that the simple nearest neighbor algorithm is very difficult\\u000a to beat for most time series problems, especially for large-scale datasets. While this may be considered good news, given\\u000a the simplicity of implementing the nearest

Lexiang Ye; Eamonn J. Keogh

2011-01-01

36

[Classification and identification of vibrio cholerae and vibrio parahaemolyticus isolates based on gyrB gene phylogenetic analysis].  

PubMed

In order to validate the usefulness of gyrB genotype for the classification and identification of Vibrio cholerae and Vibrio parahaemolyticus isolates, the phylogenetic analysis of 13 V. cholerae, 8 V. parahaemolyticus, 2 Aeromonas hydrophila and 1 Plesiomonas shigelloides strains was carried out using the partial coding sequence of gyrB, a gene that encodes the B subunit of DNA gyrase (topoisomerase type II ) in bacteria. These strains were separately clustered at species level and typed by the DNA sequences of reference strains from GenBank. CtxA positive V. cholerae strains including 8 clincical isolates of 0139 and 2 clinical isolates of 01 formed one cluster. Four V. parahaemolyticus strains of 1 isolate from 2002 Zhejiang outbreak patient ( tdh positive), 2 clinical isoltates from 2004 and 1 strain from Japan were grouped with an environmental isolate ( trh positive) from 2001. GyrB genotype is applicable to species identification of V. cholerae, V. parahaemolyticus, A. hydrophila and P. shigelloides isolates. The ctxA positive 0139 and 01 group of V. cholerae are closely related, as reflected by gyrB sequence divergence. Furthermore, the toxigenic V. parahaemolyticus strain isolated from environments may be the potential pathogen to the local prevalent and sporadic cases. PMID:17302148

Hou, Xiao-li; Cao, Qing-yi; Pan, Jin-cao; Chen, Zhi

2006-12-01

37

Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules.  

PubMed

We introduce a computational method for classification of individual DNA molecules measured by an alpha-hemolysin channel detector. We show classification with better than 99% accuracy for DNA hairpin molecules that differ only in their terminal Watson-Crick basepairs. Signal classification was done in silico to establish performance metrics (i.e., where train and test data were of known type, via single-species data files). It was then performed in solution to assay real mixtures of DNA hairpins. Hidden Markov Models (HMMs) were used with Expectation/Maximization for denoising and for associating a feature vector with the ionic current blockade of the DNA molecule. Support Vector Machines (SVMs) were used as discriminators, and were the focus of off-line training. A multiclass SVM architecture was designed to place less discriminatory load on weaker discriminators, and novel SVM kernels were used to boost discrimination strength. The tuning on HMMs and SVMs enabled biophysical analysis of the captured molecule states and state transitions; structure revealed in the biophysical analysis was used for better feature selection. PMID:12547778

Winters-Hilt, Stephen; Vercoutere, Wenonah; DeGuzman, Veronica S; Deamer, David; Akeson, Mark; Haussler, David

2003-02-01

38

A Comprehensive Guide for the Accurate Classification of Murine Hair Follicles in Distinct Hair Cycle Stages  

Microsoft Academic Search

Numerous strains of mice with defined mutations display pronounced abnormalities of hair follicle cycling, even in the absence of overt alterations of the skin and hair phenotype; however, in order to recognize even subtle, hair cycle-related abnormalities, it is critically important to be able to determine accurately and classify the major stages of the normal murine hair cycle. In this

Sven Müller-Röver; Bori Handjiski; Carina van der Veen; Stefan Eichmüller; Kerstin Foitzik; Ian A. McKay; Kurt S. Stenn; Ralf Paus

2001-01-01

39

Accurate video text detection through classification of low and high contrast images  

Microsoft Academic Search

Detection of both scene text and graphic text in video images is gaining popularity in the area of information retrieval for efficient indexing and understanding the video. In this paper, we explore a new idea of classifying low contrast and high contrast video images in order to detect accurate boundary of the text lines in video images. In this work,

Palaiahnakote Shivakumara; Weihua Huang; Trung Quy Phan; Chew Lim Tan

2010-01-01

40

ColorPhylo: A Color Code to Accurately Display Taxonomic Classifications.  

PubMed

Color may be very useful to visualise complex data. As far as taxonomy is concerned, color may help observing various species' characteristics in correlation with classification. However, choosing the number of subclasses to display is often a complex task: on the one hand, assigning a limited number of colors to taxa of interest hides the structure imbedded in the subtrees of the taxonomy; on the other hand, differentiating a high number of taxa by giving them specific colors, without considering the underlying taxonomy, may lead to unreadable results since relationships between displayed taxa would not be supported by the color code. In the present paper, an automatic color coding scheme is proposed to visualise the levels of taxonomic relationships displayed as overlay on any kind of data plot. To achieve this goal, a dimensionality reduction method allows displaying taxonomic "distances" onto a Euclidean two-dimensional space. The resulting map is projected onto a 2D color space (the Hue, Saturation, Brightness colorimetric space with brightness set to 1). Proximity in the taxonomic classification corresponds to proximity on the map and is therefore materialised by color proximity. As a result, each species is related to a color code showing its position in the taxonomic tree. The so called ColorPhylo displays taxonomic relationships intuitively and can be combined with any biological result. A Matlab version of ColorPhylo is available at http://sy.lespi.free.fr/ColorPhylo-homepage.html. Meanwhile, an ad-hoc distance in case of taxonomy with unknown edge lengths is proposed. PMID:22253532

Lespinats, Sylvain; Fertil, Bernard

2011-01-01

41

Novel exomphalos genetic mouse model: The importance of accurate phenotypic classification  

PubMed Central

Background Rodent models of abdominal wall defects (AWD) may provide insight into the pathophysiology of these conditions including gut dysfunction in gastroschisis, or pulmonary hypoplasia in exomphalos. Previously, a Scribble mutant mouse model (circletail) was reported to exhibit gastroschisis. We further characterise this AWD in Scribble knockout mice. Method Homozygous Scrib knockout mice were obtained from heterozygote matings. Fetuses were collected at E17.5–18.5 with intact amniotic membranes. Three mutants and two control fetuses were imaged by in amnio micro-MRI. Remaining fetuses were dissected, photographed and gut length/weight measured. Ileal specimens were stained for interstitial cells of Cajal (ICC), imaged using confocal microscopy and ICC quantified. Results 127 fetuses were collected, 15 (12%) exhibited AWD. Microdissection revealed 3 mutants had characteristic exomphalos phenotype with membrane-covered gut/liver herniation into the umbilical cord. A further 12 exhibited extensive AWD, with eviscerated abdominal organs and thin covering membrane (intact or ruptured). Micro-MRI confirmed these phenotypes. Gut was shorter and heavier in AWD group compared to controls but morphology/number of ICC was not different. Discussion The Scribble knockout fetus exhibits exomphalos (intact and ruptured), in contrast to the original published phenotype of gastroschisis. Detailed dissection of fetuses is essential ensuring accurate phenotyping and result reporting.

Carnaghan, Helen; Roberts, Tom; Savery, Dawn; Norris, Francesca C.; McCann, Conor J.; Copp, Andrew J.; Scambler, Peter J.; Lythgoe, Mark F.; Greene, Nicholas D.; DeCoppi, Paolo; Burns, Alan J.; Pierro, Agustino; Eaton, Simon

2013-01-01

42

Classification  

NASA Astrophysics Data System (ADS)

A supervised learning task involves constructing a mapping from input data (normally described by several features) to the appropriate outputs. A set of training examples— examples with known output values—is used by a learning algorithm to generate a model. This model is intended to approximate the mapping between the inputs and outputs. This model can be used to generate predicted outputs for inputs that have not been seen before. Within supervised learning, one type of task is a classification learning task, in which each output is one or more classes to which the input belongs. For example, we may have data consisting of observations of sunspots. In a classification learning task, our goal may be to learn to classify sunspots into one of several types. Each example may correspond to one candidate sunspot with various measurements or just an image. A learning algorithm would use the supplied examples to generate a model that approximates the mapping between each supplied set of measurements and the type of sunspot. This model can then be used to classify previously unseen sunspots based on the candidate’s measurements. The generalization performance of a learned model (how closely the target outputs and the model’s predicted outputs agree for patterns that have not been presented to the learning algorithm) would provide an indication of how well the model has learned the desired mapping. More formally, a classification learning algorithm L takes a training set T as its input. The training set consists of |T| examples or instances. It is assumed that there is a probability distribution D from which all training examples are drawn independently—that is, all the training examples are independently and identically distributed (i.i.d.). The ith training example is of the form (x_i, y_i), where x_i is a vector of values of several features and y_i represents the class to be predicted.* In the sunspot classification example given above, each training example would represent one sunspot’s classification (y_i) and the corresponding set of measurements (x_i). The output of a supervised learning algorithm is a model h that approximates the unknown mapping from the inputs to the outputs. In our example, h would map from the sunspot measurements to the type of sunspot. We may have a test set S—a set of examples not used in training that we use to test how well the model h predicts the outputs on new examples. Just as with the examples in T, the examples in S are assumed to be independent and identically distributed (i.i.d.) draws from the distribution D. We measure the error of h on the test set as the proportion of test cases that h misclassifies: 1/|S| Sigma(x,y union S)[I(h(x)!= y)] where I(v) is the indicator function—it returns 1 if v is true and 0 otherwise. In our sunspot classification example, we would identify additional examples of sunspots that were not used in generating the model, and use these to determine how accurate the model is—the fraction of the test samples that the model classifies correctly. An example of a classification model is the decision tree shown in Figure 23.1. We will discuss the decision tree learning algorithm in more detail later—for now, we assume that, given a training set with examples of sunspots, this decision tree is derived. This can be used to classify previously unseen examples of sunpots. For example, if a new sunspot’s inputs indicate that its "Group Length" is in the range 10-15, then the decision tree would classify the sunspot as being of type “E,” whereas if the "Group Length" is "NULL," the "Magnetic Type" is "bipolar," and the "Penumbra" is "rudimentary," then it would be classified as type "C." In this chapter, we will add to the above description of classification problems. We will discuss decision trees and several other classification models. In particular, we will discuss the learning algorithms that generate these classification models, how to use them to classify new

Oza, Nikunj

2012-03-01

43

CLASSIFICATION  

NSDL National Science Digital Library

Students will learn about classification Go into the Carnivorous Plant site and find 5 facts about carnivorous plants and write them in your science journal. Carnivorous Plants Using the animal classification site, click on the animals shown and write information about 2 of them in your journal. animal classification Use the animal diversity web page and write down ...

Kirby, Ms.

2009-09-23

44

Phylogenetic classification of Trichophyton mentagrophytes complex strains based on DNA sequences of nuclear ribosomal internal transcribed spacer 1 regions.  

PubMed

Using internal transcribed spacer 1 (ITS1) region ribosomal DNA sequences from 37 stock strains and clinical isolates provisionally termed Trichophyton mentagrophytes complex in Japan, we demonstrated the mutual phylogenetic relationships of these strains. Members of this complex were classified into 3 ITS1-homologous groups and 13 ITS1-identical groups by their sequences. ITS1-homologous group I consists of Arthroderma vanbreuseghemii, T. mentagrophytes human isolates, and several strains of T. mentagrophytes animal isolates. Five strains of Arthroderma simii form a cluster comprising ITS1-homologous group II. The Americano-European and African races of Arthroderma benhamiae, T. mentagrophytes var. erinacei, and one strain of a T. mentagrophytes animal isolate constitute ITS1-homologous group III. According to the phylogenetic tree constructed with Trichophyton rubrum as an outgroup, ITS1-homologous groups I and II comprised a monophyletic cluster and ITS1-homologous group III constituted another cluster which was rather distant from the others in the complex. This system was applicable to the phylogenetic analysis of closely related strains. Using this technique, human and animal isolates of T. mentagrophytes were also clearly distinguishable from each other. PMID:9705405

Makimura, K; Mochizuki, T; Hasegawa, A; Uchida, K; Saito, H; Yamaguchi, H

1998-09-01

45

Comprehensive Phylogenetic Reconstructions of African Swine Fever Virus: Proposal for a New Classification and Molecular Dating of the Virus  

PubMed Central

African swine fever (ASF) is a highly lethal disease of domestic pigs caused by the only known DNA arbovirus. It was first described in Kenya in 1921 and since then many isolates have been collected worldwide. However, although several phylogenetic studies have been carried out to understand the relationships between the isolates, no molecular dating analyses have been achieved so far. In this paper, comprehensive phylogenetic reconstructions were made using newly generated, publicly available sequences of hundreds of ASFV isolates from the past 70 years. Analyses focused on B646L, CP204L, and E183L genes from 356, 251, and 123 isolates, respectively. Phylogenetic analyses were achieved using maximum likelihood and Bayesian coalescence methods. A new lineage-based nomenclature is proposed to designate 35 different clusters. In addition, dating of ASFV origin was carried out from the molecular data sets. To avoid bias, diversity due to positive selection or recombination events was neutralized. The molecular clock analyses revealed that ASFV strains currently circulating have evolved over 300 years, with a time to the most recent common ancestor (TMRCA) in the early 18th century.

Michaud, Vincent; Randriamparany, Tantely; Albina, Emmanuel

2013-01-01

46

Analysis of genetic diversity in banana cultivars (Musa cvs.) from the South of Oman using AFLP markers and classification by phylogenetic, hierarchical clustering and principal component analyses*  

PubMed Central

Banana is an important crop grown in Oman and there is a dearth of information on its genetic diversity to assist in crop breeding and improvement programs. This study employed amplified fragment length polymorphism (AFLP) to investigate the genetic variation in local banana cultivars from the southern region of Oman. Using 12 primer combinations, a total of 1094 bands were scored, of which 1012 were polymorphic. Eighty-two unique markers were identified, which revealed the distinct separation of the seven cultivars. The results obtained show that AFLP can be used to differentiate the banana cultivars. Further classification by phylogenetic, hierarchical clustering and principal component analyses showed significant differences between the clusters found with molecular markers and those clusters created by previous studies using morphological analysis. Based on the analytical results, a consensus dendrogram of the banana cultivars is presented.

Opara, Umezuruike Linus; Jacobson, Dan; Al-Saady, Nadiya Abubakar

2010-01-01

47

DEFLATE compression algorithm corrects for overestimation of phylogenetic diversity by Grantham approach to single-nucleotide polymorphism classification.  

PubMed

Improvements in speed and cost of genome sequencing are resulting in increasing numbers of novel non-synonymous single nucleotide polymorphisms (nsSNPs) in genes known to be associated with disease. The large number of nsSNPs makes laboratory-based classification infeasible and familial co-segregation with disease is not always possible. In-silico methods for classification or triage are thus utilised. A popular tool based on multiple-species sequence alignments (MSAs) and work by Grantham, Align-GVGD, has been shown to underestimate deleterious effects, particularly as sequence numbers increase. We utilised the DEFLATE compression algorithm to account for expected variation across a number of species. With the adjusted Grantham measure we derived a means of quantitatively clustering known neutral and deleterious nsSNPs from the same gene; this was then used to assign novel variants to the most appropriate cluster as a means of binary classification. Scaling of clusters allows for inter-gene comparison of variants through a single pathogenicity score. The approach improves upon the classification accuracy of Align-GVGD while correcting for sensitivity to large MSAs. Open-source code and a web server are made available at https://github.com/aschlosberg/CompressGV. PMID:24828207

Schlosberg, Arran; Lam, Brian Y H; Yeo, Giles S H; Clifton-Bligh, Roderick J

2014-01-01

48

DEFLATE Compression Algorithm Corrects for Overestimation of Phylogenetic Diversity by Grantham Approach to Single-Nucleotide Polymorphism Classification  

PubMed Central

Improvements in speed and cost of genome sequencing are resulting in increasing numbers of novel non-synonymous single nucleotide polymorphisms (nsSNPs) in genes known to be associated with disease. The large number of nsSNPs makes laboratory-based classification infeasible and familial co-segregation with disease is not always possible. In-silico methods for classification or triage are thus utilised. A popular tool based on multiple-species sequence alignments (MSAs) and work by Grantham, Align-GVGD, has been shown to underestimate deleterious effects, particularly as sequence numbers increase. We utilised the DEFLATE compression algorithm to account for expected variation across a number of species. With the adjusted Grantham measure we derived a means of quantitatively clustering known neutral and deleterious nsSNPs from the same gene; this was then used to assign novel variants to the most appropriate cluster as a means of binary classification. Scaling of clusters allows for inter-gene comparison of variants through a single pathogenicity score. The approach improves upon the classification accuracy of Align-GVGD while correcting for sensitivity to large MSAs. Open-source code and a web server are made available at https://github.com/aschlosberg/CompressGV.

Schlosberg, Arran; Lam, Brian Y. H.; Yeo, Giles S. H.; Clifton-Bligh, Roderick J.

2014-01-01

49

Phylogenetic inference rejects sporophyte based classification of the Funariaceae (Bryophyta): rapid radiation suggests rampant homoplasy in sporophyte evolution.  

PubMed

The moss family Funariaceae, which includes the model systems Funaria hygrometrica and Physcomitrella patens, comprises 15 genera, of which three accommodate approximately 95% of the 250-400 species. Generic concepts are drawn primarily from patterns in the diversity of morphological complexity of the sporophyte. Phylogenetic inferences from ten loci sampled across the three genomic compartments yield a hypothesis that is incompatible with the current circumscription of two of the speciose genera of the Funariaceae. The single clade, comprising exemplars of Funaria with a compound annulus, is congruent with the systematic concept proposed by Fife (1985). By contrast, Entosthodon and Physcomitrium are resolved as polyphyletic entities, and even the three species of Physcomitrella are confirmed to have diverged from distinct ancestors. Although the backbone relationships within the core clade of the Funariaceae remain unresolved, the polyphyly of these genera withstands alternative hypothesis testing. Consequently, the sporophytic characters that define these lineages are clearly homoplasious suggesting that selective pressures (or their relaxation) are in fact driving the diversification rather than the conservation of sporophytic architecture in the Funariaceae. PMID:21971055

Liu, Yang; Budke, Jessica M; Goffinet, Bernard

2012-01-01

50

Bacterial classification of fish-pathogenic Mycobacterium species by multigene phylogenetic analyses and MALDI Biotyper identification system.  

PubMed

Mycobacterium marinum is difficult to distinguish from other species of Mycobacterium isolated from fish using biochemical methods. Here, we used genetic and proteomic analyses to distinguish three Mycobacterium strains: M. marinum strains MB2 and Europe were isolated from tropical and marine fish in Thailand and Europe, and Mycobacterium sp. 012931 strain was isolated from yellowtail in Japan. In phylogenetic trees based on gyrB, rpoB, and Ag85B genes, Mycobacterium sp. 012931 clustered with M. marinum strains MB2 and Europe, but in trees based on 16S rRNA, hsp65, and Ag85A genes Mycobacterium sp. 012931 did not cluster with the other strains. In proteomic analyses using a Bruker matrix-assisted laser desorption ionization Biotyper, the mass profile of Mycobacterium sp. 012931 differed from the mass profiles of the other two fish M. marinum strains. Therefore, Mycobacterium sp. 012931 is similar to M. marinum but is not the same, suggesting that it could be a subspecies of M. marinum. PMID:23229498

Kurokawa, Satoru; Kabayama, Jun; Fukuyasu, Tsuguaki; Hwang, Seong Don; Park, Chan-Il; Park, Seong-Bin; del Castillo, Carmelo S; Hikima, Jun-ichi; Jung, Tae-Sung; Kondo, Hidehiro; Hirono, Ikuo; Takeyama, Haruko; Aoki, Takashi

2013-06-01

51

Accurate classification and hemagglutinin amino acid signatures for influenza A virus host-origin association and subtyping.  

PubMed

Host-origin classification and signatures of influenza A viruses were investigated based on the HA protein for tracking of the HA host of origin. Hidden Markov models (HMMs), decision trees and associative classification for each influenza A virus subtype and its major hosts (human, avian, swine) were generated. Features of the HA protein signatures that were host-and subtype-specific were sought. Host-associated signatures that occurred in different subtypes of the virus were identified. Evaluation of the classification models based on ROC curves and support and confidence ratings for the amino acid class-association rules was performed. Host classification based on the HA subtype achieved accuracies between 91.2% and 100% using decision trees after feature selection. Host-specific class association rules for avian-host origins gave better support and confidence ratings, followed by human and finally swine origin. This finding indicated the lower specificity of the swine host, perhaps pointing to its ability to mix different strains. PMID:24418567

ElHefnawi, Mahmoud; Sherif, Fayroz F

2014-01-20

52

Topology representing network enables highly accurate classification of protein images taken by cryo electron-microscope without masking  

Microsoft Academic Search

In single-particle analysis, a three-dimensional (3-D) structure of a protein is constructed using electron microscopy (EM). As these images are very noisy in general, the primary process of this 3-D reconstruction is the classification of images according to their Euler angles, the images in each classified group then being averaged to reduce the noise level. In our newly developed strategy

Toshihiko Ogura; Kenji Iwasaki; Chikara Sato

2003-01-01

53

A non-contact method based on multiple signal classification algorithm to reduce the measurement time for accurately heart rate detection  

NASA Astrophysics Data System (ADS)

Non-contact methods for the assessment of vital signs are of great interest for specialists due to the benefits obtained in both medical and special applications, such as those for surveillance, monitoring, and search and rescue. This paper investigates the possibility of implementing a digital processing algorithm based on the MUSIC (Multiple Signal Classification) parametric spectral estimation in order to reduce the observation time needed to accurately measure the heart rate. It demonstrates that, by proper dimensioning the signal subspace, the MUSIC algorithm can be optimized in order to accurately assess the heart rate during an 8-28 s time interval. The validation of the processing algorithm performance was achieved by minimizing the mean error of the heart rate after performing simultaneous comparative measurements on several subjects. In order to calculate the error the reference value of heart rate was measured using a classic measurement system through direct contact.

Bechet, P.; Mitran, R.; Munteanu, M.

2013-08-01

54

Photometric brown dwarf classification. A method to identify and accurately classify large samples of brown dwarfs without spectroscopy  

NASA Astrophysics Data System (ADS)

We have developed a method ``photo-type'' to identify and accurately classify L and T dwarfs, onto the standard system, from photometry alone. We combine SDSS, UKIDSS and WISE data and classify point sources by comparing the izYJHKW1W2 colours against template colours for quasars, stars, and brown dwarfs. In a sample of 6.5×106 bright point sources, J < 17.5, from 3150 deg2, we identify and type 898 L and T dwarfs, making this the largest homogeneously selected sample of brown dwarfs to date. The sample includes 713 (125) new (previously known) L dwarfs and 21 (39) T dwarfs. For the previously-known sources, the scatter in the plot of photo-type vs spectral type indicates that our photo-types are accurate to 1.5 (1.0) sub-types rms for L (T) dwarfs. Peculiar objects and candidate unresolved binaries are identified.

Skrzypek, N.; Warren, S. J.

55

Development of accurate classification method based on the analysis of volatile organic compounds from human exhaled air.  

PubMed

Analysis of exhaled air leads to the development of fast accurate and non-invasive diagnostics. A comprehensive analysis of the entire range of volatile organic compounds (VOCs) in exhaled air samples will enable the identification of VOCs unique for certain patient groups. This study demonstrates proof of principle of our developed method tested on a smoking/non-smoking study population. Thermal desorption and gas chromatography coupled to time-of-flight mass spectrometry were used to analyse exhaled air samples. The VOC profiles obtained from each individual were combined into one final database based on similarity of mass spectra and retention indexes (RI), which offers the possibility for a reliable selection of compounds of interest. As proof of principle we correctly classified all subjects from population of smoking (N=11) and non-smoking (N=11) based on the VOC profiles available in their exhaled air. Support vector machine (SVM) analysis identified 4 VOCs as biomarkers of recent exposure to cigarette smoke: 2,5-dimethyl hexane, dodecane, 2,5-dimethylfuran and 2-methylfuran. This approach contributes to future development of fast, accurate and non-invasive diagnostics of inflammatory diseases including pulmonary diseases. PMID:18055279

Van Berkel, J J B N; Dallinga, J W; Möller, G M; Godschalk, R W L; Moonen, E; Wouters, E F M; Van Schooten, F J

2008-01-01

56

Classification  

NASA Technical Reports Server (NTRS)

A supervised learning task involves constructing a mapping from input data (normally described by several features) to the appropriate outputs. Within supervised learning, one type of task is a classification learning task, in which each output is one or more classes to which the input belongs. In supervised learning, a set of training examples---examples with known output values---is used by a learning algorithm to generate a model. This model is intended to approximate the mapping between the inputs and outputs. This model can be used to generate predicted outputs for inputs that have not been seen before. For example, we may have data consisting of observations of sunspots. In a classification learning task, our goal may be to learn to classify sunspots into one of several types. Each example may correspond to one candidate sunspot with various measurements or just an image. A learning algorithm would use the supplied examples to generate a model that approximates the mapping between each supplied set of measurements and the type of sunspot. This model can then be used to classify previously unseen sunspots based on the candidate's measurements. This chapter discusses methods to perform machine learning, with examples involving astronomy.

Oza, Nikunj C.

2011-01-01

57

Accurate classification of MLH1/MSH2 missense variants with multivariate analysis of protein polymorphisms-mismatch repair (MAPP-MMR).  

PubMed

Lynch syndrome, also known as hereditary nonpolyposis colon cancer (HNPCC), is the most common known genetic syndrome for colorectal cancer (CRC). MLH1/MSH2 mutations underlie approximately 90% of Lynch syndrome families. A total of 24% of these mutations are missense. Interpreting missense variation is extremely challenging. We have therefore developed multivariate analysis of protein polymorphisms-mismatch repair (MAPP-MMR), a bioinformatic algorithm that effectively classifies MLH1/MSH2 deleterious and neutral missense variants. We compiled a large database (n>300) of MLH1/MSH2 missense variants with associated clinical and molecular characteristics. We divided this database into nonoverlapping training and validation sets and tested MAPP-MMR. MAPP-MMR significantly outperformed other missense variant classification algorithms (sensitivity, 94%; specificity, 96%; positive predictive value [PPV] 98%; negative predictive value [NPV], 89%), such as SIFT and PolyPhen. MAPP-MMR is an effective bioinformatic tool for missense variant interpretation that accurately distinguishes MLH1/MSH2 deleterious variants from neutral variants. PMID:18383312

Chao, Elizabeth C; Velasquez, Jonathan L; Witherspoon, Mavee S L; Rozek, Laura S; Peel, David; Ng, Pauline; Gruber, Stephen B; Watson, Patrice; Rennert, Gad; Anton-Culver, Hoda; Lynch, Henry; Lipkin, Steven M

2008-06-01

58

From learning taxonomies to phylogenetic learning: Integration of 16S rRNA gene data into FAME-based bacterial classification  

Microsoft Academic Search

BACKGROUND: Machine learning techniques have shown to improve bacterial species classification based on fatty acid methyl ester (FAME) data. Nonetheless, FAME analysis has a limited resolution for discrimination of bacteria at the species level. In this paper, we approach the species classification problem from a taxonomic point of view. Such a taxonomy or tree is typically obtained by applying clustering

Bram Slabbinck; Willem Waegeman; Peter Dawyndt; Paul De Vos; Bernard De Baets

2010-01-01

59

Phylogenetics problems  

NSDL National Science Digital Library

Students receive information about cladistics and apply this phylogenetic approach to two problems, collecting data, determining whether traits are ancestral or derived, and using this information to select the most parsimonious tree.

Deel, Sarah; Walser-Kuntz, Debby

60

Rapid identification and classification of Mycobacterium spp. using whole-cell protein barcodes with matrix assisted laser desorption ionization time of flight mass spectrometry in comparison with multigene phylogenetic analysis.  

PubMed

The need of quick diagnostics and increasing number of bacterial species isolated necessitate development of a rapid and effective phenotypic identification method. Mass spectrometry (MS) profiling of whole cell proteins has potential to satisfy the requirements. The genus Mycobacterium contains more than 154 species that are taxonomically very close and require use of multiple genes including 16S rDNA for phylogenetic identification and classification. Six strains of five Mycobacterium species were selected as model bacteria in the present study because of their 16S rDNA similarity (98.4-99.8%) and the high similarity of the concatenated 16S rDNA, rpoB and hsp65 gene sequences (95.9-99.9%), requiring high identification resolution. The classification of the six strains by MALDI TOF MS protein barcodes was consistent with, but at much higher resolution than, that of the multi-locus sequence analysis of using 16S rDNA, rpoB and hsp65. The species were well differentiated using MALDI TOF MS and MALDI BioTyper™ software after quick preparation of whole-cell proteins. Several proteins were selected as diagnostic markers for species confirmation. An integration of MALDI TOF MS, MALDI BioTyper™ software and diagnostic protein fragments provides a robust phenotypic approach for bacterial identification and classification. PMID:22284888

Wang, Jun; Chen, Wen Feng; Li, Qing X

2012-02-24

61

GB Virus C\\/Hepatitis G Virus Groups and Subgroups: Classification by a Restriction Fragment Length Polymorphism Method Based on Phylogenetic Analysis of the 59 Untranslated Region  

Microsoft Academic Search

A phylogenetic tree based on 150 5* untranslated region sequences deposited in GenBank database allowed segregation of the sequences into three major groups, including two subgroups, i.e., 1, 2a, 2b, and 3, supported by bootstrap analysis. Restriction site analysis of these sequences predicted that HinfI and either AatII or AciI could be used for genomic typing with 99.4% accuracy. cDNA

J. F. QUARLERI; V. L. MATHET; M. FELD; D. FERRARIO; M. P. DELLA LATTA; R. VERDUN; D. O. SANCHEZ; J. R. OUBINA

1999-01-01

62

An Exploration of Hyperion Hyperspectral Imagery Combined with Different Supervised Classification Approaches Towards Obtaining More Accurate Land Use/Cover Cartography  

NASA Astrophysics Data System (ADS)

Land use and land cover (LULC) constitutes a key variable of the Earth's system that has in general shown a close correlation with human activities and the physical environment. Describing the pattern and the spatial distribution of LULC is traditionally based on remote sensing data analysis and, evidently, one of the most commonly techniques applied has been image classification. The main objective of the present study has been to evaluate the combined use of Hyperion hyperspectral imagery with a range of supervised classification algorithms widely available today for discriminating LULC classes in a typical Mediterranean setting. Accuracy assessment of the derived thematic maps was based on the analysis of the classification confusion matrix statistics computed for each classification map, using for consistency the same set of validation points. Those were selected on the basis of photo-interpretation of high resolution aerial imagery and of panchromatic imagery available for the studied region at the time of the Hyperion overpass. Results indicated close classification accuracy between the different classifiers with the SVMs outperforming the other classification approaches. The higher classification accuracy by SVMs was attributed principally to the ability of this classifier to identify an optimal separating hyperplane for classes' separation which allows a low generalisation error, thus producing the best possible classes' separation. Although all classifiers produced close results, SVMs generally appeared most useful in describing the spatial distribution and the cover density of each land cover category. All in all, this study demonstrated that, provided that a Hyperion hyperspectral imagery can be made available at regular time intervals over a given region, when combined with SVMs classifiers, can potentially enable a wider approach in land use/cover mapping. This can be of particular importance, especially for regions like in the Mediterranean basin, since it can be related to mapping and monitoring of land degradation and desertification phenomena which are evident in such areas. KEYWORDS: land cover/use mapping, Hyperion, classification, Mediterranean

Igityan, Nune

2014-05-01

63

A preliminary phylogenetic analysis of the New World Helopini (Coleoptera, Tenebrionidae, Tenebrioninae) indicates the need for profound rearrangements of the classification  

PubMed Central

Abstract Helopini is a diverse tribe in the subfamily Tenebrioninae with a worldwide distribution. The New World helopine species have not been reviewed recently and several doubts emerge regarding their generic assignment as well as the naturalness of the tribe and subordinate taxa. To assess these questions, a preliminary cladistic analysis was conducted with emphasis on sampling the genera distributed in the New World, but including representatives from other regions. The parsimony analysis includes 30 ingroup species from America, Europe and Asia of the subtribes Helopina and Cylindrinotina, plus three outgroups, and 67 morphological characters. Construction of the matrix resulted in the discovery of morphological character states not previously reported for the tribe, particularly from the genitalia of New World species. A consensus of the 12 most parsimonious trees supports the monophyly of the tribe based on a unique combination of characters, including one synapomorphy. None of the subtribes or the genera of the New World represented by more than one species (Helops Fabricius, Nautes Pascoe and Tarpela Bates) were recovered as monophyletic. Helopina was recovered as paraphyletic in relation to Cylindrinotina. One Nearctic species of Helops and one Palearctic species of Tarpela (subtribe Helopina) were more closely related to species of Cylindrinotina. A relatively derived clade, mainly composed by Neotropical species, was found; it includes seven species of Tarpela, seven species of Nautes, and three species of Helops, two Nearctic and one Neotropical. Our results reveal the need to deeply re-evaluate the current classification of the tribe and subordinated taxa, but a broader taxon sampling and further character exploration is needed in order to fully recognize monophyletic groups at different taxonomic levels (from subtribes to genera).

Cifuentes-Ruiz, Paulina; Zaragoza-Caballero, Santiago; Ochoterena-Booth, Helga; Moron, Miguel Angel

2014-01-01

64

Phylogenetic and Physicochemical Analyses Enhance the Classification of Rare Non-Synonymous Single Nucleotide Variants in Type 1 and 2 Long QT Syndrome  

PubMed Central

Background Hundreds of non-synonymous single nucleotide variants (nsSNVs) have been identified in the two most common LQTS-susceptibility genes (KCNQ1 and KCNH2). Unfortunately, a ~3% background rate of rare KCNQ1 and KCNH2 nsSNVs amongst healthy individuals complicates the ability to distinguish rare pathogenic mutations from similarly rare yet presumably innocuous variants. Methods and Results In this study, 4 tools [1) conservation across species, 2) Grantham values, 3) SIFT, and 4) PolyPhen] were used to predict “pathogenic” or “benign” status for nsSNVs identified across 388 clinically “definite” LQTS cases and 1344 ostensibly healthy controls. From these data, estimated predictive values (EPVs) were determined for each tool independently, in concert with previously published protein topology-derived EPVs, and synergistically when ? 3 tools were in agreement. Overall, all 4 tools displayed a statistically significant ability to distinguish between case-derived and control-derived nsSNVs in KCNQ1, whereas each tool, except Grantham values, displayed a similar ability to differentiate KCNH2 nsSNVs. Collectively, when at least 3 of the 4 tools agreed on the “pathogenic” status of C-terminal nsSNVs located outside the KCNH2/Kv11.1 cyclic nucleotide binding domain, the topology-specific EPV improved from 56% to 91%. Conclusions While in silico prediction tools should not be used to predict independently the pathogenicity of a novel, rare nSNV, our results support the potential clinical utility of the synergistic use of these tools to enhance the classification of nsSNVs, particularly for Kv11.1’s difficult to interpret C-terminal region.

Giudicessi, John R.; Kapplinger, Jamie D.; Tester, David J.; Alders, Marielle; Salisbury, Benjamin A.; Wilde, Arthur A.M.; Ackerman, Michael J.

2013-01-01

65

Molecular Classifications  

Microsoft Academic Search

The field of glioma classification is currently entering a new era with the introduction of paradigms based on molecular information.\\u000a Rather than supplanting traditional morphology-based classification schemes, it is anticipated that emerging molecular biologic,\\u000a genomic, transcriptomic, and proteomic data will complement and augment existing morphologic and immunophenotypic data, providing\\u000a for a more accurate and refined stratification of glioma patients for

Gregory N. Fuller

66

Combining multiple hypothesis testing and affinity propagation clustering leads to accurate, robust and sample size independent classification on gene expression data  

PubMed Central

Background A feature selection method in microarray gene expression data should be independent of platform, disease and dataset size. Our hypothesis is that among the statistically significant ranked genes in a gene list, there should be clusters of genes that share similar biological functions related to the investigated disease. Thus, instead of keeping N top ranked genes, it would be more appropriate to define and keep a number of gene cluster exemplars. Results We propose a hybrid FS method (mAP-KL), which combines multiple hypothesis testing and affinity propagation (AP)-clustering algorithm along with the Krzanowski & Lai cluster quality index, to select a small yet informative subset of genes. We applied mAP-KL on real microarray data, as well as on simulated data, and compared its performance against 13 other feature selection approaches. Across a variety of diseases and number of samples, mAP-KL presents competitive classification results, particularly in neuromuscular diseases, where its overall AUC score was 0.91. Furthermore, mAP-KL generates concise yet biologically relevant and informative N-gene expression signatures, which can serve as a valuable tool for diagnostic and prognostic purposes, as well as a source of potential disease biomarkers in a broad range of diseases. Conclusions mAP-KL is a data-driven and classifier-independent hybrid feature selection method, which applies to any disease classification problem based on microarray data, regardless of the available samples. Combining multiple hypothesis testing and AP leads to subsets of genes, which classify unknown samples from both, small and large patient cohorts with high accuracy.

2012-01-01

67

Stratification of co-evolving genomic groups using ranked phylogenetic profiles  

PubMed Central

Background Previous methods of detecting the taxonomic origins of arbitrary sequence collections, with a significant impact to genome analysis and in particular metagenomics, have primarily focused on compositional features of genomes. The evolutionary patterns of phylogenetic distribution of genes or proteins, represented by phylogenetic profiles, provide an alternative approach for the detection of taxonomic origins, but typically suffer from low accuracy. Herein, we present rank-BLAST, a novel approach for the assignment of protein sequences into genomic groups of the same taxonomic origin, based on the ranking order of phylogenetic profiles of target genes or proteins across the reference database. Results The rank-BLAST approach is validated by computing the phylogenetic profiles of all sequences for five distinct microbial species of varying degrees of phylogenetic proximity, against a reference database of 243 fully sequenced genomes. The approach - a combination of sequence searches, statistical estimation and clustering - analyses the degree of sequence divergence between sets of protein sequences and allows the classification of protein sequences according to the species of origin with high accuracy, allowing taxonomic classification of 64% of the proteins studied. In most cases, a main cluster is detected, representing the corresponding species. Secondary, functionally distinct and species-specific clusters exhibit different patterns of phylogenetic distribution, thus flagging gene groups of interest. Detailed analyses of such cases are provided as examples. Conclusion Our results indicate that the rank-BLAST approach can capture the taxonomic origins of sequence collections in an accurate and efficient manner. The approach can be useful both for the analysis of genome evolution and the detection of species groups in metagenomics samples.

Freilich, Shiri; Goldovsky, Leon; Gottlieb, Assaf; Blanc, Eric; Tsoka, Sophia; Ouzounis, Christos A

2009-01-01

68

ICGA-PSO-ELM approach for accurate multiclass cancer classification resulting in reduced gene sets in which genes encoding secreted proteins are highly represented.  

PubMed

A combination of Integer-Coded Genetic Algorithm (ICGA) and Particle Swarm Optimization (PSO), coupled with the neural-network-based Extreme Learning Machine (ELM), is used for gene selection and cancer classification. ICGA is used with PSO-ELM to select an optimal set of genes, which is then used to build a classifier to develop an algorithm (ICGA_PSO_ELM) that can handle sparse data and sample imbalance. We evaluate the performance of ICGA-PSO-ELM and compare our results with existing methods in the literature. An investigation into the functions of the selected genes, using a systems biology approach, revealed that many of the identified genes are involved in cell signaling and proliferation. An analysis of these gene sets shows a larger representation of genes that encode secreted proteins than found in randomly selected gene sets. Secreted proteins constitute a major means by which cells interact with their surroundings. Mounting biological evidence has identified the tumor microenvironment as a critical factor that determines tumor survival and growth. Thus, the genes identified by this study that encode secreted proteins might provide important insights to the nature of the critical biological features in the microenvironment of each tumor type that allow these cells to thrive and proliferate. PMID:21233525

Saraswathi, Saras; Sundaram, Suresh; Sundararajan, Narasimhan; Zimmermann, Michael; Nilsen-Hamilton, Marit

2011-01-01

69

Drawing Rooted Phylogenetic Networks  

Microsoft Academic Search

The evolutionary history of a collection of species is usually represented by a phylogenetic tree. Sometimes, phylogenetic networks are used as a means of representing reticulate evolution or of showing uncertainty and incompatibilities in evolutionary datasets. This is often done using unrooted phylogenetic networks such as split networks, due in part, to the availability of software (SplitsTree) for their computation

Daniel H. Huson

2009-01-01

70

Directional biases in phylogenetic structure quantification: a Mediterranean case study  

PubMed Central

Recent years have seen an increasing effort to incorporate phylogenetic hypotheses to the study of community assembly processes. The incorporation of such evolutionary information has been eased by the emergence of specialized software for the automatic estimation of partially resolved supertrees based on published phylogenies. Despite this growing interest in the use of phylogenies in ecological research, very few studies have attempted to quantify the potential biases related to the use of partially resolved phylogenies and to branch length accuracy, and no work has examined how tree shape may affect inference of community phylogenetic metrics. In this study, using a large plant community and elevational dataset, we tested the influence of phylogenetic resolution and branch length information on the quantification of phylogenetic structure; and also explored the impact of tree shape (stemminess) on the loss of accuracy in phylogenetic structure quantification due to phylogenetic resolution. For this purpose, we used 9 sets of phylogenetic hypotheses of varying resolution and branch lengths to calculate three indices of phylogenetic structure: the mean phylogenetic distance (NRI), the mean nearest taxon distance (NTI) and phylogenetic diversity (stdPD) metrics. The NRI metric was the less sensitive to phylogenetic resolution, stdPD showed an intermediate sensitivity, and NTI was the most sensitive one; NRI was also less sensitive to branch length accuracy than NTI and stdPD, the degree of sensitivity being strongly dependent on the dating method and the sample size. Directional biases were generally towards type II errors. Interestingly, we detected that tree shape influenced the accuracy loss derived from the lack of phylogenetic resolution, particularly for NRI and stdPD. We conclude that well-resolved molecular phylogenies with accurate branch length information are needed to identify the underlying phylogenetic structure of communities, and also that sensitivity of phylogenetic structure measures to low phylogenetic resolution can strongly differ depending on phylogenetic tree shape.

Molina-Venegas, Rafael; Roquet, Cristina

2014-01-01

71

Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses.  

PubMed

BACKGROUND: Cymbidium orchids, including some 50 species, are the famous flowers, and they possess high commercial value in the floricultural industry. Furthermore, the values of different orchids are great differences. However, species identification is very difficult. To a certain degree, chloroplast DNA sequence data are a versatile tool for species identification and phylogenetic implications in plants. Different chloroplast loci have been utilized for evaluating phylogenetic relationships at each classification level among plant species, including at the interspecies and intraspecies levels. However, there is no evidence that a short sequence can distinguish all plant species from each other in order to infer phylogenetic relationships. Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution. RESULTS: The complete nucleotide sequences of eight individuals from a total of five Cymbidium species' chloroplast (cp) genomes were determined using Illumina sequencing technology of the total DNA via a combination of de novo and reference-guided assembly. The length of the Cymbidium cp genome is about 155 kb. The cp genomes contain 123 unique genes, and the IR regions contain 24 duplicates. Although the genomes, including genome structure, gene order and orientation, are similar to those of other orchids, they are not evolutionarily conservative. The cp genome of Cymbidium evolved moderately with more than 3% sequence divergence, which could provide enough information for phylogeny. Rapidly evolving chloroplast genome regions were identified and 11 new divergence hotspot regions were disclosed for further phylogenetic study and species identification in Orchidaceae. CONCLUSIONS: Phylogenomic analyses were conducted using 10 complete chloroplast genomes from seven orchid species. These data accurately identified the individuals and established the phylogenetic relationships between the species. The results reveal that phylogenomics based on organelle genome sequencing lights the species identification---organelle-scale "barcodes", and is also an effective approach for studying whole populations and phylogenetic characteristics of Cymbidium. PMID:23597078

Yang, Jun-Bo; Tang, Min; Li, Hong-Tao; Zhang, Zhi-Rong; Li, De-Zhu

2013-04-18

72

CREST - Classification Resources for Environmental Sequence Tags  

PubMed Central

Sequencing of taxonomic or phylogenetic markers is becoming a fast and efficient method for studying environmental microbial communities. This has resulted in a steadily growing collection of marker sequences, most notably of the small-subunit (SSU) ribosomal RNA gene, and an increased understanding of microbial phylogeny, diversity and community composition patterns. However, to utilize these large datasets together with new sequencing technologies, a reliable and flexible system for taxonomic classification is critical. We developed CREST (Classification Resources for Environmental Sequence Tags), a set of resources and tools for generating and utilizing custom taxonomies and reference datasets for classification of environmental sequences. CREST uses an alignment-based classification method with the lowest common ancestor algorithm. It also uses explicit rank similarity criteria to reduce false positives and identify novel taxa. We implemented this method in a web server, a command line tool and the graphical user interfaced program MEGAN. Further, we provide the SSU rRNA reference database and taxonomy SilvaMod, derived from the publicly available SILVA SSURef, for classification of sequences from bacteria, archaea and eukaryotes. Using cross-validation and environmental datasets, we compared the performance of CREST and SilvaMod to the RDP Classifier. We also utilized Greengenes as a reference database, both with CREST and the RDP Classifier. These analyses indicate that CREST performs better than alignment-free methods with higher recall rate (sensitivity) as well as precision, and with the ability to accurately identify most sequences from novel taxa. Classification using SilvaMod performed better than with Greengenes, particularly when applied to environmental sequences. CREST is freely available under a GNU General Public License (v3) from http://apps.cbu.uib.no/crest and http://lcaclassifier.googlecode.com.

