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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



Phylogenetic classification and molecular evolution of knotted1 homeobox genes  

Microsoft Academic Search

Homeobox genes encode a family of DNA-binding regulatory proteins which are crucial for development. The first plant homeobox\\u000a gene identified was knotted1 which plays a major role in leaf development. The knotted1 gene has a homeobox which encodes a homeodomain (HD) and HD proteins have been shown to function as transcription factors.\\u000a A phylogenetic classification of the KNOTTED1 HD is

A. D. Deshpande; W. Ramakrishna; G. P. Mulay; V. S. Gupta; P. K. Ranjekar



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.



Accurate Reconstruction of Insertion-Deletion Histories by Statistical Phylogenetics  

PubMed Central

The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for finite substitution models (Dayhoff's probability matrices and Felsenstein's pruning algorithm) to arbitrary-length sequences. In this paper, we report results of a simulation-based benchmark of several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes.

Westesson, Oscar; Lunter, Gerton; Paten, Benedict; Holmes, Ian



Phylogenetic and functional classification of ATP-binding cassette (ABC) systems.  


ATP binding cassette (ABC) systems constitute one of the most abundant superfamilies of proteins. They are involved in the transport of a wide variety of substances, but also in many cellular processes and in their regulation. In this paper, we made a comparative analysis of the properties of ABC systems and we provide a phylogenetic and functional classification. This analysis will be helpful to accurately annotate ABC systems discovered during the sequencing of the genome of living organisms and to identify the partners of the ABC ATPases. PMID:12370001

Bouige, Philippe; Laurent, David; Piloyan, Linda; Dassa, Elie



The ABC of ABCS: a phylogenetic and functional classification of ABC systems in living organisms.  


ATP binding cassette (ABC) systems constitute one of the most abundant superfamilies of proteins. They are involved not only in the transport of a wide variety of substances, but also in many cellular processes and in their regulation. In this paper, we made a comparative analysis of the properties of ABC systems and we provide a phylogenetic and functional classification. This analysis will be helpful to accurately annotate ABC systems discovered during the sequencing of the genome of living organisms and to identify the partners of the ABC ATPases. PMID:11421270

Dassa, E; Bouige, P


Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models.  


Metagenomics projects collect DNA from uncharacterized environments that may contain thousands of species per sample. One main challenge facing metagenomic analysis is phylogenetic classification of raw sequence reads into groups representing the same or similar taxa, a prerequisite for genome assembly and for analyzing the biological diversity of a sample. New sequencing technologies have made metagenomics easier, by making sequencing faster, and more difficult, by producing shorter reads than previous technologies. Classifying sequences from reads as short as 100 base pairs has until now been relatively inaccurate, requiring researchers to use older, long-read technologies. We present Phymm, a classifier for metagenomic data, that has been trained on 539 complete, curated genomes and can accurately classify reads as short as 100 base pairs, a substantial improvement over previous composition-based classification methods. We also describe how combining Phymm with sequence alignment algorithms improves accuracy. PMID:19648916

Brady, Arthur; Salzberg, Steven L



Accurate cancer classification using expressions of very few genes.  


We aim at finding the smallest set of genes that can ensure highly accurate classification of cancers from microarray data by using supervised machine learning algorithms. The significance of finding the minimum gene subsets is three-fold: 1) It greatly reduces the computational burden and "noise" arising from irrelevant genes