Lanzen, Anders; J?rgensen, Steffen L.; Huson, Daniel H.; Gorfer, Markus; Grindhaug, Svenn Helge; Jonassen, Inge; ?vreas, Lise; Urich, Tim

2012-01-01

73

Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics  

PubMed Central

Recent implementations of path sampling (PS) and stepping-stone sampling (SS) have been shown to outperform the harmonic mean estimator (HME) and a posterior simulation-based analog of Akaike’s information criterion through Markov chain Monte Carlo (AICM), in Bayesian model selection of demographic and molecular clock models. Almost simultaneously, a Bayesian model averaging approach was developed that avoids conditioning on a single model but averages over a set of relaxed clock models. This approach returns estimates of the posterior probability of each clock model through which one can estimate the Bayes factor in favor of the maximum a posteriori (MAP) clock model; however, this Bayes factor estimate may suffer when the posterior probability of the MAP model approaches 1. Here, we compare these two recent developments with the HME, stabilized/smoothed HME (sHME), and AICM, using both synthetic and empirical data. Our comparison shows reassuringly that MAP identification and its Bayes factor provide similar performance to PS and SS and that these approaches considerably outperform HME, sHME, and AICM in selecting the correct underlying clock model. We also illustrate the importance of using proper priors on a large set of empirical data sets.

Baele, Guy; Li, Wai Lok Sibon; Drummond, Alexei J.; Suchard, Marc A.; Lemey, Philippe

2013-01-01

74

Accurate model selection of relaxed molecular clocks in bayesian phylogenetics.  

PubMed

Recent implementations of path sampling (PS) and stepping-stone sampling (SS) have been shown to outperform the harmonic mean estimator (HME) and a posterior simulation-based analog of Akaike's information criterion through Markov chain Monte Carlo (AICM), in bayesian model selection of demographic and molecular clock models. Almost simultaneously, a bayesian model averaging approach was developed that avoids conditioning on a single model but averages over a set of relaxed clock models. This approach returns estimates of the posterior probability of each clock model through which one can estimate the Bayes factor in favor of the maximum a posteriori (MAP) clock model; however, this Bayes factor estimate may suffer when the posterior probability of the MAP model approaches 1. Here, we compare these two recent developments with the HME, stabilized/smoothed HME (sHME), and AICM, using both synthetic and empirical data. Our comparison shows reassuringly that MAP identification and its Bayes factor provide similar performance to PS and SS and that these approaches considerably outperform HME, sHME, and AICM in selecting the correct underlying clock model. We also illustrate the importance of using proper priors on a large set of empirical data sets. PMID:23090976

Baele, Guy; Li, Wai Lok Sibon; Drummond, Alexei J; Suchard, Marc A; Lemey, Philippe

2013-02-01

75

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

Microsoft Academic Search

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. \\

Frederick A. Matsen III; Robin B. Kodner; E. Virginia Armbrust

2010-01-01

76

Phylogenetic relationships among arecoid palms (Arecaceae: Arecoideae)  

PubMed Central

Background and Aims The Arecoideae is the largest and most diverse of the five subfamilies of palms (Arecaceae/Palmae), containing >50 % of the species in the family. Despite its importance, phylogenetic relationships among Arecoideae are poorly understood. Here the most densely sampled phylogenetic analysis of Arecoideae available to date is presented. The results are used to test the current classification of the subfamily and to identify priority areas for future research. Methods DNA sequence data for the low-copy nuclear genes PRK and RPB2 were collected from 190 palm species, covering 103 (96 %) genera of Arecoideae. The data were analysed using the parsimony ratchet, maximum likelihood, and both likelihood and parsimony bootstrapping. Key Results and Conclusions Despite the recovery of paralogues and pseudogenes in a small number of taxa, PRK and RPB2 were both highly informative, producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Simultaneous analyses of the combined data sets provided additional resolution and support. Two areas of incongruence between PRK and RPB2 were strongly supported by the bootstrap relating to the placement of tribes Chamaedoreeae, Iriarteeae and Reinhardtieae; the causes of this incongruence remain uncertain. The current classification within Arecoideae was strongly supported by the present data. Of the 14 tribes and 14 sub-tribes in the classification, only five sub-tribes from tribe Areceae (Basseliniinae, Linospadicinae, Oncospermatinae, Rhopalostylidinae and Verschaffeltiinae) failed to receive support. Three major higher level clades were strongly supported: (1) the RRC clade (Roystoneeae, Reinhardtieae and Cocoseae), (2) the POS clade (Podococceae, Oranieae and Sclerospermeae) and (3) the core arecoid clade (Areceae, Euterpeae, Geonomateae, Leopoldinieae, Manicarieae and Pelagodoxeae). However, new data sources are required to elucidate ambiguities that remain in phylogenetic relationships among and within the major groups of Arecoideae, as well as within the Areceae, the largest tribe in the palm family.

Baker, William J.; Norup, Maria V.; Clarkson, James J.; Couvreur, Thomas L. P.; Dowe, John L.; Lewis, Carl E.; Pintaud, Jean-Christophe; Savolainen, Vincent; Wilmot, Tomas; Chase, Mark W.

2011-01-01

77

Phylogenetic reconstruction of the wolf spiders (Araneae: Lycosidae) using sequences from the 12S rRNA, 28S rRNA, and NADH1 genes: implications for classification, biogeography, and the evolution of web building behavior.  

PubMed

Current knowledge of the evolutionary relationships amongst the wolf spiders (Araneae: Lycosidae) is based on assessment of morphological similarity or phylogenetic analysis of a small number of taxa. In order to enhance the current understanding of lycosid relationships, phylogenies of 70 lycosid species were reconstructed by parsimony and Bayesian methods using three molecular markers; the mitochondrial genes 12S rRNA, NADH1, and the nuclear gene 28S rRNA. The resultant trees from the mitochondrial markers were used to assess the current taxonomic status of the Lycosidae and to assess the evolutionary history of sheet-web construction in the group. The results suggest that a number of genera are not monophyletic, including Lycosa, Arctosa, Alopecosa, and Artoria. At the subfamilial level, the status of Pardosinae needs to be re-assessed, and the position of a number of genera within their respective subfamilies is in doubt (e.g., Hippasa and Arctosa in Lycosinae and Xerolycosa, Aulonia and Hygrolycosa in Venoniinae). In addition, a major clade of strictly Australasian taxa may require the creation of a new subfamily. The analysis of sheet-web building in Lycosidae revealed that the interpretation of this trait as an ancestral state relies on two factors: (1) an asymmetrical model favoring the loss of sheet-webs and (2) that the suspended silken tube of Pirata is directly descended from sheet-web building. Paralogous copies of the nuclear 28S rRNA gene were sequenced, confounding the interpretation of the phylogenetic analysis and suggesting that a cautionary approach should be taken to the further use of this gene for lycosid phylogenetic analysis. PMID:16503280

Murphy, Nicholas P; Framenau, Volker W; Donnellan, Stephen C; Harvey, Mark S; Park, Yung-Chul; Austin, Andrew D

2006-03-01

78

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes  

PubMed Central

New microbial genomes are constantly being sequenced, and it is crucial to accurately determine their taxonomic identities and evolutionary relationships. Here we report PhyloPhlAn, a new method to assign microbial phylogeny and putative taxonomy using >400 proteins optimized from among 3,737 genomes. This method measures the sequence diversity of all clades, classifies genomes from deep-branching candidate divisions through closely-related subspecies, and improves consistency between phylogenetic and taxonomic groupings. PhyloPhlAn improved taxonomic accuracy for existing and newly-sequenced genomes, detecting 157 erroneous labels, correcting 46, and placing or refining 130 new genomes. We provide examples of accurate classifications from subspecies (Sulfolobus spp.) to phyla, and of preliminary rooting of deep-branching candidate divisions, including consistent statistical support for Caldiserica (formerly candidate division OP5). PhyloPhlAn will thus be useful for both phylogenetic assessment and taxonomic quality control of newly-sequenced genomes. The final phylogenies, conserved protein sequences, and open-source implementation are available online.

Segata, Nicola; Bornigen, Daniela; Morgan, Xochitl C.; Huttenhower, Curtis

2013-01-01

79

Phylogenetic relationships of some filamentous cyanoprokaryotic species.  

PubMed

The polyphasic approach is the most progressive system that has been suggested for distinguishing and phylogenetically classifying Cyanoprokaryota (Cyanobacteria/Cyanophyta). Several oscillatorialean genera (Lyngbya, Phormidium, Plectonema, and Leptolyngbya) have problematic phylogenetic position and taxonomic state because of their heterogeneity and polyphyletic nature. To accurately resolve the phylogenetic relationship of some filamentous species (Nodosilinea bijugata, Phormidium molle, Phormidium papyraceum), we have performed phylogenetic analyses based on 16S rRNA gene and the phycocyanin operon (PC-IGS) by using maximum-likelihood (ML) tree inference methods. These analyses were combined with morphological re-evaluation. Our phylogenetic analyses support the taxonomic separation of genus Nodosilinea from the polyphyletic genus Leptolyngbya. Investigated Nodosilinea strains always formed a coherent genetic cluster supported with a high bootstrap value. The molecular phylogeny confirmed also the monophyly of the Wilmottia group. In addition, data reveal that although P. papyraceum is morphologically similar to Wilmottia murrayi, this species is genetically distinct. Strains from the newly formed genus Phormidesmis and some Phormidium priestleyi strains were clustered in a separate clade different from the typical Phormidium species, but without strong bootstrap support. PMID:24596450

Stoyanov, Plamen; Moten, Dzhemal; Mladenov, Rumen; Dzhambazov, Balik; Teneva, Ivanka

2014-01-01

80

Phylogenetic Relationships of Some Filamentous Cyanoprokaryotic Species  

PubMed Central

The polyphasic approach is the most progressive system that has been suggested for distinguishing and phylogenetically classifying Cyanoprokaryota (Cyanobacteria/Cyanophyta). Several oscillatorialean genera (Lyngbya, Phormidium, Plectonema, and Leptolyngbya) have problematic phylogenetic position and taxonomic state because of their heterogeneity and polyphyletic nature. To accurately resolve the phylogenetic relationship of some filamentous species (Nodosilinea bijugata, Phormidium molle, Phormidium papyraceum), we have performed phylogenetic analyses based on 16S rRNA gene and the phycocyanin operon (PC-IGS) by using maximum-likelihood (ML) tree inference methods. These analyses were combined with morphological re-evaluation. Our phylogenetic analyses support the taxonomic separation of genus Nodosilinea from the polyphyletic genus Leptolyngbya. Investigated Nodosilinea strains always formed a coherent genetic cluster supported with a high bootstrap value. The molecular phylogeny confirmed also the monophyly of the Wilmottia group. In addition, data reveal that although P. papyraceum is morphologically similar to Wilmottia murrayi, this species is genetically distinct. Strains from the newly formed genus Phormidesmis and some Phormidium priestleyi strains were clustered in a separate clade different from the typical Phormidium species, but without strong bootstrap support.

Stoyanov, Plamen; Moten, Dzhemal; Mladenov, Rumen; Dzhambazov, Balik; Teneva, Ivanka

2014-01-01

81

Journey into Phylogenetic Systematics  

NSDL National Science Digital Library

This straightforward and informative site from the Museum of Paleontology (UCMP) at the University of California at Berkeley offers an excellent introduction to Phylogenetic Systematics, the reconstruction of "the pattern of events that have led to the distribution and diversity of life." The site is organized into several sections, addressing "the philosophy, methodology, and implications of cladistic analysis." Descriptive summaries are made more useful with links to the UCMP Glossary of Phylogenetic Terms, and interested users may seek greater depth by linking directly to the UCMP's additional resources.

82

The revised classification of eukaryotes  

PubMed Central

This revision of the classification of eukaryotes, which updates that of Adl et al. (2005), retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.

Adl, Sina M.; Simpson, Alastair. G.; Lane, Christopher E.; Lukes, Julius; Bass, David; Bowser, Samuel S.; Brown, Matt; Burki, Fabien; Dunthorn, Micah; Hampl, Vladimir; Heiss, Aaron; Hoppenrath, Mona; Lara, Enrique; leGall, Line; Lynn, Denis H.; McManus, Hilary; Mitchell, Edward A. D.; Mozley-Stanridge, Sharon E.; Parfrey, Laura Wegener; Pawlowski, Jan; Rueckert, Sonja; Shadwick, Laura; Schoch, Conrad; Smirnov, Alexey; Spiegel, Frederick W.

2012-01-01

83

ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.  

PubMed

Accurate and rapid characterization of influenza A virus (IAV) hemagglutinin (HA) and neuraminidase (NA) sequences with respect to subtype and clade is at the basis of extended diagnostic services and implicit to molecular epidemiologic studies. ClassyFlu is a new tool and web service for the classification of IAV sequences of the HA and NA gene into subtypes and phylogenetic clades using discriminatively trained profile hidden Markov models (HMMs), one for each subtype or clade. ClassyFlu merely requires as input unaligned, full-length or partial HA or NA DNA sequences. It enables rapid and highly accurate assignment of HA sequences to subtypes H1-H17 but particularly focusses on the finer grained assignment of sequences of highly pathogenic avian influenza viruses of subtype H5N1 according to the cladistics proposed by the H5N1 Evolution Working Group. NA sequences are classified into subtypes N1-N10. ClassyFlu was compared to semiautomatic classification approaches using BLAST and phylogenetics and additionally for H5 sequences to the new "Highly Pathogenic H5N1 Clade Classification Tool" (IRD-CT) proposed by the Influenza Research Database. Our results show that both web tools (ClassyFlu and IRD-CT), although based on different methods, are nearly equivalent in performance and both are more accurate and faster than semiautomatic classification. A retraining of ClassyFlu to altered cladistics as well as an extension of ClassyFlu to other IAV genome segments or fragments thereof is undemanding. This is exemplified by unambiguous assignment to a distinct cluster within subtype H7 of sequences of H7N9 viruses which emerged in China early in 2013 and caused more than 130 human infections. http://bioinf.uni-greifswald.de/ClassyFlu is a free web service. For local execution, the ClassyFlu source code in PERL is freely available. PMID:24404173

Van der Auwera, Sandra; Bulla, Ingo; Ziller, Mario; Pohlmann, Anne; Harder, Timm; Stanke, Mario

2014-01-01

84

Charles Darwin, beetles and phylogenetics  

NASA Astrophysics Data System (ADS)

Here, we review Charles Darwin’s relation to beetles and developments in coleopteran systematics in the last two centuries. Darwin was an enthusiastic beetle collector. He used beetles to illustrate different evolutionary phenomena in his major works, and astonishingly, an entire sub-chapter is dedicated to beetles in “The Descent of Man”. During his voyage on the Beagle, Darwin was impressed by the high diversity of beetles in the tropics, and he remarked that, to his surprise, the majority of species were small and inconspicuous. However, despite his obvious interest in the group, he did not get involved in beetle taxonomy, and his theoretical work had little immediate impact on beetle classification. The development of taxonomy and classification in the late nineteenth and earlier twentieth century was mainly characterised by the exploration of new character systems (e.g. larval features and wing venation). In the mid-twentieth century, Hennig’s new methodology to group lineages by derived characters revolutionised systematics of Coleoptera and other organisms. As envisioned by Darwin and Ernst Haeckel, the new Hennigian approach enabled systematists to establish classifications truly reflecting evolution. Roy A. Crowson and Howard E. Hinton, who both made tremendous contributions to coleopterology, had an ambivalent attitude towards the Hennigian ideas. The Mickoleit school combined detailed anatomical work with a classical Hennigian character evaluation, with stepwise tree building, comparatively few characters and a priori polarity assessment without explicit use of the outgroup comparison method. The rise of cladistic methods in the 1970s had a strong impact on beetle systematics. Cladistic computer programs facilitated parsimony analyses of large data matrices, mostly morphological characters not requiring detailed anatomical investigations. Molecular studies on beetle phylogeny started in the 1990s with modest taxon sampling and limited DNA data. This has changed dramatically. With very large data sets and high throughput sampling, phylogenetic questions can be addressed without prior knowledge of morphological characters. Nevertheless, molecular studies have not lead to the great breakthrough in beetle systematics—yet. Especially the phylogeny of the extremely species rich suborder Polyphaga remains incompletely resolved. Coordinated efforts of molecular workers and of morphologists using innovative techniques may lead to more profound insights in the near future. The final aim is to develop a well-founded phylogeny, which truly reflects the evolution of this immensely species rich group of organisms.

Beutel, Rolf G.; Friedrich, Frank; Leschen, Richard A. B.

2009-11-01

85

Iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family Bolbitiaceae.  

PubMed

Reconciling traditional classifications, morphology, and the phylogenetic relationships of brown-spored agaric mushrooms has proven difficult in many groups, due to extensive convergence in morphological features. Here, we address the monophyly of the Bolbitiaceae, a family with over 700 described species and examine the higher-level relationships within the family using a newly constructed multilocus dataset (ITS, nrLSU rDNA and EF1-alpha). We tested whether the fast-evolving Internal Transcribed Spacer (ITS) sequences can be accurately aligned across the family, by comparing the outcome of two iterative alignment refining approaches (an automated and a manual) and various indel-treatment strategies. We used PRANK to align sequences in both cases. Our results suggest that--although PRANK successfully evades overmatching of gapped sites, referred previously to as alignment overmatching--it infers an unrealistically high number of indel events with natively generated guide-trees. This 'alignment undermatching' could be avoided by using more rigorous (e.g. ML) guide trees. The trees inferred in this study support the monophyly of the core Bolbitiaceae, with the exclusion of Panaeolus, Agrocybe, and some of the genera formerly placed in the family. Bolbitius and Conocybe were found monophyletic, however, Pholiotina and Galerella require redefinition. The phylogeny revealed that stipe coverage type is a poor predictor of phylogenetic relationships, indicating the need for a revision of the intrageneric relationships within Conocybe. PMID:23418526

Tóth, Annamária; Hausknecht, Anton; Krisai-Greilhuber, Irmgard; Papp, Tamás; Vágvölgyi, Csaba; Nagy, László G

2013-01-01

86

Insights into the evolution of sorbitol metabolism: phylogenetic analysis of SDR196C family  

PubMed Central

Background Short chain dehydrogenases/reductases (SDR) are NAD(P)(H)-dependent oxidoreductases with a highly conserved 3D structure and of an early origin, which has allowed them to diverge into several families and enzymatic activities. The SDR196C family (http://www.sdr-enzymes.org) groups bacterial sorbitol dehydrogenases (SDH), which are of great industrial interest. In this study, we examine the phylogenetic relationship between the members of this family, and based on the findings and some sequence conserved blocks, a new and a more accurate classification is proposed. Results The distribution of the 66 bacterial SDH species analyzed was limited to Gram-negative bacteria. Six different bacterial families were found, encompassing ?-, ?- and ?-proteobacteria. This broad distribution in terms of bacteria and niches agrees with that of SDR, which are found in all forms of life. A cluster analysis of sorbitol dehydrogenase revealed different types of gene organization, although with a common pattern in which the SDH gene is surrounded by sugar ABC transporter proteins, another SDR, a kinase, and several gene regulators. According to the obtained trees, six different lineages and three sublineages can be discerned. The phylogenetic analysis also suggested two different origins for SDH in ?-proteobacteria and four origins for ?-proteobacteria. Finally, this subdivision was further confirmed by the differences observed in the sequence of the conserved blocks described for SDR and some specific blocks of SDH, and by a functional divergence analysis, which made it possible to establish new consensus sequences and specific fingerprints for the lineages and sub lineages. Conclusion SDH distribution agrees with that observed for SDR, indicating the importance of the polyol metabolism, as an alternative source of carbon and energy. The phylogenetic analysis pointed to six clearly defined lineages and three sub lineages, and great variability in the origin of this gene, despite its well conserved 3D structure. This suggests that SDH are very old and emerged early during the evolution. This study also opens up a new and more accurate classification of SDR196C family, introducing two numbers at the end of the family name, which indicate the lineage and the sublineage of each member, i.e, SDR196C6.3.

2012-01-01

87

CORE: A Phylogenetically-Curated 16S rDNA Database of the Core Oral Microbiome  

PubMed Central

Comparing bacterial 16S rDNA sequences to GenBank and other large public databases via BLAST often provides results of little use for identification and taxonomic assignment of the organisms of interest. The human microbiome, and in particular the oral microbiome, includes many taxa, and accurate identification of sequence data is essential for studies of these communities. For this purpose, a phylogenetically curated 16S rDNA database of the core oral microbiome, CORE, was developed. The goal was to include a comprehensive and minimally redundant representation of the bacteria that regularly reside in the human oral cavity with computationally robust classification at the level of species and genus. Clades of cultivated and uncultivated taxa were formed based on sequence analyses using multiple criteria, including maximum-likelihood-based topology and bootstrap support, genetic distance, and previous naming. A number of classification inconsistencies for previously named species, especially at the level of genus, were resolved. The performance of the CORE database for identifying clinical sequences was compared to that of three publicly available databases, GenBank nr/nt, RDP and HOMD, using a set of sequencing reads that had not been used in creation of the database. CORE offered improved performance compared to other public databases for identification of human oral bacterial 16S sequences by a number of criteria. In addition, the CORE database and phylogenetic tree provide a framework for measures of community divergence, and the focused size of the database offers advantages of efficiency for BLAST searching of large datasets. The CORE database is available as a searchable interface and for download at http://microbiome.osu.edu.

Griffen, Ann L.; Beall, Clifford J.; Firestone, Noah D.; Gross, Erin L.; DiFranco, James M.; Hardman, Jori H.; Vriesendorp, Bastienne; Faust, Russell A.; Janies, Daniel A.; Leys, Eugene J.

2011-01-01

88

Phylogenetic trees in bioinformatics  

SciTech Connect

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

Burr, Tom L [Los Alamos National Laboratory

2008-01-01

89

The Phylogenetic Diversity of Metagenomes  

PubMed Central

Phylogenetic diversity—patterns of phylogenetic relatedness among organisms in ecological communities—provides important insights into the mechanisms underlying community assembly. Studies that measure phylogenetic diversity in microbial communities have primarily been limited to a single marker gene approach, using the small subunit of the rRNA gene (SSU-rRNA) to quantify phylogenetic relationships among microbial taxa. In this study, we present an approach for inferring phylogenetic relationships among microorganisms based on the random metagenomic sequencing of DNA fragments. To overcome challenges caused by the fragmentary nature of metagenomic data, we leveraged fully sequenced bacterial genomes as a scaffold to enable inference of phylogenetic relationships among metagenomic sequences from multiple phylogenetic marker gene families. The resulting metagenomic phylogeny can be used to quantify the phylogenetic diversity of microbial communities based on metagenomic data sets. We applied this method to understand patterns of microbial phylogenetic diversity and community assembly along an oceanic depth gradient, and compared our findings to previous studies of this gradient using SSU-rRNA gene and metagenomic analyses. Bacterial phylogenetic diversity was highest at intermediate depths beneath the ocean surface, whereas taxonomic diversity (diversity measured by binning sequences into taxonomically similar groups) showed no relationship with depth. Phylogenetic diversity estimates based on the SSU-rRNA gene and the multi-gene metagenomic phylogeny were broadly concordant, suggesting that our approach will be applicable to other metagenomic data sets for which corresponding SSU-rRNA gene sequences are unavailable. Our approach opens up the possibility of using metagenomic data to study microbial diversity in a phylogenetic context.

Kembel, Steven W.; Eisen, Jonathan A.; Pollard, Katherine S.; Green, Jessica L.

2011-01-01

90

Spectral classification  

NASA Astrophysics Data System (ADS)

Taxonomic classification of astronomically observed stellar objects is described in terms of spectral properties. Stars receive a classification containing a letter, number, and a Roman numeral, which relates the star to other stars of higher or lower Roman numerals. The citation indicates the stellar chromatic emission in relation to the wavelengths of other stars. Standards are chosen from the available objects detected. Various classification schemes such as the MK, HD, and the Barbier-Chalonge-Divan systems are defined, including examples of indexing differences. Details delineating the separations between classifications are discussed with reference to the information content in spectral and in photometric classification schemes. The parameters usually used for classification include the temperature, luminosity, reddening, binarity, rotation, magnetic field, and elemental abundance or composition. The inclusion of recently discovered extended wavelength characteristics in nominal classifications is outlined, together with techniques involved in automated classification.

Jaschek, C.

91

[Phylogenetic analysis of chloroplast DNA of 18 Solanaceae species].  

PubMed

Chloroplast DNA of 18 Solanaceae species classified into 9 different tribes was analyzed using combined amplified fragment length polymorphism (AFLP) analysis. UPGMA phylogenetic tree was constructed based on the observed data set. In general, the conclusions of this study confirmed the morphology-based classification of these species. Cluster analysis has placed Mandragora into a monophiletic branch and grouped Schizantus and Capsicum into the independent clusters. PMID:15067941

Komarnyts'ky?, S I; Komarnyts'ky?, I K

2003-01-01

92

Editor's Note: Classification Matters  

NSDL National Science Digital Library

Classification skills, so foundational to science, must be taught. While children have a passion and drive to organize and categorize their experiences, sometimes the way they organize them doesn't lead to a worthwhile or accurate scientific understanding. Just as putting a pencil in the hands of a child doesn't automatically teach them to write, having a child sort rocks won't lead to an understanding of classification. The articles in this issue aim to help you teach students how to classify successfully and with purpose.

Ohana, Chris

2009-03-01

93

Toric ideals of phylogenetic invariants  

Microsoft Academic Search

Statistical models of evolution are algebraic varieties in the space of joint probability distributions on the leaf colorations of a phylogenetic tree. The phylogenetic invariants of a model are the polynomials which vanish on the variety. Several widely used models for biological sequences have transition matrices that can be diagonalized by means of the Fourier transform of an abelian group.

Bernd Sturmfels; Seth Sullivant

2004-01-01

94

Toric Ideals of Phylogenetic Invariants  

Microsoft Academic Search

Statistical models of evolution are algebraic varieties in the space of joint probability distri- butions on the leaf colorations of a phylogenetic tree. The phylogenetic invariants of a model are the polynomials which vanish on the variety. Several widely used models for biological se- quences have transition matrices that can be diagonalized by means of the Fourier transform of an

Bernd Sturmfels; Seth Sullivant

2005-01-01

95

Phylogenetic Quantification of Intra-tumour Heterogeneity  

PubMed Central

Intra-tumour genetic heterogeneity is the result of ongoing evolutionary change within each cancer. The expansion of genetically distinct sub-clonal populations may explain the emergence of drug resistance, and if so, would have prognostic and predictive utility. However, methods for objectively quantifying tumour heterogeneity have been missing and are particularly difficult to establish in cancers where predominant copy number variation prevents accurate phylogenetic reconstruction owing to horizontal dependencies caused by long and cascading genomic rearrangements. To address these challenges, we present MEDICC, a method for phylogenetic reconstruction and heterogeneity quantification based on a Minimum Event Distance for Intra-tumour Copy-number Comparisons. Using a transducer-based pairwise comparison function, we determine optimal phasing of major and minor alleles, as well as evolutionary distances between samples, and are able to reconstruct ancestral genomes. Rigorous simulations and an extensive clinical study show the power of our method, which outperforms state-of-the-art competitors in reconstruction accuracy, and additionally allows unbiased numerical quantification of tumour heterogeneity. Accurate quantification and evolutionary inference are essential to understand the functional consequences of tumour heterogeneity. The MEDICC algorithms are independent of the experimental techniques used and are applicable to both next-generation sequencing and array CGH data.

Schwarz, Roland F.; Trinh, Anne; Sipos, Botond; Brenton, James D.; Goldman, Nick; Markowetz, Florian

2014-01-01

96

Norovirus classification and proposed strain nomenclature  

Microsoft Academic Search

Without a virus culture system, genetic analysis becomes the principal method to classify norovirus (NoV) strains. Currently, classification of NoV strains beneath the species level has been based on sequences from different regions of the viral genome. As a result, the phylogenetic insights of some virus were not appropriately interpreted, and no consensus has been reached to establish a uniform

Du-Ping Zheng; Tamie Ando; Rebecca L. Fankhauser; R. Suzanne Beard; Roger I. Glass; Stephan S. Monroe

2006-01-01

97

Gene functional classification from heterogeneous data  

Microsoft Academic Search

In our attempts to understand cellular function at the molecular level, we must be able to synthesize information from disparate types of genomic data. We consider the problem of inferring gene functional classifications from a heterogeneous data set consisting of DNA microarray expression measurements and phylogenetic profiles from whole-genome sequence comparisons. We demonstrate the application of the support vector machine

Paul Pavlidis; Jason Weston; Jinsong Cai; William Noble Grundy

2001-01-01

98

A phylogenomics approach for selecting robust sets of phylogenetic markers  

PubMed Central

Reconstructing the evolutionary relationships of species is a major goal in biology. Despite the increasing number of completely sequenced genomes, a large number of phylogenetic projects rely on targeted sequencing and analysis of a relatively small sample of marker genes. The selection of these phylogenetic markers should ideally be based on accurate predictions of their combined, rather than individual, potential to accurately resolve the phylogeny of interest. Here we present and validate a new phylogenomics strategy to efficiently select a minimal set of stable markers able to reconstruct the underlying species phylogeny. In contrast to previous approaches, our methodology does not only rely on the ability of individual genes to reconstruct a known phylogeny, but it also explores the combined power of sets of concatenated genes to accurately infer phylogenetic relationships of species not previously analyzed. We applied our approach to two broad sets of cyanobacterial and ascomycetous fungal species, and provide two minimal sets of six and four genes, respectively, necessary to fully resolve the target phylogenies. This approach paves the way for the informed selection of phylogenetic markers in the effort of reconstructing the tree of life.

Capella-Gutierrez, Salvador; Kauff, Frank; Gabaldon, Toni

2014-01-01

99

An Optimization-Based Sampling Scheme for Phylogenetic Trees  

NASA Astrophysics Data System (ADS)

Much modern work in phylogenetics depends on statistical sampling approaches to phylogeny construction to estimate probability distributions of possible trees for any given input data set. Our theoretical understanding of sampling approaches to phylogenetics remains far less developed than that for optimization approaches, however, particularly with regard to the number of sampling steps needed to produce accurate samples of tree partition functions. Despite the many advantages in principle of being able to sample trees from sophisticated probabilistic models, we have little theoretical basis for concluding that the prevailing sampling approaches do in fact yield accurate samples from those models within realistic numbers of steps. We propose a novel approach to phylogenetic sampling intended to be both efficient in practice and more amenable to theoretical analysis than the prevailing methods. The method depends on replacing the standard tree rearrangement moves with an alternative Markov model in which one solves a theoretically hard but practically tractable optimization problem on each step of sampling. The resulting method can be applied to a broad range of standard probability models, yielding practical algorithms for efficient sampling and rigorous proofs of accurate sampling for some important special cases. We demonstrate the efficiency and versatility of the method in an analysis of uncertainty in tree inference over varying input sizes. In addition to providing a new practical method for phylogenetic sampling, the technique is likely to prove applicable to many similar problems involving sampling over combinatorial objects weighted by a likelihood model.

Misra, Navodit; Blelloch, Guy; Ravi, R.; Schwartz, Russell

100

Rational disagreements in phylogenetics.  

PubMed

This paper addresses the general problem of how to rationally choose an algorithm for phylogenetic inference. Specifically, the controversy between maximum likelihood (ML) and maximum parsimony (MP) perspectives is reframed within the philosophical issue of theory choice. A Kuhnian approach in which rationality is bounded and value-laden is offered and construed through the notion of a Style of Modeling. A Style is divided into four stages: collecting remnant models, constructing models of taxonomical identity, implementing modeling algorithms, and finally inferring and confirming evolutionary trees or cladograms. The identification and investigation of styles is useful for exploring sociological and epistemological issues such as individuating scientific communities and assessing the rationality of algorithm choice. Regarding the last point, this paper suggests that the values motivating ML and MP perspectives are justified but only contextually; these algorithms also have normative force because they can be therapeutic by allowing us to rationally choose among several competing trees, nonetheless this force is limited and cannot be used in order to decide the controversy tout court. PMID:19229637

Mc Manus, Fabrizzio Guerrero

2009-06-01

101

Phylogenetic lineages in Entomophthoromycota.  

PubMed

Entomophthoromycota is one of six major phylogenetic lineages among the former phylum Zygomycota. These early terrestrial fungi share evolutionarily ancestral characters such as coenocytic mycelium and gametangiogamy as a sexual process resulting in zygospore formation. Previous molecular studies have shown the monophyly of Entomophthoromycota, thus justifying raising the taxonomic status of these fungi to a phylum. Multi-gene phylogenies have identified five major lineages of Entomophthoromycota. In this review we provide a detailed discussion about the biology and taxonomy of these lineages: I) Basidiobolus (Basidiobolomycetes: Basidiobolaceae; primarily saprobic); II) Conidiobolus (Entomophthoromycetes, Ancylistaceae; several clades of saprobes and invertebrate pathogens), as well as three rapidly evolving entomopathogenic lineages in the family Entomophthoraceae centering around; III) Batkoa; IV) Entomophthora and allied genera; and V) the subfamily Erynioideae which includes Zoophthora and allied genera. Molecular phylogenic analysis has recently determined the relationships of several taxa that were previously unresolved based on morphology alone: Eryniopsis, Macrobiotophthora, Massospora, Strongwellsea and two as yet undescribed genera of Basidiobolaceae. PMID:24027349

Gryganskyi, A P; Humber, R A; Smith, M E; Hodge, K; Huang, B; Voigt, K; Vilgalys, R

2013-06-01

102

Toric ideals of phylogenetic invariants.  

PubMed

Statistical models of evolution are algebraic varieties in the space of joint probability distributions on the leaf colorations of a phylogenetic tree. The phylogenetic invariants of a model are the polynomials which vanish on the variety. Several widely used models for biological sequences have transition matrices that can be diagonalized by means of the Fourier transform of an Abelian group. Their phylogenetic invariants form a toric ideal in the Fourier coordinates. We determine generators and Gröbner bases for these toric ideals. For the Jukes-Cantor and Kimura models on a binary tree, our Gröbner bases consist of certain explicitly constructed polynomials of degree at most four. PMID:15882142

Sturmfels, Bernd; Sullivant, Seth

2005-05-01

103

Toric ideals of phylogenetic invariants.  

PubMed

Statistical models of evolution are algebraic varieties in the space of joint probability distributions on the leaf colorations of a phylogenetic tree. The phylogenetic invariants of a model are the polynomials which vanish on the variety. Several widely used models for biological sequences have transition matrices that can be diagonalized by means of the Fourier transform of an abelian group. Their phylogenetic invariants form a toric ideal in the Fourier coordinates. We determine generators and Gröbner bases for these toric ideals. For the Jukes-Cantor and Kimura models on a binary tree, our Gröbner bases consist of certain explicitly constructed polynomials of degree at most four. PMID:15767777

Sturmfels, Bernd; Sullivant, Seth

2005-03-01

104

Contextual classification of multispectral image data: Approximate algorithm  

NASA Technical Reports Server (NTRS)

An approximation to a classification algorithm incorporating spatial context information in a general, statistical manner is presented which is computationally less intensive. Classifications that are nearly as accurate are produced.

Tilton, J. C. (principal investigator)

1980-01-01

105

Evaluating Support for the Current Classification of Eukaryotic Diversity  

Microsoft Academic Search

Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic groups within the five-kingdom classification—plants, animals, fungi, and protists—have been transformed through numerous permutations into the current system of six “supergroups.” The intent of the supergroup classification system is to unite microbial and macroscopic eukaryotes based on phylogenetic inference. This supergroup approach is

Laura Wegener Parfrey; Erika Barbero; Elyse Lasser; Micah Dunthorn; Debashish Bhattacharya; David J Patterson; Laura A Katz

2006-01-01

106

Evaluating Support for the Current Classification of Eukaryotic Diversity  

Microsoft Academic Search

Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic groups within the five-kingdom classification—plants, animals, fungi, and protists—have been transformed through numerous permutations into the current system of six ''supergroups.'' The intent of the supergroup classification system is to unite microbial and macroscopic eukaryotes based on phylogenetic inference. This supergroup approach is

Laura Wegener Parfrey; Erika Barbero; Elyse Lasser; Micah Saul Dunthorn; Debashish Bhattacharya; David J. Patterson; Laura A. Katz

2005-01-01

107

Anole classification: A response to Poe.  

PubMed

A recent correspondence (Poe 2013; hereafter referred to simply as 'Poe,' 'he,' or 'his') criticized our monographic revision of anole classification (Nicholson et al. 2012; hereafter referred to as 'our'). In tone and content, Poe expresses his distress with the idea that his preferred concept of a single, large genus, containing all living members of the family Dactyloidae, might be divided into eight smaller genera. We acknowledge that science benefits from vigorous, intellectual debate, but would have preferred his commentary to be more constructive, objective, and scientifically accurate. We therefore present this rebuttal to explain how Poe erred in characterizing our work, and missed the opportunity to present an alternative comprehensive taxonomy to replace the one against which he argues so strenuously. In this contribution we explain, and correct, Poe's errors and misrepresentations, and argue that our taxonomy is likely to be adopted because it 1) eliminates the obvious problem that will arise if the family Dactyloidae contains only a single large genus (i.e., that a single genus obscures the evolution and diversity within the group and misrepresents or cloaks it), 2) conforms with the long historical trend of dissecting large, cumbersome groups into smaller sub-units, 3) is consistent with all recent phylogenetic studies for anoles in membership within clades we recognize as genera, and 4) aids in associating these lizards with the ancient land masses that shaped their history.  PMID:24943416

Nicholson, K E; Crother, B I; Guyer, C; Savage, J M

2014-01-01

108

Spatial patterns of phylogenetic diversity.  

PubMed

Ecologists and conservation biologists have historically used species-area and distance-decay relationships as tools to predict the spatial distribution of biodiversity and the impact of habitat loss on biodiversity. These tools treat each species as evolutionarily equivalent, yet the importance of species' evolutionary history in their ecology and conservation is becoming increasingly evident. Here, we provide theoretical predictions for phylogenetic analogues of the species-area and distance-decay relationships. We use a random model of community assembly and a spatially explicit flora dataset collected in four Mediterranean-type regions to provide theoretical predictions for the increase in phylogenetic diversity - the total phylogenetic branch-length separating a set of species - with increasing area and the decay in phylogenetic similarity with geographic separation. These developments may ultimately provide insights into the evolution and assembly of biological communities, and guide the selection of protected areas. PMID:21166972

Morlon, Hélène; Schwilk, Dylan W; Bryant, Jessica A; Marquet, Pablo A; Rebelo, Anthony G; Tauss, Catherine; Bohannan, Brendan J M; Green, Jessica L

2011-02-01

109

Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods  

PubMed Central

Host population structure has a major influence on epidemiological dynamics. However, in particular for sexually transmitted diseases, quantitative data on population contact structure are hard to obtain. Here, we introduce a new method that quantifies host population structure based on phylogenetic trees, which are obtained from pathogen genetic sequence data. Our method is based on a maximum-likelihood framework and uses a multi-type branching process, under which each host is assigned to a type (subpopulation). In a simulation study, we show that our method produces accurate parameter estimates for phylogenetic trees in which each tip is assigned to a type, as well for phylogenetic trees in which the type of the tip is unknown. We apply the method to a Latvian HIV-1 dataset, quantifying the impact of the intravenous drug user epidemic on the heterosexual epidemic (known tip states), and identifying superspreader dynamics within the men-having-sex-with-men epidemic (unknown tip states).

Stadler, Tanja; Bonhoeffer, Sebastian

2013-01-01

110

Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods.  

PubMed

Host population structure has a major influence on epidemiological dynamics. However, in particular for sexually transmitted diseases, quantitative data on population contact structure are hard to obtain. Here, we introduce a new method that quantifies host population structure based on phylogenetic trees, which are obtained from pathogen genetic sequence data. Our method is based on a maximum-likelihood framework and uses a multi-type branching process, under which each host is assigned to a type (subpopulation). In a simulation study, we show that our method produces accurate parameter estimates for phylogenetic trees in which each tip is assigned to a type, as well for phylogenetic trees in which the type of the tip is unknown. We apply the method to a Latvian HIV-1 dataset, quantifying the impact of the intravenous drug user epidemic on the heterosexual epidemic (known tip states), and identifying superspreader dynamics within the men-having-sex-with-men epidemic (unknown tip states). PMID:23382421

Stadler, Tanja; Bonhoeffer, Sebastian

2013-03-19

111

Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method, Primer Choice, and Error  

PubMed Central

Nuclear large subunit ribosomal DNA is widely used in fungal phylogenetics and to an increasing extent also amplicon-based environmental sequencing. The relatively short reads produced by next-generation sequencing, however, makes primer choice and sequence error important variables for obtaining accurate taxonomic classifications. In this simulation study we tested the performance of three classification methods: 1) a similarity-based method (BLAST + Metagenomic Analyzer, MEGAN); 2) a composition-based method (Ribosomal Database Project naïve Bayesian classifier, NBC); and, 3) a phylogeny-based method (Statistical Assignment Package, SAP). We also tested the effects of sequence length, primer choice, and sequence error on classification accuracy and perceived community composition. Using a leave-one-out cross validation approach, results for classifications to the genus rank were as follows: BLAST + MEGAN had the lowest error rate and was particularly robust to sequence error; SAP accuracy was highest when long LSU query sequences were classified; and, NBC runs significantly faster than the other tested methods. All methods performed poorly with the shortest 50–100 bp sequences. Increasing simulated sequence error reduced classification accuracy. Community shifts were detected due to sequence error and primer selection even though there was no change in the underlying community composition. Short read datasets from individual primers, as well as pooled datasets, appear to only approximate the true community composition. We hope this work informs investigators of some of the factors that affect the quality and interpretation of their environmental gene surveys.

Porter, Teresita M.; Golding, G. Brian

2012-01-01

112

Molecular identification of hepatitis B virus genotypes/subgenotypes: Revised classification hurdles and updated resolutions  

PubMed Central

The clinical course of infections with the hepatitis B virus (HBV) substantially varies between individuals, as a consequence of a complex interplay between viral, host, environmental and other factors. Due to the high genetic variability of HBV, the virus can be categorized into different HBV genotypes and subgenotypes, which considerably differ with respect to geographical distribution, transmission routes, disease progression, responses to antiviral therapy or vaccination, and clinical outcome measures such as cirrhosis or hepatocellular carcinoma. However, HBV (sub)genotyping has caused some controversies in the past due to misclassifications and incorrect interpretations of different genotyping methods. Thus, an accurate, holistic and dynamic classification system is essential. In this review article, we aimed at highlighting potential pitfalls in genetic and phylogenetic analyses of HBV and suggest novel terms for HBV classification. Analyzing full-length genome sequences when classifying genotypes and subgenotypes is the foremost prerequisite of this classification system. Careful attention must be paid to all aspects of phylogenetic analysis, such as bootstrapping values and meeting the necessary thresholds for (sub)genotyping. Quasi-subgenotype refers to subgenotypes that were incorrectly suggested to be novel. As many of these strains were misclassified due to genetic differences resulting from recombination, we propose the term “recombino-subgenotype”. Moreover, immigration is an important confounding facet of global HBV distribution and substantially changes the geographic pattern of HBV (sub)genotypes. We therefore suggest the term “immigro-subgenotype” to distinguish exotic (sub)genotypes from native ones. We are strongly convinced that applying these two proposed terms in HBV classification will help harmonize this rapidly progressing field and allow for improved prophylaxis, diagnosis and treatment.

Pourkarim, Mahmoud Reza; Amini-Bavil-Olyaee, Samad; Kurbanov, Fuat; Van Ranst, Marc; Tacke, Frank

2014-01-01

113

Phylogenetic Analysis of a Spontaneous Cocoa Bean Fermentation Metagenome Reveals New Insights into Its Bacterial and Fungal Community Diversity  

PubMed Central

This is the first report on the phylogenetic analysis of the community diversity of a single spontaneous cocoa bean box fermentation sample through a metagenomic approach involving 454 pyrosequencing. Several sequence-based and composition-based taxonomic profiling tools were used and evaluated to avoid software-dependent results and their outcome was validated by comparison with previously obtained culture-dependent and culture-independent data. Overall, this approach revealed a wider bacterial (mainly ?-Proteobacteria) and fungal diversity than previously found. Further, the use of a combination of different classification methods, in a software-independent way, helped to understand the actual composition of the microbial ecosystem under study. In addition, bacteriophage-related sequences were found. The bacterial diversity depended partially on the methods used, as composition-based methods predicted a wider diversity than sequence-based methods, and as classification methods based solely on phylogenetic marker genes predicted a more restricted diversity compared with methods that took all reads into account. The metagenomic sequencing analysis identified Hanseniaspora uvarum, Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus as the prevailing species. Also, the presence of occasional members of the cocoa bean fermentation process was revealed (such as Erwinia tasmaniensis, Lactobacillus brevis, Lactobacillus casei, Lactobacillus rhamnosus, Lactococcus lactis, Leuconostoc mesenteroides, and Oenococcus oeni). Furthermore, the sequence reads associated with viral communities were of a restricted diversity, dominated by Myoviridae and Siphoviridae, and reflecting Lactobacillus as the dominant host. To conclude, an accurate overview of all members of a cocoa bean fermentation process sample was revealed, indicating the superiority of metagenomic sequencing over previously used techniques.

Illeghems, Koen; De Vuyst, Luc; Papalexandratou, Zoi; Weckx, Stefan

2012-01-01

114

Molecular phylogenetics and evolutionary history of ariid catfishes revisited: a comprehensive sampling  

PubMed Central

Background Ariids or sea catfishes are one of the two otophysan fish families (out of about 67 families in four orders) that inhabit mainly marine and brackish waters (although some species occur strictly in fresh waters). The group includes over 150 species placed in ~29 genera and two subfamilies (Galeichthyinae and Ariinae). Despite their global distribution, ariids are largely restricted to the continental shelves due in part to their specialized reproductive behavior (i.e., oral incubation). Thus, among marine fishes, ariids offer an excellent opportunity for inferring historical biogeographic scenarios. Phylogenetic hypotheses available for ariids have focused on restricted geographic areas and comprehensive phylogenies are still missing. This study inferred phylogenetic hypotheses for 123 ariid species in 28 genera from different biogeographic provinces using both mitochondrial and nuclear sequences (up to ~4 kb). Results While the topologies obtained support the monophyly of basal groups, up to ten genera validated in previous morphological studies were incongruent with the molecular topologies. New World ariines were recovered as paraphyletic and Old World ariines were grouped into a well-supported clade that was further divided into subclades mainly restricted to major Gondwanan landmasses. A general area cladogram derived from the area cladograms of ariines and three other fish groups was largely congruent with the geological area cladogram of Gondwana. Nonetheless, molecular clock estimations provided variable results on the timing of ariine diversification (~105-41 mya). Conclusion This study provides the most comprehensive phylogeny of sea catfishes to date and highlights the need for re-assessment of their classification. While from a topological standpoint the evolutionary history of ariines is mostly congruent with vicariance associated with the sequence of events during Gondwanan fragmentation, ambiguous divergence time estimations hinders assessing the vicariant hypothesis on a temporal framework. Further examination of ariid fossils might provide the basis for more accurate inferences on the timing of ariine diversification.

Betancur-R, Ricardo

2009-01-01

115

Two issues in archaeological phylogenetics: taxon construction and outgroup selection.  

PubMed

Cladistics is widely used in biology and paleobiology to construct phylogenetic hypotheses, but rarely has it been applied outside those disciplines. There is, however, no reason to suppose that cladistics is not applicable to anything that evolves by cladogenesis and produces a nested hierarchy of taxa. This includes cultural phenomena such as languages and tools recovered from archaeological contexts. Two methodological issues assume primacy in attempts to extend cladistics to archaeological materials: the construction of analytical taxa and the selection of appropriate outgroups. In biology the species is the primary taxonomic unit used, irrespective of the debates that have arisen in phylogenetic theory over the nature of species. Also in biology the phylogenetic history of a group of taxa usually is well enough known that an appropriate taxon can be selected as an outgroup. No analytical unit parallel to the species exists in archaeology, and thus taxa have to be constructed specifically for phylogenetic analysis. One method of constructing taxa is paradigmatic classification, which defines classes (taxa) on the basis of co-occurring, unweighted character states. Once classes have been created, a form of occurrence seriation-an archaeological method based on the theory of cultural transmission and heritability-offers an objective basis for selecting an outgroup. PMID:12051970

O'Brien, Michael J; Lyman, R Lee; Saab, Youssef; Saab, Elias; Darwent, John; Glover, Daniel S

2002-03-21

116

Absolute Pitch in Boreal Chickadees and Humans: Exceptions that Test a Phylogenetic Rule  

ERIC Educational Resources Information Center

This research examined generality of the phylogenetic rule that birds discriminate frequency ranges more accurately than mammals. Human absolute pitch chroma possessors accurately tracked transitions between frequency ranges. Independent tests showed that they used note naming (pitch chroma) to remap the tones into ranges; neither possessors nor…

Weisman, Ronald G.; Balkwill, Laura-Lee; Hoeschele, Marisa; Moscicki, Michele K.; Bloomfield, Laurie L.; Sturdy, Christopher B.

2010-01-01

117

Classification of packed executables for accurate computer virus detection  

Microsoft Academic Search

Executable packing is the most common technique used by computer virus writers to obfuscate malicious code and evade detection by anti-virus software. Universal unpackers have been proposed that can detect and extract encrypted code from packed executables, therefore potentially revealing hidden viruses that can then be detected by traditional signature-based anti-virus software. However, universal unpackers are computationally expensive and scanning

Roberto Perdisci; Andrea Lanzi; Wenke Lee

2008-01-01

118

Efficient and Accurate Value Prediction Using Dynamic Classification  

Microsoft Academic Search

In an effort to increase instruction level parallelism in superscalar microprocessors, several recent works have proposed using value prediction mechanisms to break the data dependency links between value-producing and value-consuming instructions. Some of these mechanisms achieve very high prediction accuracies, albeit at considerable hardware cost. Other mechanisms have low hardware cost but obtain mediocre prediction performance. In this paper, we

Bohuslav Rychlik; John W. Faistl; Bryon P. Krug; Albert Y. Kurland; John J. Sung; Miroslav N. Velev; John P. Shen

1998-01-01

119

Phylogenetic Approaches Toward Crocodylian History  

NASA Astrophysics Data System (ADS)

A review of crocodylian phylogeny reveals a more complex history than might have been anticipated from a direct reading of the fossil record without consideration of phylogenetic relationships. The three main extant crocodylian lineagesGavialoidea, Alligatoroidea, Crocodyloideaare known from fossils in the Late Cretaceous, and the group is found nearly worldwide during the Cenozoic. Some groups have distributions that are best explained by the crossing of marine barriers during the Tertiary. Early Tertiary crocodylian faunas are phylogenetically composite, and clades tend to be morphologically uniform and geographically widespread. Later in the Tertiary, Old World crocodylian faunas are more endemic. Crocodylian phylogeneticists face numerous challenges, the most important being the phylogenetic relationships and time of divergence of the two living gharials (Gavialis gangeticus and Tomistoma schlegelii), the relationships among living true crocodiles (Crocodylus), and the relationships among caimans.

Brochu, Christopher A.

120

Fast and accurate methods for phylogenomic analyses  

PubMed Central

Background Species phylogenies are not estimated directly, but rather through phylogenetic analyses of different gene datasets. However, true gene trees can differ from the true species tree (and hence from one another) due to biological processes such as horizontal gene transfer, incomplete lineage sorting, and gene duplication and loss, so that no single gene tree is a reliable estimate of the species tree. Several methods have been developed to estimate species trees from estimated gene trees, differing according to the specific algorithmic technique used and the biological model used to explain differences between species and gene trees. Relatively little is known about the relative performance of these methods. Results We report on a study evaluating several different methods for estimating species trees from sequence datasets, simulating sequence evolution under a complex model including indels (insertions and deletions), substitutions, and incomplete lineage sorting. The most important finding of our study is that some fast and simple methods are nearly as accurate as the most accurate methods, which employ sophisticated statistical methods and are computationally quite intensive. We also observe that methods that explicitly consider errors in the estimated gene trees produce more accurate trees than methods that assume the estimated gene trees are correct. Conclusions Our study shows that highly accurate estimations of species trees are achievable, even when gene trees differ from each other and from the species tree, and that these estimations can be obtained using fairly simple and computationally tractable methods.

2011-01-01

121

Classification Skills: Visual and Verbal Presentation Modes.  

ERIC Educational Resources Information Center

A classification task with two experimental conditions, a visual presentation mode and a verbal presentation mode, was presented to 20 adult subjects and to 108 children, ages 3 years, 9 months to 7 years, 2 months. Among children, verbal presentation elicited a significantly greater number of accurate functional classifications than did the…

Pine, Shirley J.; Grimes, Karin B.

122

Integrating Classification and Association Rule Mining  

Microsoft Academic Search

Classification rule mining aims to discover a small set of rules in the database that forms an accurate classifier. Association rule mining finds all the rules existing in the database that satisfy some minimum support and minimum confidence constraints. For association rule mining, the target of discovery is not pre-determined, while for classification rule mining there is one and only

Bing Liu; Wynne Hsu; Yiming Ma

1998-01-01

123

Classification of Instructional Programs: 2000 Edition.  

ERIC Educational Resources Information Center

This third revision of the Classification of Instructional Programs (CIP) updates and modifies education program classifications, providing a taxonomic scheme that supports the accurate tracking, assessment, and reporting of field of study and program completions activity. This edition has also been adopted as the standard field of study taxonomy…

Morgan, Robert L.; Hunt, E. Stephen

124

A Comparison of Phylogenetic Network Methods Using Computer Simulation  

PubMed Central

Background We present a series of simulation studies that explore the relative performance of several phylogenetic network approaches (statistical parsimony, split decomposition, union of maximum parsimony trees, neighbor-net, simulated history recombination upper bound, median-joining, reduced median joining and minimum spanning network) compared to standard tree approaches, (neighbor-joining and maximum parsimony) in the presence and absence of recombination. Principal Findings In the absence of recombination, all methods recovered the correct topology and branch lengths nearly all of the time when the substitution rate was low, except for minimum spanning networks, which did considerably worse. At a higher substitution rate, maximum parsimony and union of maximum parsimony trees were the most accurate. With recombination, the ability to infer the correct topology was halved for all methods and no method could accurately estimate branch lengths. Conclusions Our results highlight the need for more accurate phylogenetic network methods and the importance of detecting and accounting for recombination in phylogenetic studies. Furthermore, we provide useful information for choosing a network algorithm and a framework in which to evaluate improvements to existing methods and novel algorithms developed in the future.

Woolley, Steven M.; Posada, David; Crandall, Keith A.

2008-01-01

125

Grading More Accurately  

ERIC Educational Resources Information Center

Grades matter. College grading systems, however, are often ad hoc and prone to mistakes. This essay focuses on one factor that contributes to high-quality grading systems: grading accuracy (or "efficiency"). I proceed in several steps. First, I discuss the elements of "efficient" (i.e., accurate) grading. Next, I present analytical results…

Rom, Mark Carl

2011-01-01

126

Interpreting the universal phylogenetic tree.  

PubMed

The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist. PMID:10900003

Woese, C R

2000-07-18

127

PHYLOGENETIC APPROACHES TOWARD CROCODYLIAN HISTORY  

Microsoft Academic Search

? Abstract A review of crocodylian phylogeny reveals a more complex history than might have been anticipated from a direct reading of the fossil record with- out consideration of phylogenetic relationships. The three main extant crocodylian lineages—Gavialoidea, Alligatoroidea, Crocodyloidea—are known from fossils in the Late Cretaceous, and the group is found nearly worldwide during the Cenozoic. Some groups have distributions

Christopher A. Brochu

2003-01-01

128

Phylogenetic Approaches Toward Crocodylian History  

Microsoft Academic Search

A review of crocodylian phylogeny reveals a more complex history than might have been anticipated from a direct reading of the fossil record without consideration of phylogenetic relationships. The three main extant crocodylian lineagesGavialoidea, Alligatoroidea, Crocodyloideaare known from fossils in the Late Cretaceous, and the group is found nearly worldwide during the Cenozoic. Some groups have distributions that are best

Christopher A. Brochu

2003-01-01

129

Early dinosaurs: A phylogenetic study  

Microsoft Academic Search

Early dinosaur evolution has been the subject of several phylogenetic studies and the position of certain basal forms is currently debated. This is the case for the oldest known members of the group, excavated from the Late Triassic Ischigualastian beds of South America, such as Herrerasaurus, Eoraptor, Pisanosaurus, Saturnalia and Staurikosaurus. A new cladistic analysis of the early dinosaur radiation

Max C. Langer; Michael J. Benton

2006-01-01

130

Polytomies and Bayesian phylogenetic inference  

Microsoft Academic Search

Bayesian phylogenetic analyses are now very popular in systematics and molecular evolution because they allow the use of much more realistic models than currently possible with maximum likelihood methods. There are, however, ag rowing number of examples in which large Bayesian posterior clade probabilities are associated with very short edge lengths and low values for non-Bayesian measures of support such

Paul O. Lewis; Mark T. Holder; Kent E. Holsinger

2005-01-01

131

Accurate monotone cubic interpolation  

NASA Technical Reports Server (NTRS)

Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.

Huynh, Hung T.

1991-01-01

132

Accurate Finite Difference Algorithms  

NASA Technical Reports Server (NTRS)

Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

Goodrich, John W.

1996-01-01

133

Accurate Unlexicalized Parsing  

Microsoft Academic Search

We demonstrate that an unlexicalized PCFG can parse much more accurately than previously shown, by making use of simple, linguistically motivated state splits, which break down false independence assumptions latent in a vanilla treebank grammar. Indeed, its performance of 86.36% (LP\\/LR F PCFG models, and surprisingly close to the current state-of-the-art. This result has potential uses beyond establishing a strong

Dan Klein; Christopher D. Manning

2003-01-01

134

Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies.  

PubMed

Gobioidei is one of the largest suborders of teleost fishes, with nearly 2000 extant species currently recognized. They have a worldwide distribution and show a spectacular variety in morphology, ecology, and behavior. Despite their importance, phylogenetic relationships among many groups of gobioids (including some of the major lineages) still remain poorly understood. In this study, we analyze sequence data of five molecular markers (two mitochondrial and three nuclear) averaging 6000 bp for 222 species of gobioids. Our study is the first to include both multiple nuclear and mitochondrial genes to reconstruct a comprehensive multilocus phylogeny of gobioids encompassing most major lineages representing the overall diversity of one of the most speciose vertebrate lineages. Two separate datasets are produced and used to specifically address the phylogenetic placement of Rhyacichthyidae and Odontobutidae, and the phylogenetic relationships among gobioid lineages. Our results strongly support that the initial split in the gobioid tree separated a clade containing Rhyacichthyidae+Odontobutidae as the sister group of all other lineages. The family Eleotrididae branches off the gobioid tree after the Rhyacichthyidae+Odontobutidae clade, followed by the Butidae as sister group to the Gobiidae. Additionally, several major monophyletic groups are confidently identified within the two major Gobiidae subclades, the gobiine-like gobiids and the gobionelline-like gobiids. Robustness of the phylogenetic trees inferred here is significantly higher than that of previous studies, hence our results provide the most compelling molecular phylogenetic hypothesis of Gobioidei thus far. For the first time, we provide a comprehensive sampling of European gobies that traditionally have been divided into "transverse" gobies and "sand gobies". We show that the European gobies cluster in three distinct lineages, the Pomatoschistus-, Aphia-, and Gobius-lineages. The former resolved within the gobionelline-like gobiids and the latter two within the gobiine-like gobiids. These findings have significant implications for our understanding of the phylogeographic origin of European gobies in the light of the closure of the Paratethys. A rogue taxon analysis identified Kraemeria as an unstable taxon decreasing support at the base of the gobiine-like gobiids. Removal of this rogue taxon significantly increased phylogenetic resolution in that part of the tree and revealed additional insights into early bursts of cladogenesis of the gobiine-like gobiids. PMID:23911892

Agorreta, Ainhoa; San Mauro, Diego; Schliewen, Ulrich; Van Tassell, James L; Kova?i?, Marcelo; Zardoya, Rafael; Rüber, Lukas

2013-12-01

135

Form classification  

NASA Astrophysics Data System (ADS)

The problem of form classification is to assign a single-page form image to one of a set of predefined form types or classes. We classify the form images using low level pixel density information from the binary images of the documents. In this paper, we solve the form classification problem with a classifier based on the k-means algorithm, supported by adaptive boosting. Our classification method is tested on the NIST scanned tax forms data bases (special forms databases 2 and 6) which include machine-typed and handwritten documents. Our method improves the performance over published results on the same databases, while still using a simple set of image features.

Reddy, K. V. Umamaheswara; Govindaraju, Venu

2008-01-01

136

Identification of medicinal Dendrobium species by phylogenetic analyses using matK and rbcL sequences  

Microsoft Academic Search

Species identification of five Dendrobium plants was conducted using phylogenetic analysis and the validity of the method was verified. Some Dendrobium plants (Orchidaceae) have been used as herbal medicines but the difficulty in identifying their botanical origin by traditional\\u000a methods prevented their full modern utilization. Based on the emerging field of molecular systematics as a powerful classification\\u000a tool, a phylogenetic

Haruka Asahina; Junichi Shinozaki; Kazuo Masuda; Yasujiro Morimitsu; Motoyoshi Satake

2010-01-01

137

Classification Fun  

NSDL National Science Digital Library

Taxonomic information shows the evolutionary relationships between organisms. In this lesson plan, students will classify organisms by kingdom and apply their own understanding of classification to identify organisms. The students should already have an understanding of the basics of the five kindoms and the seven categories of classification. The document includes a pre-test on the topic to gauge student understanding and two classroom activities. The activity is intended for sixth grade students, and should take three to four class periods to complete.

Shubinski, Carol

2012-06-11

138

Learning classification trees  

NASA Technical Reports Server (NTRS)

Algorithms for learning classification trees have had successes in artificial intelligence and statistics over many years. How a tree learning algorithm can be derived from Bayesian decision theory is outlined. This introduces Bayesian techniques for splitting, smoothing, and tree averaging. The splitting rule turns out to be similar to Quinlan's information gain splitting rule, while smoothing and averaging replace pruning. Comparative experiments with reimplementations of a minimum encoding approach, Quinlan's C4 and Breiman et al. Cart show the full Bayesian algorithm is consistently as good, or more accurate than these other approaches though at a computational price.

Buntine, Wray

1991-01-01

139

Phylogenetics of Saccharomycetales, the ascomycete yeasts.  

PubMed

Ascomycete yeasts (phylum Ascomycota: subphylum Saccharomycotina: class Saccharomycetes: order Saccharomycetales) comprise a monophyletic lineage with a single order of about 1000 known species. These yeasts live as saprobes, often in association with plants, animals and their interfaces. A few species account for most human mycotic infections, and fewer than 10 species are plant pathogens. Yeasts are responsible for important industrial and biotechnological processes, including baking, brewing and synthesis of recombinant proteins. Species such as Saccharomyces cerevisiae are model organisms in research, some of which led to a Nobel Prize. Yeasts usually reproduce asexually by budding, and their sexual states are not enclosed in a fruiting body. The group also is well defined by synapomorphies visible at the ultrastructural level. Yeast identification and classification changed dramatically with the availability of DNA sequencing. Species identification now benefits from a constantly updated sequence database and no longer relies on ambiguous growth tests. A phylogeny based on single gene analyses has shown the order to be remarkably divergent despite morphological similarities among members. The limits of many previously described genera are not supported by sequence comparisons, and multigene phylogenetic studies are under way to provide a stable circumscription of genera, families and orders. One recent multigene study has resolved species of the Saccharomycetaceae into genera that differ markedly from those defined by analysis of morphology and growth responses, and similar changes are likely to occur in other branches of the yeast tree as additional sequences become available. PMID:17486976

Suh, Sung-Oui; Blackwell, Meredith; Kurtzman, Cletus P; Lachance, Marc-André

2006-01-01

140

EM for phylogenetic topology reconstruction on nonhomogeneous data  

PubMed Central

Background The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly dealing with the long-branch attraction problem. The correct reconstruction of 4-taxon trees is crucial for making quartet-based methods work and being able to recover large phylogenies. Methods We adapt the well known expectation-maximization algorithm to evolutionary Markov models on phylogenetic 4-taxon trees. We then use this algorithm to estimate the substitution parameters, compute the corresponding likelihood, and to infer the most likely quartet. Results In this paper we consider an expectation-maximization method for maximizing the likelihood of (time nonhomogeneous) evolutionary Markov models on trees. We study its success on reconstructing 4-taxon topologies and its performance as input method in quartet-based phylogenetic reconstruction methods such as QFIT and QuartetSuite. Our results show that the method proposed here outperforms neighbor-joining and the usual (time-homogeneous continuous-time) maximum likelihood methods on 4-leaved trees with among-lineage instantaneous rate heterogeneity, and perform similarly to usual continuous-time maximum-likelihood when data satisfies the assumptions of both methods. Conclusions The method presented in this paper is well suited for reconstructing the topology of any number of taxa via quartet-based methods and is highly accurate, specially regarding largely divergent trees and time nonhomogeneous data.

2014-01-01

141

Accurate searching using XML and topic maps.  

PubMed

Most clinical data is narrative text and often not accessible and searchable at the clinical workstation. We have therefore developed a search engine that allows indexing, searching and linking different kinds of data using web technologies. Text matching methods fail to represent implicit relationships between data, e.g. the relationship between HIV and AIDS. The ISO topic maps standard provides a data model that allows representing arbitrary relationships between resources. Such relationships form the basis for context sensitive searching and accurate search results. XML standards are used for the interchange of data relationships. Our approach has been applied to medical classification systems and clinical practice guidelines with promising results. PMID:14664036

Schweiger, Ralf; Hölzer, Simon; Dudeck, Joachim

2003-01-01

142

Increased Taxon Sampling Greatly Reduces Phylogenetic Error  

Microsoft Academic Search

Several authors have argued recently that extensive taxon sampling has a positive and important effect on the accuracy of phylogenetic estimates. However, other authors have argued that there is little beneét of extensive taxon sampling, and so phylogenetic problems can or should be reduced to a few exemplar taxa as a means of reducing the computational complexity of the phylogenetic

Derrick J. Zwickl; David M. Hillis

2002-01-01

143

Image Classification  

NSDL National Science Digital Library

In this exercise, students get experience with image classification. Images are an increasingly important source of information about land cover and land use over time because comparisons of historic and current images can provide an estimate of change in the landscape.

Cote, Paul; Welch, Brian C.

2008-10-14

144

Classifying Classification  

ERIC Educational Resources Information Center

This article describes the experience of a group of first-grade teachers as they tackled the science process of classification, a targeted learning objective for the first grade. While the two-year process was not easy and required teachers to teach in a new, more investigation-oriented way, the benefits were great. The project helped teachers and…

Novakowski, Janice

2009-01-01

145

Phylogenetic diversity of nonmarine picocyanobacteria.  

PubMed

We studied the phylogenetic diversity of nonmarine picocyanobacteria broadening the sequence data set with 43 new sequences of the 16S rRNA gene. The sequences were derived from monoclonal strains isolated from four volcanic high-altitude athalassohaline lakes in Mexico, five glacial ultraoligotrophic North Patagonian lakes and six Italian lakes of glacial, volcanic and morenic origin. The new sequences fall into a number of both novel and previously described clades within the phylogenetic tree of 16S rRNA gene. The new cluster of Lake Nahuel Huapi (North Patagonia) forms a sister clade to the subalpine cluster II and the marine Synechococcus subcluster 5.2. Our finding of the novel clade of 'halotolerants' close to the marine subcluster 5.3 (Synechococcus RCC307) constitutes an important demonstration that euryhaline and marine strains affiliate closely. The intriguing results obtained shed new light on the importance of the nonmarine halotolerants in the phylogenesis of picocyanobacteria. PMID:23528076

Callieri, Cristiana; Coci, Manuela; Corno, Gianluca; Macek, Miroslav; Modenutti, Beatriz; Balseiro, Esteban; Bertoni, Roberto

2013-08-01

146

Classification in Australia.  

National Technical Information Service (NTIS)

Despite some inroads by the Library of Congress Classification and short-lived experimentation with Universal Decimal Classification and Bliss Classification, Dewey Decimal Classification, with its ability in recent editions to be hospitable to local need...

J. McKinlay

1980-01-01

147

Phylogenetic methods in drug discovery.  

PubMed

In recent decades, growth of computing power has facilitated powerful techniques for reconstructing evolutionary relationships from online genetic and proteomic databases. These methods are useful tools for pharmacologists for analyzing relationships between receptors and associated enzymes. Phylogenetic analysis can help generate hypotheses and leads for experimentation. Reconstruction of molecular phylogenies for the nonspecialist is described in this article using the example of the orphaned g protein coupled receptor GPR18. PMID:23895575

Ashton, John C

2013-12-01

148

Algebraic Invariants of Phylogenetic Trees  

Microsoft Academic Search

Abstract One of the restrictions used,in all of the works,done,on phylogenetic,in- variants for group-based,models,has been that the group,be abelian. In my thesis, I aim to generalize the method of invariants for group-based models of DNA sequence,evolution to include nonabelian,groups. By using a non- abelian group to act one the nucleotides, one could capture the structure of the symmetric model for

Mike Hansen

149

Phylogenetic analysis of gene expression.  

PubMed

Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary changes in morphological, physiological, and developmental characters of interest. This will provide entirely new opportunities to identify genes related to particular phenotypes. There are, however, 3 key challenges that must be addressed for such studies to realize their potential. First, data on gene expression must be measured from multiple species, some of which may be field-collected, and parameterized in such a way that they can be compared across species. Second, it will be necessary to develop comparative phylogenetic methods suitable for large multidimensional datasets. In most phylogenetic comparative studies to date, the number n of independent observations (independent contrasts) has been greater than the number p of variables (characters). The behavior of comparative methods for these classic problems is now well understood under a wide variety of conditions. In studies of gene expression, and in studies based on other high-throughput tools, the number n of samples is dwarfed by the number p of variables. The estimated covariance matrices will be singular, complicating their analysis and interpretation, and prone to spurious results. Third, new approaches are needed to investigate the expression of the many genes whose phylogenies are not congruent with species phylogenies due to gene loss, gene duplication, and incomplete lineage sorting. Here we outline general considerations of project design for phylogenetic analyses of gene expression and suggest solutions to these three categories of challenges. These topics are relevant to high-throughput phenotypic data well beyond gene expression. PMID:23748631

Dunn, Casey W; Luo, Xi; Wu, Zhijin

2013-11-01

150

Phylogenetic Analysis of the Kinesin Superfamily from Physcomitrella  

PubMed Central

Kinesins are an ancient superfamily of microtubule dependent motors. They participate in an extensive and diverse list of essential cellular functions, including mitosis, cytokinesis, cell polarization, cell elongation, flagellar development, and intracellular transport. Based on phylogenetic relationships, the kinesin superfamily has been subdivided into 14 families, which are represented in most eukaryotic phyla. The functions of these families are sometimes conserved between species, but important variations in function across species have been observed. Plants possess most kinesin families including a few plant specific families. With the availability of an ever increasing number of genome sequences from plants, it is important to document the complete complement of kinesins present in a given organism. This will help develop a molecular framework to explore the function of each family using genetics, biochemistry, and cell biology. The moss Physcomitrella patens has emerged as a powerful model organism to study gene function in plants, which makes it a key candidate to explore complex gene families, such as the kinesin superfamily. Here we report a detailed phylogenetic characterization of the 71 kinesins of the kinesin superfamily in Physcomitrella. We found a remarkable conservation of families and subfamily classes with Arabidopsis, which is important for future comparative analysis of function. Some of the families, such as kinesins 14s are composed of fewer members in moss, while other families, such as the kinesin 12s are greatly expanded. To improve the comparison between species, and to simplify communication between research groups, we propose a classification of subfamilies based on our phylogenetic analysis.

Shen, Zhiyuan; Collatos, Angelo R.; Bibeau, Jeffrey P.; Furt, Fabienne; Vidali, Luis

2012-01-01

151

Phylogenetic analysis of antibiotic glycosyltransferases.  

PubMed

Catalyzed by a family of enzymes called glycosyltransferases, glycosylation reactions are essential for the bioactivities of secondary metabolites such as antibiotics. Due to the special characters of antibiotic glycosyltransferases (AGts), antibiotics can function by attaching some unusual deoxy-sugars to their aglycons. Comprehensive similarity searches on the amino acid sequences of AGts have been performed. We reconstructed the molecular phylogeny of AGts with neighbor-joining, maximum-likelihood, and Bayesian methods of phylogenetic inference. The phylogenetic trees show a distinct separation of polyene macrolide (PEM) AGts and other polyketide AGts. The former are more like eukaryotic glycosyltransferases and were deduced to be the results of horizontal gene transfer from eukaryotes. Protein tertiary structural comparison also indicated that some glycopeptide AGts (Gtf-proteins) have a close evolutionary relationship with MurGs, essential glycosyltransferases involved in maturation of bacterial cell walls. The evolutionary relationship of glycopeptide antibiotic biosynthetic gene clusters was speculated according to the phylogenetic analysis of Gtf-proteins. Considering the fact that polyketide AGts and Gtf-proteins are all GT Family 1 members and their aglycon acceptor biosynthetic patterns are very similar, we deduced that AGts and the synthases of their aglycon acceptors have some evolutionary relevance. Finally, the evolutionary origins of AGts that do not fall into GT Family 1 are discussed, suggesting that their ancestral proteins appear to be derived from various proteins responsible for primary metabolism. PMID:17334710

Liang, Dongmei; Qiao, Jianjun

2007-03-01

152

Accurate measurement of time  

NASA Astrophysics Data System (ADS)

The paper discusses current methods for accurate measurements of time by conventional atomic clocks, with particular attention given to the principles of operation of atomic-beam frequency standards, atomic hydrogen masers, and atomic fountain and to the potential use of strings of trapped mercury ions as a time device more stable than conventional atomic clocks. The areas of application of the ultraprecise and ultrastable time-measuring devices that tax the capacity of modern atomic clocks include radio astronomy and tests of relativity. The paper also discusses practical applications of ultraprecise clocks, such as navigation of space vehicles and pinpointing the exact position of ships and other objects on earth using the GPS.

Itano, Wayne M.; Ramsey, Norman F.

1993-07-01

153

Accurate quantum chemical calculations  

NASA Technical Reports Server (NTRS)

An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

1989-01-01

154

A new classification method to overcome over-branching  

Microsoft Academic Search

Classification is an important technique in data mining. The decision trees built by most of the existing classification algorithms\\u000a commonly feature over-branching, which will lead to poor efficiency in the subsequent classification period. In this paper,\\u000a we present a new value-oriented classification method, which aims at building accurately proper-sized decision trees while\\u000a reducing over-branching as much as possible, based on

Aoying Zhou; Weining Qian; Hailei Qian; Wen Jin

2002-01-01

155

Maximum Parsimony on Phylogenetic networks  

PubMed Central

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

2012-01-01

156

Triangle Classification  

NSDL National Science Digital Library

This geometry lesson from Illuminations presents the Triangle Classification problem. Students will attempt to classify the triangles formed in a plane when a randomly selected point is connected to the endpoints of a given line segment. Students should have access to a computer with internet access for the lesson. The material is intended for grades 9-12 and should require 1 class period to complete.

2010-12-29

157

Primate Classification  

NSDL National Science Digital Library

In this lesson students learn how classification of organisms is based on evolutionary relationships. They will also learn how primates are categorized, and how they are related. Students transfer examples (names) of primates from their location in an outline hierarchy of primate groups into a set of nested boxes reflecting that same hierarchy. A cladogram can then be drawn illustrating how these groups are related in an evolutionary way.

158

Multicriteria PCF Design: An Accurate Photonic Crystal Fiber Design Tool  

Microsoft Academic Search

Summary form only given. In recent years there has been a major development in optical communications and a new generation of fibers was introduced. These fibers, called Photonic Crystal Fibers (PCF) have unusual propagation properties. This paper presents multicriteria PCF design tool, which is an accurate PCF design based on multicriteria classification. This method combines the deductive and the inductive

Imen Sassi; Nabil Belacel; Yassine Bouslimani; Habib Hamam

2009-01-01

159

Quartet-Net: A Quartet-Based Method to Reconstruct Phylogenetic Networks  

PubMed Central

Phylogenetic networks can model reticulate evolutionary events such as hybridization, recombination, and horizontal gene transfer. However, reconstructing such networks is not trivial. Popular character-based methods are computationally inefficient, whereas distance-based methods cannot guarantee reconstruction accuracy because pairwise genetic distances only reflect partial information about a reticulate phylogeny. To balance accuracy and computational efficiency, here we introduce a quartet-based method to construct a phylogenetic network from a multiple sequence alignment. Unlike distances that only reflect the relationship between a pair of taxa, quartets contain information on the relationships among four taxa; these quartets provide adequate capacity to infer a more accurate phylogenetic network. In applications to simulated and biological data sets, we demonstrate that this novel method is robust and effective in reconstructing reticulate evolutionary events and it has the potential to infer more accurate phylogenetic distances than other conventional phylogenetic network construction methods such as Neighbor-Joining, Neighbor-Net, and Split Decomposition. This method can be used in constructing phylogenetic networks from simple evolutionary events involving a few reticulate events to complex evolutionary histories involving a large number of reticulate events. A software called “Quartet-Net” is implemented and available at http://sysbio.cvm.msstate.edu/QuartetNet/.

Yang, Jialiang; Grunewald, Stefan; Wan, Xiu-Feng

2013-01-01

160

Higher-Level Phylogenetic Relationships of Homobasidiomycetes (Mushroom-Forming Fungi) Inferred from Four rDNA Regions  

Microsoft Academic Search

Homobasidiomycetes include approximately 13,000 described species of mushroom-forming fungi and related taxa. The higher-level classification of this ecologically important group has been unsettled for over 100 years. The goals of the present study were to evaluate a recent phylogenetic classification by Hibbett and Thorn that divided the homobasidiomycetes into eight major unranked clades, and to infer the higher-order relationships among

Manfred Binder; David S. Hibbett

2002-01-01

161

Phylogenetic positions of RH blood group-related genes in cyclostomes.  

PubMed

The RH gene family in vertebrates consists of four major genes (RH, RHAG, RHBG, and RHCG). They are thought to have emerged in the common ancestor of vertebrates after two rounds of whole genome duplication (2R-WGD). To analyze the detailed phylogenetic relationships within the RH gene family, we determined three types of cDNA sequence that belong to the RH gene family in lamprey (Lethenteron reissneri) and designated them as RHBG-like, RHCG-like1, and RHCG-like2. Phylogenetic analyses clearly showed that RHCG-like1 and RHCG-like2 genes, which were probably duplicated in the lamprey lineage, are orthologs of gnathostome RHCG. In contrast, the clear phylogenetic position of the RHBG-like gene could not be obtained. Probably some convergent events for cyclostome RHBG-like genes prevented the accurate identification of their phylogenetic positions. PMID:24720951

Suzuki, Akinori; Endo, Kouhei; Kitano, Takashi

2014-06-10

162

Constraint Classification for Multiclass Classification and Ranking  

Microsoft Academic Search

The constraint classification framework captures many flavors of mul- ticlass classification including winner-take-all multiclass classification, multilabel classification and ranking. We present a meta-algorithm for learning in this framework that learns via a single linear classifier in high dimension. We discuss distribution independent as well as margin-based generalization bounds and present empirical and theoretical evidence showing that constraint classification benefits over

Sariel Har-peled; Dan Roth; Dav Zimak

2002-01-01

163

Phylogenetic placement of the Spirosomaceae.  

PubMed

Comparative analysis of 16S rRNA sequences shows that the family Spirosomaceae belongs within the eubacterial phylum defined by the flavobacteria and bacteriodes. Its constituent genera, Spirosoma, Flectobacillus, and Runella form a monophyletic grouping therein. The phylogenetic assignment is based not only upon evolutionary distance analysis, but also upon sequence signatures and higher order structural synapomorphies in 16S rRNA. Another genus peripherally associated with the Spirosomaceae, Ancylobacter ("Microcyclus"), does not cluster with the flavobacteria and their relatives, but rather belongs to the alpha subdivision of the purple bacteria. PMID:11538307

Woese, C R; Maloy, S; Mandelco, L; Raj, H D

1990-03-01

164

Choosing among Partition Models in Bayesian Phylogenetics  

PubMed Central

Bayesian phylogenetic analyses often depend on Bayes factors (BFs) to determine the optimal way to partition the data. The marginal likelihoods used to compute BFs, in turn, are most commonly estimated using the harmonic mean (HM) method, which has been shown to be inaccurate. We describe a new more accurate method for estimating the marginal likelihood of a model and compare it with the HM method on both simulated and empirical data. The new method generalizes our previously described stepping-stone (SS) approach by making use of a reference distribution parameterized using samples from the posterior distribution. This avoids one challenging aspect of the original SS method, namely the need to sample from distributions that are close (in the Kullback–Leibler sense) to the prior. We specifically address the choice of partition models and find that using the HM method can lead to a strong preference for an overpartitioned model. In contrast to the HM method and the original SS method, we show using simulated data that the generalized SS method is strikingly more precise (repeatable BF values of the same data and partition model) and yields BF values that are much more reasonable than those produced by the HM method. Comparisons of HM and generalized SS methods on an empirical data set demonstrate that the generalized SS method tends to choose simpler partition schemes that are more in line with expectation based on inferred patterns of molecular evolution. The generalized SS method shares with thermodynamic integration the need to sample from a series of distributions in addition to the posterior. Such dedicated path-based Markov chain Monte Carlo analyses appear to be a cost of estimating marginal likelihoods accurately.

Fan, Yu; Wu, Rui; Chen, Ming-Hui; Kuo, Lynn; Lewis, Paul O.

2011-01-01

165

The phylogenetic diversity of eukaryotic transcription.  

PubMed

Eukaryotic transcription is a highly regulated process involving interactions between large numbers of proteins. To analyse the phylogenetic distribution of the components of this process, six crown eukaryote group genomes were queried with a reference set of transcription-associated (TA) proteins. On average, one in 10 proteins encoded by these genomes were found to be homologous to sequences in the reference set. Analysis of families identified using an accurate sequence clustering algorithm and containing both TA proteins and eukaryotic sequences showed that in two-thirds of the families the homologues originate from a single kingdom. Furthermore, in only 15% of the fungal-specific clusters are the homologues present in both budding and fission yeast, as compared with the metazoan-specific clusters where 53% of the homologues originate from two or more species. Families whose members comprise general transcription factor or RNA polymerase subunits exhibit a low degree of taxon specificity, suggesting that the transcription initiation complex is highly conserved. This contrasts with transcriptional regulator families, that are primarily taxon-specific, indicating proteins controlling gene activation exhibit considerable sequence diversity across the eukaryotic domain. PMID:12527774

Coulson, Richard M R; Ouzounis, Christos A

2003-01-15

166

LABEL: Fast and Accurate Lineage Assignment with Assessment of H5N1 and H9N2 Influenza A Hemagglutinins  

PubMed Central

The evolutionary classification of influenza genes into lineages is a first step in understanding their molecular epidemiology and can inform the subsequent implementation of control measures. We introduce a novel approach called Lineage Assignment By Extended Learning (LABEL) to rapidly determine cladistic information for any number of genes without the need for time-consuming sequence alignment, phylogenetic tree construction, or manual annotation. Instead, LABEL relies on hidden Markov model profiles and support vector machine training to hierarchically classify gene sequences by their similarity to pre-defined lineages. We assessed LABEL by analyzing the annotated hemagglutinin genes of highly pathogenic (H5N1) and low pathogenicity (H9N2) avian influenza A viruses. Using the WHO/FAO/OIE H5N1 evolution working group nomenclature, the LABEL pipeline quickly and accurately identified the H5 lineages of uncharacterized sequences. Moreover, we developed an updated clade nomenclature for the H9 hemagglutinin gene and show a similarly fast and reliable phylogenetic assessment with LABEL. While this study was focused on hemagglutinin sequences, LABEL could be applied to the analysis of any gene and shows great potential to guide molecular epidemiology activities, accelerate database annotation, and provide a data sorting tool for other large-scale bioinformatic studies.

Shepard, Samuel S.; Davis, C. Todd; Bahl, Justin; Rivailler, Pierre; York, Ian A.; Donis, Ruben O.

2014-01-01

167

Beach Classification  

NSDL National Science Digital Library

This activity provides students with an in-class practice of landscape interpretation using slides of beaches shown by the instructor. Students view a select number of slides and are asked to classify each beach shown using the Wright and Short Beach Classification: dissipative, reflexive, and intermediate by visually identifying landforms and processes of each beach type. The outcome of this activity is that students have practice identifying landforms and processes and applying their observations and interpretations of geomorphic features and processes for an applied purpose. Designed for a geomorphology course Has minimal/no quantitative component

Davis, Lisa

168

Phylogenetic Origins of Brain Organisers  

PubMed Central

The regionalisation of the nervous system begins early in embryogenesis, concomitant with the establishment of the anteroposterior (AP) and dorsoventral (DV) body axes. The molecular mechanisms that drive axis induction appear to be conserved throughout the animal kingdom and may be phylogenetically older than the emergence of bilateral symmetry. As a result of this process, groups of patterning genes that are equally well conserved are expressed at specific AP and DV coordinates of the embryo. In the emerging nervous system of vertebrate embryos, this initial pattern is refined by local signalling centres, secondary organisers, that regulate patterning, proliferation, and axonal pathfinding in adjacent neuroepithelium. The main secondary organisers for the AP neuraxis are the midbrain-hindbrain boundary, zona limitans intrathalamica, and anterior neural ridge and for the DV neuraxis the notochord, floor plate, and roof plate. A search for homologous secondary organisers in nonvertebrate lineages has led to controversy over their phylogenetic origins. Based on a recent study in hemichordates, it has been suggested that the AP secondary organisers evolved at the base of the deuterostome superphylum, earlier than previously thought. According to this view, the lack of signalling centres in some deuterostome lineages is likely to reflect a secondary loss due to adaptive processes. We propose that the relative evolutionary flexibility of secondary organisers has contributed to a broader morphological complexity of nervous systems in different clades.

Robertshaw, Ellen; Kiecker, Clemens

2012-01-01

169

Using invariants for phylogenetic tree construction  

Microsoft Academic Search

Phylogenetic invariants are certain polynomials in the joint probability\\u000adistribution of a Markov model on a phylogenetic tree. Such polynomials are of\\u000atheoretical interest in the field of algebraic statistics and they are also of\\u000apractical interest--they can be used to construct phylogenetic trees. This\\u000apaper is a self-contained introduction to the algebraic, statistical, and\\u000acomputational challenges involved in the

Nicholas Eriksson

2007-01-01

170

Classification in Australia.  

ERIC Educational Resources Information Center

Despite some inroads by the Library of Congress Classification and short-lived experimentation with Universal Decimal Classification and Bliss Classification, Dewey Decimal Classification, with its ability in recent editions to be hospitable to local needs, remains the most widely used classification system in Australia. Although supplemented at…

McKinlay, John

171

Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human  

Microsoft Academic Search

Accurate predictions of orthology and paralogy relationships are necessary to infer human molecular function from experiments in model organisms. Previous genome-scale approaches to predicting these relationships have been limited by their use of protein similarity and their failure to take into account multiple splicing events and gene prediction errors. We have developed PhyOP, a new phylogenetic orthology prediction pipeline based

Leo Goodstadt; Chris P. Ponting

2006-01-01

172

PHYML Online - a web server for fast maximum likelihood-based phylogenetic inference  

Microsoft Academic Search

PHYML Online is a web interface to PHYML, a soft- ware that implements a fast and accurate heuristic for estimating maximum likelihood phylogenies from DNA and protein sequences. This tool provides the user with a number of options, e.g. nonparametric bootstrap and estimation of various evolutionary parameters, in order to perform comprehensive phylogenetic analyses on large datasets in reason- able

Stéphane Guindon; Franck Lethiec; Patrice Duroux; Olivier Gascuel

2005-01-01

173

Reanalysis and Simulation Suggest a Phylogenetic Microarray Does Not Accurately Profile Microbial Communities  

PubMed Central

The second generation (G2) PhyloChip is designed to detect over 8700 bacteria and archaeal and has been used over 50 publications and conference presentations. Many of those publications reveal that the PhyloChip measures of species richness greatly exceed statistical estimates of richness based on other methods. An examination of probes downloaded from Greengenes suggested that the system may have the potential to distort the observed community structure. This may be due to the sharing of probes by taxa; more than 21% of the taxa in that downloaded data have no unique probes. In-silico simulations using these data showed that a population of 64 taxa representing a typical anaerobic subterranean community returned 96 different taxa, including 15 families incorrectly called present and 19 families incorrectly called absent. A study of nasal and oropharyngeal microbial communities by Lemon et al (2010) found some 1325 taxa using the G2 PhyloChip, however, about 950 of these taxa have, in the downloaded data, no unique probes and cannot be definitively called present. Finally, data from Brodie et al (2007), when re-examined, indicate that the abundance of the majority of detected taxa, are highly correlated with one another, suggesting that many probe sets do not act independently. Based on our analyses of downloaded data, we conclude that outputs from the G2 PhyloChip should be treated with some caution, and that the presence of taxa represented solely by non-unique probes be independently verified.

Midgley, David J.; Greenfield, Paul; Shaw, Janet M.; Oytam, Yalchin; Li, Dongmei; Kerr, Caroline A.; Hendry, Philip

2012-01-01

174

Staghorn classification: Platform for morphometry assessment  

PubMed Central

Introduction: The majority of staghorn classifications do not incorporate volumetric stone burden assessment. Accurate volumetric data can easily be acquired with the ever-increasingly available computerized tomography (CT) scan. This manuscript reviews the available staghorn stone classifications and rationalizes the morphometry-based classification. Materials and Methods: A Pubmed search was performed for articles concerning staghorn classification and morphometry. Twenty abstracts were shortlisted from a total of 43 published abstracts. In view of the paucity of manuscripts on staghorn morphometry (4), older staghorn classifications were analyzed with the aim to determine the most optimum one having relevance to the percutaneous nephrolithotomy (PCNL) monotherapy outcome. Results: All available staghorn classifications are limited with non-widespread applicability. The traditional partial and complete staghorn are limited due to non-descript stone volumetric data and considerable overlap of the intermediate ones in either group. A lack of standardized definition limits intergroup comparison as well. Staghorn morphometry is a recent addition to the clinical classification profiling of a staghorn calculus. It comprises extensive CT volumetric stone distribution assessment of a staghorn in a given pelvi–calyceal anatomy. It allowsmeaningful clinical classification of staghorn stones from a contemporary PCNL monotherapy perspective. Conclusions: Morphometry-based classification affords clinically relevant nomenclature in predicting the outcome of PCNL for staghorn stones. Further research is required to reduce the complexity associated with measuring the volumetric stone distribution in a given calyceal system.

Mishra, Shashikant; Bhattu, Amit S.; Sabnis, Ravindra B.; Desai, Mahesh R.

2014-01-01

175

Using a multigene phylogenetic analysis to assess generic delineation and character evolution in Verrucariaceae ( Verrucariales, Ascomycota)  

Microsoft Academic Search

Verrucariaceae are a family of mostly crustose lichenized ascomycetes colonizing various habitats ranging from marine and fresh water to arid environments. Phylogenetic relationships among members of the Verrucariaceae are mostly unknown and the current morphology-based classification has never been confronted to molecular data. A multilocus phylogeny (nuLSU, nuSSU and RPB1) was reconstructed for 83 taxa representing all main genera of

Cécile Gueidan; Claude Roux; François Lutzoni

2007-01-01

176

Hazard classification methodology  

SciTech Connect

This document outlines the hazard classification methodology used to determine the hazard classification of the NIF LTAB, OAB, and the support facilities on the basis of radionuclides and chemicals. The hazard classification determines the safety analysis requirements for a facility.

Brereton, S.J.

1996-07-22

177

Remote Sensing Information Classification  

NASA Technical Reports Server (NTRS)

This viewgraph presentation reviews the classification of Remote Sensing data in relation to epidemiology. Classification is a way to reduce the dimensionality and precision to something a human can understand. Classification changes SCALAR data into NOMINAL data.

Rickman, Douglas L.

2008-01-01

178

Classification and knowledge  

NASA Technical Reports Server (NTRS)

Automated procedures to classify objects are discussed. The classification problem is reviewed, and the relation of epistemology and classification is considered. The classification of stellar spectra and of resolved images of galaxies is addressed.

Kurtz, Michael J.

1989-01-01

179

Relaxed Phylogenetics and Dating with Confidence  

Microsoft Academic Search

In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to

Alexei J Drummond; Simon Y. W Ho; Matthew J Phillips; Andrew Rambaut

2006-01-01

180

A tree kernel to analyse phylogenetic profiles  

Microsoft Academic Search

Motivation: The phylogenetic profile of a protein is a string that encodes the presence or absence of the protein in every fully sequenced genome. Because proteins that participate in a common structural complex or metabolic pathway are likely to evolve in a correlated fashion, the phylogenetic profiles of such proteins are often 'similar' or at least 'related' to each other.

Jean-philippe Vert

2002-01-01

181

The challenge of constructing large phylogenetic trees  

Microsoft Academic Search

The amount of sequence data available to reconstruct the evolutionary history of genes and species has increased 20-fold in the past decade. Consequently the size of phylogenetic analyses has grown as well, and phylogenetic methods, algorithms and their implementations have struggled to keep pace. Computational and other challenges raised by this burgeoning database emerge at several stages of analysis, from

Michael J. Sanderson; Amy C. Driskell

2003-01-01

182

Quartet-based methods to reconstruct phylogenetic networks  

PubMed Central

Background Phylogenetic networks are employed to visualize evolutionary relationships among a group of nucleotide sequences, genes or species when reticulate events like hybridization, recombination, reassortant and horizontal gene transfer are believed to be involved. In comparison to traditional distance-based methods, quartet-based methods consider more information in the reconstruction process and thus have the potential to be more accurate. Results We introduce QuartetSuite, which includes a set of new quartet-based methods, namely QuartetS, QuartetA, and QuartetM, to reconstruct phylogenetic networks from nucleotide sequences. We tested their performances and compared them with other popular methods on two simulated nucleotide sequence data sets: one generated from a tree topology and the other from a complicated evolutionary history containing three reticulate events. We further validated these methods to two real data sets: a bacterial data set consisting of seven concatenated genes of 36 bacterial species and an influenza data set related to recently emerging H7N9 low pathogenic avian influenza viruses in China. Conclusion QuartetS, QuartetA, and QuartetM have the potential to accurately reconstruct evolutionary scenarios from simple branching trees to complicated networks containing many reticulate events. These methods could provide insights into the understanding of complicated biological evolutionary processes such as bacterial taxonomy and reassortant of influenza viruses.

2014-01-01

183

A phylogenetic model for understanding the effect of gene duplication on cancer progression.  

PubMed

As biotechnology advances rapidly, a tremendous amount of cancer genetic data has become available, providing an unprecedented opportunity for understanding the genetic mechanisms of cancer. To understand the effects of duplications and deletions on cancer progression, two genomes (normal and tumor) were sequenced from each of five stomach cancer patients in different stages (I, II, III and IV). We developed a phylogenetic model for analyzing stomach cancer data. The model assumes that duplication and deletion occur in accordance with a continuous time Markov Chain along the branches of a phylogenetic tree attached with five extended branches leading to the tumor genomes. Moreover, coalescence times of the phylogenetic tree follow a coalescence process. The simulation study suggests that the maximum likelihood approach can accurately estimate parameters in the phylogenetic model. The phylogenetic model was applied to the stomach cancer data. We found that the expected number of changes (duplication and deletion) per gene for the tumor genomes is significantly higher than that for the normal genomes. The goodness-of-fit test suggests that the phylogenetic model with constant duplication and deletion rates can adequately fit the duplication data for the normal genomes. The analysis found nine duplicated genes that are significantly associated with stomach cancer. PMID:24371277

Ma, Qin; Reeves, Jaxk H; Liberles, David A; Yu, Lili; Chang, Zheng; Zhao, Jing; Cui, Juan; Xu, Ying; Liu, Liang

2014-03-01

184

Phylogenetic fields of species: cross-species patterns of phylogenetic structure and geographical coexistence  

PubMed Central

Differential coexistence among species underlies geographical patterns of biodiversity. Understanding such patterns has relied either on ecological or historical approaches applied separately. Recently, macroecology and community phylogenetics have tried to integrate both ecological and historical approaches. However, macroecology is mostly non-phylogenetic, whereas community phylogenetics is largely focused on local scales. Here, we propose a conceptual framework to link macroecology and community phylogenetics by exploring the evolutionary context of large-scale species coexistence, introducing the phylogenetic field concept. This is defined as the phylogenetic structure of species co-occurrence within a focal species' geographical range. We developed concepts and methods for analysing phylogenetic fields and applied them to study coexistence patterns of the bat family Phyllostomidae. Our analyses showed that phyllostomid bats coexist mostly with closely related species, revealing a north–south gradient from overdispersed to clustered phylogenetic fields. Patterns at different phylogenetic levels (i.e. all species versus close relatives only) presented the same gradient. Results support the tropical niche conservatism hypothesis, potentially mediated by higher speciation rates in the region of origin coupled with shared environmental preferences among species. The phylogenetic field approach enables species-based community phylogenetics, instead of those that are site-based, allowing the description of historical processes at more appropriate macroecological and biogeographic scales.

Villalobos, Fabricio; Rangel, Thiago F.; Diniz-Filho, Jose Alexandre F.

2013-01-01

185

Phylogenetic fields of species: cross-species patterns of phylogenetic structure and geographical coexistence.  

PubMed

Differential coexistence among species underlies geographical patterns of biodiversity. Understanding such patterns has relied either on ecological or historical approaches applied separately. Recently, macroecology and community phylogenetics have tried to integrate both ecological and historical approaches. However, macroecology is mostly non-phylogenetic, whereas community phylogenetics is largely focused on local scales. Here, we propose a conceptual framework to link macroecology and community phylogenetics by exploring the evolutionary context of large-scale species coexistence, introducing the phylogenetic field concept. This is defined as the phylogenetic structure of species co-occurrence within a focal species' geographical range. We developed concepts and methods for analysing phylogenetic fields and applied them to study coexistence patterns of the bat family Phyllostomidae. Our analyses showed that phyllostomid bats coexist mostly with closely related species, revealing a north-south gradient from overdispersed to clustered phylogenetic fields. Patterns at different phylogenetic levels (i.e. all species versus close relatives only) presented the same gradient. Results support the tropical niche conservatism hypothesis, potentially mediated by higher speciation rates in the region of origin coupled with shared environmental preferences among species. The phylogenetic field approach enables species-based community phylogenetics, instead of those that are site-based, allowing the description of historical processes at more appropriate macroecological and biogeographic scales. PMID:23390100

Villalobos, Fabricio; Rangel, Thiago F; Diniz-Filho, José Alexandre F

2013-04-01

186

Phylogenetic analyses of plastid and nuclear DNA sequences indicate a rapid late Miocene radiation of the temperate bamboo tribe Arundinarieae (Poaceae, Bambusoideae)  

Microsoft Academic Search

Background: Arundinarieae are a large tribe of temperate woody bamboos for which phylogenetics are poorly understood because of limited taxon sampling and lack of informative characters.Aims: This study assessed phylogenetic relationships, origins and classification of Arundinarieae.Methods: DNA sequences (plastid trnL-F; nuclear ITS) were used for parsimony and Bayesian inference including 41 woody bamboo taxa. Divergence dates were estimated using a

Trevor R. Hodkinson; Grainne Ní Chonghaile; Sarawood Sungkaew; Mark W. Chase; Nicolas Salamin; Chris M. A. Stapleton

2010-01-01

187

Revising angiotensinogen from phylogenetic and genetic variants perspectives.  

PubMed

Angiotensinogen (AGT) belongs to the serpin superfamily. It acts as the unique substrate of all angiotensin peptides, which generates a spectrum of angiotensin peptides in the renin-angiotensin system and regulates hypertension. This serpin belongs to the multiple member group V2 of the intron encoded vertebrate serpin classification. Despite huge advancements in the understanding of angiotensinogen based on biochemical properties and its roles in the RAS, phylogenetic history of AGT remains forgotten. To date, there is no comprehensive study illustrating the phylogenetic history of AGT. Herein, we investigated phylogenetic traits of AGT gene across vertebrates. Gene structures of AGT gene from selected ray-finned fishes varied in exon I and II with insertions of two novel introns in the core domain for ray-finned fishes at the position 77c and 233c. We that found AGT loci is conserved from lampreys to human and estimated to be older than 500 MY. By comparing AGT protein in 57 vertebrate genomes, we illustrated that the reactive center loop (RCL) of AGT protein became from inhibitory (in lampreys, GTEAKAETVVGIMPI†SMPPT) to non-inhibitory (in human, EREPTESTQQLNKPE†VLEVT) during period of 500 MY. We identified 690 AGT variants by analysis of 1092 human genomes with top three variation classes belongs to SNPs (89.7%), somatic SNVs (5.2%) and deletion (2.9%). There are 32 key residues out of 121 missense variants, which are deleterious for AGT protein, computed by combination of SIFT and PolyPhen V2 methods. These results may have clinical implications for understanding hypertension. PMID:24631685

Kumar, Abhishek; Sarde, Sandeep J; Bhandari, Anita

2014-04-01

188

Phylogenetic relationships matter: antifungal susceptibility among clinically relevant yeasts.  

PubMed

The objective of this study was 2-fold: to evaluate whether phylogenetically closely related yeasts share common antifungal susceptibility profiles (ASPs) and whether these ASPs can be predicted from phylogeny. To address this question, 9,627 yeast strains were collected and tested for their antifungal susceptibility. Isolates were reidentified by considering recent changes in taxonomy and nomenclature. A phylogenetic (PHYLO) code based on the results of multilocus sequence analyses (large-subunit rRNA, small-subunit rRNA, translation elongation factor 1?, RNA polymerase II subunits 1 and 2) and the classification of the cellular neutral sugar composition of coenzyme Q and 18S ribosomal DNA was created to group related yeasts into PHYLO groups. The ASPs were determined for fluconazole, itraconazole, and voriconazole in each PHYLO group. The majority (95%) of the yeast strains were Ascomycetes. After reclassification, a total of 23 genera and 54 species were identified, resulting in an increase of 64% of genera and a decrease of 5% of species compared with the initial identification. These taxa were assigned to 17 distinct PHYLO groups (Ascomycota, n=13; Basidiomycota, n=4). ASPs for azoles were similar among members of the same PHYLO group and different between the various PHYLO groups. Yeast phylogeny may be an additional tool to significantly enhance the assessment of MIC values and to predict antifungal susceptibility, thereby more rapidly initiating appropriate patient management. PMID:24366735

Schmalreck, A F; Lackner, M; Becker, K; Fegeler, W; Czaika, V; Ulmer, H; Lass-Flörl, C

2014-03-01

189

Phylogenetic analysis of mitochondrial outer membrane ?-barrel channels.  

PubMed

Transport of molecules across mitochondrial outer membrane is pivotal for a proper function of mitochondria. The transport pathways across the membrane are formed by ion channels that participate in metabolite exchange between mitochondria and cytoplasm (voltage-dependent anion-selective channel, VDAC) as well as in import of proteins encoded by nuclear genes (Tom40 and Sam50/Tob55). VDAC, Tom40, and Sam50/Tob55 are present in all eukaryotic organisms, encoded in the nuclear genome, and have ?-barrel topology. We have compiled data sets of these protein sequences and studied their phylogenetic relationships with a special focus on the position of Amoebozoa. Additionally, we identified these protein-coding genes in Acanthamoeba castellanii and Dictyostelium discoideum to complement our data set and verify the phylogenetic position of these model organisms. Our analysis show that mitochondrial ?-barrel channels from Archaeplastida (plants) and Opisthokonta (animals and fungi) experienced many duplication events that resulted in multiple paralogous isoforms and form well-defined monophyletic clades that match the current model of eukaryotic evolution. However, in representatives of Amoebozoa, Chromalveolata, and Excavata (former Protista), they do not form clearly distinguishable clades, although they locate basally to the plant and algae branches. In most cases, they do not posses paralogs and their sequences appear to have evolved quickly or degenerated. Consequently, the obtained phylogenies of mitochondrial outer membrane ?-channels do not entirely reflect the recent eukaryotic classification system involving the six supergroups: Chromalveolata, Excavata, Archaeplastida, Rhizaria, Amoebozoa, and Opisthokonta. PMID:22155732

Wojtkowska, Ma?gorzata; J?kalski, Marcin; Pie?kowska, Joanna R; Stobienia, Olgierd; Karachitos, Andonis; Przytycka, Teresa M; Weiner, January; Kmita, Hanna; Maka?owski, Wojciech

2012-01-01

190

Phylogenetic study of the species within the family Streptomycetaceae.  

PubMed

Species of the genus Streptomyces, which constitute the vast majority of taxa within the family Streptomycetaceae, are a predominant component of the microbial population in soils throughout the world and have been the subject of extensive isolation and screening efforts over the years because they are a major source of commercially and medically important secondary metabolites. Taxonomic characterization of Streptomyces strains has been a challenge due to the large number of described species, greater than any other microbial genus, resulting from academic and industrial activities. The methods used for characterization have evolved through several phases over the years from those based largely on morphological observations, to subsequent classifications based on numerical taxonomic analyses of standardized sets of phenotypic characters and, most recently, to the use of molecular phylogenetic analyses of gene sequences. The present phylogenetic study examines almost all described species (615 taxa) within the family Streptomycetaceae based on 16S rRNA gene sequences and illustrates the species diversity within this family, which is observed to contain 130 statistically supported clades, as well as many unsupported and single member clusters. Many of the observed clades are consistent with earlier morphological and numerical taxonomic studies, but it is apparent that insufficient variation is present in the 16S rRNA gene sequence within the species of this family to permit bootstrap-supported resolution of relationships between many of the individual clusters. PMID:22045019

Labeda, D P; Goodfellow, M; Brown, R; Ward, A C; Lanoot, B; Vanncanneyt, M; Swings, J; Kim, S-B; Liu, Z; Chun, J; Tamura, T; Oguchi, A; Kikuchi, T; Kikuchi, H; Nishii, T; Tsuji, K; Yamaguchi, Y; Tase, A; Takahashi, M; Sakane, T; Suzuki, K I; Hatano, K

2012-01-01

191

[Comparative leaf anatomy and phylogenetic relationships of 11 species of Laeliinae with emphasis on Brassavola (Orchidaceae)].  

PubMed

Brassavola inhabits a wide altitude range and habitat types from Northern Mexico to Northern Argentina. Classification schemes in plants have normally used vegetative and floral characters, but when species are very similar, as in this genus, conflicts arise in species delimitation, and alternative methods should be applied. In this study we explored the taxonomic and phylogenetic value of the anatomical structure of leaves in Brassavola; as ingroup, seven species of Brassavola were considered, and as an outgroup Guarianthe skinneri, Laelia anceps, Rhyncholaelia digbyana and Rhyncholaelia glauca were evaluated. Leaf anatomical characters were studied in freehand cross sections of the middle portion with a light microscope. Ten vegetative anatomical characters were selected and coded for the phylogenetic analysis. Phylogenetic reconstruction was carried out under maximum parsimony using the program NONA through WinClada. Overall, Brassavola species reveal a wide variety of anatomical characters, many of them associated with xeromorphic plants: thick cuticle, hypodermis and cells of the mesophyll with spiral thickenings in the secondary wall. Moreover, mesophyll is either homogeneous or heterogeneous, often with extravascular bundles of fibers near the epidermis at both terete and flat leaves. All vascular bundles are collateral, arranged in more than one row in the mesophyll. The phylogenetic analysis did not resolve internal relationships of the genus; we obtained a polytomy, indicating that the anatomical characters by themselves have little phylogenetic value in Brassavola. We concluded that few anatomical characters are phylogenetically important; however, they would provide more support to elucidate the phylogenetic relantionships in the Orchidaceae and other plant groups if they are used in conjunction with morphological and/or molecular characters. PMID:22017111

Noguera-Savelli, Eliana; Jáuregui, Damelis

2011-09-01

192

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

PubMed

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/. PMID:23554899

Kelly, Steven; Maini, Philip K

2013-01-01

193

Accurate \\  

Microsoft Academic Search

We analyse a system in which, due to entanglement between the spin and\\u000aspatial degrees of freedom, the reduced transmitted state has the shape of the\\u000afreely propagating pulse translated in the complex co-ordinate plane. In the\\u000acase an apparently \\

D. Sokolovski; R. Sala Mayato

2009-01-01

194

Sparse and accurate high resolution SAR imaging  

NASA Astrophysics Data System (ADS)

We investigate the usage of an adaptive method, the Iterative Adaptive Approach (IAA), in combination with a maximum a posteriori (MAP) estimate to reconstruct high resolution SAR images that are both sparse and accurate. IAA is a nonparametric weighted least squares algorithm that is robust and user parameter-free. IAA has been shown to reconstruct SAR images with excellent side lobes suppression and high resolution enhancement. We first reconstruct the SAR images using IAA, and then we enforce sparsity by using MAP with a sparsity inducing prior. By coupling these two methods, we can produce a sparse and accurate high resolution image that are conducive for feature extractions and target classification applications. In addition, we show how IAA can be made computationally efficient without sacrificing accuracies, a desirable property for SAR applications where the size of the problems is quite large. We demonstrate the success of our approach using the Air Force Research Lab's "Gotcha Volumetric SAR Data Set Version 1.0" challenge dataset. Via the widely used FFT, individual vehicles contained in the scene are barely recognizable due to the poor resolution and high side lobe nature of FFT. However with our approach clear edges, boundaries, and textures of the vehicles are obtained.

Vu, Duc; Zhao, Kexin; Rowe, William; Li, Jian

2012-05-01

195

Improving Automatic Query Classification via Semi-Supervised Learning  

Microsoft Academic Search

Accurate topical classification of user queries allows for increased effectiveness and efficiency in general-purpose web search systems. Such classification becomes critical if the system is to return results not just from a general web collection but from topic-specific back-end databases as well. Maintaining sufficient classification recall is very difficult as web queries are typically short, yielding few features per query.

Steven M. Beitzel; Eric C. Jensen; Ophir Frieder; David D. Lewis; Abdur Chowdhury; Aleksander Kolcz

2005-01-01

196

Land capability classification — a basis for farm conservation planning  

Microsoft Academic Search

Inadequacies evident in present?day farm planning procedures require that attention be given to land classification — the starting point of land?use planning. It is suggested that soils, correctly classified and accurately mapped, provide the only reliable basis for developing a land capability classification. A study of several systems in current use, including that of the United States, enables important principles

D. M. Scotney

1971-01-01

197

Complete mitochondrial genomes elucidate phylogenetic relationships of the deep-sea octocoral families Coralliidae and Paragorgiidae  

NASA Astrophysics Data System (ADS)

In the past decade, molecular phylogenetic analyses of octocorals have shown that the current morphological taxonomic classification of these organisms needs to be revised. The latest phylogenetic analyses show that most octocorals can be divided into three main clades. One of these clades contains the families Coralliidae and Paragorgiidae. These families share several taxonomically important characters and it has been suggested that they may not be monophyletic; with the possibility of the Coralliidae being a derived branch of the Paragorgiidae. Uncertainty exists not only in the relationship of these two families, but also in the classification of the two genera that make up the Coralliidae, Corallium and Paracorallium. Molecular analyses suggest that the genus Corallium is paraphyletic, and it can be divided into two main clades, with the Paracorallium as members of one of these clades. In this study we sequenced the whole mitochondrial genome of five species of Paragorgia and of five species of Corallium to use in a phylogenetic analysis to achieve two main objectives; the first to elucidate the phylogenetic relationship between the Paragorgiidae and Coralliidae and the second to determine whether the genera Corallium and Paracorallium are monophyletic. Our results show that other members of the Coralliidae share the two novel mitochondrial gene arrangements found in a previous study in Corallium konojoi and Paracorallium japonicum; and that the Corallium konojoi arrangement is also found in the Paragorgiidae. Our phylogenetic reconstruction based on all the protein coding genes and ribosomal RNAs of the mitochondrial genome suggest that the Coralliidae are not a derived branch of the Paragorgiidae, but rather a monophyletic sister branch to the Paragorgiidae.

Figueroa, Diego F.; Baco, Amy R.

2014-01-01

198

Accurate Monitor 1.2  

NSDL National Science Digital Library

With many computer users developing their own Web sites, some of them may be interested in monitoring how search engines may be ranking their site. This latest edition of Accurate Monitor may prove useful, as it allows individuals to find the position of their Web site in search engines like Altavista and Google. Additionally, Accurate Monitor can generate advanced statistics and monitor plugins, along with providing a flexible interface system. This version of Accurate Monitor is compatible with all systems running Windows 95 and higher.

2003-01-01

199

A statistical approach to root system classification  

PubMed Central

Plant root systems have a key role in ecology and agronomy. In spite of fast increase in root studies, still there is no classification that allows distinguishing among distinctive characteristics within the diversity of rooting strategies. Our hypothesis is that a multivariate approach for “plant functional type” identification in ecology can be applied to the classification of root systems. The classification method presented is based on a data-defined statistical procedure without a priori decision on the classifiers. The study demonstrates that principal component based rooting types provide efficient and meaningful multi-trait classifiers. The classification method is exemplified with simulated root architectures and morphological field data. Simulated root architectures showed that morphological attributes with spatial distribution parameters capture most distinctive features within root system diversity. While developmental type (tap vs. shoot-borne systems) is a strong, but coarse classifier, topological traits provide the most detailed differentiation among distinctive groups. Adequacy of commonly available morphologic traits for classification is supported by field data. Rooting types emerging from measured data, mainly distinguished by diameter/weight and density dominated types. Similarity of root systems within distinctive groups was the joint result of phylogenetic relation and environmental as well as human selection pressure. We concluded that the data-define classification is appropriate for integration of knowledge obtained with different root measurement methods and at various scales. Currently root morphology is the most promising basis for classification due to widely used common measurement protocols. To capture details of root diversity efforts in architectural measurement techniques are essential.

Bodner, Gernot; Leitner, Daniel; Nakhforoosh, Alireza; Sobotik, Monika; Moder, Karl; Kaul, Hans-Peter

2013-01-01

200

A statistical approach to root system classification.  

PubMed

Plant root systems have a key role in ecology and agronomy. In spite of fast increase in root studies, still there is no classification that allows distinguishing among distinctive characteristics within the diversity of rooting strategies. Our hypothesis is that a multivariate approach for "plant functional type" identification in ecology can be applied to the classification of root systems. The classification method presented is based on a data-defined statistical procedure without a priori decision on the classifiers. The study demonstrates that principal component based rooting types provide efficient and meaningful multi-trait classifiers. The classification method is exemplified with simulated root architectures and morphological field data. Simulated root architectures showed that morphological attributes with spatial distribution parameters capture most distinctive features within root system diversity. While developmental type (tap vs. shoot-borne systems) is a strong, but coarse classifier, topological traits provide the most detailed differentiation among distinctive groups. Adequacy of commonly available morphologic traits for classification is supported by field data. Rooting types emerging from measured data, mainly distinguished by diameter/weight and density dominated types. Similarity of root systems within distinctive groups was the joint result of phylogenetic relation and environmental as well as human selection pressure. We concluded that the data-define classification is appropriate for integration of knowledge obtained with different root measurement methods and at various scales. Currently root morphology is the most promising basis for classification due to widely used common measurement protocols. To capture details of root diversity efforts in architectural measurement techniques are essential. PMID:23914200

Bodner, Gernot; Leitner, Daniel; Nakhforoosh, Alireza; Sobotik, Monika; Moder, Karl; Kaul, Hans-Peter

2013-01-01

201

Phylogenetic relationships in the family Resedaceae L  

Microsoft Academic Search

A study was made on the phylogenetic relationships of species of the family Resedaceae, based on morphological features, chromosome meiotic behaviour, karyotype features, size and fertility of pollen grains, nucleotypic parameters, seed protein profiles and esterase isozyme patterns.

J. J. González-Aguilera; A. M. Fernández-Peralta

1984-01-01

202

Document Classification for Computer Science Related Articles  

Microsoft Academic Search

Document classification based on content is a general task that appears in a wide spectrum of tasks from text retrieval to automatic browsing tools or database maintenance. It is expen- sive when performed manually-even though this is still the most accurate method. In this project we have implemented a simple probabilistic document classifier based on corpus sim- ilarity from a

Ana Fuentes Martínez; Flavius Gruian

203

Pathogenesis, classification and treatment of inflammatory myopathies  

Microsoft Academic Search

The inflammatory myopathies—collectively, myositis—are a heterogeneous group of chronic muscle disorders that differ in response to immunosuppressive treatment. Insufficient knowledge of the molecular pathways that drive pathogenesis (and underlie the clinical differences between subtypes) has hindered accurate classification, which in turn has been detrimental for clinical research. Nevertheless, new insights into pathogenesis are paving the way for improvements in diagnosis,

Mei Zong; Ingrid E. Lundberg

2011-01-01

204

Speaker Classification Concepts: Past, Present and Future  

Microsoft Academic Search

Speaker classification requires a sufficiently accurate functional description of speaker attributes and the resources used in speaking, to be able to produce new utterances mimicking the speaker's current physical, emotional and cognitive state, with the correct dialect, social class markers and speech habits. We lack adequate functional knowledge of why and how speakers produce the utterances they do, as well

David R. Hill; Peter Ladefoged

2007-01-01

205

Phylogenetic Distribution of Fungal Sterols  

PubMed Central

Background Ergosterol has been considered the “fungal sterol” for almost 125 years; however, additional sterol data superimposed on a recent molecular phylogeny of kingdom Fungi reveals a different and more complex situation. Methodology/Principal Findings The interpretation of sterol distribution data in a modern phylogenetic context indicates that there is a clear trend from cholesterol and other ?5 sterols in the earliest diverging fungal species to ergosterol in later diverging fungi. There are, however, deviations from this pattern in certain clades. Sterols of the diverse zoosporic and zygosporic forms exhibit structural diversity with cholesterol and 24-ethyl -?5 sterols in zoosporic taxa, and 24-methyl sterols in zygosporic fungi. For example, each of the three monophyletic lineages of zygosporic fungi has distinctive major sterols, ergosterol in Mucorales, 22-dihydroergosterol in Dimargaritales, Harpellales, and Kickxellales (DHK clade), and 24-methyl cholesterol in Entomophthorales. Other departures from ergosterol as the dominant sterol include: 24-ethyl cholesterol in Glomeromycota, 24-ethyl cholest-7-enol and 24-ethyl-cholesta-7,24(28)-dienol in rust fungi, brassicasterol in Taphrinales and hypogeous pezizalean species, and cholesterol in Pneumocystis. Conclusions/Significance Five dominant end products of sterol biosynthesis (cholesterol, ergosterol, 24-methyl cholesterol, 24-ethyl cholesterol, brassicasterol), and intermediates in the formation of 24-ethyl cholesterol, are major sterols in 175 species of Fungi. Although most fungi in the most speciose clades have ergosterol as a major sterol, sterols are more varied than currently understood, and their distribution supports certain clades of Fungi in current fungal phylogenies. In addition to the intellectual importance of understanding evolution of sterol synthesis in fungi, there is practical importance because certain antifungal drugs (e.g., azoles) target reactions in the synthesis of ergosterol. These findings also invalidate use of ergosterol as an indicator of biomass of certain fungal taxa (e.g., Glomeromycota). Data from this study are available from the Assembling the Fungal Tree of Life (AFTOL) Structural and Biochemical Database: http://aftol.umn.edu.

Weete, John D.; Abril, Maritza; Blackwell, Meredith

2010-01-01

206

Polyhedral Geometry of Phylogenetic Rogue Taxa  

Microsoft Academic Search

It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of\\u000a the optimal phylogenetic tree in surprising ways. However, little is known about this “rogue taxon” effect. In this paper\\u000a we characterize the behavior of balanced minimum evolution (BME) phylogenetics on data sets of this type using tools from

María Angélica Cueto; Frederick A. Matsen

2011-01-01

207

Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting  

PubMed Central

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the phylogenetic relationships among the sequences under study to make more accurate predictions. The program is guaranteed to report all sets of motifs with the lowest parsimony scores, calculated with respect to the phylogenetic tree relating the input species. We report the results of this algorithm on several data sets of interest. A large number of known functional binding sites are identified by our method, but we also find several highly conserved motifs for which no function is yet known.

Blanchette, Mathieu; Tompa, Martin

2002-01-01

208

Identifying Less Accurately Measured Students  

Microsoft Academic Search

Abstract Some students are less accurately measured,by typical reading tests than other students. By asking teachers to identify students whose performance,on state reading tests would likely underestimate their reading skills, this study sought to learn about characteristics of less accurately measured,students while also evaluating how well teachers can make such judgments. Twenty students identified by eight teachers participated in structured

Ross Moen; Kristi Liu; Martha Thurlow; Adam Lekwa; Sarah Scullin; Kristin Hausmann

209

How does cognition evolve? Phylogenetic comparative psychology  

PubMed Central

Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution.

Matthews, Luke J.; Hare, Brian A.; Nunn, Charles L.; Anderson, Rindy C.; Aureli, Filippo; Brannon, Elizabeth M.; Call, Josep; Drea, Christine M.; Emery, Nathan J.; Haun, Daniel B. M.; Herrmann, Esther; Jacobs, Lucia F.; Platt, Michael L.; Rosati, Alexandra G.; Sandel, Aaron A.; Schroepfer, Kara K.; Seed, Amanda M.; Tan, Jingzhi; van Schaik, Carel P.; Wobber, Victoria

2014-01-01

210

Many-core algorithms for statistical phylogenetics  

PubMed Central

Motivation: Statistical phylogenetics is computationally intensive, resulting in considerable attention meted on techniques for parallelization. Codon-based models allow for independent rates of synonymous and replacement substitutions and have the potential to more adequately model the process of protein-coding sequence evolution with a resulting increase in phylogenetic accuracy. Unfortunately, due to the high number of codon states, computational burden has largely thwarted phylogenetic reconstruction under codon models, particularly at the genomic-scale. Here, we describe novel algorithms and methods for evaluating phylogenies under arbitrary molecular evolutionary models on graphics processing units (GPUs), making use of the large number of processing cores to efficiently parallelize calculations even for large state-size models. Results: We implement the approach in an existing Bayesian framework and apply the algorithms to estimating the phylogeny of 62 complete mitochondrial genomes of carnivores under a 60-state codon model. We see a near 90-fold speed increase over an optimized CPU-based computation and a >140-fold increase over the currently available implementation, making this the first practical use of codon models for phylogenetic inference over whole mitochondrial or microorganism genomes. Availability and implementation: Source code provided in BEAGLE: Broad-platform Evolutionary Analysis General Likelihood Evaluator, a cross-platform/processor library for phylogenetic likelihood computation (http://beagle-lib.googlecode.com/). We employ a BEAGLE-implementation using the Bayesian phylogenetics framework BEAST (http://beast.bio.ed.ac.uk/). Contact: msuchard@ucla.edu; a.rambaut@ed.ac.uk

Suchard, Marc A.; Rambaut, Andrew

2009-01-01

211

Models for automatic classification of video sequences  

NASA Astrophysics Data System (ADS)

In this paper, we explore a technique for automatic classification of video sequences, (such as a TV broadcast, movies). This technique analyzes the incoming video sequences and classifies them into categories. It can be viewed as an on-line parser for video signals. We present two techniques for automatic classification. In the first technique, the incoming video sequence is analyzed to extract the motion information. This information is optimally projected onto a single dimension. This projection information is then used to train Hidden Markov Models (HMMs) that efficiently and accurately classify the incoming video sequence. Preliminary results with 50 different test sequences (25 Sports and 25 News sequences) indicae a classification accuracy of 90% by the HMM models. In the second technique, 24 full-length motion picture trailers are classified using HMMs. This classification is compared with the internet movie database and we find that they correlate well. Only two out of 24 trailers were classified incorrectly.

Iyengar, Giridharan; Lippman, Andrew B.

1997-12-01

212

Genotypic Identification of Fusarium Species from Ocular Sources: Comparison to Morphologic Classification and Antifungal Sensitivity Testing (An AOS Thesis)  

PubMed Central

Purpose Ocular infections caused by fungal organisms can cause significant ocular morbidity, particularly when diagnosis and treatment are delayed. Rapid and accurate identification of Fusarium species at the subgenus level using current diagnostic standards is timely and insensitive. The purpose of this study is to examine the usefulness of polymerase chain reaction (PCR) analysis of the internal transcribed spacer (ITS) regions (ITS1, 5.8S, and ITS2) in detecting and differentiating Fusarium species from isolates of ocular infections, and to assess the correlation between the genotypic and morphologic classification. Methods Fifty-eight isolates from 52 patients diagnosed with Fusarium ocular infections were retrieved from storage at the Bascom Palmer Eye Institute’s ocular microbiology laboratory. Morphologic classification was determined at both a general and a reference microbiology laboratory. DNA was extracted and purified, and the ITS region was amplified and sequenced. Following DNA sequences, alignment and phylogenetic analysis were done. Susceptibility to antifungal drugs was measured according to the Clinical and Laboratory Standards Institute reference method. Results Sequence analysis demonstrated 15 unique sequences among the 58 isolates. The grouping showed that the 58 isolates were distributed among 4 main species complexes. At the species level, morphologic classification correlated with genotypic classification in 25% and 97% of the isolates in a general microbiology and a reference mycology laboratory, respectively. Conclusions The sequence variation within the ITS provides a sufficient quantitative basis for the development of a molecular diagnostic approach to the Fusarium pathogens isolated from ocular infections. Morphology based on microscopic and macroscopic observations yields inconsistent results, particularly at nonreference laboratories, emphasizing the need for a more reproducible test with less user-dependent variability. Fusarium solani tends to be more resistant to certain antifungals (azoles).

Alfonso, Eduardo C.

2008-01-01

213

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods  

PubMed Central

Accurate genome-wide identification of orthologs is a central problem in comparative genomics, a fact reflected by the numerous orthology identification projects developed in recent years. However, only a few reports have compared their accuracy, and indeed, several recent efforts have not yet been systematically evaluated. Furthermore, orthology is typically only assessed in terms of function conservation, despite the phylogeny-based original definition of Fitch. We collected and mapped the results of nine leading orthology projects and methods (COG, KOG, Inparanoid, OrthoMCL, Ensembl Compara, Homologene, RoundUp, EggNOG, and OMA) and two standard methods (bidirectional best-hit and reciprocal smallest distance). We systematically compared their predictions with respect to both phylogeny and function, using six different tests. This required the mapping of millions of sequences, the handling of hundreds of millions of predicted pairs of orthologs, and the computation of tens of thousands of trees. In phylogenetic analysis or in functional analysis where high specificity is required, we find that OMA and Homologene perform best. At lower functional specificity but higher coverage level, OrthoMCL outperforms Ensembl Compara, and to a lesser extent Inparanoid. Lastly, the large coverage of the recent EggNOG can be of interest to build broad functional grouping, but the method is not specific enough for phylogenetic or detailed function analyses. In terms of general methodology, we observe that the more sophisticated tree reconstruction/reconciliation approach of Ensembl Compara was at times outperformed by pairwise comparison approaches, even in phylogenetic tests. Furthermore, we show that standard bidirectional best-hit often outperforms projects with more complex algorithms. First, the present study provides guidance for the broad community of orthology data users as to which database best suits their needs. Second, it introduces new methodology to verify orthology. And third, it sets performance standards for current and future approaches.

Altenhoff, Adrian M.; Dessimoz, Christophe

2009-01-01

214

Computational Prediction of Phylogenetically Conserved Sequence Motifs for Five Different Candidate Genes in Type II Diabetic Nephropathy  

PubMed Central

Background: Computational identification of phylogenetic motifs helps to understand the knowledge about known functional features that includes catalytic site, substrate binding epitopes, and protein-protein interfaces. Furthermore, they are strongly conserved among orthologs, indicating their evolutionary importance. The study aimed to analyze five candidate genes involved in type II diabetic nephropathy and to predict phylogenetic motifs from their corresponding orthologous protein sequences. Methods: AKR1B1, APOE, ENPP1, ELMO1 and IGFBP1 are the genes that have been identified as an important target for type II diabetic nephropathy through experimental studies. Their corresponding protein sequences, structures, orthologous sequences were retrieved from UniprotKB, PDB, and PHOG database respectively. Multiple sequence alignments were constructed using ClustalW and phylogenetic motifs were identified using MINER. The occurrence of amino acids in the obtained phylogenetic motifs was generated using WebLogo and false positive expectations were calculated against phylogenetic similarity. Results: In total, 17 phylogenetic motifs were identified from the five proteins and the residues such as glycine, leucine, tryptophan, aspartic acid were found in appreciable frequency whereas arginine identified in all the predicted PMs. The result implies that these residues can be important to the functional and structural role of the proteins and calculated false positive expectations implies that they were generally conserved in traditional sense. Conclusion: The prediction of phylogenetic motifs is an accurate method for detecting functionally important conserved residues. The conserved motifs can be used as a potential drug target for type II diabetic nephropathy.

Sindhu, T; Rajamanikandan, S; Srinivasan, P

2012-01-01

215

Evaluating Support for the Current Classification of Eukaryotic Diversity  

PubMed Central

Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic groups within the five-kingdom classification—plants, animals, fungi, and protists—have been transformed through numerous permutations into the current system of six “supergroups.” The intent of the supergroup classification system is to unite microbial and macroscopic eukaryotes based on phylogenetic inference. This supergroup approach is increasing in popularity in the literature and is appearing in introductory biology textbooks. We evaluate the stability and support for the current six-supergroup classification of eukaryotes based on molecular genealogies. We assess three aspects of each supergroup: (1) the stability of its taxonomy, (2) the support for monophyly (single evolutionary origin) in molecular analyses targeting a supergroup, and (3) the support for monophyly when a supergroup is included as an out-group in phylogenetic studies targeting other taxa. Our analysis demonstrates that supergroup taxonomies are unstable and that support for groups varies tremendously, indicating that the current classification scheme of eukaryotes is likely premature. We highlight several trends contributing to the instability and discuss the requirements for establishing robust clades within the eukaryotic tree of life.

Parfrey, Laura Wegener; Barbero, Erika; Lasser, Elyse; Dunthorn, Micah; Bhattacharya, Debashish; Patterson, David J; Katz, Laura A

2006-01-01

216

Measuring community similarity with phylogenetic networks.  

PubMed

Environmental drivers of biodiversity can be identified by relating patterns of community similarity to ecological factors. Community variation has traditionally been assessed by considering changes in species composition and more recently by incorporating phylogenetic information to account for the relative similarity of taxa. Here, we describe how an important class of measures including Bray-Curtis, Canberra, and UniFrac can be extended to allow community variation to be computed on a phylogenetic network. We focus on phylogenetic split systems, networks that are produced by the widely used median network and neighbor-net methods, which can represent incongruence in the evolutionary history of a set of taxa. Calculating ? diversity over a split system provides a measure of community similarity averaged over uncertainty or conflict in the available phylogenetic signal. Our freely available software, Network Diversity, provides 11 qualitative (presence-absence, unweighted) and 14 quantitative (weighted) network-based measures of community similarity that model different aspects of community richness and evenness. We demonstrate the broad applicability of network-based diversity approaches by applying them to three distinct data sets: pneumococcal isolates from distinct geographic regions, human mitochondrial DNA data from the Indonesian island of Nias, and proteorhodopsin sequences from the Sargasso and Mediterranean Seas. Our results show that major expected patterns of variation for these data sets are recovered using network-based measures, which indicates that these patterns are robust to phylogenetic uncertainty and conflict. Nonetheless, network-based measures of community similarity can differ substantially from measures ignoring phylogenetic relationships or from tree-based measures when incongruent signals are present in the underlying data. Network-based measures provide a methodology for assessing the robustness of ?-diversity results in light of incongruent phylogenetic signal and allow ? diversity to be calculated over widely used network structures such as median networks. PMID:22915830

Parks, Donovan H; Beiko, Robert G

2012-12-01

217

NASA Position Classification Handbook  

NASA Technical Reports Server (NTRS)

The NASA Position Classification Handbook provides: a concise unitary reference document covering most aspects of position classification within NASA, information regarding the characteristics of NASA's own position classification program--the NASA Supplemental Classification System--and its origins, information concerning responsibilities of various levels of NASA management for position classification, and information concerning overall operation of a classification program. The provisions of this handbook pertain to the position classification function agency-wide. Although it will be particularly useful to personnel specialists, it also can serve as a convenient reference on position classification for line managers and supervisors and administrative personnel who deal with personnel management matters. Recommendations or questions concerning the content of this handbook should be directed to Director, Personnel Programs Division (Code NP), NASA Headquarters.

1987-01-01

218

Determining Horizontal Gene Transfers in Species Classification: Unique Scenario  

Microsoft Academic Search

\\u000a The problem of species classification, taking into account the mechanisms of reticulate evolution such as horizontal gene\\u000a transfer (HGT), species hybridization,or gene duplication, is very delicate. In this paper, we describe a new algorithm for\\u000a determining a unique scenario of HGT events in a given additive tree (i.e., a phylogenetic tree) representing the evolution\\u000a of a group of species. The

Vladimir Makarenkov; Alix Boc; Abdoulaye Baniré Diallo

219

Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection  

PubMed Central

The marginal likelihood is commonly used for comparing different evolutionary models in Bayesian phylogenetics and is the central quantity used in computing Bayes Factors for comparing model fit. A popular method for estimating marginal likelihoods, the harmonic mean (HM) method, can be easily computed from the output of a Markov chain Monte Carlo analysis but often greatly overestimates the marginal likelihood. The thermodynamic integration (TI) method is much more accurate than the HM method but requires more computation. In this paper, we introduce a new method, steppingstone sampling (SS), which uses importance sampling to estimate each ratio in a series (the “stepping stones”) bridging the posterior and prior distributions. We compare the performance of the SS approach to the TI and HM methods in simulation and using real data. We conclude that the greatly increased accuracy of the SS and TI methods argues for their use instead of the HM method, despite the extra computation needed.

Xie, Wangang; Lewis, Paul O.; Fan, Yu; Kuo, Lynn; Chen, Ming-Hui

2011-01-01

220

A Bayesian phylogenetic method to estimate unknown sequence ages.  

PubMed

Heterochronous data sets comprise molecular sequences sampled at different points in time. If the temporal range of the sampled sequences is large relative to the rate of mutation, the sampling times can directly calibrate evolutionary rates to calendar time. Here, we extend this calibration process to provide a full probabilistic method that utilizes temporal information in heterochronous data sets to estimate sampling times (leaf-ages) for sequenced for which this information unavailable. Our method is similar to relaxing the constraints of the molecular clock on specific lineages within a phylogenetic tree. Using a combination of synthetic and empirical data sets, we demonstrate that the method estimates leaf-ages reliably and accurately. Potential applications of our approach include incorporating samples of uncertain or radiocarbon-infinite age into ancient DNA analyses, evaluating the temporal signal in a particular sequence or data set, and exploring the reliability of sequence ages that are somehow contentious. PMID:20889726

Shapiro, Beth; Ho, Simon Y W; Drummond, Alexei J; Suchard, Marc A; Pybus, Oliver G; Rambaut, Andrew

2011-02-01

221

A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages  

PubMed Central

Heterochronous data sets comprise molecular sequences sampled at different points in time. If the temporal range of the sampled sequences is large relative to the rate of mutation, the sampling times can directly calibrate evolutionary rates to calendar time. Here, we extend this calibration process to provide a full probabilistic method that utilizes temporal information in heterochronous data sets to estimate sampling times (leaf-ages) for sequenced for which this information unavailable. Our method is similar to relaxing the constraints of the molecular clock on specific lineages within a phylogenetic tree. Using a combination of synthetic and empirical data sets, we demonstrate that the method estimates leaf-ages reliably and accurately. Potential applications of our approach include incorporating samples of uncertain or radiocarbon-infinite age into ancient DNA analyses, evaluating the temporal signal in a particular sequence or data set, and exploring the reliability of sequence ages that are somehow contentious.

Shapiro, Beth; Drummond, Alexei J.; Suchard, Marc A.; Pybus, Oliver G.; Rambaut, Andrew

2011-01-01

222

Characterization of a branch of the phylogenetic tree  

SciTech Connect

We use a combination of analytic models and computer simulations to gain insight into the dynamics of evolution. Our results suggest that certain interesting phenomena should eventually emerge from the fossil record. For example, there should be a ''tortoise and hare effect'': Those genera with the smallest species death rate are likely to survive much longer than genera with large species birth and death rates. A complete characterization of the behavior of a branch of the phylogenetic tree corresponding to a genus and accurate mathematical representations of the various stages are obtained. We apply our results to address certain controversial issues that have arisen in paleontology such as the importance of punctuated equilibrium and whether unique Cambrian phyla have survived to the present.

Samuel, Stuart A.; Weng, Gezhi

2003-04-11

223

Webpage classification through summarization  

Microsoft Academic Search

Web-page classification is much more difficult than pure-text classification due to a large variety of noisy information embedded in Web pages. In this paper, we propose a new Web-page classification algorithm based on Web summarization for improving the accuracy. We first give empirical evidence that ideal Web-page summaries generated by human editors can indeed improve the performance of Web-page classification

Dou Shen; Zheng Chen; Qiang Yang; Hua-Jun Zeng; Benyu Zhang; Yuchang Lu; Wei-Ying Ma

2004-01-01

224

New Classification of Headache  

PubMed Central

The Headache Classification Committee of the International Headache Society has developed a new classification system for headache, cranial neuralgia, and facial pain. The value of the classification for the practising clinician is that it forces him or her to take a more careful history in order to determine the nature of the headache. This article reviews the classification system and gives examples of case histories and subsequent diagnoses.

Gawel, Marek J.

1992-01-01

225

Conflicting phylogenetic position of Schizosaccharomyces pombe.  

PubMed

The phylogenetic position of the fission yeast Schizosaccharomyces pombe in the fungal Tree of Life is still controversial. Three alternative phylogenetic positions have been proposed in the literature, namely (1) a position basal to the Hemiascomycetes and Euascomycetes, (2) a position as a sister group to the Euascomycetes with the Hemiascomycetes as a basal branch, or (3) a sister group to the Hemiascomycetes with Euascomycetes as a basal branch. Here we compared 91 clusters of orthologous proteins containing a single orthologue that are shared by 19 eukaryote genomes. The major part of these 91 orthologues supports a phylogenetic position of S. pombe as a basal lineage among the Ascomycota, thus supporting the second proposition. Interestingly, part of the orthologous proteins supported a fourth, not yet described alternative, in which S. pombe is basal to both Basidiomycota and Ascomycota. Both topologies of phylogenetic trees are well supported. We believe that both reflect correctly the phylogenetic history of the species concerned. This apparent paradox may point to a heterogeneous nuclear genome of the fungi. Importantly, this needs to be taken in consideration for a correct understanding of the fungal Tree of Life. PMID:16904286

Kuramae, Eiko E; Robert, Vincent; Snel, Berend; Boekhout, Teun

2006-10-01

226

Worldwide Phylogenetic Relationship of Avian Poxviruses  

PubMed Central

Poxvirus infections have been found in 230 species of wild and domestic birds worldwide in both terrestrial and marine environments. This ubiquity raises the question of how infection has been transmitted and globally dispersed. We present a comprehensive global phylogeny of 111 novel poxvirus isolates in addition to all available sequences from GenBank. Phylogenetic analysis of the Avipoxvirus genus has traditionally relied on one gene region (4b core protein). In this study we expanded the analyses to include a second locus (DNA polymerase gene), allowing for a more robust phylogenetic framework, finer genetic resolution within specific groups, and the detection of potential recombination. Our phylogenetic results reveal several major features of avipoxvirus evolution and ecology and propose an updated avipoxvirus taxonomy, including three novel subclades. The characterization of poxviruses from 57 species of birds in this study extends the current knowledge of their host range and provides the first evidence of the phylogenetic effect of genetic recombination of avipoxviruses. The repeated occurrence of avian family or order-specific grouping within certain clades (e.g., starling poxvirus, falcon poxvirus, raptor poxvirus, etc.) indicates a marked role of host adaptation, while the sharing of poxvirus species within prey-predator systems emphasizes the capacity for cross-species infection and limited host adaptation. Our study provides a broad and comprehensive phylogenetic analysis of the Avipoxvirus genus, an ecologically and environmentally important viral group, to formulate a genome sequencing strategy that will clarify avipoxvirus taxonomy.

Foster, Jeffrey T.; Dan, Adam; Ip, Hon S.; Egstad, Kristina F.; Parker, Patricia G.; Higashiguchi, Jenni M.; Skinner, Michael A.; Hofle, Ursula; Kreizinger, Zsuzsa; Dorrestein, Gerry M.; Solt, Szabolcs; Sos, Endre; Kim, Young Jun; Uhart, Marcela; Pereda, Ariel; Gonzalez-Hein, Gisela; Hidalgo, Hector; Blanco, Juan-Manuel; Erdelyi, Karoly

2013-01-01

227

Prioritizing Populations for Conservation Using Phylogenetic Networks  

PubMed Central

In the face of inevitable future losses to biodiversity, ranking species by conservation priority seems more than prudent. Setting conservation priorities within species (i.e., at the population level) may be critical as species ranges become fragmented and connectivity declines. However, existing approaches to prioritization (e.g., scoring organisms by their expected genetic contribution) are based on phylogenetic trees, which may be poor representations of differentiation below the species level. In this paper we extend evolutionary isolation indices used in conservation planning from phylogenetic trees to phylogenetic networks. Such networks better represent population differentiation, and our extension allows populations to be ranked in order of their expected contribution to the set. We illustrate the approach using data from two imperiled species: the spotted owl Strix occidentalis in North America and the mountain pygmy-possum Burramys parvus in Australia. Using previously published mitochondrial and microsatellite data, we construct phylogenetic networks and score each population by its relative genetic distinctiveness. In both cases, our phylogenetic networks capture the geographic structure of each species: geographically peripheral populations harbor less-redundant genetic information, increasing their conservation rankings. We note that our approach can be used with all conservation-relevant distances (e.g., those based on whole-genome, ecological, or adaptive variation) and suggest it be added to the assortment of tools available to wildlife managers for allocating effort among threatened populations.

Volkmann, Logan; Martyn, Iain; Moulton, Vincent; Spillner, Andreas; Mooers, Arne O.

2014-01-01

228

Phylogenetic tree shapes resolve disease transmission patterns  

PubMed Central

Background and Objectives: Whole-genome sequencing is becoming popular as a tool for understanding outbreaks of communicable diseases, with phylogenetic trees being used to identify individual transmission events or to characterize outbreak-level overall transmission dynamics. Existing methods to infer transmission dynamics from sequence data rely on well-characterized infectious periods, epidemiological and clinical metadata which may not always be available, and typically require computationally intensive analysis focusing on the branch lengths in phylogenetic trees. We sought to determine whether the topological structures of phylogenetic trees contain signatures of the transmission patterns underlying an outbreak. Methodology: We use simulated outbreaks to train and then test computational classifiers. We test the method on data from two real-world outbreaks. Results: We show that different transmission patterns result in quantitatively different phylogenetic tree shapes. We describe topological features that summarize a phylogeny’s structure and find that computational classifiers based on these are capable of predicting an outbreak’s transmission dynamics. The method is robust to variations in the transmission parameters and network types, and recapitulates known epidemiology of previously characterized real-world outbreaks. Conclusions and implications: There are simple structural properties of phylogenetic trees which, when combined, can distinguish communicable disease outbreaks with a super-spreader, homogeneous transmission and chains of transmission. This is possible using genome data alone, and can be done during an outbreak. We discuss the implications for management of outbreaks.

Colijn, Caroline; Gardy, Jennifer

2014-01-01

229

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

PubMed Central

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.

2010-01-01

230

Shower Classification Software  

NASA Astrophysics Data System (ADS)

We describe the Shower Classification Software (SCS) which makes an automatic shower classification of plotted meteors. This tool is developed to help observers make shower classification procedure fast and allows them to check calculations done by hand. The programme is available for Linux and Windows operating systems and can be obtained from http://www.pkim.org/?q=pl/scs.

Zloczewski, K.; Wisniewski, M.; Lelit, M.; Polakowski, K.

2009-06-01

231

Classification Line-up  

NSDL National Science Digital Library

This activity was designed for blind learners, but all types of learners can use it to organize an interactive model for learning the classification system (taxonomy) of living things. Learners with visual impairments as well as sighted learners can explore the classification categories (kingdom, phylum, class, order, family, genus, species) and practice the classification of organisms.

Blind, Perkins S.

2011-11-16

232

Analysis of the peroxiredoxin family: using active site structure and sequence information for global classification and residue analysis  

PubMed Central

Peroxiredoxins (Prxs) are a widespread and highly expressed family of cysteine-based peroxidases that react very rapidly with H2O2, organic peroxides, and peroxynitrite. Correct subfamily classification has been problematic since Prx subfamilies are frequently not correlated with phylogenetic distribution and diverge in their preferred reductant, oligomerization state, and tendency towards overoxidation. We have developed a method that uses the Deacon Active Site Profiler (DASP) tool to extract functional site profiles from structurally characterized proteins, to computationally define subfamilies, and to identify new Prx subfamily members from GenBank(nr). For the 58 literature-defined Prx test proteins, 57 were correctly assigned and none were assigned to the incorrect subfamily. The >3500 putative Prx sequences identified were then used to analyze residue conservation in the active site of each Prx subfamily. Our results indicate that the existence and location of the resolving cysteine varies in some subfamilies (e.g. Prx5) to a greater degree than previously appreciated and that interactions at the A interface (common to Prx5, Tpx and higher order AhpC/Prx1 structures) are important for stabilization of the correct active site geometry. Interestingly, this method also allows us to further divide the AhpC/Prx1 into four groups that are correlated with functional characteristics. The DASP method provides more accurate subfamily classification than PSI-BLAST for members of the Prx family and can now readily be applied to other large protein families.

Nelson, Kimberly J.; Knutson, Stacy T.; Soito, Laura; Klomsiri, Chananat; Poole, Leslie B.; Fetrow, Jacquelyn S.

2010-01-01

233

Cirrhosis Classification Based on Texture Classification of Random Features  

PubMed Central

Accurate staging of hepatic cirrhosis is important in investigating the cause and slowing down the effects of cirrhosis. Computer-aided diagnosis (CAD) can provide doctors with an alternative second opinion and assist them to make a specific treatment with accurate cirrhosis stage. MRI has many advantages, including high resolution for soft tissue, no radiation, and multiparameters imaging modalities. So in this paper, multisequences MRIs, including T1-weighted, T2-weighted, arterial, portal venous, and equilibrium phase, are applied. However, CAD does not meet the clinical needs of cirrhosis and few researchers are concerned with it at present. Cirrhosis is characterized by the presence of widespread fibrosis and regenerative nodules in the hepatic, leading to different texture patterns of different stages. So, extracting texture feature is the primary task. Compared with typical gray level cooccurrence matrix (GLCM) features, texture classification from random features provides an effective way, and we adopt it and propose CCTCRF for triple classification (normal, early, and middle and advanced stage). CCTCRF does not need strong assumptions except the sparse character of image, contains sufficient texture information, includes concise and effective process, and makes case decision with high accuracy. Experimental results also illustrate the satisfying performance and they are also compared with typical NN with GLCM.

Shao, Ying; Guo, Dongmei; Zheng, Yuanjie; Zhao, Zuowei; Qiu, Tianshuang

2014-01-01

234

Accurate Replication in Genetic Programming  

Microsoft Academic Search

Abstract One characteristic tendency of genetic program - ming is the production of considerably larger trees than expected It has been suggested that this is related to the ability of individuals to replicate ac - curately In this paper we present theoretical anal - ysis which shows that, for certain specific cases, the pressure for accurate replication induces an increase

Nicholas Freitag Mcphee; Justin Darwin Miller

1995-01-01

235

CORE: A Phylogenetically-Curated 16S rDNA Database of the Core Oral Microbiome  

Microsoft Academic Search

Comparing bacterial 16S rDNA sequences to GenBank and other large public databases via BLAST often provides results of little use for identification and taxonomic assignment of the organisms of interest. The human microbiome, and in particular the oral microbiome, includes many taxa, and accurate identification of sequence data is essential for studies of these communities. For this purpose, a phylogenetically

Ann L. Griffen; Clifford J. Beall; Noah D. Firestone; Erin L. Gross; James M. DiFranco; Jori H. Hardman; Bastienne Vriesendorp; Russell A. Faust; Daniel A. Janies; Eugene J. Leys

2011-01-01

236

The phylogenetic significance of colour patterns in marine teleost larvae  

PubMed Central

Ichthyologists, natural-history artists, and tropical-fish aquarists have described, illustrated, or photographed colour patterns in adult marine fishes for centuries, but colour patterns in marine fish larvae have largely been neglected. Yet the pelagic larval stages of many marine fishes exhibit subtle to striking, ephemeral patterns of chromatophores that warrant investigation into their potential taxonomic and phylogenetic significance. Colour patterns in larvae of over 200 species of marine teleosts, primarily from the western Caribbean, were examined from digital colour photographs, and their potential utility in elucidating evolutionary relationships at various taxonomic levels was assessed. Larvae of relatively few basal marine teleosts exhibit erythrophores, xanthophores, or iridophores (i.e. nonmelanistic chromatophores), but one or more of those types of chromatophores are visible in larvae of many basal marine neoteleosts and nearly all marine percomorphs. Whether or not the presence of nonmelanistic chromatophores in pelagic marine larvae diagnoses any major teleost taxonomic group cannot be determined based on the preliminary survey conducted, but there is a trend toward increased colour from elopomorphs to percomorphs. Within percomorphs, patterns of nonmelanistic chromatophores may help resolve or contribute evidence to existing hypotheses of relationships at multiple levels of classification. Mugilid and some beloniform larvae share a unique ontogenetic transformation of colour pattern that lends support to the hypothesis of a close relationship between them. Larvae of some tetraodontiforms and lophiiforms are strikingly similar in having the trunk enclosed in an inflated sac covered with xanthophores, a character that may help resolve the relationships of these enigmatic taxa. Colour patterns in percomorph larvae also appear to diagnose certain groups at the interfamilial, familial, intergeneric, and generic levels. Slight differences in generic colour patterns, including whether the pattern comprises xanthophores or erythrophores, often distinguish species. The homology, ontogeny, and possible functional significance of colour patterns in larvae are discussed. Considerably more investigation of larval colour patterns in marine teleosts is needed to assess fully their value in phylogenetic reconstruction.

Baldwin, Carole C

2013-01-01

237

How reliable are human phylogenetic hypotheses?  

PubMed Central

Cladistic analysis of cranial and dental evidence has been widely used to generate phylogenetic hypotheses about humans and their fossil relatives. However, the reliability of these hypotheses has never been subjected to external validation. To rectify this, we applied identical methods to equivalent evidence from two groups of extant higher primates for whom reliable molecular phylogenies are available, the hominoids and papionins. We found that the phylogenetic hypotheses based on the craniodental data were incompatible with the molecular phylogenies for the groups. Given the robustness of the molecular phylogenies, these results indicate that little confidence can be placed in phylogenies generated solely from higher primate craniodental evidence. The corollary of this is that existing phylogenetic hypotheses about human evolution are unlikely to be reliable. Accordingly, new approaches are required to address the problem of hominin phylogeny.

Collard, Mark; Wood, Bernard

2000-01-01

238

Phylogenetic conservatism of extinctions in marine bivalves.  

PubMed

Evolutionary histories of species and lineages can influence their vulnerabilities to extinction, but the importance of this effect remains poorly explored for extinctions in the geologic past. When analyzed using a standardized taxonomy within a phylogenetic framework, extinction rates of marine bivalves estimated from the fossil record for the last approximately 200 million years show conservatism at multiple levels of evolutionary divergence, both within individual families and among related families. The strength of such phylogenetic clustering varies over time and is influenced by earlier extinction history, especially by the demise of volatile taxa in the end-Cretaceous mass extinction. Analyses of the evolutionary roles of ancient extinctions and predictive models of vulnerability of taxa to future natural and anthropogenic stressors should take phylogenetic relationships and extinction history into account. PMID:19661426

Roy, Kaustuv; Hunt, Gene; Jablonski, David

2009-08-01

239

Construction of the Platform for Phylogenetic Analysis  

NASA Astrophysics Data System (ADS)

Based on discussing the history of advancement to building the tree of life using genetic and genomic information, effective strategies and methods for the construction of the tree of life, this paper carried out business process analysis and application design. It implements a phylogenetic analysis platform for the land plants based on this analysis. The platform extracts molecular data from the international public databases in batch, which is automated acquisition, cleaning function for users to understand the situation of peer data. The process of phylogenetic reconstruction includes several public modes and tools, such as batch extraction, multiple sequence alignment, cleaning & editing, tree reconstruction, phylogeny evaluation and visualization. All these procedures demand a number of interactive interfaces for phylogenetic tree automatic generation and decision-making aids experiment.

Meng, Zhen; Lin, Xiaoguang; He, Xing; Gao, Yanping; Liu, Hongmei; Liu, Yong; Zhou, Yuanchun; Li, Jianhui; Chen, Zhiduan; Zhang, Shouzhou; Li, Yong

240

A Novel Approach for Compressing Phylogenetic Trees  

NASA Astrophysics Data System (ADS)

Phylogenetic trees are tree structures that depict relationships between organisms. Popular analysis techniques often produce large collections of candidate trees, which are expensive to store. We introduce TreeZip, a novel algorithm to compress phylogenetic trees based on their shared evolutionary relationships. We evaluate TreeZip's performance on fourteen tree collections ranging from 2,505 trees on 328 taxa to 150,000 trees on 525 taxa corresponding to 0.6 MB to 434 MB in storage. Our results show that TreeZip is very effective, typically compressing a tree file to less than 2% of its original size. When coupled with standard compression methods such as 7zip, TreeZip can compress a file to less than 1% of its original size. Our results strongly suggest that TreeZip is very effective at compressing phylogenetic trees, which allows for easier exchange of data with colleagues around the world.

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

241

Phylogenetic diversity of phytopathogenic mycoplasmalike organisms.  

PubMed

By using specific primers, the 16S rRNA genes of Japanese mycoplasmalike organisms (MLOs) were amplified by polymerase chain reactions from MLO-enriched fractions of plants infected with each of six different MLOs. Each of the polymerase chain reaction fragments (length, 1,370 nucleotides) was directly sequenced in both strands by using 17 oligonucleotide primers. A phylogenetic tree constructed by using the sequence data showed that these Japanese MLOs are phylogenetically diverse microorganisms that fall into three groups, group I (onion yellows, tomato yellows, mulberry dwarf, and paulownia witches' broom MLOs), group II (tsuwabuki witches' broom MLO), and group III (rice yellow dwarf MLO). A high level of sequence homology (99%) between the Oenothera hookeri MLO and the severe strain of the western aster yellows MLO on the one hand and group I MLOs on the other indicates that the O. hookeri MLO and the severe strain of the western aster yellows MLO belong to group I and suggests that these MLOs, isolated from two geographically separated locations, descended from a very similar ancestor. Although group I contains phylogenetically identical MLOs, the organisms are transmitted by diverse insect vectors. The three MLO groups are more closely related to Acholeplasma laidlawii than to Mycoplasma gallisepticum. Thus, although MLOs are phylogenetically diverse, they are evolutionarily distant from other mollicutes. These data, together with other information (including phylogenetic relationships, vector specificity, plant-pathogenic properties, and habitat in plant phloem sieve tubes), suggest that MLOs could be classified into at least three phylogenetic groups (groups I through III). PMID:8347505

Namba, S; Oyaizu, H; Kato, S; Iwanami, S; Tsuchizaki, T

1993-07-01

242

Threat Diversity Will Erode Mammalian Phylogenetic Diversity in the Near Future  

PubMed Central

To reduce the accelerating rate of phylogenetic diversity loss, many studies have searched for mechanisms that could explain why certain species are at risk, whereas others are not. In particular, it has been demonstrated that species might be affected by both extrinsic threat factors as well as intrinsic biological traits that could render a species more sensitive to extinction; here, we focus on extrinsic factors. Recently, the International Union for Conservation of Nature developed a new classification of threat types, including climate change, urbanization, pollution, agriculture and aquaculture, and harvesting/hunting. We have used this new classification to analyze two main factors that could explain the expected future loss of mammalian phylogenetic diversity: 1. differences in the type of threats that affect mammals and 2. differences in the number of major threats that accumulate for a single species. Our results showed that Cetartiodactyla, Diprotodontia, Monotremata, Perissodactyla, Primates, and Proboscidea could lose a high proportion of their current phylogenetic diversity in the coming decades. In contrast, Chiroptera, Didelphimorphia, and Rodentia could lose less phylogenetic diversity than expected if extinctions were random. Some mammalian clades, including Marsupiala, Chiroptera, and a subclade of Primates, are affected by particular threat types, most likely due solely to their geographic locations and associations with particular habitats. However, regardless of the geography, habitat, and taxon considered, it is not the threat type, but the threat diversity that determines the extinction risk for species and clades. Thus, some mammals might be randomly located in areas subjected to a large diversity of threats; they might also accumulate detrimental traits that render them sensitive to different threats, which is a characteristic that could be associated with large body size. Any action reducing threat diversity is expected to have a significant impact on future mammalian phylogeny.

Jono, Clementine M. A.; Pavoine, Sandrine

2012-01-01

243

Comparative genomic analysis and phylogenetic position of Theileria equi  

PubMed Central

Background Transmission of arthropod-borne apicomplexan parasites that cause disease and result in death or persistent infection represents a major challenge to global human and animal health. First described in 1901 as Piroplasma equi, this re-emergent apicomplexan parasite was renamed Babesia equi and subsequently Theileria equi, reflecting an uncertain taxonomy. Understanding mechanisms by which apicomplexan parasites evade immune or chemotherapeutic elimination is required for development of effective vaccines or chemotherapeutics. The continued risk of transmission of T. equi from clinically silent, persistently infected equids impedes the goal of returning the U. S. to non-endemic status. Therefore comparative genomic analysis of T. equi was undertaken to: 1) identify genes contributing to immune evasion and persistence in equid hosts, 2) identify genes involved in PBMC infection biology and 3) define the phylogenetic position of T. equi relative to sequenced apicomplexan parasites. Results The known immunodominant proteins, EMA1, 2 and 3 were discovered to belong to a ten member gene family with a mean amino acid identity, in pairwise comparisons, of 39%. Importantly, the amino acid diversity of EMAs is distributed throughout the length of the proteins. Eight of the EMA genes were simultaneously transcribed. As the agents that cause bovine theileriosis infect and transform host cell PBMCs, we confirmed that T. equi infects equine PBMCs, however, there is no evidence of host cell transformation. Indeed, a number of genes identified as potential manipulators of the host cell phenotype are absent from the T. equi genome. Comparative genomic analysis of T. equi revealed the phylogenetic positioning relative to seven apicomplexan parasites using deduced amino acid sequences from 150 genes placed it as a sister taxon to Theileria spp. Conclusions The EMA family does not fit the paradigm for classical antigenic variation, and we propose a novel model describing the role of the EMA family in persistence. T. equi has lost the putative genes for host cell transformation, or the genes were acquired by T. parva and T. annulata after divergence from T. equi. Our analysis identified 50 genes that will be useful for definitive phylogenetic classification of T. equi and closely related organisms.

2012-01-01

244

A molecular phylogenetic analysis of the Scarabaeinae (dung beetles).  

PubMed

The dung beetles (Scarabaeinae) include ca. 5000 species and exhibit a diverse array of morphologies and behaviors. This variation presumably reflects the adaptation to a diversity of food types and the different strategies used to avoid competition for vertebrate dung, which is the primary breeding environment for most species. The current classification gives great weight to the major behavioral types, separating the ball rollers and the tunnelers, but existing phylogenetic studies have been based on limited taxonomic or biogeographic sampling and have been contradictory. Here, we present a molecular phylogenetic analysis of 214 species of Scarabaeinae, representing all 12 traditionally recognized tribes and six biogeographical regions, using partial gene sequences from one nuclear (28S) and two mitochondrial (cox1, rrnL) genes. Length variation in 28S (588-621 bp) and rrnL (514-523 bp) was subjected to a thorough evaluation of alternative alignments, gap-coding methods, and tree searches using model-based (Bayesian and likelihood), maximum parsimony, and direct optimization analyses. The small-bodied, non-dung-feeding Sarophorus+Coptorhina were basal in all reconstructions. These were closely related to rolling Odontoloma+Dicranocara, suggesting an early acquisition of rolling behavior. Smaller tribes and most genera were monophyletic, while Canthonini and Dichotomiini each consisted of multiple paraphyletic lineages at hierarchical levels equivalent to the smaller tribes. Plasticity of rolling and tunneling was evidenced by a lack of monophyly (S-H test, p > 0.05) and several reversals within clades. The majority of previously unrecognized clades were geographical, including the well-supported Neotropical Phanaeini+Eucraniini, and a large Australian clade of rollers as well as tunneling Coptodactyla and Demarziella. Only three lineages, Gymnopleurini, Copris+Microcopris and Onthophagus, were widespread and therefore appear to be dispersive at a global scale. A reconstruction of biogeographical characters recovered 38-48 transitions between regions and an African origin for most lineages. Dispersal-vicariance analysis supported an African origin with links to all other regions and little back-migration. Our results provide a new synthesis of global-scale dung beetle evolution, demonstrating the great plasticity of behavioral and morphological traits and the importance of biogeographic distributions as the basis for a new classification. PMID:17656114

Monaghan, Michael T; Inward, Daegan J G; Hunt, Toby; Vogler, Alfried P

2007-11-01

245

The phylogenetic relationship among Ectothiorhodospiraceae: a reevaluation of their taxonomy on the basis of 16S rDNA analyses  

Microsoft Academic Search

Sequences of the 16S rRNA gene were determined from all type strains of the recognized Ectothiorhodospira species and from a number of additional strains. For the first time, these data resolve the phylogenetic relationships of\\u000a the Ectothiorhodospiraceae in detail, confirm the established species, and improve the classification of strains of uncertain\\u000a affiliation. Two major groups that are recognized as separate

Johannes F. Imhoff; Jörg Süling

1996-01-01

246

Genetic Classification of \\  

Microsoft Academic Search

To determine the phylogenetic position of two new rickettsial strains isolated from ticks in China, 16S ribosomal DNA, gltA, and ompA (apart from the tandem repeat units) genes were amplified by PCR and sequenced. The phylogenetic relationships between these strains and other rickettsiae were inferred from the comparison of sequences of the three genes by the parsimony, neighbor-joining, and maximum-likelihood

J. Z. ZHANG; M. Y. FAN; Y. M. WU; P. E. FOURNIER; V. ROUX; D. RAOULT; CNRS UPRES-A

2000-01-01

247

Time-Accurate Computational Simulation  

NASA Technical Reports Server (NTRS)

Time accurate CFD may offer a faster approach to S&C aerodynamic database population than the conventional point by point steady state CFD. We would directly simulate -, -sweeps or other configuration movements typically of measurement sequence in wind tunnels. A second objective is to demonstrate potential applications to assessment of S&C dynamic derivatives by simulating vehicle motions such as free to roll, and nonlinearity such as the trends of aerodynamic forces near CL-max or flow hysteresis.

Pao, S. Paul; Buning, Pieter G.

2004-01-01

248

From accurate machining towards accurate measurements with MICROSCOPE  

NASA Astrophysics Data System (ADS)

Observing any violation of the Equivalence Principle at a level as low as 10 -15 needs both a very soft and stable environment and a very accurate instrument The MICROSCOPE space laboratory allows testing of the universality of free fall with two masses made of a Platinum Rhodium alloy and a Titanium alloy in a 10 pico-g environment The two test-masses are accurately controlled by electrostatic forces to follow a common geodesic within a CNES drag-free microsatellite Accurate centring and alignment of the test-masses is mandatory to prevent any artefact signal due to the Earth s gravity gradient or any on-board gravity gradient To this purpose the MICROSCOPE instrument called Twin-Space Accelerometer for Gravitation Experimentation T-SAGE has been designed to minimise the gravity gradient disturbances A laboratory model and a first representative model for vibration tests have been produced integrated and tested These models have allowed verification of the manufacturing and integration processes and of their accuracy which gives a first budget for the expected centring and alignment of the flight-models This paper describes the micro-meter machining and integration challenges of T-SAGE and their impact on the instrument performance In particular the shape of the test-mass has an effect on the differential accelerometer output due to the gravity gradient and also on the instrument capacitive position output used for the electrostatic servo-loop First results obtained with the fully integrated models are also presented to assess the

Rodrigues, M.; Touboul, P.; Chhun, R.; Hudson, D.; Foulon, B.; Flinoise, P.; Bodoville, G.; Lebat, V.

249

Empirical profile mixture models for phylogenetic reconstruction  

Microsoft Academic Search

Motivation: Previous studies have shown that accounting for site- specific amino acid replacement patterns using mixtures of stationary probability profiles offers a promising approach for improving the robustness of phylogenetic reconstructions in the presence of satu- ration. However, such profile mixture models were introduced only in a Bayesian context, and are not yet available in a Maximum Like- lihood framework.

Le Si Quang; Olivier Gascuel; Nicolas Lartillot

2008-01-01

250

Phylogenetic invariants for stationary base composition  

Microsoft Academic Search

Changing base composition during the evolution of biological sequences can mislead some of the phylogenetic inference techniques in current use. However, detecting whether such a process has occurred may be dicult, since convergent evolution may lead to similar base frequencies emerging from dierent lineages. To study this situation, algebraic models of biologicalsequence evolution are intro- duced in which the base

Elizabeth S. Allman; John A. Rhodes

2006-01-01

251

Construction of the Platform for Phylogenetic Analysis  

Microsoft Academic Search

Based on discussing the history of advancement to building the tree of life using genetic and genomic information, effective strategies and methods for the construction of the tree of life, this paper carried out business process analysis and application design. It implements a phylogenetic analysis platform for the land plants based on this analysis. The platform extracts molecular data from

Zhen Meng; Xiaoguang Lin; Xing He; Yanping Gao; Hongmei Liu; Yong Liu; Yuanchun Zhou; Jianhui Li; Zhiduan Chen; Shouzhou Zhang; Yong Li

2011-01-01

252

Phylogenetic Inference via Sequential Monte Carlo  

PubMed Central

Bayesian inference provides an appealing general framework for phylogenetic analysis, able to incorporate a wide variety of modeling assumptions and to provide a coherent treatment of uncertainty. Existing computational approaches to Bayesian inference based on Markov chain Monte Carlo (MCMC) have not, however, kept pace with the scale of the data analysis problems in phylogenetics, and this has hindered the adoption of Bayesian methods. In this paper, we present an alternative to MCMC based on Sequential Monte Carlo (SMC). We develop an extension of classical SMC based on partially ordered sets and show how to apply this framework—which we refer to as PosetSMC—to phylogenetic analysis. We provide a theoretical treatment of PosetSMC and also present experimental evaluation of PosetSMC on both synthetic and real data. The empirical results demonstrate that PosetSMC is a very promising alternative to MCMC, providing up to two orders of magnitude faster convergence. We discuss other factors favorable to the adoption of PosetSMC in phylogenetics, including its ability to estimate marginal likelihoods, its ready implementability on parallel and distributed computing platforms, and the possibility of combining with MCMC in hybrid MCMC–SMC schemes. Software for PosetSMC is available at http://www.stat.ubc.ca/ bouchard/PosetSMC.

Sankararaman, Sriram; Jordan, Michael I.

2012-01-01

253

Phylogenetic and phylogenomic overview of the Polyporales.  

PubMed

We present a phylogenetic and phylogenomic overview of the Polyporales. The newly sequenced genomes of Bjerkandera adusta, Ganoderma sp., and Phlebia brevispora are introduced and an overview of 10 currently available Polyporales genomes is provided. The new genomes are 39 500 000-49 900 00 bp and encode for 12 910-16 170 genes. We searched available genomes for single-copy genes and performed phylogenetic informativeness analyses to evaluate their potential for phylogenetic systematics of the Polyporales. Phylogenomic datasets (25, 71, 356 genes) were assembled for the 10 Polyporales species with genome data and compared with the most comprehensive dataset of Polyporales to date (six-gene dataset for 373 taxa, including taxa with missing data). Maximum likelihood and Bayesian phylogenetic analyses of genomic datasets yielded identical topologies, and the corresponding clades also were recovered in the 373-taxa dataset although with different support values in some datasets. Three previously recognized lineages of Polyporales, antrodia, core polyporoid and phlebioid clades, are supported in most datasets, while the status of the residual polyporoid clade remains uncertain and certain taxa (e.g. Gelatoporia, Grifola, Tyromyces) apparently do not belong to any of the major lineages of Polyporales. The most promising candidate single-copy genes are presented, and nodes in the Polyporales phylogeny critical for the suprageneric taxonomy of the order are identified and discussed. PMID:23935031

Binder, Manfred; Justo, Alfredo; Riley, Robert; Salamov, Asaf; Lopez-Giraldez, Francesc; Sjökvist, Elisabet; Copeland, Alex; Foster, Brian; Sun, Hui; Larsson, Ellen; Larsson, Karl-Henrik; Townsend, Jeffrey; Grigoriev, Igor V; Hibbett, David S

2013-01-01

254

Tree models for macroevolution and phylogenetic analysis.  

PubMed

It has long been recognized that phylogenetic trees are more unbalanced than those generated by a Yule process. Recently, the degree of this imbalance has been quantified using the large set of phylogenetic trees available in the TreeBASE data set. In this article, a more precise analysis of imbalance is undertaken. Trees simulated under a range of models are compared with trees from TreeBASE and two smaller data sets. Several simple models can match the amount of imbalance measured in real data. Most of them also match the variance of imbalance among empirical trees to a remarkable degree. Statistics are developed to measure balance and to distinguish between trees with the same overall imbalance. The match between models and data for these statistics is investigated. In particular, age-dependent (Bellman-Harris) branching process are studied in detail. It remains difficult to separate the process of macroevolution from biases introduced by sampling. The lessons for phylogenetic analysis are clearer. In particular, the use of the usual proportional to distinguishable arrangements (uniform) prior on tree topologies in Bayesian phylogenetic analysis is not recommended. PMID:21865338

Jones, Graham R

2011-12-01

255

A phylogenetic analysis of the brassicales clade based on an alignment-free sequence comparison method.  

PubMed

Phylogenetic analyses reveal the evolutionary derivation of species. A phylogenetic tree can be inferred from multiple sequence alignments of proteins or genes. The alignment of whole genome sequences of higher eukaryotes is a computational intensive and ambitious task as is the computation of phylogenetic trees based on these alignments. To overcome these limitations, we here used an alignment-free method to compare genomes of the Brassicales clade. For each nucleotide sequence a Chaos Game Representation (CGR) can be computed, which represents each nucleotide of the sequence as a point in a square defined by the four nucleotides as vertices. Each CGR is therefore a unique fingerprint of the underlying sequence. If the CGRs are divided by grid lines each grid square denotes the occurrence of oligonucleotides of a specific length in the sequence (Frequency Chaos Game Representation, FCGR). Here, we used distance measures between FCGRs to infer phylogenetic trees of Brassicales species. Three types of data were analyzed because of their different characteristics: (A) Whole genome assemblies as far as available for species belonging to the Malvidae taxon. (B) EST data of species of the Brassicales clade. (C) Mitochondrial genomes of the Rosids branch, a supergroup of the Malvidae. The trees reconstructed based on the Euclidean distance method are in general agreement with single gene trees. The Fitch-Margoliash and Neighbor joining algorithms resulted in similar to identical trees. Here, for the first time we have applied the bootstrap re-sampling concept to trees based on FCGRs to determine the support of the branchings. FCGRs have the advantage that they are fast to calculate, and can be used as additional information to alignment based data and morphological characteristics to improve the phylogenetic classification of species in ambiguous cases. PMID:22952468

Hatje, Klas; Kollmar, Martin

2012-01-01

256

Security classification of information  

SciTech Connect

Certain governmental information must be classified for national security reasons. However, the national security benefits from classifying information are usually accompanied by significant costs -- those due to a citizenry not fully informed on governmental activities, the extra costs of operating classified programs and procuring classified materials (e.g., weapons), the losses to our nation when advances made in classified programs cannot be utilized in unclassified programs. The goal of a classification system should be to clearly identify that information which must be protected for national security reasons and to ensure that information not needing such protection is not classified. This document was prepared to help attain that goal. This document is the first of a planned four-volume work that comprehensively discusses the security classification of information. Volume 1 broadly describes the need for classification, the basis for classification, and the history of classification in the United States from colonial times until World War 2. Classification of information since World War 2, under Executive Orders and the Atomic Energy Acts of 1946 and 1954, is discussed in more detail, with particular emphasis on the classification of atomic energy information. Adverse impacts of classification are also described. Subsequent volumes will discuss classification principles, classification management, and the control of certain unclassified scientific and technical information. 340 refs., 6 tabs.

Quist, A.S.

1989-09-01

257

Security classification of information  

SciTech Connect

This document is the second of a planned four-volume work that comprehensively discusses the security classification of information. The main focus of Volume 2 is on the principles for classification of information. Included herein are descriptions of the two major types of information that governments classify for national security reasons (subjective and objective information), guidance to use when determining whether information under consideration for classification is controlled by the government (a necessary requirement for classification to be effective), information disclosure risks and benefits (the benefits and costs of classification), standards to use when balancing information disclosure risks and benefits, guidance for assigning classification levels (Top Secret, Secret, or Confidential) to classified information, guidance for determining how long information should be classified (classification duration), classification of associations of information, classification of compilations of information, and principles for declassifying and downgrading information. Rules or principles of certain areas of our legal system (e.g., trade secret law) are sometimes mentioned to .provide added support to some of those classification principles.

Quist, A.S.

1993-04-01

258

Phyloclimatic modeling: combining phylogenetics and bioclimatic modeling.  

PubMed

We investigate the impact of past climates on plant diversification by tracking the "footprint" of climate change on a phylogenetic tree. Diversity within the cosmopolitan carnivorous plant genus Drosera (Droseraceae) is focused within Mediterranean climate regions. We explore whether this diversity is temporally linked to Mediterranean-type climatic shifts of the mid-Miocene and whether climate preferences are conservative over phylogenetic timescales. Phyloclimatic modeling combines environmental niche (bioclimatic) modeling with phylogenetics in order to study evolutionary patterns in relation to climate change. We present the largest and most complete such example to date using Drosera. The bioclimatic models of extant species demonstrate clear phylogenetic patterns; this is particularly evident for the tuberous sundews from southwestern Australia (subgenus Ergaleium). We employ a method for establishing confidence intervals of node ages on a phylogeny using replicates from a Bayesian phylogenetic analysis. This chronogram shows that many clades, including subgenus Ergaleium and section Bryastrum, diversified during the establishment of the Mediterranean-type climate. Ancestral reconstructions of bioclimatic models demonstrate a pattern of preference for this climate type within these groups. Ancestral bioclimatic models are projected into palaeo-climate reconstructions for the time periods indicated by the chronogram. We present two such examples that each generate plausible estimates of ancestral lineage distribution, which are similar to their current distributions. This is the first study to attempt bioclimatic projections on evolutionary time scales. The sundews appear to have diversified in response to local climate development. Some groups are specialized for Mediterranean climates, others show wide-ranging generalism. This demonstrates that Phyloclimatic modeling could be repeated for other plant groups and is fundamental to the understanding of evolutionary responses to climate change. PMID:17060200

Yesson, C; Culham, A

2006-10-01

259

Classification images: A review.  

PubMed

Classification images have recently become a widely used tool in visual psychophysics. Here, I review the development of classification image methods over the past fifteen years. I provide some historical background, describing how classification images and related methods grew out of established statistical and mathematical frameworks and became common tools for studying biological systems. I describe key developments in classification image methods: use of optimal weighted sums based on the linear observer model, formulation of classification images in terms of the generalized linear model, development of statistical tests, use of priors to reduce dimensionality, methods for experiments with more than two response alternatives, a variant using multiplicative noise, and related methods for examining nonlinearities in visual processing, including second-order Volterra kernels and principal component analysis. I conclude with a selective review of how classification image methods have led to substantive findings in three representative areas of vision research, namely, spatial vision, perceptual organization, and visual search. PMID:21536726

Murray, Richard F

2011-01-01

260

Automatic lexical classification: bridging research and practice.  

PubMed

Natural language processing (NLP)--the automatic analysis, understanding and generation of human language by computers--is vitally dependent on accurate knowledge about words. Because words change their behaviour between text types, domains and sub-languages, a fully accurate static lexical resource (e.g. a dictionary, word classification) is unattainable. Researchers are now developing techniques that could be used to automatically acquire or update lexical resources from textual data. If successful, the automatic approach could considerably enhance the accuracy and portability of language technologies, such as machine translation, text mining and summarization. This paper reviews the recent and on-going research in automatic lexical acquisition. Focusing on lexical classification, it discusses the many challenges that still need to be met before the approach can benefit NLP on a large scale. PMID:20603372

Korhonen, Anna

2010-08-13

261

Multilocus phylogeny of the New-World mud turtles (Kinosternidae) supports the traditional classification of the group.  

PubMed

A goal of modern taxonomy is to develop classifications that reflect current phylogenetic relationships and are as stable as possible given the inherent uncertainties in much of the tree of life. Here, we provide an in-depth phylogenetic analysis, based on 14 nuclear loci comprising 10,305 base pairs of aligned sequence data from all but two species of the turtle family Kinosternidae, to determine whether recent proposed changes to the group's classification are justified and necessary. We conclude that those proposed changes were based on (1) mtDNA gene tree anomalies, (2) preliminary analyses that do not fully capture the breadth of geographic variation necessary to motivate taxonomic changes, and (3) changes in rank that are not motivated by non-monophyletic groups. Our recommendation, for this and other similar cases, is that taxonomic changes be made only when phylogenetic results that are statistically well-supported and corroborated by multiple independent lines of genetic evidence indicate that non-monophyletic groups are currently recognized and need to be corrected. We hope that other members of the phylogenetics community will join us in proposing taxonomic changes only when the strongest phylogenetic data demand such changes, and in so doing that we can move toward stable, phylogenetically informed classifications of lasting value. PMID:24704303

Spinks, Phillip Q; Thomson, Robert C; Gidi?, Müge; Bradley Shaffer, H

2014-07-01

262

Coarse Iris Classification by Learned Visual Dictionary  

Microsoft Academic Search

In state-of-the-art iris recognition systems, the input iris image has to be compared with a large number of templates in\\u000a database. When the scale of iris database increases, they are much less efficient and accurate. In this paper, we propose\\u000a a novel iris classification method to attack this problem in iris recognition systems. Firstly, we learned a small finite\\u000a dictionary

Xianchao Qiu; Zhenan Sun; Tieniu Tan

2007-01-01

263

Phylogenetic Species Recognition and Species Concepts in Fungi  

Microsoft Academic Search

Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology 31, 000–000. The operational species concept, i.e., the one used to recognize species, is contrasted to the theoretical species concept. A phylogenetic approach to recognize fungal species based on concordance of multiple gene genealogies is compared to those based on morphology and reproductive behavior. Examples where Phylogenetic Species

John W. Taylor; David J. Jacobson; Scott Kroken; Takao Kasuga; David M. Geiser; David S. Hibbett; Matthew C. Fisher

2000-01-01

264

Older Adults Are Less Accurate Than Younger Adults at Identifying Symptoms of Anxiety and Depression  

PubMed Central

The present study examined age differences in the discrimination between anxiety and depressive symptoms in a community sample of 374 adults, ages 18–93. Older adults were less accurate and more likely than younger adults to label symptoms as neither anxiety nor depression. Both older and younger adults were more accurate in their classification of depressive than anxiety symptoms. These findings suggest that additional efforts are needed to educate the general public, particularly older adults, about anxiety and its symptoms.

Wetherell, Julie Loebach; Petkus, Andrew J.; McChesney, Kathleen; Stein, Murray B.; Judd, Patricia H.; Rockwell, Enid; Sewell, Daniel D.; Patterson, Thomas L.

2009-01-01

265

Classification of HIV-1 Sequences Using Profile Hidden Markov Models  

PubMed Central

Accurate classification of HIV-1 subtypes is essential for studying the dynamic spatial distribution pattern of HIV-1 subtypes and also for developing effective methods of treatment that can be targeted to attack specific subtypes. We propose a classification method based on profile Hidden Markov Model that can accurately identify an unknown strain. We show that a standard method that relies on the construction of a positive training set only, to capture unique features associated with a particular subtype, can accurately classify sequences belonging to all subtypes except B and D. We point out the drawbacks of the standard method; namely, an arbitrary choice of threshold to distinguish between true positives and true negatives, and the inability to discriminate between closely related subtypes. We then propose an improved classification method based on construction of a positive as well as a negative training set to improve discriminating ability between closely related subtypes like B and D. Finally, we show how the improved method can be used to accurately determine the subtype composition of Common Recombinant Forms of the virus that are made up of two or more subtypes. Our method provides a simple and highly accurate alternative to other classification methods and will be useful in accurately annotating newly sequenced HIV-1 strains.

Dwivedi, Sanjiv K.; Sengupta, Supratim

2012-01-01

266

Predict amine solution properties accurately  

SciTech Connect

Improved process design begins with using accurate physical property data. Especially in the preliminary design stage, physical property data such as density viscosity, thermal conductivity and specific heat can affect the overall performance of absorbers, heat exchangers, reboilers and pump. These properties can also influence temperature profiles in heat transfer equipment and thus control or affect the rate of amine breakdown. Aqueous-amine solution physical property data are available in graphical form. However, it is not convenient to use with computer-based calculations. Developed equations allow improved correlations of derived physical property estimates with published data. Expressions are given which can be used to estimate physical properties of methyldiethanolamine (MDEA), monoethanolamine (MEA) and diglycolamine (DGA) solutions.

Cheng, S.; Meisen, A. [Univ. of British Columbia, Vancouver, British Columbia (Canada); Chakma, A. [Univ. of Calgary, Alberta (Canada)

1996-02-01

267

Toric ideals of homogeneous phylogenetic models  

Microsoft Academic Search

We consider the model of phylogenetic trees in which every node of the tree is an observed, binary random variable and the transition probabilities are given by the same matrix on each edge of the tree. The ideal of invariants of this model is a toric ideal in ℂ[p;i1;…i;n;]. We are able to compute the Göbner basis and minimal generating

Nicholas Eriksson

2004-01-01

268

Parametric Analysis of Alignment and Phylogenetic Uncertainty  

Microsoft Academic Search

To infer a phylogenetic tree from a set of DNA sequences, typically a multiple alignment is first used to obtain homologous\\u000a bases. The inferred phylogeny can be very sensitive to how the alignment was created. We develop tools for analyzing the robustness\\u000a of phylogeny to perturbations in alignment parameters in the NW algorithm. Our main tool is parametric alignment, with

Anna-Sapfo Malaspinas; Nicholas Eriksson; Peter Huggins

2011-01-01

269

Sterols of the phylum Zygomycota: Phylogenetic implications  

Microsoft Academic Search

The sterol composition of 42 fungal species representing six of the eight orders of the Zygomycota was determined using gas-liquid\\u000a chromatography-mass spectrometry to assess whether the distribution of major sterols in this phylum has taxonomic or phylogenetic\\u000a relevance. Ergosterol, 22-dihydroergosterol, 24-methyl cholesterol, cholesterol, and desmosterol were detected as the major\\u000a sterols among the species studied. Ergosterol was the major sterol

J. D. Weete; S. R. Gandhi

1997-01-01

270

A phylogenetic analysis of Aquifex pyrophilus  

NASA Technical Reports Server (NTRS)

The 16S rRNA of the bacterion Aquifex pyrophilus, a microaerophilic, oxygen-reducing hyperthermophile, has been sequenced directly from the the PCR amplified gene. Phylogenetic analyses show the Aq. pyrophilus lineage to be probably the deepest (earliest) in the (eu)bacterial tree. The addition of this deep branching to the bacterial tree further supports the argument that the Bacteria are of thermophilic ancestry.

Burggraf, S.; Olsen, G. J.; Stetter, K. O.; Woese, C. R.

1992-01-01

271

Phylogenetic Network for European mtDNA  

Microsoft Academic Search

The sequence in the first hypervariable segment (HVS-I) of the control region has been used as a source of evo- lutionary information in most phylogenetic analyses of mtDNA. Population genetic inference would benefit from a better understanding of the variation in the mtDNA coding region, but, thus far, complete mtDNA sequences have been rare. We determined the nucleotide sequence in

Saara Finnilä; Mervi S. Lehtonen; Kari Majamaa

2001-01-01

272

Asteroid taxonomic classifications  

NASA Technical Reports Server (NTRS)

Asteroid taxonomic classification according to the schemes of Tholen (1984) and Baracci et al. (1987) are presented in a table. Inconsistent data are indicated. Special notions are given for unusual spectra, noisy and very noisy data, and data too noisy to permit classification.

Tholen, D. J.

1989-01-01

273

Contextual classification of cracks  

Microsoft Academic Search

We describe a technique for improving the classification of fragmented cues for cracks. Evidence propagation on Bayesian networks represent search within the context of each cue. The algorithm was applied to a data-set of cracks, and results demonstrate that con- textual classification of the cues leads to significantly improved error rates.

Noel Bryson; R. N. Dixon; J. Jeffrey Hunter; Christopher J. Taylor

1994-01-01

274

Scalable packet classification  

Microsoft Academic Search

Packet classification is important for applications such as firewalls, intrusion detection, and differentiated services. Existing algorithms for packet classification reported in the literature scale poorly in either time or space as filter databases grow in size. Hardware solutions such as TCAMs do not scale to large classifiers. However, even for large classifiers (say 100,000 rules), any packet is likely to

Florin Baboescu; George Varghese

2001-01-01

275

A classification of \\  

Microsoft Academic Search

This paper focuses on protein sequences family classification from Gracilaria changii seaweed species using back-propagation classifier. Classification of protein sequence family is to infer the function of an unknown protein by analysing its structural similarity to a given family of proteins. The use of sequence alignment technique to classify the protein sequence is less efficient because the entire sequence is

Nur Shazila Mohamed; Zulaiha Ali Othman; Azuraliza Abu Bakar

2009-01-01

276

Tradeoffs for Packet Classification  

Microsoft Academic Search

We present an algorithmic framework for solving the packet classification problem that allows various access time vs. memory tradeoffs. It reduces the multi-dimensional packet classification problem to solving a few instances of the one-dimensional IP lookup problem. It gives the best known lookup performance with moderately large memory space. Further- more, it efficiently supports a reasonable number of additions and

Anja Feldmann; S. Muthukrishnan

2000-01-01

277

Periscope video ship classification  

Microsoft Academic Search

Automatic classification of surface ships by means of imaging sensors through the submarine's periscope is of interest to the naval underwater warfare center of the US Navy. In this paper we discuss a testbed designed for periscope video ship classification based on model-based automatic target recognition paradigm, will present the performance results for the application of some of the existing

Firooz A. Sadjadi; Jack Osullivan

1996-01-01

278

Classification of agroforestry systems  

Microsoft Academic Search

Classification of agroforestry (AF) systems is necessary in order to provide a framework for evaluating systems and developing action plans for their improvement. The AF Systems Inventory (AFSI) being undertaken by ICRAF provides the background information for an approach to classification.

P. K. R. Nair

1985-01-01

279

Classification: Theory and Practice.  

ERIC Educational Resources Information Center

In response to recent trends towards automated bibliographic control, this issue of "Drexel Library Quarterly" discusses present day bibliographic classification schemes and offers some insight into the future. This volume contains essays which: (1) define "classification"; (2) provide historical background; (3) examine the Dewey Decimal System,…

Painter, Ann F., Ed.

1974-01-01

280

Engineering rock mass classifications  

Microsoft Academic Search

This book is a reference on rock mass classification, consolidating into one handy source information widely scattered through the literature. Includes new, unpublished material and case histories. Presents the fundamental concepts of classification schemes and critically appraises their practical application in industrial projects such as tunneling and mining.

Z. T. Bieniawski

1989-01-01

281

Phylogenetic reassessment of Hyaloscyphaceae sensu lato (Helotiales, Leotiomycetes) based on multigene analyses.  

PubMed

Hyaloscyphaceae is the largest family in Helotiales, Leotiomycetes. It is mainly characterized by minute apothecia with well-differentiated hairs, but its taxonomic delimitation and infrafamilial classification remain ambiguous. This study performed molecular phylogenetic analyses using multiple genes including the ITS-5.8S rDNA, the D1-D2 region of large subunit of rDNA, RNA polymerase II subunit 2, and the mitochondrial small subunit. The primary objective was to evaluate the phylogenetic utility of morphological characters traditionally used in the taxonomy of Hyaloscyphaceae through reassessment of the monophyly of this family and its genera. The phylogenetic analyses inferred Hyaloscyphaceae as being a heterogeneous assemblage of a diverse group of fungi and not supported as monophyletic. Among the three tribes of Hyaloscyphaceae only Lachneae formed a monophyletic lineage. The presence of hairs is rejected as a synapomorphy, since morphologically diversified hairs have originated independently during the evolution of Helotiales. The true- and false-subiculum in Arachnopezizeae are hypothesized to have evolved through different evolutionary processes; the true-subiculum is likely the product of a single evolutionary origin, while the false-subiculum is hypothesized to have originated multiple times. Since Hyaloscyphaceae sensu lato was not resolved as monophyletic, Hyaloscyphaceae sensu stricto is redefined and only applied to the genus Hyaloscypha. PMID:24528638

Han, Jae-Gu; Hosoya, Tsuyoshi; Sung, Gi-Ho; Shin, Hyeon-Dong

2014-02-01

282

mtDNA Diversity and Phylogenetic State of Korean Cattle Breed, Chikso  

PubMed Central

In order to analyze the genetic diversity and phylogenetic status of the Korean Chikso breed, we determined sequences of mtDNA cytochrome b (cyt b) gene and performed phylogenetic analysis using 239 individuals from 5 Chikso populations. Five non-synonymous mutations of a total of 15 polymorphic sites were identified among 239 cyt b coding sequences. Thirteen haplotypes were defined, and haplotype diversity was 0.4709 ranging from 0.2577 to 0.6114. Thirty-five haplotypes (C1–C35) were classified among 9 Asia and 3 European breeds. C2 was a major haplotype that contained 206 sequences (64.6%) from all breeds used. C3–C13 haplotypes were Chikso-specific haplotypes. C1 and C2 haplotypes contained 80.5% of cyt b sequences of Hanwoo, Yanbian, Zaosheng and JB breeds. In phylogenetic analyses, the Chikso breed was contained into B. taurus lineage and was genetically more closely related to two Chinese breeds than to Korean brown cattle, Hanwoo. These results suggest that Chikso and Hanwoo have a genetic difference based on the mtDNA cyt b gene as well as their coat color, sufficient for classification as a separate breed.

Kim, Jae-Hwan; Byun, Mi Jeong; Kim, Myung-Jick; Suh, Sang Won; Ko, Yeoung-Gyu; Lee, Chang Woo; Jung, Kyoung-Sub; Kim, Eun Sung; Yu, Dae Jung; Kim, Woo Hyun; Choi, Seong-Bok

2013-01-01

283

Two New Rapid SNP-Typing Methods for Classifying Mycobacterium tuberculosis Complex into the Main Phylogenetic Lineages  

PubMed Central

There is increasing evidence that strain variation in Mycobacterium tuberculosis complex (MTBC) might influence the outcome of tuberculosis infection and disease. To assess genotype-phenotype associations, phylogenetically robust molecular markers and appropriate genotyping tools are required. Most current genotyping methods for MTBC are based on mobile or repetitive DNA elements. Because these elements are prone to convergent evolution, the corresponding genotyping techniques are suboptimal for phylogenetic studies and strain classification. By contrast, single nucleotide polymorphisms (SNP) are ideal markers for classifying MTBC into phylogenetic lineages, as they exhibit very low degrees of homoplasy. In this study, we developed two complementary SNP-based genotyping methods to classify strains into the six main human-associated lineages of MTBC, the “Beijing” sublineage, and the clade comprising Mycobacterium bovis and Mycobacterium caprae. Phylogenetically informative SNPs were obtained from 22 MTBC whole-genome sequences. The first assay, referred to as MOL-PCR, is a ligation-dependent PCR with signal detection by fluorescent microspheres and a Luminex flow cytometer, which simultaneously interrogates eight SNPs. The second assay is based on six individual TaqMan real-time PCR assays for singleplex SNP-typing. We compared MOL-PCR and TaqMan results in two panels of clinical MTBC isolates. Both methods agreed fully when assigning 36 well-characterized strains into the main phylogenetic lineages. The sensitivity in allele-calling was 98.6% and 98.8% for MOL-PCR and TaqMan, respectively. Typing of an additional panel of 78 unknown clinical isolates revealed 99.2% and 100% sensitivity in allele-calling, respectively, and 100% agreement in lineage assignment between both methods. While MOL-PCR and TaqMan are both highly sensitive and specific, MOL-PCR is ideal for classification of isolates with no previous information, whereas TaqMan is faster for confirmation. Furthermore, both methods are rapid, flexible and comparably inexpensive.

Stucki, David; Malla, Bijaya; Hostettler, Simon; Huna, Thembela; Feldmann, Julia; Yeboah-Manu, Dorothy; Borrell, Sonia; Fenner, Lukas; Comas, Inaki; Coscolla, Mireia; Gagneux, Sebastien

2012-01-01

284

Consequences of recombination on traditional phylogenetic analysis.  

PubMed Central

We investigate the shape of a phylogenetic tree reconstructed from sequences evolving under the coalescent with recombination. The motivation is that evolutionary inferences are often made from phylogenetic trees reconstructed from population data even though recombination may well occur (mtDNA or viral sequences) or does occur (nuclear sequences). We investigate the size and direction of biases when a single tree is reconstructed ignoring recombination. Standard software (PHYLIP) was used to construct the best phylogenetic tree from sequences simulated under the coalescent with recombination. With recombination present, the length of terminal branches and the total branch length are larger, and the time to the most recent common ancestor smaller, than for a tree reconstructed from sequences evolving with no recombination. The effects are pronounced even for small levels of recombination that may not be immediately detectable in a data set. The phylogenies when recombination is present superficially resemble phylogenies for sequences from an exponentially growing population. However, exponential growth has a different effect on statistics such as Tajima's D. Furthermore, ignoring recombination leads to a large overestimation of the substitution rate heterogeneity and the loss of the molecular clock. These results are discussed in relation to viral and mtDNA data sets.

Schierup, M H; Hein, J

2000-01-01

285

PAML 4: phylogenetic analysis by maximum likelihood.  

PubMed

PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html). PMID:17483113

Yang, Ziheng

2007-08-01

286

A Consistent Phylogenetic Backbone for the Fungi  

PubMed Central

The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data—a common practice in phylogenomic analyses—introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses.

Ebersberger, Ingo; de Matos Simoes, Ricardo; Kupczok, Anne; Gube, Matthias; Kothe, Erika; Voigt, Kerstin; von Haeseler, Arndt

2012-01-01

287

Marine turtle mitogenome phylogenetics and evolution.  

PubMed

The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phylogeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1 Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution. PMID:22750111

Duchene, Sebastián; Frey, Amy; Alfaro-Núñez, Alonzo; Dutton, Peter H; Thomas P Gilbert, M; Morin, Phillip A

2012-10-01

288

Phylogenetic inferences reveal a large extent of novel biodiversity in chemically rich tropical marine cyanobacteria.  

PubMed

Benthic marine cyanobacteria are known for their prolific biosynthetic capacities to produce structurally diverse secondary metabolites with biomedical application and their ability to form cyanobacterial harmful algal blooms. In an effort to provide taxonomic clarity to better guide future natural product drug discovery investigations and harmful algal bloom monitoring, this study investigated the taxonomy of tropical and subtropical natural product-producing marine cyanobacteria on the basis of their evolutionary relatedness. Our phylogenetic inferences of marine cyanobacterial strains responsible for over 100 bioactive secondary metabolites revealed an uneven taxonomic distribution, with a few groups being responsible for the vast majority of these molecules. Our data also suggest a high degree of novel biodiversity among natural product-producing strains that was previously overlooked by traditional morphology-based taxonomic approaches. This unrecognized biodiversity is primarily due to a lack of proper classification systems since the taxonomy of tropical and subtropical, benthic marine cyanobacteria has only recently been analyzed by phylogenetic methods. This evolutionary study provides a framework for a more robust classification system to better understand the taxonomy of tropical and subtropical marine cyanobacteria and the distribution of natural products in marine cyanobacteria. PMID:23315747

Engene, Niclas; Gunasekera, Sarath P; Gerwick, William H; Paul, Valerie J

2013-03-01

289

Identifying early events of gene expression in breast cancer with systems biology phylogenetics.  

PubMed

Advanced omics technologies such as deep sequencing and spectral karyotyping are revealing more of cancer heterogeneity at the genetic, genomic, gene expression, epigenetic, proteomic, and metabolomic levels. With this increasing body of emerging data, the task of data analysis becomes critical for mining and modeling to better understand the relevant underlying biological processes. However, the multiple levels of heterogeneity evident within and among populations, healthy and diseased, complicate the mining and interpretation of biological data, especially when dealing with hundreds to tens of thousands of variables. Heterogeneity occurs in many diseases, such as cancers, autism, macular degeneration, and others. In cancer, heterogeneity has hampered the search for validated biomarkers for early detection, and it has complicated the task of finding clonal (driver) and nonclonal (nonexpanded or passenger) aberrations. We show that subtyping of cancer (classification of specimens) should be an a priori step to the identification of early events of cancers. Studying early events in oncogenesis can be done on histologically normal tissues from diseased individuals (HNTDI), since they most likely have been exposed to the same mutagenic insults that caused the cancer in their neighboring tissues. Polarity assessment of HNTDI data variables by using healthy specimens as outgroup(s), followed by the application of parsimony phylogenetic analysis, produces a hierarchical classification of specimens that reveals the early events of the disease ontogeny within its subtypes as shared derived changes (abnormal changes) or synapomorphies in phylogenetic terminology. PMID:23548567

Abu-Asab, M S; Abu-Asab, N; Loffredo, C A; Clarke, R; Amri, H

2013-01-01

290

The bacterial species dilemma and the genomic-phylogenetic species concept  

PubMed Central

The number of species of Bacteria and Archaea (ca 5000) is surprisingly small considering their early evolution, genetic diversity and residence in all ecosystems. The bacterial species definition accounts in part for the small number of named species. The primary procedures required to identify new species of Bacteria and Archaea are DNA–DNA hybridization and phenotypic characterization. Recently, 16S rRNA gene sequencing and phylogenetic analysis have been applied to bacterial taxonomy. Although 16S phylogeny is arguably excellent for classification of Bacteria and Archaea from the Domain level down to the family or genus, it lacks resolution below that level. Newer approaches, including multilocus sequence analysis, and genome sequence and microarray analyses, promise to provide necessary information to better understand bacterial speciation. Indeed, recent data using these approaches, while meagre, support the view that speciation processes may occur at the subspecies level within ecological niches (ecovars) and owing to biogeography (geovars). A major dilemma for bacterial taxonomists is how to incorporate this new information into the present hierarchical system for classification of Bacteria and Archaea without causing undesirable confusion and contention. This author proposes the genomic–phylogenetic species concept (GPSC) for the taxonomy of prokaryotes. The aim is twofold. First, the GPSC would provide a conceptual and testable framework for bacterial taxonomy. Second, the GPSC would replace the burdensome requirement for DNA hybridization presently needed to describe new species. Furthermore, the GPSC is consistent with the present treatment at higher taxonomic levels.

Staley, James T

2006-01-01

291

Molecular phylogenetic analysis of mudflat snails (Gastropoda: Euthyneura: Amphiboloidea) supports an Australasian centre of origin.  

PubMed

Amphiboloidea is a small but widespread group of snails found exclusively, and often abundantly, in mudflat and associated salt marsh or mangrove habitat. This study uses molecular data from three loci (COI, 16S and 28S) to infer phylogenetic relationships in Amphiboloidea and examine its position in Euthyneura. All but two of the named extant species of Amphiboloidea and additional undescribed taxa from across Southeast Asia and the Arabian Gulf were sampled. In contrast to the current morphology-based classification dividing Amphiboloidea into three families, analysis of molecular data supports revision of the classification to comprise two families. Maningrididae is a monotypic family basal to Amphibolidae, which is revised to comprise three subfamilies: Amphibolinae, Phallomedusinae and Salinatorinae. Sequence divergence between Asian populations of Naranjia is relatively large and possibly indicative of species complexes divergent across the Strait of Malacca. Salinatorrosacea and Salinator burmana do not cluster with other Salinator species, and require generic reassignment. In addition, sequences were obtained from an undescribed species of Lactiforis from the Malay Peninsula. Reconstruction of ancestral distributions indicates a plesiomorphic distribution and centre of origin in Australasia, with two genera subsequently diversifying throughout Asia. Increasing the sampling density of amphiboloid taxa in a phylogenetic analysis of Euthyneura did not resolve the identity of the sister taxon to Amphibolidae, but confirmed its inclusion in Pulmonata/Panpulmonata. PMID:22210412

Golding, Rosemary E

2012-04-01

292

CTEP Simplified Disease Classification Overview  

Cancer.gov

CTEP Simplified Disease Classification Overview The CTEP Simplified Disease Classification (CTEP SDC) v1.0 is a restructured, more intuitive classification of diseases, designed to meet the needs of CTEP while still allowing reporting based on the

293

Intraregional classification of wine via ICP-MS elemental fingerprinting.  

PubMed

The feasibility of elemental fingerprinting in the classification of wines according to their provenance vineyard soil was investigated in the relatively small geographical area of a single wine district. Results for the Stellenbosch wine district (Western Cape Wine Region, South Africa), comprising an area of less than 1000km(2), suggest that classification of wines from different estates (120 wines from 23 estates) is indeed possible using accurate elemental data and multivariate statistical analysis based on a combination of principal component analysis, cluster analysis, and discriminant analysis. This is the first study to demonstrate the successful classification of wines at estate level in a single wine district in South Africa. The elements B, Ba, Cs, Cu, Mg, Rb, Sr, Tl and Zn were identified as suitable indicators. White and red wines were grouped in separate data sets to allow successful classification of wines. Correlation between wine classification and soil type distributions in the area was observed. PMID:24996361

Coetzee, P P; van Jaarsveld, F P; Vanhaecke, F

2014-12-01

294

Transcriptomic Biomarkers for the Accurate Diagnosis of Myocarditis  

PubMed Central

Background Lymphocytic myocarditis is a clinically important condition that is difficult to diagnose and distinguish. We hypothesized that the transcriptome obtained from an endomyocardial biopsy (EMB) would yield clinically relevant and accurate molecular signatures. Methods and results Microarray analysis was performed on samples from patients with histologically proven lymphocytic myocarditis (n=16) and idiopathic dilated cardiomyopathy (IDCM, n=32) to develop accurate diagnostic transcriptome-based biomarkers (TBB) using multiple classification algorithms. We identified 9,878 genes differentially expressed in lymphocytic myocarditis vs. IDCM (FC>1.2, FDR<5%), from which a TBB containing 62 genes was identified, which distinguished myocarditis with 100% sensitivity (95% CI: 46-100%) and 100% specificity (95% CI: 66-100%) and which was generalizable to a broad range of secondary cardiomyopathies associated with inflammation (n=27), ischemic cardiomyopathy (n=8) and the normal heart (n=11). Multiple classification algorithms and quantitative realtime RT-PCR analysis further reduced this subset to a highly robust molecular signature of 13 genes, which still performed with 100% accuracy. Conclusions Together these findings demonstrate that transcriptomic biomarkers from a single EMB can improve the clinical detection of patients with inflammatory diseases of the heart. This approach advances the clinical management and treatment of cardiac disorders with highly variable outcome.

Heidecker, Bettina; Kittleson, Michelle M.; Kasper, Edward K.; Wittstein, Ilan S.; Champion, Hunter C.; Russell, Stuart D.; Hruban, Ralph H.; Rodriguez, E. Rene; Baughman, Kenneth L.; Hare, Joshua M.

2012-01-01

295

Structured sparse models for classification  

NASA Astrophysics Data System (ADS)

The main focus of this thesis is the modeling and classification of high dimensional data using structured sparsity. Sparse models, where data is assumed to be well represented as a linear combination of a few elements from a dictionary, have gained considerable attention in recent years, and its use has led to state-of-the-art results in many signal and image processing tasks. The success of sparse modeling is highly due to its ability to efficiently use the redundancy of the data and find its underlying structure. On a classification setting, we capitalize on this advantage to properly model and separate the structure of the classes. We design and validate modeling solutions to challenging problems arising in computer vision and remote sensing. We propose both supervised and unsupervised schemes for the modeling of human actions from motion imagery under a wide variety of acquisition condi- tions. In the supervised case, the main goal is to classify the human actions in the video given a predefined set of actions to learn from. In the unsupervised case, the main goal is to an- alyze the spatio-temporal dynamics of the individuals in the scene without having any prior information on the actions themselves. We also propose a model for remotely sensed hysper- spectral imagery, where the main goal is to perform automatic spectral source separation and mapping at the subpixel level. Finally, we present a sparse model for sensor fusion to exploit the common structure and enforce collaboration of hyperspectral with LiDAR data for better mapping capabilities. In all these scenarios, we demonstrate that these data can be expressed as a combination of atoms from a class-structured dictionary. These data representation becomes essentially a "mixture of classes," and by directly exploiting the sparse codes, one can attain highly accurate classification performance with relatively unsophisticated classifiers.

Castrodad, Alexey

296

Target classification algorithm based on feature aided tracking  

NASA Astrophysics Data System (ADS)

An effective target classification algorithm based on feature aided tracking (FAT) is proposed, using the length of target (target extent) as the classification information. To implement the algorithm, the Rao-Blackwellised unscented Kalman filter (RBUKF) is used to jointly estimate the kinematic state and target extent; meanwhile the joint probability data association (JPDA) algorithm is exploited to implement multi-target data association aided by target down-range extent. Simulation results under different condition show the presented algorithm is both accurate and robust, and it is suitable for the application of near spaced targets tracking and classification under the environment of dense clutters.

Zhan, Ronghui; Zhang, Jun

2013-03-01

297

Accurate models for EUV lithography  

NASA Astrophysics Data System (ADS)

Accurate modeling of EUV Lithography is a mandatory step in driving the technology towards its foreseen insertion point for 22-16nm node patterning. The models are needed to correct EUV designs for imaging effects, and to understand and improve the CD fingerprint of the exposure tools. With a full-field EUV ADT from ASML now available in the IMEC cleanroom, wafer data can be collected to calibrate accurate models and check if the existing modeling infrastructure can be extended to EUV lithography. As a first topic, we have measured the CD on wafer of a typical OPC dataset at different flare levels and modeled the evolution of wafer CD through flare, reticle CD, and pitch using Brion's Tachyon OPC engine. The modeling first requires the generation of a flare map using long-range kernels to model the EUV specific long-range flare. The accuracy of the flare map can be established independently from the CD measurements, by using the traditional disappearing pad test for flare determination (Kirk test). The flare map is then used as background intensity in the calibration of the traditional optical models with short-range kernels. For a structure set of 600 features and over a flare range of 4-6%, an rms fit value of 0.9nm was obtained. As a second aspect of the modeling, we have calibrated a full resist model to process window data. The full resist model is then used in a combination with experimental measurements of reticle CD, slit intensity uniformity, focal plane behavior, and EUV thick mask effects to model the evolution of wafer CD across the exposure field. The modeled evolution of CD across the exposure field was found to be a good match to the experimentally seen evolution of CD across the field, and confirms that the 4 factors mentioned above are main contributions to the CD uniformity across the field. As such the modeling work enables a better understanding of the errors contributing to CD variation across the field for EUV technology.

Hendrickx, Eric; Lorusso, Gian F.; Jiang, Jiong; Chen, Luoqi; Liu, Wei; van Setten, Eelco; Hansen, Steve

2009-10-01

298

Hyperspectral Data Classification Using Factor Graphs  

NASA Astrophysics Data System (ADS)

Accurate classification of hyperspectral data is still a competitive task and new classification methods are developed to achieve desired tasks of hyperspectral data use. The objective of this paper is to develop a new method for hyperspectral data classification ensuring the classification model properties like transferability, generalization, probabilistic interpretation, etc. While factor graphs (undirected graphical models) are unfortunately not widely employed in remote sensing tasks, these models possess important properties such as representation of complex systems to model estimation/decision making tasks. In this paper we present a new method for hyperspectral data classification using factor graphs. Factor graph (a bipartite graph consisting of variables and factor vertices) allows factorization of a more complex function leading to definition of variables (employed to store input data), latent variables (allow to bridge abstract class to data), and factors (defining prior probabilities for spectral features and abstract classes; input data mapping to spectral features mixture and further bridging of the mixture to an abstract class). Latent variables play an important role by defining two-level mapping of the input spectral features to a class. Configuration (learning) on training data of the model allows calculating a parameter set for the model to bridge the input data to a class. The classification algorithm is as follows. Spectral bands are separately pre-processed (unsupervised clustering is used) to be defined on a finite domain (alphabet) leading to a representation of the data on multinomial distribution. The represented hyperspectral data is used as input evidence (evidence vector is selected pixelwise) in a configured factor graph and an inference is run resulting in the posterior probability. Variational inference (Mean field) allows to obtain plausible results with a low calculation time. Calculating the posterior probability for each class and comparison of the probabilities leads to classification. Since the factor graphs operate on input data represented on an alphabet (the represented data transferred into multinomial distribution) the number of training samples can be relatively low. Classification assessment on Salinas hyperspectral data benchmark allowed to obtain a competitive accuracy of classification. Employment of training data consisting of 20 randomly selected points for a class allowed to obtain the overall classification accuracy equal to 85.32% and Kappa equal to 0.8358. Representation of input data on a finite domain discards the curse of dimensionality problem allowing to use large hyperspectral data with a moderately high number of bands.

Makarau, A.; Müller, R.; Palubinskas, G.; Reinartz, P.

2012-07-01

299

Biomarker Selection and Classification of "-Omics" Data Using a Two-Step Bayes Classification Framework  

PubMed Central

Identification of suitable biomarkers for accurate prediction of phenotypic outcomes is a goal for personalized medicine. However, current machine learning approaches are either too complex or perform poorly. Here, a novel two-step machine-learning framework is presented to address this need. First, a Naïve Bayes estimator is used to rank features from which the top-ranked will most likely contain the most informative features for prediction of the underlying biological classes. The top-ranked features are then used in a Hidden Naïve Bayes classifier to construct a classification prediction model from these filtered attributes. In order to obtain the minimum set of the most informative biomarkers, the bottom-ranked features are successively removed from the Naïve Bayes-filtered feature list one at a time, and the classification accuracy of the Hidden Naïve Bayes classifier is checked for each pruned feature set. The performance of the proposed two-step Bayes classification framework was tested on different types of -omics datasets including gene expression microarray, single nucleotide polymorphism microarray (SNParray), and surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) proteomic data. The proposed two-step Bayes classification framework was equal to and, in some cases, outperformed other classification methods in terms of prediction accuracy, minimum number of classification markers, and computational time.

Assawamakin, Anunchai; Prueksaaroon, Supakit; Kulawonganunchai, Supasak; Shaw, Philip James; Varavithya, Vara; Ruangrajitpakorn, Taneth; Tongsima, Sissades

2013-01-01

300

Automated Protein Subfamily Identification and Classification  

PubMed Central

Function prediction by homology is widely used to provide preliminary functional annotations for genes for which experimental evidence of function is unavailable or limited. This approach has been shown to be prone to systematic error, including percolation of annotation errors through sequence databases. Phylogenomic analysis avoids these errors in function prediction but has been difficult to automate for high-throughput application. To address this limitation, we present a computationally efficient pipeline for phylogenomic classification of proteins. This pipeline uses the SCI-PHY (Subfamily Classification in Phylogenomics) algorithm for automatic subfamily identification, followed by subfamily hidden Markov model (HMM) construction. A simple and computationally efficient scoring scheme using family and subfamily HMMs enables classification of novel sequences to protein families and subfamilies. Sequences representing entirely novel subfamilies are differentiated from those that can be classified to subfamilies in the input training set using logistic regression. Subfamily HMM parameters are estimated using an information-sharing protocol, enabling subfamilies containing even a single sequence to benefit from conservation patterns defining the family as a whole or in related subfamilies. SCI-PHY subfamilies correspond closely to functional subtypes defined by experts and to conserved clades found by phylogenetic analysis. Extensive comparisons of subfamily and family HMM performances show that subfamily HMMs dramatically improve the separation between homologous and non-homologous proteins in sequence database searches. Subfamily HMMs also provide extremely high specificity of classification and can be used to predict entirely novel subtypes. The SCI-PHY Web server at http://phylogenomics.berkeley.edu/SCI-PHY/ allows users to upload a multiple sequence alignment for subfamily identification and subfamily HMM construction. Biologists wishing to provide their own subfamily definitions can do so. Source code is available on the Web page. The Berkeley Phylogenomics Group PhyloFacts resource contains pre-calculated subfamily predictions and subfamily HMMs for more than 40,000 protein families and domains at http://phylogenomics.berkeley.edu/phylofacts/.

Brown, Duncan P; Krishnamurthy, Nandini; Sjolander, Kimmen

2007-01-01

301

An Alignment-Free Approach for Eukaryotic ITS2 Annotation and Phylogenetic Inference  

PubMed Central

The ITS2 gene class shows a high sequence divergence among its members that have complicated its annotation and its use for reconstructing phylogenies at a higher taxonomical level (beyond species and genus). Several alignment strategies have been implemented to improve the ITS2 annotation quality and its use for phylogenetic inferences. Although, alignment based methods have been exploited to the top of its complexity to tackle both issues, no alignment-free approaches have been able to successfully address both topics. By contrast, the use of simple alignment-free classifiers, like the topological indices (TIs) containing information about the sequence and structure of ITS2, may reveal to be a useful approach for the gene prediction and for assessing the phylogenetic relationships of the ITS2 class in eukaryotes. Thus, we used the TI2BioP (Topological Indices to BioPolymers) methodology [1], [2], freely available at http://ti2biop.sourceforge.net/ to calculate two different TIs. One class was derived from the ITS2 artificial 2D structures generated from DNA strings and the other from the secondary structure inferred from RNA folding algorithms. Two alignment-free models based on Artificial Neural Networks were developed for the ITS2 class prediction using the two classes of TIs referred above. Both models showed similar performances on the training and the test sets reaching values above 95% in the overall classification. Due to the importance of the ITS2 region for fungi identification, a novel ITS2 genomic sequence was isolated from Petrakia sp. This sequence and the test set were used to comparatively evaluate the conventional classification models based on multiple sequence alignments like Hidden Markov based approaches, revealing the success of our models to identify novel ITS2 members. The isolated sequence was assessed using traditional and alignment-free based techniques applied to phylogenetic inference to complement the taxonomy of the Petrakia sp. fungal isolate.

Hidalgo-Yanes, Pedro I.; Perez-Castillo, Yunierkis; Molina-Ruiz, Reinaldo; Marchal, Kathleen; Vasconcelos, Vitor; Antunes, Agostinho

2011-01-01

302

Accurate ab Initio Spin Densities  

PubMed Central

We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of ? and ? electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740].

2012-01-01

303

Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships  

PubMed Central

Background Camellia is an economically and phylogenetically important genus in the family Theaceae. Owing to numerous hybridization and polyploidization, it is taxonomically and phylogenetically ranked as one of the most challengingly difficult taxa in plants. Sequence comparisons of chloroplast (cp) genomes are of great interest to provide a robust evidence for taxonomic studies, species identification and understanding mechanisms that underlie the evolution of the Camellia species. Results The eight complete cp genomes and five draft cp genome sequences of Camellia species were determined using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. The Camellia cp genomes exhibited typical circular structure that was rather conserved in genomic structure and the synteny of gene order. Differences of repeat sequences, simple sequence repeats, indels and substitutions were further examined among five complete cp genomes, representing a wide phylogenetic diversity in the genus. A total of fifteen molecular markers were identified with more than 1.5% sequence divergence that may be useful for further phylogenetic analysis and species identification of Camellia. Our results showed that, rather than functional constrains, it is the regional constraints that strongly affect sequence evolution of the cp genomes. In a substantial improvement over prior studies, evolutionary relationships of the section Thea were determined on basis of phylogenomic analyses of cp genome sequences. Conclusions Despite a high degree of conservation between the Camellia cp genomes, sequence variation among species could still be detected, representing a wide phylogenetic diversity in the genus. Furthermore, phylogenomic analysis was conducted using 18 complete cp genomes and 5 draft cp genome sequences of Camellia species. Our results support Chang’s taxonomical treatment that C. pubicosta may be classified into sect. Thea, and indicate that taxonomical value of the number of ovaries should be reconsidered when classifying the Camellia species. The availability of these cp genomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the phylogeny of the genus Camellia.

2014-01-01

304

New insights into myosin evolution and classification.  

PubMed

Myosins are eukaryotic actin-dependent molecular motors important for a broad range of functions like muscle contraction, vision, hearing, cell motility, and host cell invasion of apicomplexan parasites. Myosin heavy chains consist of distinct head, neck, and tail domains and have previously been categorized into 18 different classes based on phylogenetic analysis of their conserved heads. Here we describe a comprehensive phylogenetic examination of many previously unclassified myosins, with particular emphasis on sequences from apicomplexan and other chromalveolate protists including the model organism Toxoplasma, the malaria parasite Plasmodium, and the ciliate Tetrahymena. Using different phylogenetic inference methods and taking protein domain architectures, specific amino acid polymorphisms, and organismal distribution into account, we demonstrate a hitherto unrecognized common origin for ciliate and apicomplexan class XIV myosins. Our data also suggest common origins for some apicomplexan myosins and class VI, for classes II and XVIII, for classes XII and XV, and for some microsporidian myosins and class V, thereby reconciling evolutionary history and myosin structure in several cases and corroborating the common coevolution of myosin head, neck, and tail domains. Six novel myosin classes are established to accommodate sequences from chordate metazoans (class XIX), insects (class XX), kinetoplastids (class XXI), and apicomplexans and diatom algae (classes XXII, XXIII, and XXIV). These myosin (sub)classes include sequences with protein domains (FYVE, WW, UBA, ATS1-like, and WD40) previously unknown to be associated with myosin motors. Regarding the apicomplexan "myosome," we significantly update class XIV classification, propose a systematic naming convention, and discuss possible functions in these parasites. PMID:16505385

Foth, Bernardo J; Goedecke, Marc C; Soldati, Dominique

2006-03-01

305

Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences.  

PubMed

Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed by using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used; however, all NJ trees still supported most of the same terminal groupings as the MP and ML trees did. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, by both parsimony and likelihood tests. Our analyses suggest that weighted MP and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife values or are consistent with morphology-based classification schemes. Analyses also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several groups revealed by these data to be nonmonophyletic include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets. PMID:12118409

Moncalvo, J M; Lutzoni, F M; Rehner, S A; Johnson, J; Vilgalys, R

2000-06-01

306

Phylogenetic relationships of Malaysia's long-tailed macaques, Macaca fascicularis, based on cytochrome b sequences  

PubMed Central

Abstract Phylogenetic relationships among Malaysia’s long-tailed macaques have yet to be established, despite abundant genetic studies of the species worldwide. The aims of this study are to examine the phylogenetic relationships of Macaca fascicularis in Malaysia and to test its classification as a morphological subspecies. A total of 25 genetic samples of M. fascicularis yielding 383 bp of Cytochrome b (Cyt b) sequences were used in phylogenetic analysis along with one sample each of M. nemestrina and M. arctoides used as outgroups. Sequence character analysis reveals that Cyt b locus is a highly conserved region with only 23% parsimony informative character detected among ingroups. Further analysis indicates a clear separation between populations originating from different regions; the Malay Peninsula versus Borneo Insular, the East Coast versus West Coast of the Malay Peninsula, and the island versus mainland Malay Peninsula populations. Phylogenetic trees (NJ, MP and Bayesian) portray a consistent clustering paradigm as Borneo’s population was distinguished from Peninsula’s population (99% and 100% bootstrap value in NJ and MP respectively and 1.00 posterior probability in Bayesian trees). The East coast population was separated from other Peninsula populations (64% in NJ, 66% in MP and 0.53 posterior probability in Bayesian). West coast populations were divided into 2 clades: the North-South (47%/54% in NJ, 26/26% in MP and 1.00/0.80 posterior probability in Bayesian) and Island-Mainland (93% in NJ, 90% in MP and 1.00 posterior probability in Bayesian). The results confirm the previous morphological assignment of 2 subspecies, M. f. fascicularis and M. f. argentimembris, in the Malay Peninsula. These populations should be treated as separate genetic entities in order to conserve the genetic diversity of Malaysia’s M. fascicularis. These findings are crucial in aiding the conservation management and translocation process of M. fascicularis populations in Malaysia.

Abdul-Latiff, Muhammad Abu Bakar; Ruslin, Farhani; Fui, Vun Vui; Abu, Mohd-Hashim; Rovie-Ryan, Jeffrine Japning; Abdul-Patah, Pazil; Lakim, Maklarin; Roos, Christian; Yaakop, Salmah; Md-Zain, Badrul Munir

2014-01-01

307

Phylogenetic relationships of Malaysia's long-tailed macaques, Macaca fascicularis, based on cytochrome b sequences.  

PubMed

Phylogenetic relationships among Malaysia's long-tailed macaques have yet to be established, despite abundant genetic studies of the species worldwide. The aims of this study are to examine the phylogenetic relationships of Macaca fascicularis in Malaysia and to test its classification as a morphological subspecies. A total of 25 genetic samples of M. fascicularis yielding 383 bp of Cytochrome b (Cyt b) sequences were used in phylogenetic analysis along with one sample each of M. nemestrina and M. arctoides used as outgroups. Sequence character analysis reveals that Cyt b locus is a highly conserved region with only 23% parsimony informative character detected among ingroups. Further analysis indicates a clear separation between populations originating from different regions; the Malay Peninsula versus Borneo Insular, the East Coast versus West Coast of the Malay Peninsula, and the island versus mainland Malay Peninsula populations. Phylogenetic trees (NJ, MP and Bayesian) portray a consistent clustering paradigm as Borneo's population was distinguished from Peninsula's population (99% and 100% bootstrap value in NJ and MP respectively and 1.00 posterior probability in Bayesian trees). The East coast population was separated from other Peninsula populations (64% in NJ, 66% in MP and 0.53 posterior probability in Bayesian). West coast populations were divided into 2 clades: the North-South (47%/54% in NJ, 26/26% in MP and 1.00/0.80 posterior probability in Bayesian) and Island-Mainland (93% in NJ, 90% in MP and 1.00 posterior probability in Bayesian). The results confirm the previous morphological assignment of 2 subspecies, M. f. fascicularis and M. f. argentimembris, in the Malay Peninsula. These populations should be treated as separate genetic entities in order to conserve the genetic diversity of Malaysia's M. fascicularis. These findings are crucial in aiding the conservation management and translocation process of M. fascicularis populations in Malaysia. PMID:24899832

Abdul-Latiff, Muhammad Abu Bakar; Ruslin, Farhani; Fui, Vun Vui; Abu, Mohd-Hashim; Rovie-Ryan, Jeffrine Japning; Abdul-Patah, Pazil; Lakim, Maklarin; Roos, Christian; Yaakop, Salmah; Md-Zain, Badrul Munir

2014-01-01

308

Phylogenetic relationships in Brassicaceae tribe Alysseae inferred from nuclear ribosomal and chloroplast DNA sequence data.  

PubMed

Numerous molecular systematic studies within Brassicaceae have resulted in a strongly improved classification of the family, as morphologically defined units at and above the generic level were often found to poorly reflect phylogenetic relationships. Here, we focus on tribe Alysseae, which despite its size (accounting for about 7% of all species) has only received limited coverage in previous phylogenetic studies. Specifically, we want to test phylogenetic hypotheses implied by current tribal and generic circumscriptions and to put diversification within tribe Alysseae into a temporal context. To this end, sequence data from the nrDNA ITS and two plastid regions (ndhF gene, trnL-F intergenic spacer) were obtained for 176 accessions, representing 16 out of 17 currently recognized genera of the tribe, and were phylogenetically analysed, among others, using a relaxed molecular clock. Due to large discrepancies with respect to published ages of Brassicaceae, age estimates concerning Alysseae are, however, burdened with considerable uncertainty. The tribe is monophyletic and contains four strongly supported major clades and Alyssum homalocarpum, whose relationships among each other remain uncertain due to incongruences between nuclear and plastid DNA markers. The largest genus of the tribe, Alyssum, is not monophyletic and contains, apart from A. homalocarpum, two distinct lineages, corresponding to sections Alyssum, Psilonema, Gamosepalum and to sections Odontarrhena and Meniocus, respectively. Clypeola, whose monophyly is supported only by the plastid data, is very closely related to and possibly nested within the second Alyssum lineage. Species of the genus Fibigia intermingle with those of Alyssoides, Clastopus, Degenia, and Physoptychis, rendering Fibigia polyphyletic. The monotypic genera Leptoplax and Physocardamum are embedded in Bornmuellera. PMID:23850498

Rešetnik, Ivana; Satovic, Zlatko; Schneeweiss, Gerald M; Liber, Zlatko

2013-12-01

309

Mineral Classification Exercise  

NSDL National Science Digital Library

This exercise is designed to help students think about the properties of minerals that are most useful for mineral classification and identification. Students are given a set of minerals and asked to come up with a hierarchical classification scheme (a "key") that can be used to identify different mineral species. They compare their results with the products of other groups. They test the various schemes by applying them to unknown samples. While doing this exercise, the students develop observational and interpretational skill. They also begin to think about the nature of classification systems.

Perkins, Dexter

310

Acoustic classification of zooplankton  

NASA Astrophysics Data System (ADS)

Work on the forward problem in zooplankton bioacoustics has resulted in the identification of three categories of acoustic scatterers: elastic-shelled (e.g. pteropods), fluid-like (e.g. euphausiids), and gas-bearing (e.g. siphonophores). The relationship between backscattered energy and animal biomass has been shown to vary by a factor of ~19,000 across these categories, so that to make accurate estimates of zooplankton biomass from acoustic backscatter measurements of the ocean, the acoustic characteristics of the species of interest must be well-understood. This thesis describes the development of both feature based and model based classification techniques to invert broadband acoustic echoes from individual zooplankton for scatterer type, as well as for particular parameters such as animal orientation. The feature based Empirical Orthogonal Function Classifier (EOFC) discriminates scatterer types by identifying characteristic modes of variability in the echo spectra, exploiting only the inherent characteristic structure of the acoustic signatures. The model based Model Parameterisation Classifier (MPC) classifies based on correlation of observed echo spectra with simplified parameterisations of theoretical scattering models for the three classes. The Covariance Mean Variance Classifiers (CMVC) are a set of advanced model based techniques which exploit the full complexity of the theoretical models by searching the entire physical model parameter space without employing simplifying parameterisations. Three different CMVC algorithms were developed: the Integrated Score Classifier (ISC), the Pairwise Score Classifier (PSC) and the Bayesian Probability Classifier (BPC); these classifiers assign observations to a class based on similarities in covariance, mean, and variance, while accounting for model ambiguity and validity. These feature based and model based inversion techniques were successfully applied to several thousand echoes acquired from broadband (~350 kHz-750 kHz) insonifications of live zooplankton collected on Georges Bank and the Gulf of Maine to determine scatterer class. CMVC techniques were also applied to echoes from fluid-like zooplankton (Antarctic krill) to invert for angle of orientation using generic and animal-specific theoretical and empirical models. Application of these inversion techniques in situ will allow correct apportionment of backscattered energy to animal biomass, significantly improving estimates of zooplankton biomass based on acoustic surveys. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)

Martin Traykovski, Linda V.

1998-11-01

311

Multiple sequence alignment: a major challenge to large-scale phylogenetics  

PubMed Central

Over the last decade, dramatic advances have been made in developing methods for large-scale phylogeny estimation, so that it is now feasible for investigators with moderate computational resources to obtain reasonable solutions to maximum likelihood and maximum parsimony, even for datasets with a few thousand sequences. There has also been progress on developing methods for multiple sequence alignment, so that greater alignment accuracy (and subsequent improvement in phylogenetic accuracy) is now possible through automated methods. However, these methods have not been tested under conditions that reflect properties of datasets confronted by large-scale phylogenetic estimation projects. In this paper we report on a study that compares several alignment methods on a benchmark collection of nucleotide sequence datasets of up to 78,132 sequences. We show that as the number of sequences increases, the number of alignment methods that can analyze the datasets decreases. Furthermore, the most accurate alignment methods are unable to analyze the very largest datasets we studied, so that only moderately accurate alignment methods can be used on the largest datasets. As a result, alignments computed for large datasets have relatively large error rates, and maximum likelihood phylogenies computed on these alignments also have high error rates. Therefore, the estimation of highly accurate multiple sequence alignments is a major challenge for Tree of Life projects, and more generally for large-scale systematics studies.

Liu, Kevin; Linder, C. Randal; Warnow, Tandy

2011-01-01

312

Constitutional Classifications and the \\  

Microsoft Academic Search

In this essay the author discusses the use of genetic information to classify individuals for purposes of the law, and more specifically, the impact of the so-called “gay gene” on legal classifications.

Susan J. Becker

2002-01-01

313

Classification of perinatal death.  

PubMed Central

Three paediatric pathologists, one perinatal paediatrician, one obstetrician, and one epidemiologist separately used information collected on 239 babies in an attempt to validate the Wigglesworth classification of perinatal deaths. This was first done using clinical data only, then using the combination of clinical and gross necropsy findings and finally using clinical, gross necropsy, histological and any other information (for example, chromosome analyses, microbiological investigations). Only 14 (6%) of deaths changed groups within the Wigglesworth classification when gross necropsy findings were considered as well as clinical findings, and altogether only 21 (9%) changed classification when complete investigations were available. There was an unacceptable amount (15%) of disagreement between the classifiers, largely the result of failure to comply with the rules laid down for classification. We set out amendments to Wigglesworth's original definitions to clarify certain ambiguities.

Keeling, J W; MacGillivray, I; Golding, J; Wigglesworth, J; Berry, J; Dunn, P M

1989-01-01

314

Classification: Theory and Practice.  

National Technical Information Service (NTIS)

In response to recent trends towards automated bibliographic control, this issue of 'Drexel Library Quarterly' discusses present day bibliographic classification schemes and offers some insight into the future. This volume contains essays which: (1) defin...

A. F. Painter

1974-01-01

315

A comparison of material classification techniques for ultrasound inverse imaging  

NASA Astrophysics Data System (ADS)

The conjugate gradient method with edge preserving regularization (CGEP) is applied to the ultrasound inverse scattering problem for the early detection of breast tumors. To accelerate image reconstruction, several different pattern classification schemes are introduced into the CGEP algorithm. These classification techniques are compared for a full-sized, two-dimensional breast model. One of these techniques uses two parameters, the sound speed and attenuation, simultaneously to perform classification based on a Bayesian classifier and is called bivariate material classification (BMC). The other two techniques, presented in earlier work, are univariate material classification (UMC) and neural network (NN) classification. BMC is an extension of UMC, the latter using attenuation alone to perform classification, and NN classification uses a neural network. Both noiseless and noisy cases are considered. For the noiseless case, numerical simulations show that the CGEP-BMC method requires 40% fewer iterations than the CGEP method, and the CGEP-NN method requires 55% fewer. The CGEP-BMC and CGEP-NN methods yield more accurate reconstructions than the CGEP method. A quantitative comparison of the CGEP-BMC, CGEP-NN, and GN-UMC methods shows that the CGEP-BMC and CGEP-NN methods are more robust to noise than the GN-UMC method, while all three are similar in computational complexity.

Zhang, Xiaodong; Broschat, Shira L.; Flynn, Patrick J.

2002-01-01

316

Ultrametric networks: a new tool for phylogenetic analysis  

PubMed Central

Background The large majority of optimization problems related to the inference of distance?based trees used in phylogenetic analysis and classification is known to be intractable. One noted exception is found within the realm of ultrametric distances. The introduction of ultrametric trees in phylogeny was inspired by a model of evolution driven by the postulate of a molecular clock, now dismissed, whereby phylogeny could be represented by a weighted tree in which the sum of the weights of the edges separating any given leaf from the root is the same for all leaves. Both, molecular clocks and rooted ultrametric trees, fell out of fashion as credible representations of evolutionary change. At the same time, ultrametric dendrograms have shown good potential for purposes of classification in so far as they have proven to provide good approximations for additive trees. Most of these approximations are still intractable, but the problem of finding the nearest ultrametric distance matrix to a given distance matrix with respect to the L? distance has been long known to be solvable in polynomial time, the solution being incarnated in any minimum spanning tree for the weighted graph subtending to the matrix. Results This paper expands this subdominant ultrametric perspective by studying ultrametric networks, consisting of the collection of all edges involved in some minimum spanning tree. It is shown that, for a graph with n vertices, the construction of such a network can be carried out by a simple algorithm in optimal time O(n2) which is faster by a factor of n than the direct adaptation of the classical O(n3) paradigm by Warshall for computing the transitive closure of a graph. This algorithm, called UltraNet, will be shown to be easily adapted to compute relaxed networks and to support the introduction of artificial points to reduce the maximum distance between vertices in a pair. Finally, a few experiments will be discussed to demonstrate the applicability of subdominant ultrametric networks. Availability http://www.dei.unipd.it/~ciompin/main/Ultranet/Ultranet.html

2013-01-01

317

Progressive Classification Using Support Vector Machines  

NASA Technical Reports Server (NTRS)

An algorithm for progressive classification of data, analogous to progressive rendering of images, makes it possible to compromise between speed and accuracy. This algorithm uses support vector machines (SVMs) to classify data. An SVM is a machine learning algorithm that builds a mathematical model of the desired classification concept by identifying the critical data points, called support vectors. Coarse approximations to the concept require only a few support vectors, while precise, highly accurate models require far more support vectors. Once the model has been constructed, the SVM can be applied to new observations. The cost of classifying a new observation is proportional to the number of support vectors in the model. When computational resources are limited, an SVM of the appropriate complexity can be produced. However, if the constraints are not known when the model is constructed, or if they can change over time, a method for adaptively responding to the current resource constraints is required. This capability is particularly relevant for spacecraft (or any other real-time systems) that perform onboard data analysis. The new algorithm enables the fast, interactive application of an SVM classifier to a new set of data. The classification process achieved by this algorithm is characterized as progressive because a coarse approximation to the true classification is generated rapidly and thereafter iteratively refined. The algorithm uses two SVMs: (1) a fast, approximate one and (2) slow, highly accurate one. New data are initially classified by the fast SVM, producing a baseline approximate classification. For each classified data point, the algorithm calculates a confidence index that indicates the likelihood that it was classified correctly in the first pass. Next, the data points are sorted by their confidence indices and progressively reclassified by the slower, more accurate SVM, starting with the items most likely to be incorrectly classified. The user can halt this reclassification process at any point, thereby obtaining the best possible result for a given amount of computation time. Alternatively, the results can be displayed as they are generated, providing the user with real-time feedback about the current accuracy of classification.

Wagstaff, Kiri; Kocurek, Michael

2009-01-01

318

INVENTORY AND CLASSIFICATION OF GREAT LAKES COASTAL WETLANDS FOR MONITORING AND ASSESSMENT AT LARGE SPATIAL SCALES  

EPA Science Inventory

Monitoring aquatic resources for regional assessments requires an accurate and comprehensive inventory of the resource and useful classification of exosystem similarities. Our research effort to create an electronic database and work with various ways to classify coastal wetlands...

319

Abduction in Classification Tasks  

Microsoft Academic Search

\\u000a The aim of this paper is to show how abduction can be used in classification tasks when we deal with incomplete data. Some\\u000a classifiers, even if based on decision tree induction like C4.5 1, produce as output a set of rules in order to classify new\\u000a given examples. Most of these rule-based classifiers make the assumption that at classification time

Maurizio Atzori; Paolo Mancarella; Franco Turini

2003-01-01

320

Periscope video ship classification  

NASA Astrophysics Data System (ADS)

Automatic classification of surface ships by means of imaging sensors through the submarine's periscope is of interest to the naval underwater warfare center of the US Navy. In this paper we discuss a testbed designed for periscope video ship classification based on model-based automatic target recognition paradigm, will present the performance results for the application of some of the existing algorithms and will present a sequential tree based technique for ship recognition.

Sadjadi, Firooz A.; OSullivan, Jack

1996-05-01

321

Nearest neighbor pattern classification  

Microsoft Academic Search

The nearest neighbor decision rule assigns to an unclassified sample point the classification of the nearest of a set of previously classified points. This rule is independent of the underlying joint distribution on the sample points and their classifications, and hence the probability of errorRof such a rule must be at least as great as the Bayes probability of errorR^{ast}--the

P. Hart

1967-01-01

322

Occupational Classification System Manual  

NSDL National Science Digital Library

Researchers may gain insight into the Bureau of Labor Statistics and Census Bureau occupational codes via the Occupational Classification System Manual (OCSM). A list of Major Occupation Group titles (MOGs) is provided as well as links to the Census Occupation Index--an alphabetical list of approximately 30,000 occupational titles. Further guidance in locating the proper occupation classification for research queries is outlined in the articles "Using the OCSM" and "Using the Census Index."

323

Rough classification and accuracy assessment  

Microsoft Academic Search

In search for methods to handle imprecision in geographical information this paper explores the use of rough classification to represent uncertainty. Rough classification is based on rough set theory, where an uncertain set is specified by giving an upper and a lower approximation. Novel measures are presented to assess a single rough classification, to compare a rough classification to a

Ola Ahlqvist; Johannes Keukelaar; Karim Oukbir

2000-01-01

324

Feature selection for collective classification  

Microsoft Academic Search

When in addition to node contents and labels, relations (links) between nodes and some unlabeled nodes are available, collective classification algorithms can be used. Collective classification algorithms, like ICA (iterative classification algorithm), determine labels for the unlabeled nodes based on the contents and\\/or labels of the neighboring nodes. Feature selection algorithms have been shown to improve classification accuracy for traditional

Baris Senliol; Atakan Aral; Zehra Cataltepe

2009-01-01

325

Phylogenetic relatedness and the determinants of competitive outcomes.  

PubMed

Recent hypotheses argue that phylogenetic relatedness should predict both the niche differences that stabilise coexistence and the average fitness differences that drive competitive dominance. These still largely untested predictions complicate Darwin's hypothesis that more closely related species less easily coexist, and challenge the use of community phylogenetic patterns to infer competition. We field parameterised models of competitor dynamics with pairs of 18 California annual plant species, and then related species' niche and fitness differences to their phylogenetic distance. Stabilising niche differences were unrelated to phylogenetic distance, while species' average fitness showed phylogenetic structure. This meant that more distant relatives had greater competitive asymmetry, which should favour the coexistence of close relatives. Nonetheless, coexistence proved unrelated to phylogeny, due in part to increasing variance in fitness differences with phylogenetic distance, a previously overlooked property of such relationships. Together, these findings question the expectation that distant relatives should more readily coexist. PMID:24766326

Godoy, Oscar; Kraft, Nathan J B; Levine, Jonathan M

2014-07-01

326

Classification of genomic signals using dynamic time warping  

PubMed Central

Background Classification methods of DNA most commonly use comparison of the differences in DNA symbolic records, which requires the global multiple sequence alignment. This solution is often inappropriate, causing a number of imprecisions and requires additional user intervention for exact alignment of the similar segments. The similar segments in DNA represented as a signal are characterized by a similar shape of the curve. The DNA alignment in genomic signals may adjust whole sections not only individual symbols. The dynamic time warping (DTW) is suitable for this purpose and can replace the multiple alignment of symbolic sequences in applications, such as phylogenetic analysis. Methods The proposed method is composed of three main parts. The first part represent conversion of symbolic representation of DNA sequences in the form of a string of A,C,G,T symbols to signal representation in the form of cumulated phase of complex components defined for each symbol. Next part represents signals size adjustment realized by standard signal preprocessing methods: median filtration, detrendization and resampling. The final part necessary for genomic signals comparison is position and length alignment of genomic signals by dynamic time warping (DTW). Results The application of the DTW on set of genomic signals was evaluated in dendrogram construction using cluster analysis. The resulting tree was compared with a classical phylogenetic tree reconstructed using multiple alignment. The classification of genomic signals using the DTW is evolutionary closer to phylogeny of organisms. This method is more resistant to errors in the sequences and less dependent on the number of input sequences. Conclusions Classification of genomic signals using dynamic time warping is an adequate variant to phylogenetic analysis using the symbolic DNA sequences alignment; in addition, it is robust, quick and more precise technique.

2013-01-01

327

What should an ideal spinal injury classification system consist of? A methodological review and conceptual proposal for future classifications  

PubMed Central

Since Böhler published the first categorization of spinal injuries based on plain radiographic examinations in 1929, numerous classifications have been proposed. Despite all these efforts, however, only a few have been tested for reliability and validity. This methodological, conceptual review summarizes that a spinal injury classification system should be clinically relevant, reliable and accurate. The clinical relevance of a classification is directly related to its content validity. The ideal content of a spinal injury classification should only include injury characteristics of the vertebral column, is primarily based on the increasingly routinely performed CT imaging, and is clearly distinctive from severity scales and treatment algorithms. Clearly defined observation and conversion criteria are crucial determinants of classification systems’ reliability and accuracy. Ideally, two principle spinal injury characteristics should be easy to discern on diagnostic images: the specific location and morphology of the injured spinal structure. Given the current evidence and diagnostic imaging technology, descriptions of the mechanisms of injury and ligamentous injury should not be included in a spinal injury classification. The presence of concomitant neurologic deficits can be integrated in a spinal injury severity scale, which in turn can be considered in a spinal injury treatment algorithm. Ideally, a validation pathway of a spinal injury classification system should be completed prior to its clinical and scientific implementation. This review provides a methodological concept which might be considered prior to the synthesis of new or modified spinal injury classifications.

Audige, Laurent; Hanson, Beate; Chapman, Jens R.; Hosman, Allard J. F.

2010-01-01

328

Classification of eating impairments based on eating efficiency in children with cerebral palsy  

Microsoft Academic Search

Eating impairments in children with cerebral palsy (CP) may vary widely from mild to severe. Accurate diagnosis of the severity of eating has been hampered by the lack of a classification system which would permit stratification of this wide range of problems into mild, moderate, and severe. We propose such a classification system based on measures of (1) growth: weight,

Erika G. Gisel; Elisabet Alphonce

1995-01-01

329

A study of MODIS and AWiFS multisensor fusion for crop classification enhancement  

Microsoft Academic Search

Accurate, robust, timely and complete remote sensing-based crop classification results are critical to the mission of the National Agricultural Statistics Service (NASS), United States Department of Agriculture. However, due to cloud coverage and limited budget, in many cases, there are not enough quality AWiFS image data available for performing a reliable multitemporal crop classification. To solve this problem, extra image

Zhengwei Yang; Yangrong Ling; Claire Boryan

2009-01-01

330

A Distance Measure for Genome Phylogenetic Analysis  

NASA Astrophysics Data System (ADS)

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 ?-Proteobacteria group whose genomes are known to contain many horizontally transferred genes.

Cao, Minh Duc; Allison, Lloyd; Dix, Trevor

331

Phylogenetic relationships of Termitomyces and related taxa.  

PubMed

Phylogenetic relationships of termitophilic fungi were estimated with Bayesian as well as other phylogenetic methods from partial sequences of the nuclear encoded large subunit ribosomal DNA (nLSU-rDNA) and the mitochondrial encoded small subunit ribosomal DNA (mtSSU-rDNA). Sequences were obtained from basidiomes covering the morphological, taxonomical, and geographical span of termitophilic mushroom-forming fungi, and analysed together with sequences from termite nests and termite guts from most known genera of fungus growing termites from geographically diverse regions. Topologies of trees resulting from the combined analyses of the two ribosomal genes generally show no positive conflicts with those obtained from separate analyses. We show that termitophilic fungi constitute a strongly supported monophyletic group within lyophylloid species. The genera Sinotermitomyces and Podabrella are derived within Termitomyces, and do not form monophyletic groups. Identical sequences were frequently found among samples of basidiomes from the same continents and among fungi utilized by termites from the same continent. However, only two sequences were identical between basidiome samples and termite nest/gut samples suggesting fruiting species do not form a representative sample of termitophilic fungi. No sequences were identical between samples from Asia and Africa indicating some geographic differentiation between these continents. PMID:15000230

Frøslev, Tobias G; Aanen, Duur K; Laessøe, Thomas; Rosendahl, Søren

2003-11-01

332

Phylogenetic relationships among megabats, microbats, and primates.  

PubMed Central

We present 744 nucleotide base positions from the mitochondrial 12S rRNA gene and 236 base positions from the mitochondrial cytochrome oxidase subunit I gene for a microbat, Brachyphylla cavernarum, and a megabat, Pteropus capestratus, in phylogenetic analyses with homologous DNA sequences from Homo sapiens, Mus musculus (house mouse), and Gallus gallus (chicken). We use information on evolutionary rate differences for different types of sequence change to establish phylogenetic character weights, and we consider alternative rRNA alignment strategies in finding that this mtDNA data set clearly supports bat monophyly. This result is found despite variations in outgroup used, gap coding scheme, and order of input for DNA sequences in multiple alignment bouts. These findings are congruent with morphological characters including details of wing structure as well as cladistic analyses of amino acid sequences for three globin genes and indicate that neurological similarities between megabats and primates are due to either retention of primitive characters or to convergent evolution rather than to inheritance from a common ancestor. This finding also indicates a single origin for flight among mammals.

Mindell, D P; Dick, C W; Baker, R J

1991-01-01

333

Phylogenetic diversity of Mesorhizobium in chickpea.  

PubMed

Crop domestication, in general, has reduced genetic diversity in cultivated gene pool of chickpea (Cicer arietinum) as compared with wild species (C. reticulatum, C. bijugum). To explore impact of domestication on symbiosis, 10 accessions of chickpeas, including 4 accessions of C. arietinum, and 3 accessions of each of C. reticulatum and C. bijugum species, were selected and DNAs were extracted from their nodules. To distinguish chickpea symbiont, preliminary sequences analysis was attempted with 9 genes (16S rRNA, atpD, dnaJ, glnA, gyrB, nifH, nifK, nodD and recA) of which 3 genes (gyrB, nifK and nodD) were selected based on sufficient sequence diversity for further phylogenetic analysis. Phylogenetic analysis and sequence diversity for 3 genes demonstrated that sequences from C. reticulatum were more diverse. Nodule occupancy by dominant symbiont also indicated that C. reticulatum (60 percent) could have more various symbionts than cultivated chickpea (80 percent). The study demonstrated that wild chickpeas (C. reticulatum) could be used for selecting more diverse symbionts in the field conditions and it implies that chickpea domestication affected symbiosis negatively in addition to reducing genetic diversity. PMID:24845514

Kim, Dong Hyun; Kaashyap, Mayank; Rathore, Abhishek; Das, Roma R; Parupalli, Swathi; Upadhyaya, Hari D; Gopalakrishnan, S; Gaur, Pooran M; Singh, Sarvjeet; Kaur, Jagmeet; Yasin, Mohammad; Varshney, Rajeev K

2014-06-01

334

Phylogenetic relationships among group II intron ORFs  

PubMed Central

Group II introns are widely believed to have been ancestors of spliceosomal introns, yet little is known about their own evolutionary history. In order to address the evolution of mobile group II introns, we have compiled 71 open reading frames (ORFs) related to group II intron reverse transcriptases and subjected their derived amino acid sequences to phylogenetic analysis. The phylogenetic tree was rooted with reverse transcriptases (RTs) of non-long terminal repeat retroelements, and the inferred phylogeny reveals two major clusters which we term the mitochondrial and chloroplast-like lineages. Bacterial ORFs are mainly positioned at the bases of the two lineages but with weak bootstrap support. The data give an overview of an apparently high degree of horizontal transfer of group II intron ORFs, mostly among related organisms but also between organelles and bacteria. The Zn domain (nuclease) and YADD motif (RT active site) were lost multiple times during evolution. Differences in domain structures suggest that the oldest ORFs were concise, while the ORF in the mitochondrial lineage subsequently expanded in three locations. The data are consistent with a bacterial origin for mobile group II introns.

Zimmerly, Steven; Hausner, Georg; Wu, Xu-chu

2001-01-01

335

A molecular phylogeny and classification of Bignoniaceae.  

PubMed

Bignoniaceae are woody, trees, shrubs, and lianas found in all tropical floras of the world with lesser representation in temperate regions. Phylogenetic analyses of chloroplast sequences (rbcL, ndhF, trnL-F) were undertaken to infer evolutionary relationships in Bignoniaceae and to revise its classification. Eight clades are recognized as tribes (Bignonieae, Catalpeae, Coleeae, Crescentieae, Jacarandeae, Oroxyleae, Tecomeae, Tourrettieae); additional inclusive clades are named informally. Jacarandeae and Catalpeae are resurrected; the former is sister to the rest of the family, and the latter occupies an unresolved position within the "core" Bignoniaceae. Tribe Eccremocarpeae is included in Tourrettieae. Past classifications recognized a large Tecomeae, but this tribe is paraphyletic with respect to all other tribes. Here Tecomeae are reduced to a clade of approximately 12 genera with a worldwide distribution in both temperate and tropical ecosystems. Two large clades, Bignonieae and Crescentiina, account for over 80% of the species in the family. Coleeae and Crescentieae are each included in larger clades, the Paleotropical alliance and Tabebuia alliance, respectively; each alliance includes a grade of taxa assigned to the traditional Tecomeae. Parsimony inference suggests that the family originated in the neotropics, with at least five dispersal events leading to the Old World representatives. PMID:21622359

Olmstead, Richard G; Zjhra, Michelle L; Lohmann, Lúcia G; Grose, Susan O; Eckert, Andrew J

2009-09-01

336

Phylogenetic tree construction based on 2D graphical representation  

NASA Astrophysics Data System (ADS)

A new approach based on the two-dimensional (2D) graphical representation of the whole genome sequence [Bo Liao, Chem. Phys. Lett., 401(2005) 196.] is proposed to analyze the phylogenetic relationships of genomes. The evolutionary distances are obtained through measuring the differences among the 2D curves. The fuzzy theory is used to construct phylogenetic tree. The phylogenetic relationships of H5N1 avian influenza virus illustrate the utility of our approach.

Liao, Bo; Shan, Xinzhou; Zhu, Wen; Li, Renfa

2006-04-01

337

Best Practices for Data Sharing in Phylogenetic Research  

PubMed Central

As phylogenetic data becomes increasingly available, along with associated data on species’ genomes, traits, and geographic distributions, the need to ensure data availability and reuse become more and more acute. In this paper, we provide ten “simple rules” that we view as best practices for data sharing in phylogenetic research. These rules will help lead towards a future phylogenetics where data can easily be archived, shared, reused, and repurposed across a wide variety of projects.

Cranston, Karen; Harmon, Luke J.; O'Leary, Maureen A.; Lisle, Curtis

2014-01-01

338

Drug classification: science, politics, both or neither?  

PubMed

Governments currently classify illicit drugs for various purposes: to guide courts in the sentencing of convicted violators of drug control laws, to prioritize targets of prevention measures and to educate the public about relative risks of the various drugs. It has been proposed that classification should be conducted by scientists and drug experts rather than by politicians, so that it will reflect only accurate factual knowledge of drug effects and risks rather than political biases. Although this is an appealing goal, it is inherently impossible because rank-ordering of the drugs inevitably requires value judgements concerning the different types of harm. Such judgements, even by scientists, depend upon subjective personal criteria and not only upon scientific facts. Moreover, classification that is meant to guide the legal system in controlling dangerous drug use can function only if it is in harmony with the values and sentiments of the public. In some respects, politicians may be better attuned to public attitudes and wishes, and to what policies the public will support, than are scientific experts. The problems inherent in such drug classification are illustrated by the examples of cannabis and of salvinorin A. They raise the question as to whether the classification process really serves any socially beneficial purpose. PMID:20148796

Kalant, Harold

2010-07-01

339

Classification of N-type carbon stars  

NASA Astrophysics Data System (ADS)

Carbon stars are in an advanced state of evolution and are of interest for understanding the rapid evolutionary processes during late stages of stellar evolution. They are cool (T<4000K) stars with an atmospheric carbon to oxygen ratio (C/O) greater than one. Most other classes of stars exhibit atmospheric C/O < 1. Low resolution spectrophotometry has been used to examine the relationship between spectral class and effective temperatures in a sample of eleven cool carbon stars. Using effective temperatures from lunar occultation observations of Tsuji and Ridgeway et al, CN and C2 features have been examined for their utility as classification criteria. It is found that C2 strength is not a reliable temperature classification parameter, while CN should be useful. Comparison of the carbon star classification systems of Keenan and Morgan and that of Richer with recent derived temperatures and the results of this study indicates that the Richer classification system more accurately reflects the temperatures of cool carbon stars.

Bollwerk, W. V.

1986-06-01

340

Phylogenetic analysis with the iPlant discovery environment.  

PubMed

The iPlant Collaborative's Discovery Environment is a unified Web portal to many bioinformatics applications and analytical workflows, including various methods of phylogenetic analysis. This unit describes example protocols for phylogenetic analyses, starting at sequence retrieval from the GenBank sequence database, through to multiple sequence alignment inference and visualization of phylogenetic trees. Methods for extracting smaller sub-trees from very large phylogenies, and the comparative method of continuous ancestral character state reconstruction based on observed morphology of extant species related to their phylogenetic relationships, are also presented. PMID:23749754

Matasci, Naim; McKay, Sheldon

2013-06-01

341

Rapid and Simple Determination of the Escherichia coli Phylogenetic Group  

PubMed Central

Phylogenetic analysis has shown that Escherichia coli is composed of four main phylogenetic groups (A, B1, B2, and D) and that virulent extra-intestinal strains mainly belong to groups B2 and D. Actually, phylogenetic groups can be determined by multilocus enzyme electrophoresis or ribotyping, both of which are complex, time-consuming techniques. We describe a simple and rapid phylogenetic grouping technique based on triplex PCR. The method, which uses a combination of two genes (chuA and yjaA) and an anonymous DNA fragment, was tested with 230 strains and showed excellent correlation with reference methods.

Clermont, Olivier; Bonacorsi, Stephane; Bingen, Edouard

2000-01-01

342

Trinets encode tree-child and level-2 phylogenetic networks.  

PubMed

Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. Recently, there has been great interest in trying to develop methods to construct rooted phylogenetic networks from triplets, that is rooted trees on three species. However, although triplets determine or encode rooted phylogenetic trees, they do not in general encode rooted phylogenetic networks, which is a potential issue for any such method. Motivated by this fact, Huber and Moulton recently introduced trinets as a natural extension of rooted triplets to networks. In particular, they showed that [Formula: see text] phylogenetic networks are encoded by their trinets, and also conjectured that all "recoverable" rooted phylogenetic networks are encoded by their trinets. Here we prove that recoverable binary level-2 networks and binary tree-child networks are also encoded by their trinets. To do this we prove two decomposition theorems based on trinets which hold for all recoverable binary rooted phylogenetic networks. Our results provide some additional evidence in support of the conjecture that trinets encode all recoverable rooted phylogenetic networks, and could also lead to new approaches to construct phylogenetic networks from trinets. PMID:23680992

van Iersel, Leo; Moulton, Vincent

2014-06-01

343

Brain extraction based on locally linear representation-based classification.  

PubMed

Brain extraction is an important procedure in brain image analysis. Although numerous brain extraction methods have been presented, enhancing brain extraction methods remains challenging because brain MRI images exhibit complex characteristics, such as anatomical variability and intensity differences across different sequences and scanners. To address this problem, we present a Locally Linear Representation-based Classification (LLRC) method for brain extraction. A novel classification framework is derived by introducing the locally linear representation to the classical classification model. Under this classification framework, a common label fusion approach can be considered as a special case and thoroughly interpreted. Locality is important to calculate fusion weights for LLRC; this factor is also considered to determine that Local Anchor Embedding is more applicable in solving locally linear coefficients compared with other linear representation approaches. Moreover, LLRC supplies a way to learn the optimal classification scores of the training samples in the dictionary to obtain accurate classification. The International Consortium for Brain Mapping and the Alzheimer's Disease Neuroimaging Initiative databases were used to build a training dataset containing 70 scans. To evaluate the proposed method, we used four publicly available datasets (IBSR1, IBSR2, LPBA40, and ADNI3T, with a total of 241 scans). Experimental results demonstrate that the proposed method outperforms the four common brain extraction methods (BET, BSE, GCUT, and ROBEX), and is comparable to the performance of BEaST, while being more accurate on some datasets compared with BEaST. PMID:24525169

Huang, Meiyan; Yang, Wei; Jiang, Jun; Wu, Yao; Zhang, Yu; Chen, Wufan; Feng, Qianjin

2014-05-15

344

Ensemble classifiers based on correlation analysis for DNA microarray classification  

Microsoft Academic Search

Since accurate classification of DNA microarray is a very important issue for the treatment of cancer, it is more desirable to make a decision by combining the results of various expert classifiers rather than by depending on the result of only one classifier. In spite of the many advantages of mutually error-correlated ensemble classifiers, they are limited in performance. It

Kyung-joong Kim; Sung-bae Cho

2006-01-01

345

Feature Extraction System for Contextual Classification within Security Imaging Applications  

Microsoft Academic Search

Throughout security imaging applications, there is a persistent need for accurate contextual classification of objects within the scene so proper subsequent decisions can be made. To generate a set of scene attributes necessary for this analysis, this paper presents a novel feature extraction system composed of three divisions: an edge detection system, a segmentation system, and a recognition system. System

E. E. Danahy; K. A. Panetta; S. S. Agaian

2007-01-01

346

AMPSO: A New Particle Swarm Method for Nearest Neighborhood Classification  

Microsoft Academic Search

Nearest prototype methods can be quite successful on many pattern classification problems. In these methods, a collection of prototypes has to be found that accurately represents the input patterns. The classifier then assigns classes based on the nearest prototype in this collection. In this paper, we first use the standard particle swarm optimizer (PSO) algorithm to find those prototypes. Second,

Alejandro Cervantes; Inés María Galván; Pedro Isasi

2009-01-01

347

Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution  

PubMed Central

Over half of all vertebrates are “fishes”, which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a full sample of all bony fishes. Here we conducted a comprehensive phylogenetic study on a broad taxonomic sample of 61 actinopterygian and sarcopterygian lineages (with a chondrichthyan outgroup) using a molecular data set of 21 independent loci. These data yielded a resolved phylogenetic hypothesis for extant Osteichthyes, including 1) reciprocally monophyletic Sarcopterygii and Actinopterygii, as currently understood, with polypteriforms as the first diverging lineage within Actinopterygii; 2) a monophyletic group containing gars and bowfin (= Holostei) as sister group to teleosts; and 3) the earliest diverging lineage among teleosts being Elopomorpha, rather than Osteoglossomorpha. Relaxed-clock dating analysis employing a set of 24 newly applied fossil calibrations reveals divergence times that are more consistent with paleontological estimates than previous studies. Establishing a new phylogenetic pattern with accurate divergence dates for bony fishes illustrates several areas where the fossil record is incomplete and provides critical new insights on diversification of this important vertebrate group.

Broughton, Richard E.; Betancur-R., Ricardo; Li, Chenhong; Arratia, Gloria; Orti, Guillermo

2013-01-01

348

Phylogenetic relationships of nearctic Reticulitermes species (Isoptera: Rhinotermitidae) with particular reference to Reticulitermes arenincola Goellner.  

PubMed

DNA sequence comparisons of the mitochondrial COII, 16S, and 12S rRNA genes were used to infer phylogenetic relationships among the six known US Reticulitermes species (Reticulitermes flavipes, Reticulitermes arenincola, Reticulitermes tibialis, Reticulitermes hageni, Reticulitermes virginicus, and Reticulitermes hesperus) and the closely related European species Reticulitermes santonensis. The interspecific pairwise sequence divergence, based on uncorrected "p" distance, varied up to 10% across the COII, 4.9% across the 16S, and 3% across the 12S fragments. Phylogenetic trees were constructed using maximum parsimony, likelihood, and distance methods. The combined results suggest several phylogenetic relationships including: (i) R. flavipes, R. arenincola, and European R. santonensis are possibly conspecific; (ii) R. virginicus and R. hageni are closely related species; and (iii) R. tibialis and R. hesperus are closely related species. Interestingly, while there is apparent synonymity between R. flavipes and R. arenincola by DNA sequence, there are clear morphological differences in the soldier caste. This finding suggests a combination of molecular and morphological approaches are necessary for accurate species identification. These data lend resolution to the complex problem of Reticulitermes systematics, and will assist future efforts directed toward characterizing species distribution and ecology. PMID:15012959

Ye, Weimin; Lee, Chow-Yang; Scheffrahn, Rudolf H; Aleong, Jody M; Su, Nan-Yao; Bennett, Gary W; Scharf, Michael E

2004-03-01

349

morePhyML: improving the phylogenetic tree space exploration with PhyML 3.  

PubMed

PhyML is a widely used Maximum Likelihood (ML) phylogenetic tree inference software based on a standard hill-climbing method. Starting from an initial tree, the version 3 of PhyML explores the tree space by using "Nearest Neighbor Interchange" (NNI) or "Subtree Pruning and Regrafting" (SPR) tree swapping techniques in order to find the ML phylogenetic tree. NNI-based local searches are fast but can often get trapped in local optima, whereas it is expected that the larger (but slower to cover) SPR-based neighborhoods will lead to trees with higher likelihood. Here, I verify that PhyML infers more likely trees with SPRs than with NNIs in almost all cases. However, I also show that the SPR-based local search of PhyML often does not succeed at locating the ML tree. To improve the tree space exploration, I deliver a script, named morePhyML, which allows escaping from local optima by performing character reweighting. This ML tree search strategy, named ratchet, often leads to higher likelihood estimates. Based on the analysis of a large number of amino acid and nucleotide data, I show that morePhyML allows inferring more accurate phylogenetic trees than several other recently developed ML tree inference softwares in many cases. PMID:21925283

Criscuolo, Alexis

2011-12-01

350

Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution.  

PubMed

Over half of all vertebrates are "fishes", which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a full sample of all bony fishes. Here we conducted a comprehensive phylogenetic study on a broad taxonomic sample of 61 actinopterygian and sarcopterygian lineages (with a chondrichthyan outgroup) using a molecular data set of 21 independent loci. These data yielded a resolved phylogenetic hypothesis for extant Osteichthyes, including 1) reciprocally monophyletic Sarcopterygii and Actinopterygii, as currently understood, with polypteriforms as the first diverging lineage within Actinopterygii; 2) a monophyletic group containing gars and bowfin (= Holostei) as sister group to teleosts; and 3) the earliest diverging lineage among teleosts being Elopomorpha, rather than Osteoglossomorpha. Relaxed-clock dating analysis employing a set of 24 newly applied fossil calibrations reveals divergence times that are more consistent with paleontological estimates than previous studies. Establishing a new phylogenetic pattern with accurate divergence dates for bony fishes illustrates several areas where the fossil record is incomplete and provides critical new insights on diversification of this important vertebrate group. PMID:23788273

Broughton, Richard E; Betancur-R, Ricardo; Li, Chenhong; Arratia, Gloria; Ortí, Guillermo

2013-01-01

351

Semantic video classification with insufficient labeled samples  

NASA Astrophysics Data System (ADS)

To support more e®ective video retrieval at semantic level, we introduce a novel framework to achieve semantic video classification. This novel framework includes: (a) A semantic-senstive video content representation framework via principal video shots to enhance the quality of features (i.e., the ability of the selected low-level multimodal perceptual features to discriminate among various semantic video concepts); (b) A semantic video concept interpretation framework via flexible mixture model to bridge the semantic gap between the semantic video concepts and the low-level multimodal perceptual features; (c) A novel concept learning technique to integrate unlabeled samples with labeled samples for more accurate classifier training. Experimental results on semantic medical video classification are also presented to evaluate the performance of the proposed framework.

Luo, Hangzai; Gao, Yuli; Liu, Zhaoya; Fan, Jianping

2003-12-01

352

[Hard and soft classification method of multi-spectral remote sensing image based on adaptive thresholds].  

PubMed

Hard and soft classification techniques are the conventional methods of image classification for satellite data, but they have their own advantages and drawbacks. In order to obtain accurate classification results, we took advantages of both traditional hard classification methods (HCM) and soft classification models (SCM), and developed a new method called the hard and soft classification model (HSCM) based on adaptive threshold calculation. The authors tested the new method in land cover mapping applications. According to the results of confusion matrix, the overall accuracy of HCM, SCM, and HSCM is 71.06%, 67.86%, and 71.10%, respectively. And the kappa coefficient is 60.03%, 56.12%, and 60.07%, respectively. Therefore, the HSCM is better than HCM and SCM. Experimental results proved that the new method can obviously improve the land cover and land use classification accuracy. PMID:23841424

Hu, Tan-Gao; Xu, Jun-Feng; Zhang, Deng-Rong; Wang, Jie; Zhang, Yu-Zhou

2013-04-01

353

Sparse representation-based classification scheme for motor imagery-based brain-computer interface systems  

NASA Astrophysics Data System (ADS)

Motor imagery (MI)-based brain-computer interface systems (BCIs) normally use a powerful spatial filtering and classification method to maximize their performance. The common spatial pattern (CSP) algorithm is a widely used spatial filtering method for MI-based BCIs. In this work, we propose a new sparse representation-based classification (SRC) scheme for MI-based BCI applications. Sensorimotor rhythms are extracted from electroencephalograms and used for classification. The proposed SRC method utilizes the frequency band power and CSP algorithm to extract features for classification. We analyzed the performance of the new method using experimental datasets. The results showed that the SRC scheme provides highly accurate classification results, which were better than those obtained using the well-known linear discriminant analysis classification method. The enhancement of the proposed method in terms of the classification accuracy was verified using cross-validation and a statistical paired t-test (p < 0.001).

Shin, Younghak; Lee, Seungchan; Lee, Junho; Lee, Heung-No

2012-10-01

354

Rapid and accurate pyrosequencing of angiosperm plastid genomes  

PubMed Central

Background Plastid genome sequence information is vital to several disciplines in plant biology, including phylogenetics and molecular biology. The past five years have witnessed a dramatic increase in the number of completely sequenced plastid genomes, fuelled largely by advances in conventional Sanger sequencing technology. Here we report a further significant reduction in time and cost for plastid genome sequencing through the successful use of a newly available pyrosequencing platform, the Genome Sequencer 20 (GS 20) System (454 Life Sciences Corporation), to rapidly and accurately sequence the whole plastid genomes of the basal eudicot angiosperms Nandina domestica (Berberidaceae) and Platanus occidentalis (Platanaceae). Results More than 99.75% of each plastid genome was simultaneously obtained during two GS 20 sequence runs, to an average depth of coverage of 24.6× in Nandina and 17.3× in Platanus. The Nandina and Platanus plastid genomes shared essentially identical gene complements and possessed the typical angiosperm plastid structure and gene arrangement. To assess the accuracy of the GS 20 sequence, over 45 kilobases of sequence were generated for each genome using conventional sequencing. Overall error rates of 0.043% and 0.031% were observed in GS 20 sequence for Nandina and Platanus, respectively. More than 97% of all observed errors were associated with homopolymer runs, with ~60% of all errors associated with homopolymer runs of 5 or more nucleotides and ~50% of all errors associated with regions of extensive homopolymer runs. No substitution errors were present in either genome. Error rates were generally higher in the single-copy and noncoding regions of both plastid genomes relative to the inverted repeat and coding regions. Conclusion Highly accurate and essentially complete sequence information was obtained for the Nandina and Platanus plastid genomes using the GS 20 System. More importantly, the high accuracy observed in the GS 20 plastid genome sequence was generated for a significant reduction in time and cost over traditional shotgun-based genome sequencing techniques, although with approximately half the coverage of previously reported GS 20 de novo genome sequence. The GS 20 should be broadly applicable to angiosperm plastid genome sequencing, and therefore promises to expand the scale of plant genetic and phylogenetic research dramatically.

Moore, Michael J; Dhingra, Amit; Soltis, Pamela S; Shaw, Regina; Farmerie, William G; Folta, Kevin M; Soltis, Douglas E

2006-01-01

355

Land use/cover classification in the Brazilian Amazon using satellite images  

PubMed Central

Land use/cover classification is one of the most important applications in remote sensing. However, mapping accurate land use/cover spatial distribution is a challenge, particularly in moist tropical regions, due to the complex biophysical environment and limitations of remote sensing data per se. This paper reviews experiments related to land use/cover classification in the Brazilian Amazon for a decade. Through comprehensive analysis of the classification results, it is concluded that spatial information inherent in remote sensing data plays an essential role in improving land use/cover classification. Incorporation of suitable textural images into multispectral bands and use of segmentation-based method are valuable ways to improve land use/cover classification, especially for high spatial resolution images. Data fusion of multi-resolution images within optical sensor data is vital for visual interpretation, but may not improve classification performance. In contrast, integration of optical and radar data did improve classification performance when the proper data fusion method was used. Of the classification algorithms available, the maximum likelihood classifier is still an important method for providing reasonably good accuracy, but nonparametric algorithms, such as classification tree analysis, has the potential to provide better results. However, they often require more time to achieve parametric optimization. Proper use of hierarchical-based methods is fundamental for developing accurate land use/cover classification, mainly from historical remotely sensed data.

Lu, Dengsheng; Batistella, Mateus; Li, Guiying; Moran, Emilio; Hetrick, Scott; Freitas, Corina da Costa; Dutra, Luciano Vieira; Sant'Anna, Sidnei Joao Siqueira

2013-01-01

356

Classification of Variable Stars Using Thick-Pen Transform Method  

NASA Astrophysics Data System (ADS)

A suitable classification of variable stars is an important task for understanding galaxy structure and evaluating stellar evolution. Most traditional approaches for classification have used various features of variable stars such as period, amplitude, color index, and Fourier coefficients. Recently, by focusing only on the light curve shape, Deb and Singh proposed a classification method based on multivariate principal component analysis (PCA). They applied the PCA method to light curves and compared its results with those obtained by Fourier coefficients. In this article, we propose a new procedure based on the thick-pen transform for obtaining accurate information on the light curve shape as well as for improving the accuracy of classification. The proposed method is applied to the data sets of variable stars from the Stellar Astrophysics and Research on Exoplanets (STARE) project and a small number of stars from Massive Compact Halo Objects (MACHO).

Park, M.; Oh, H.-S.; Kim, D.

2013-04-01

357

Accurate indel prediction using paired-end short reads  

PubMed Central

Background One of the major open challenges in next generation sequencing (NGS) is the accurate identification of structural variants such as insertions and deletions (indels). Current methods for indel calling assign scores to different types of evidence or counter-evidence for the presence of an indel, such as the number of split read alignments spanning the boundaries of a deletion candidate or reads that map within a putative deletion. Candidates with a score above a manually defined threshold are then predicted to be true indels. As a consequence, structural variants detected in this manner contain many false positives. Results Here, we present a machine learning based method which is able to discover and distinguish true from false indel candidates in order to reduce the false positive rate. Our method identifies indel candidates using a discriminative classifier based on features of split read alignment profiles and trained on true and false indel candidates that were validated by Sanger sequencing. We demonstrate the usefulness of our method with paired-end Illumina reads from 80 genomes of the first phase of the 1001 Genomes Project ( http://www.1001genomes.org) in Arabidopsis thaliana. Conclusion In this work we show that indel classification is a necessary step to reduce the number of false positive candidates. We demonstrate that missing classification may lead to spurious biological interpretations. The software is available at: http://agkb.is.tuebingen.mpg.de/Forschung/SV-M/.

2013-01-01

358

Inferring Phylogenetic Networks from Gene Order Data  

PubMed Central

Existing algorithms allow us to infer phylogenetic networks from sequences (DNA, protein or binary), sets of trees, and distance matrices, but there are no methods to build them using the gene order data as an input. Here we describe several methods to build split networks from the gene order data, perform simulation studies, and use our methods for analyzing and interpreting different real gene order datasets. All proposed methods are based on intermediate data, which can be generated from genome structures under study and used as an input for network construction algorithms. Three intermediates are used: set of jackknife trees, distance matrix, and binary encoding. According to simulations and case studies, the best intermediates are jackknife trees and distance matrix (when used with Neighbor-Net algorithm). Binary encoding can also be useful, but only when the methods mentioned above cannot be used.

Morozov, Alexey Anatolievich; Galachyants, Yuri Pavlovich; Likhoshway, Yelena Valentinovna

2013-01-01

359

Complexity of the simplest phylogenetic estimation problem.  

PubMed Central

The maximum-likelihood (ML) solution to a simple phylogenetic estimation problem is obtained analytically The problem is estimation of the rooted tree for three species using binary characters with a symmetrical rate of substitution under the molecular clock. ML estimates of branch lengths and log-likelihood scores are obtained analytically for each of the three rooted binary trees. Estimation of the tree topology is equivalent to partitioning the sample space (space of possible data outcomes) into subspaces, within each of which one of the three binary trees is the ML tree. Distance-based least squares and parsimony-like methods produce essentially the same estimate of the tree topology, although differences exist among methods even under this simple model. This seems to be the simplest case, but has many of the conceptual and statistical complexities involved in phylogeny estimation. The solution to this real phylogeny estimation problem will be useful for studying the problem of significance evaluation.

Yang, Z

2000-01-01

360

Classification of depressive disorders.  

PubMed

The classification of depression is well established in major diagnostic systems and operational definitions now make the diagnosis of depression reasonably reliable. However, classification and diagnosis continue to be based on clinical presentation and course and are not currently informed by aetiological or pathophysiological considerations. It is still unclear, for example, whether or not categories such as melancholic depression represent distinct subforms of illness or whether a dimensional classification based on severity can capture clinical presentation adequately and more economically. Despite these caveats, there is some evidence that distinctions between various subforms of depression can predict treatment response and this can be useful for clinical practice as well as guiding research strategies. PMID:22923074

Cowen, Phillip J

2013-01-01

361

Extrahepatic biliary cancer: New staging classification  

PubMed Central

Tumor staging defines the point in the natural history of the malignancy when the diagnosis is made. The most common staging system for cancer is the tumor, node, metastases classification. Staging of cancers provides useful parameters in the determination of the extent of disease and prognosis. Cholangiocarcinoma are rare and refers to cancers that arise from the biliary epithelium. These tumors can occur anywhere along the biliary tree. These tumors have been previously divided into extrahepatic and intrahepatic lesions. Until recently the extrahepatic bile duct tumors have been considered as a single entity per American Joint Commission on Cancer (AJCC) staging classification. The most recent changes to the AJCC classification of bile duct cancers divide the tumors into two major categories: proximal and distal tumors. This practical classification is based on anatomy and surgical management. High quality cross-sectional computed tomography (CT) and/or magnetic resonance (MR) imaging of the abdomen are essential information to accurately stage this tumors. Imaging plays an important role in diagnosis, localization, staging and optimal management of cholangiocarcinoma. For example, it helps to localize the tumor to either perihilar or distal bile duct, both of which have different management. Further, it helps to accurately stage the disease and identify the presence of significant nodal and distant metastasis, which may preclude surgery. Also, it helps to identify the extent of local invasion, which has a major impact on the management. For example, extensive involvement of hepatic duct reaching up to second-order biliary radicals or major vascular encasement of portal vein or hepatic arteries precludes curative surgery and patient may be managed by palliative therapy. Further, imaging helps to identify any anatomical variations in the hepatic arterial or venous circulation and biliary ductal system, which is vital information for surgical planning. This review presents relevant clinical presentation and imaging acquisition and presentation for the accurate staging classification of bile duct tumors based on the new AJCC criteria. This will be performed with the assistance of anatomical diagrams and representative CT and MR images. The image interpretation must include all relevant imaging information for optimum staging. Detailed recommendations on the items required on the radiology report will be presented.

Ganeshan, Dhakshinamoorthy; Moron, Fanny E; Szklaruk, Janio

2012-01-01

362

Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria  

PubMed Central

Summary: The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades (viz., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria. The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria.

Gao, Beile

2012-01-01

363

Classification images with uncertainty  

PubMed Central

Classification image and other similar noise-driven linear methods have found increasingly wider applications in revealing psychophysical receptive field structures or perceptual templates. These techniques are relatively easy to deploy, and the results are simple to interpret. However, being a linear technique, the utility of the classification-image method is believed to be limited. Uncertainty about the target stimuli on the part of an observer will result in a classification image that is the superposition of all possible templates for all the possible signals. In the context of a well-established uncertainty model, which pools the outputs of a large set of linear frontends with a max operator, we show analytically, in simulations, and with human experiments that the effect of intrinsic uncertainty can be limited or even eliminated by presenting a signal at a relatively high contrast in a classification-image experiment. We further argue that the subimages from different stimulus-response categories should not be combined, as is conventionally done. We show that when the signal contrast is high, the subimages from the error trials contain a clear high-contrast image that is negatively correlated with the perceptual template associated with the presented signal, relatively unaffected by uncertainty. The subimages also contain a “haze” that is of a much lower contrast and is positively correlated with the superposition of all the templates associated with the erroneous response. In the case of spatial uncertainty, we show that the spatial extent of the uncertainty can be estimated from the classification subimages. We link intrinsic uncertainty to invariance and suggest that this signal-clamped classification-image method will find general applications in uncovering the underlying representations of high-level neural and psychophysical mechanisms.

Tjan, Bosco S.; Nandy, Anirvan S.

2009-01-01

364

Indigenous vs. International soil classification system in Ohangwena Region, Namibia  

NASA Astrophysics Data System (ADS)

This poster will present soil diversity in North-Central Namibia, with a focus on soil fertility. It aims to show the correspondence and differences between an international and an indigenous soil classification system. International classifications, like World Reference Base for Soil Resources (WRB), are very helpful tools to share information in soil science and agriculture. However, these classification are meaningful for large scale soil processes understanding but local specificities cannot be understood and differentiated. On the other hand, knowledge that farmers have on cultivated soils is very accurate and adapted to local agricultural use. However, their knowledge should be properly defined and translated to be used by scientists. Once their knowledge can be read by scientists, it provides very powerful tools for soil mapping and characterization. Analysis so far has focused on the area of Ondobe (30 km West from Eenhana, Ohangwena region). This area is located between two major systems, the Cuvelai floodplain to the West and the Kalahari Woodlands to the East. While all the cultivated soils from this region would be classified as Arenosols (WRB), the local classification differentiates five major soil types (Omutunda, Ehenge, Omufitu, Elondo, Ehenene). In WRB classification, these soils correspond, roughly, to specific Arenosols, respectively Hypereutric, Albic, Haplic, Rubic and Salic Arenosols. Further work will evaluate, the local variation inside each indigenous soil types. Hierarchical classification using soil field descriptors will be used to create statistic soil groups. These new groups will then be compared to each classification system.

Prudat, Brice; Kuhn, Nikolaus J.; Bloemertz, Lena

2014-05-01

365

Bias in Phylogenetic Reconstruction of Vertebrate Rhodopsin Sequences  

Microsoft Academic Search

Two spurious nodes were found in phylogenetic analyses of vertebrate rhodopsin sequences in comparison with well- established vertebrate relationships. These spurious reconstructions were well supported in bootstrap analyses and occurred independently of the method of phylogenetic analysis used (parsimony, distance, or likelihood). Use of this data set of vertebrate rhodopsin sequences allowed us to exploit established vertebrate relationships, as well

Belinda S. W. Chang; Dana L. Campbell

366

Path integral formulation and Feynman rules for phylogenetic branching models  

Microsoft Academic Search

A dynamical picture of phylogenetic evolution is given in terms of Markov models on a state space, comprising joint probability distributions for character types of taxonomic classes. Phylogenetic branching is a process which augments the number of taxa under consideration, and hence the rank of the underlying joint probability state tensor. We point out the combinatorial necessity for a second-quantized,

P. D. Jarvis; J. D. Bashford; J. G. Sumner

2005-01-01

367

Rare genomic changes as a tool for phylogenetics  

Microsoft Academic Search

DNA sequence data have offered valuable insights into the relationships between living organisms. However, most phylogenetic analyses of DNA sequences rely primarily on single nucleotide substitutions, which might not be perfect phylogenetic markers. Rare genomic changes (RGCs), such as intron indels, retroposon integrations, signature sequences, mitochondrial and chloroplast gene order changes, gene duplications and genetic code changes, provide a suite

Antonis Rokas; Peter W. H. Holland

2000-01-01

368

Mixed-up trees: the structure of phylogenetic mixtures  

Microsoft Academic Search

In this paper we apply new geometric and combinatorial methods to the study of phylogenetic mixtures. The focus of the geometric approach is to describe the geometry of phylogenetic mixture distributions for the two state random cluster model, which is a generalization of the two state symmetric (CFN) model. In particular, we show that the set of mixture distributions forms

Frederick A. Matsen; Elchanan Mossel; Mike Steel

2007-01-01

369

Exploration of phylogenetic data using a global sequence analysis method  

PubMed Central

Background Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets. Results Here we explore the phylogenetic signal present in molecular data by genomic signatures, defined as the set of frequencies of short oligonucleotides present in DNA sequences. Although violating many of the standard assumptions of traditional phylogenetic analyses – in particular explicit statements of homology inherent in character matrices – the use of the signature does permit the analysis of very long sequences, even those that are unalignable, and is therefore most useful in cases where alignment is questionable. We compare the results obtained by traditional phylogenetic methods to those inferred by the signature method for two genes: RAG1, which is easily alignable, and 18S RNA, where alignments are often ambiguous for some regions. We also apply this method to a multigene data set of 33 genes for 9 bacteria and one archea species as well as to the whole genome of a set of 16 ?-proteobacteria. In addition to delivering phylogenetic results comparable to traditional methods, the comparison of signatures for the sequences involved in the bacterial example identified putative candidates for horizontal gene transfers. Conclusion The signature method is therefore a fast tool for exploring phylogenetic data, providing not only a pretreatment for discovering new sequence relationships, but also for identifying cases of sequence evolution that could confound traditional phylogenetic analysis.

Chapus, Charles; Dufraigne, Christine; Edwards, Scott; Giron, Alain; Fertil, Bernard; Deschavanne, Patrick

2005-01-01

370

Phylogenetic analysis of some Neogene phasianid genera (Aves: Phasianidae)  

Microsoft Academic Search

Phylogenetic analysis based on osteological characters of some Neogene and Recent phasianids is performed. Phylogenetic tree\\u000a shows close relationships of Plioperdix with Ammoperdix and Tologuica with Excalfactoria. Chauvireria is at the base of the clade (Alectoris + (Coturnix + (Excalfactoria + Tologuica))). Palaeoperdix is relatively close to the lineage of large pheasants.

N. V. Zelenkov

2009-01-01

371

Shark Teeth Classification  

NSDL National Science Digital Library

On a recent autumn afternoon at Harmony Leland Elementary in Mableton, Georgia, students in a fifth-grade science class investigated the essential process of classification--the act of putting things into groups according to some common characteristics or attributes. While they may have honed these skills earlier in the week by grouping their own shoes or school supplies, this class provided the unique opportunity to classify objects that are inherently fascinating to students--shark teeth fossils! This article describes how by using the teeth to estimate the length of ancient sharks, students got a classification activity they could really sink their teeth into.

Creel, Sally; Brown, Tom; Lee, Velda

2009-03-01

372

Different Relationships between Temporal Phylogenetic Turnover and Phylogenetic Similarity and in Two Forests Were Detected by a New Null Model  

PubMed Central

Background Ecologists have been monitoring community dynamics with the purpose of understanding the rates and causes of community change. However, there is a lack of monitoring of community dynamics from the perspective of phylogeny. Methods/Principle Findings We attempted to understand temporal phylogenetic turnover in a 50 ha tropical forest (Barro Colorado Island, BCI) and a 20 ha subtropical forest (Dinghushan in southern China, DHS). To obtain temporal phylogenetic turnover under random conditions, two null models were used. The first shuffled names of species that are widely used in community phylogenetic analyses. The second simulated demographic processes with careful consideration on the variation in dispersal ability among species and the variations in mortality both among species and among size classes. With the two models, we tested the relationships between temporal phylogenetic turnover and phylogenetic similarity at different spatial scales in the two forests. Results were more consistent with previous findings using the second null model suggesting that the second null model is more appropriate for our purposes. With the second null model, a significantly positive relationship was detected between phylogenetic turnover and phylogenetic similarity in BCI at a 10 m×10 m scale, potentially indicating phylogenetic density dependence. This relationship in DHS was significantly negative at three of five spatial scales. This could indicate abiotic filtering processes for community assembly. Using variation partitioning, we found phylogenetic similarity contributed to variation in temporal phylogenetic turnover in the DHS plot but not in BCI plot. Conclusions/Significance The mechanisms for community assembly in BCI and DHS vary from phylogenetic perspective. Only the second null model detected this difference indicating the importance of choosing a proper null model.

Huang, Jian-Xiong; Zhang, Jian; Shen, Yong; Lian, Ju-yu; Cao, Hong-lin; Ye, Wan-hui; Wu, Lin-fang; Bin, Yue

2014-01-01

373

Classification of Composite Defects Using the Signature Classification Development System.  

National Technical Information Service (NTIS)

The Johns Hopkins University Applied Physics Laboratory and the Carderock Division of the Naval Surface Warfare Center are developing a Signature Classification Development System (SCDS) to transfer classification technology to nondestructive evaluation (...

J. S. Lin L. M. Brown C. A. Lebowitz

1996-01-01

374

Phylogenetic relationship among horseshoe crab species: effect of substitution models on phylogenetic analyses.  

PubMed

The horseshoe crabs, known as living fossils, have maintained their morphology almost unchanged for the past 150 million years. The little morphological differentiation among horseshoe crab lineages has resulted in substantial controversy concerning the phylogenetic relationship among the extant species of horseshoe crabs, especially among the three species in the Indo-Pacific region. Previous studies suggest that the three species constitute a phylogenetically unresolvable trichotomy, the result of a cladogenetic process leading to the formation of all three Indo-Pacific species in a short geological time. Data from two mitochondrial genes (for 16S ribosomal rRNA and cytochrome oxidase subunit I) and one nuclear gene (for coagulogen) in the four species of horseshoe crabs and outgroup species were used in a phylogenetic analysis with various substitution models. All three genes yield the same tree topology, with Tachypleus-gigas and Carcinoscorpius-rotundicauda grouped together as a monophyletic taxon. This topology is significantly better than all the alternatives when evaluated with the RELL (resampling estimated log-likelihood) method. PMID:12116485

Xia, X

2000-03-01

375

Open Reading Frame Phylogenetic Analysis on the Cloud  

PubMed Central

Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus.

2013-01-01

376

Student interpretations of phylogenetic trees in an introductory biology course  

NASA Astrophysics Data System (ADS)

Phylogenetic trees are a common visual representation in biology, and the most important visual representation used in evolutionary biology. Thus, phylogenetic trees have also become an important component of biology education. We sought to determine what forms of reasoning are utilized by introductory biology students to interpret taxa relatedness on phylogenetic trees, what percentage of students correctly interpret taxa relatedness, and how these results alter in response to instruction and over time. Our students demonstrated a tendency for counting synapomorphies and nodes, rather than more common misinterpretations found in current literature. Students also struggled mightily with correctly interpreting phylogenetic trees, including many who exhibited memorization of correct reasoning. Broad initial instruction achieved little for phylogenetic tree understanding. More targeted instruction on evolutionary relationships improved understanding, but to a still unacceptable level. It appears these visual representations, which can directly affect student understanding of evolution, represent a formidable challenge for instructors.

Dees, Jonathan Andrew

377

Evolution of the Chaperone/Usher Assembly Pathway: Fimbrial Classification Goes Greek†  

PubMed Central

Summary: Many Proteobacteria use the chaperone/usher pathway to assemble proteinaceous filaments on the bacterial surface. These filaments can curl into fimbrial or nonfimbrial surface structures (e.g., a capsule or spore coat). This article reviews the phylogeny of operons belonging to the chaperone/usher assembly class to explore the utility of establishing a scheme for subdividing them into clades of phylogenetically related gene clusters. Based on usher amino acid sequence comparisons, our analysis shows that the chaperone/usher assembly class is subdivided into six major phylogenetic clades, which we have termed ?-, ?-, ?-, ?-, ?-, and ?-fimbriae. Members of each clade share related operon structures and encode fimbrial subunits with similar protein domains. The proposed classification system offers a simple and convenient method for assigning newly discovered chaperone/usher systems to one of the six major phylogenetic groups.

Nuccio, Sean-Paul; Baumler, Andreas J.

2007-01-01

378

Phylogenetic analysis and temporal diversification of mosquitoes (Diptera: Culicidae) based on nuclear genes and morphology  

PubMed Central

Background Phylogenetic analyses provide a framework for examining the evolution of morphological and molecular diversity, interpreting patterns in biogeography, and achieving a stable classification. The generic and suprageneric relationships within mosquitoes (Diptera: Culicidae) are poorly resolved, making these subjects difficult to address. Results We carried out maximum parsimony and maximum likelihood, including Bayesian, analyses on a data set consisting of six nuclear genes and 80 morphological characters to assess their ability to resolve relationships among 25 genera. We also estimated divergence times based on sequence data and fossil calibration points, using Bayesian relaxed clock methods. Strong support was recovered for the basal position and monophyly of the subfamily Anophelinae and the tribes Aedini and Sabethini of subfamily Culicinae. Divergence times for major culicid lineages date to the early Cretaceous. Conclusions Deeper relationships within the family remain poorly resolved, suggesting the need for additional taxonomic sampling. Our results support the notion of rapid radiations early in the diversification of mosquitoes.

2009-01-01

379

Phylogenetic relationships among eighteen neotropical Culicini species.  

PubMed

The subgeneric relationships among 8 generic and infrageneric taxa of the Culicini tribe were examined by cladistic analysis based on 30 larval mouthpart characters (maxillae and mandibles) of 7 subgenera of Culex L. and 1 of Deinocerites Theobald. We analyzed 18 ingroup species as well as Deinocerites melanophylum Dyar and Knab as a sister group, and Aedes taeniorhynchus Wiedemann as an outgroup. A parsimony analysis using the Nona program resulted in 2 trees each of 109 steps (consistency and retention indices = 0.88). The topologies obtained were similar to the current classification of the tribe, based on nonexplicit methods mainly including adult characters, with 2 exceptions. In the present work, the monophyly of the tribe Culicini (Culex + Deinocerites) was supported by 4 synapomorphies. The subgenus Lutzia Theobald formed the most basal clade in the tribe Culicini and the placement of Phenacomyia Harbach and Peyton as a subgenus was validated by its location as a sister group of the subgenus Culex and other subgenera. The subgenus Carrollia Lutz was the most robust taxon, supported by 5 synapomorphies, and was congruent with the infragroups of the current classification. The relationships among Deinocerites, Anoedioporpa Dyar, Microculex Theobald, and Melanoconion Theobald were unresolved, but were placed in the most internal clade of the tribe. The 1st exception to the accepted classification was the poorly resolved boundary between Anoedioporpa and Microculex The 2nd was the strong support (with 11 synapomorphies) for the inclusion of Deinocerites as a subgenus of Culex in the Culicini, which is proposed here. PMID:10901630

Navarro, J C; Liria, J

2000-06-01

380

Hospital discharge diagnoses: how accurate are they and their international classification of diseases (ICD) codes?  

PubMed

The accuracy of the discharge diagnoses recorded in hospital medical records, and the accuracy of their ICD codes, were retrospectively examined in 174 randomly chosen hospital patients. There was a 29% error rate in the recorded ICD codes when compared at a three digit level to the results obtained by retrospectively reviewing the records, establishing diagnoses and coding them. The error rate increased when medical records coders, rather than medically trained personnel, undertook the task of establishing the discharge diagnoses. PMID:2797577

Smith, M W

1989-09-27

381

Accurate Parental Classification of Overweight Adolescents' Weight Status: Does It Matter?  

Microsoft Academic Search

OBJECTIVE.Our goal was to explore whether parents of overweight adolescents who recognize that their children are overweight engage in behaviors that are likely to help their adolescents with long-term weight management. METHODS.The study population included overweight adolescents (BMI 85th percen- tile) who participated in Project EAT (Eating Among Teens) I (1999) and II (2004) and their parents who were interviewed

Dianne Neumark-Sztainer; Melanie Wall; Patricia van den Berg

2010-01-01

382

Phylogenetic and biochemical characterization of the oil-producing yeast Lipomyces starkeyi.  

PubMed

Lipomyces starkeyi is an oleaginous yeast, and has been classified in four distinct groups, i.e., sensu stricto and custers ?, ?, and ?. Recently, L. starkeyi clusters ?, ?, and ? were recognized independent species, Lipomyces mesembrius, Lipomyces doorenjongii, and Lipomyces kockii, respectively. In this study, we investigated phylogenetic relationships within L. starkeyi, including 18 Japanese wild strains, and its related species, based on internal transcribed spacer sequences and evaluated biochemical characters which reflected the phylogenetic tree. Phylogenetic analysis showed that most of Japanese wild strains formed one clade and this clade is more closely related to L. starkeyi s.s. clade including one Japanese wild strain than other clades. Only three Japanese wild strains were genetically distinct from L. starkeyi. Lipomyces mesembrius and L. doorenjongii shared one clade, while L. kockii was genetically distinct from the other three species. Strains in L. starkeyi s.s. clade converted six sugars, D-glucose, D-xylose, L-arabinose, D-galactose, D-mannose, and D-cellobiose to produce high total lipid yields. The Japanese wild strains in subclades B, C, and D converted D-glucose, D-galactose, and D-mannose to produce high total lipid yields. Lipomyces mesembrius was divided into two subclades. Lipomyces mesembrius CBS 7737 converted D-xylose, L-arabinose, D-galactose, and D-cellobiose, while the other L. mesembrius strains did not. Lipomyces doorenjongii converted all the sugars except D-cellobiose. In comparison to L. starkeyi, L. mesembrius, and L. doorenjongii, L. kockii produced higher total lipid yields from D-glucose, D-galactose, and D-mannose. The type of sugar converted depended on the subclade classification elucidated in this study. PMID:21927827

Oguri, Emiko; Masaki, Kazuo; Naganuma, Takafumi; Iefuji, Haruyuki

2012-02-01

383

Library of Congress Classification  

Microsoft Academic Search

The Library of Congress Classification (LCC), being a system originally and specifically designed for the Library's own collection, generally eschews alternatives. Within the LCC schedules, alternatives are found occasionally in earlier editions; there are no alternative numbers in recently developed or revised schedules. On the other hand, many alternative numbers representing different treatment of specific types of materials such as

Lois Mai Chan

1995-01-01

384

Booklet Classification Study.  

ERIC Educational Resources Information Center

Research studies using booklet classification were implemented by the American College Testing Program to investigate the linkage between the National Assessment of Educational Progress (NAEP) Achievement Levels Descriptions and the cutpoints set to represent student performance with respect to the achievement levels. This paper describes the…

Hanson, Bradley A.; Bay, Luz; Loomis, Susan Cooper

385

The Classification Conundrum.  

ERIC Educational Resources Information Center

Argues against the five-kingdom scheme of classification as using inconsistent criteria, ending up with divisions that are forced, not natural. Advocates an approach using cell type/complexity and modification of the metabolic machinery, recommending the five-kingdom scheme as starting point for class discussion on taxonomy and its conceptual…

Granger, Charles R.

1983-01-01

386

Inhibition in Multiclass Classification  

Microsoft Academic Search

The role of inhibition is investigated in a multiclass support vector machine formalism inspired by the brain structure of insects. The so-called mushroom bodies have a set of output neurons, or classification functions, that compete with each to encode a particular input. Strongly active output neurons depress or inhibit the remaining outputs without knowing which is correct or incorrect. Accordingly,

Ramón Huerta; Shankar Vembu; José M. Amigó; Thomas Nowotny; Charles Elkan

387

Inhibition in Multiclass Classification  

Microsoft Academic Search

The role of inhibition is investigated in a multiclass support vector machine formalism inspired by the brain structure of insects. The so-called mushroom bodies have a set of output neurons, or classification functions, that compete with each other to encode a particular input. Strongly active output neurons depress or inhibit the remaining outputs without knowing which is correct or incorrect.

Ramón Huerta; Shankar Vembu; José M. Amigó; Thomas Nowotny; Charles Elkan

2012-01-01

388

BLOG INFORMATION CLASSIFICATION  

Microsoft Academic Search

nformation Classification is the categorization of the huge amount of data in an efficient and useful way. In the current scenario data is growing exponentially due to the rise of internet rich applications. One such source of information is the blogs. Blogs are web logs maintained by their authors that contain information related to a certain topic and also contain

Nishant Patel

2012-01-01

389

Classification of partial discharges  

Microsoft Academic Search

For a long time, classification of partial discharges was performed by eye, by studying discharge patterns at the ellipse of an oscilloscope screen. The introduction of digital processing techniques allowed automation of the recognition procedure. These procedures are reported and applied to a number of actual HV constructions which suffer from partial discharges. The results of these tests show that

F. H. Kreuger; E. Gulski; A. Krivda

1993-01-01

390

Improving Student Question Classification  

ERIC Educational Resources Information Center

Students in introductory programming classes often articulate their questions and information needs incompletely. Consequently, the automatic classification of student questions to provide automated tutorial responses is a challenging problem. This paper analyzes 411 questions from an introductory Java programming course by reducing the natural…

Heiner, Cecily; Zachary, Joseph L.

2009-01-01

391

Equivalent Diagnostic Classification Models  

ERIC Educational Resources Information Center

Rupp and Templin (2008) do a good job at describing the ever expanding landscape of Diagnostic Classification Models (DCM). In many ways, their review article clearly points to some of the questions that need to be answered before DCMs can become part of the psychometric practitioners toolkit. Apart from the issues mentioned in this article that…

Maris, Gunter; Bechger, Timo

2009-01-01

392

Classification of community hospitals.  

PubMed Central

This articles describes the methodology, results, and potential applications of a study conducted by the authors to classify the nation's community hospitals. The classification system is offered as a preferable alternative to the system presently used by the Social Security Administration to implement Section 223 of the Social Security Amendments of 1972 (P.L. 92-603).

Phillip, P J; Iyer, R N

1975-01-01

393

Automatic Video Classification  

Microsoft Academic Search

Within the past few years video usage has grown in a multi-fold fashion. One of the major reasons for this explosive video growth is the rising Internet bandwidth speeds. As of today, a significant human effort is needed to categorize these video data files. A successful automatic video classification method can substantially help to reduce the growing amount of cluttered

Don Jayakody

2009-01-01

394

Homographs: Classification and Identification.  

ERIC Educational Resources Information Center

Homographs are defined in this study as sets of word forms which are spelled alike but which have entirely or partially different meanings and which may have different syntactic functions (that is, they belong to more than one form class or to more than one subclass of a form class). This report deals with the classification and identification of…

Pacak, M.; Henisz, Bozena

1968-01-01

395

A Classification of Flexibacteria  

Microsoft Academic Search

SUMMARY About go strains of gliding microbes (flexibacteria) have been considered. Data obtained by Lewin & Lounsbery (1969) and Mandel & Lewin (1969) have been used by Fager (1969) in a computer programme designed to indicate affinities and thereby possible relationships. Largely on the basis of Fager's analysis, a classification of these organisms is here proposed. Including a few species

R. A. LEWIN

1969-01-01

396

Human Body Motions Classification  

Microsoft Academic Search

This paper deals with video based parameteriza- tion and classification of human body motions. The main task of this work is to develop and verify the procedures for observing of muscle and brain activity. The developed procedures have no negative impact to brain activity (the tracking does not affect the measured EEG signals). The procedures required only standard hardware equipment

J. Havlik; J. Uhlir; Z. Horcik

397

Automatic Classification in Information Retrieval.  

ERIC Educational Resources Information Center

Addresses the application of automatic classification methods to the problems associated with computerized document retrieval. Different kinds of classifications are described, and both document and term clustering methods are discussed. References and notes are provided. (Author/JD)

van Rijsbergen, C. J.

1978-01-01

398

Seismic texture classification. Final report.  

National Technical Information Service (NTIS)

The seismic texture classification method, is a seismic attribute that can both recognize the general reflectivity styles and locate variations from these. The seismic texture classification performs a statistic analysis for the seismic section (or volume...

R. Vinther

1997-01-01

399

Standard Industrial Classification Manual, 1972.  

National Technical Information Service (NTIS)

The Standard Industrial Classification was developed for use in the classification of establishments by type of activity in which they are engaged; for purposes of facilitating the collection, tabulation, presentation, and analysis of data relating to est...

1972-01-01

400

Free classification of American English dialects by native and non-native listeners  

PubMed Central

Most second language acquisition research focuses on linguistic structures, and less research has examined the acquisition of sociolinguistic patterns. The current study explored the perceptual classification of regional dialects of American English by native and non-native listeners using a free classification task. Results revealed similar classification strategies for the native and non-native listeners. However, the native listeners were more accurate overall than the non-native listeners. In addition, the non-native listeners were less able to make use of constellations of cues to accurately classify the talkers by dialect. However, the non-native listeners were able to attend to cues that were either phonologically or sociolinguistically relevant in their native language. These results suggest that non-native listeners can use information in the speech signal to classify talkers by regional dialect, but that their lack of signal-independent cultural knowledge about variation in the second language leads to less accurate classification performance.

Clopper, Cynthia G.; Bradlow, Ann R.

2009-01-01

401

High intraindividual variation in internal transcibed spacer sequences in Aeschynanthus (Gesneriaceae): implications for phylogenetics.  

PubMed

Aeschynanthus (Gesneriaceae) is a large genus of tropical epiphytes that is widely distributed from the Himalayas and China throughout South-East Asia to New Guinea and the Solomon Islands. Polymerase chain reaction (PCR) consensus sequences of the internal transcribed spacers (ITS) of Aeschynanthus nuclear ribosomal DNA showed sequence polymorphism that was difficult to interpret. Cloning individual sequences from the PCR product generated a phylogenetic tree of 23 Aeschynanthus species (two clones per species). The intraindividual clone pairs varied from 0 to 5.01%. We suggest that the high intraindividual sequence variation results from low molecular drive in the ITS of Aeschynanthus. However, this study shows that, despite the variation found within some individuals, it is still possible to use these data to reconstruct phylogenetic relationships of the species, suggesting that clone variation, although persistent, does not pre-date the divergence of Aeschynanthus species. The Aeschynanthus analysis revealed two major clades with different but overlapping geographic distributions and reflected classification based on morphology (particularly seed hair type). PMID:10983824

Denduangboripant, J; Cronk, Q C

2000-07-22

402

Phylogenetic relationships of the operculate land snail genus Cyclophorus Montfort, 1810 in Thailand.  

PubMed

Operculate land snails of the genus Cyclophorus are distributed widely in sub-tropical and tropical Asia. Shell morphology is traditionally used for species identification in Cyclophorus but their shells exhibit considerable variation both within and between populations; species limits have been extremely difficult to determine and are poorly understood. Many currently recognized species have discontinuous distributions over large ranges but geographical barriers and low mobility of snails are likely to have led to long periods of isolation resulting in cryptic speciation of allopatric populations. As a contribution towards solving these problems, we reconstructed the molecular phylogeny of 87 Cyclophorus specimens, representing 29 nominal species (of which one was represented by four subspecies), plus three related out-group species. Molecular phylogenetic analyses were used to investigate geographic limits and speciation scenarios. The analyses of COI, 16S rRNA and 28S rRNA gene fragments were performed using neighbour-joining (NJ), maximum likelihood (ML), and Bayesian inference (BI) methods. All the obtained phylogenetic trees were congruent with each other and in most cases confirmed the species level classification. However, at least three nominate species were polyphyletic. Both C. fulguratus and C. volvulus appear to be species complexes, suggesting that populations of these species from different geographical areas of Thailand are cryptic species. C. aurantiacus pernobilis is distinct and likely to be a different species from the other members of the C. aurantiacus species complex. PMID:24076249

Nantarat, Nattawadee; Tongkerd, Piyoros; Sutcharit, Chirasak; Wade, Christopher M; Naggs, Fred; Panha, Somsak

2014-01-01

403

Morphological Phylogenetic Analysis of Seven Varieties of Ficus deltoidea Jack from the Malay Peninsula of Malaysia  

PubMed Central

This study is the first report to suggest a morphological phylogenetic framework for the seven varieties of Ficus deltoidea Jack (Ficus: Moraceae) from the Malay Peninsula of Malaysia. Several molecular-based classifications on the genus Ficus had been proposed, but neither had discussed the relationship between seven varieties of F. deltoidea to its allies nor within the varieties. The relationship between seven varieties of F. deltoidea is still debated due to the extreme morphological variabilities and ambiguous boundaries between taxa. Thus, the correct identification of these varieties is important as several morphological characters are variety-specific. To test the monophyly and further resolved the relationship in F. deltoidea, a morphological phylogenetic analysis was conducted based on herbarium specimens representing the seven varieties of F. deltoidea that were collected from the Malay Peninsula of Malaysia, by using related species of the genus Ficus; F. grossularioides, F. ischnopoda and F. oleifolia as the outgroups. Parsimony and neighbour-joining analyses indicated that F. deltoidea is monophyletic, in that the seven varieties of F. deltoidea nested into two clades; clade subspecies deltoidea (var. deltoidea, var. bilobata, var. angustifolia, var. kunstleri and var. trengganuensis) and clade subspecies motleyana (var. intermedia and var. motleyana).

Fatihah, Hasan N. N.; Mat, Nashriyah; Zaimah, Abdul R. N.; Zuhailah, Mazlan N.; Norhaslinda, Haron; Khairil, Mahmud; Ghani, Abdul Y.; Ali, Abdul M.

2012-01-01

404

High intraindividual variation in internal transcibed spacer sequences in Aeschynanthus (Gesneriaceae): implications for phylogenetics.  

PubMed Central

Aeschynanthus (Gesneriaceae) is a large genus of tropical epiphytes that is widely distributed from the Himalayas and China throughout South-East Asia to New Guinea and the Solomon Islands. Polymerase chain reaction (PCR) consensus sequences of the internal transcribed spacers (ITS) of Aeschynanthus nuclear ribosomal DNA showed sequence polymorphism that was difficult to interpret. Cloning individual sequences from the PCR product generated a phylogenetic tree of 23 Aeschynanthus species (two clones per species). The intraindividual clone pairs varied from 0 to 5.01%. We suggest that the high intraindividual sequence variation results from low molecular drive in the ITS of Aeschynanthus. However, this study shows that, despite the variation found within some individuals, it is still possible to use these data to reconstruct phylogenetic relationships of the species, suggesting that clone variation, although persistent, does not pre-date the divergence of Aeschynanthus species. The Aeschynanthus analysis revealed two major clades with different but overlapping geographic distributions and reflected classification based on morphology (particularly seed hair type).

Denduangboripant, J; Cronk, Q C

2000-01-01

405

Phylogenetics of Cancer Crabs (Crustacea: Decapoda: Brachyura)  

Microsoft Academic Search

We used morphological, mitochondrial DNA sequence, paleontological, and biogeographical information to examine the evolutionary history of crabs of the genus Cancer. Phylogenies inferred from adult morphology and DNA sequence of the cytochrome oxidase I (COI) gene were each well resolved and well supported, but differed substantially in topology. Four lines of evidence suggested that the COI data set accurately reflected

Michelle K. Harrison; Bernard J. Crespi

1999-01-01

406

Phylogeny and genus-level classification of mantellid frogs (Amphibia, Anura)  

Microsoft Academic Search

We propose a novel classification of frogs in the family Mantellidae, based on published phylogenetic information and on a new analysis of molecular data. Our molecular tree for 53 mantellid species is based on 2419 base pairs of the mitochondrial 12S rRNA, 16S rRNA, tRNAVal and cytochrome b genes, and of the nuclear rhodopsin gene. Because the genus Mantidactylus Boulenger

Frank Glaw; Miguel Vences

2006-01-01

407

Efficient Fingercode Classification  

NASA Astrophysics Data System (ADS)

In this paper, we present an efficient fingerprint classification algorithm which is an essential component in many critical security application systems e. g. systems in the e-government and e-finance domains. Fingerprint identification is one of the most important security requirements in homeland security systems such as personnel screening and anti-money laundering. The problem of fingerprint identification involves searching (matching) the fingerprint of a person against each of the fingerprints of all registered persons. To enhance performance and reliability, a common approach is to reduce the search space by firstly classifying the fingerprints and then performing the search in the respective class. Jain et al. proposed a fingerprint classification algorithm based on a two-stage classifier, which uses a K-nearest neighbor classifier in its first stage. The fingerprint classification algorithm is based on the fingercode representation which is an encoding of fingerprints that has been demonstrated to be an effective fingerprint biometric scheme because of its ability to capture both local and global details in a fingerprint image. We enhance this approach by improving the efficiency of the K-nearest neighbor classifier for fingercode-based fingerprint classification. Our research firstly investigates the various fast search algorithms in vector quantization (VQ) and the potential application in fingerprint classification, and then proposes two efficient algorithms based on the pyramid-based search algorithms in VQ. Experimental results on DB1 of FVC 2004 demonstrate that our algorithms can outperform the full search algorithm and the original pyramid-based search algorithms in terms of computational efficiency without sacrificing accuracy.

Sun, Hong-Wei; Law, Kwok-Yan; Gollmann, Dieter; Chung, Siu-Leung; Li, Jian-Bin; Sun, Jia-Guang

408

Accurate estimation of sigma(exp 0) using AIRSAR data  

NASA Technical Reports Server (NTRS)

During recent years signature analysis, classification, and modeling of Synthetic Aperture Radar (SAR) data as well as estimation of geophysical parameters from SAR data have received a great deal of interest. An important requirement for the quantitative use of SAR data is the accurate estimation of the backscattering coefficient sigma(exp 0). In terrain with relief variations radar signals are distorted due to the projection of the scene topography into the slant range-Doppler plane. The effect of these variations is to change the physical size of the scattering area, leading to errors in the radar backscatter values and incidence angle. For this reason the local incidence angle, derived from sensor position and Digital Elevation Model (DEM) data must always be considered. Especially in the airborne case, the antenna gain pattern can be an additional source of radiometric error, because the radar look angle is not known precisely as a result of the the aircraft motions and the local surface topography. Consequently, radiometric distortions due to the antenna gain pattern must also be corrected for each resolution cell, by taking into account aircraft displacements (position and attitude) and position of the backscatter element, defined by the DEM data. In this paper, a method to derive an accurate estimation of the backscattering coefficient using NASA/JPL AIRSAR data is presented. The results are evaluated in terms of geometric accuracy, radiometric variations of sigma(exp 0), and precision of the estimated forest biomass.

Holecz, Francesco; Rignot, Eric

1995-01-01

409

Novel Accurate Bacterial Discrimination by MALDI-Time-of-Flight MS Based on Ribosomal Proteins Coding in S10-spc-alpha Operon at Strain Level S10-GERMS  

NASA Astrophysics Data System (ADS)

Matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is one of the most widely used mass-based approaches for bacterial identification and classification because of the simple sample preparation and extremely rapid analysis within a few minutes. To establish the accurate MALDI-TOF MS bacterial discrimination method at strain level, the ribosomal subunit proteins coded in the S 10-spc-alpha operon, which encodes half of the ribosomal subunit protein and is highly conserved in eubacterial genomes, were selected as reliable biomarkers. This method, named the S10-GERMS method, revealed that the strains of genus Pseudomonas were successfully identified and discriminated at species and strain levels, respectively; therefore, the S10-GERMS method was further applied to discriminate the pathovar of P. syringae. The eight selected biomarkers (L24, L30, S10, S12, S14, S16, S17, and S19) suggested the rapid discrimination of P. syringae at the strain (pathovar) level. The S10-GERMS method appears to be a powerful tool for rapid and reliable bacterial discrimination and successful phylogenetic characterization. In this article, an overview of the utilization of results from the S10-GERMS method is presented, highlighting the characterization of the Lactobacillus casei group and discrimination of the bacteria of genera Bacillus and Sphingopyxis despite only two and one base difference in the 16S rRNA gene sequence, respectively.

Tamura, Hiroto; Hotta, Yudai; Sato, Hiroaki

2013-08-01

410

Clinical classification of pulmonary hypertension  

Microsoft Academic Search

In 1998, during the Second World Symposium on Pulmonary Hypertension (PH) held in Evian, France, a clinical classification of PH was proposed. The aim of the Evian classification was to individualize different categories sharing similarities in pathophysiological mechanisms, clinical presentation, and therapeutic options. The Evian classification is now well accepted and widely used in clinical practice, especially in specialized centers.

Gerald Simonneau; Nazzareno Galiè; Lewis J Rubin; David Langleben; Werner Seeger; Guido Domenighetti; Simon Gibbs; Didier Lebrec; Rudolf Speich; Maurice Beghetti; Stuart Rich; Alfred Fishman

2004-01-01

411

76 FR 59031 - Classification Challenge Regulations  

Federal Register 2010, 2011, 2012, 2013

...Classification challenge, Classified information...PART 1907--CHALLENGES TO CLASSIFICATION...classification challenge. (b) Agency...classification challenges shall be reviewed...a) Formal challenges shall be directed...promptly forward the challenge to the...

2011-09-23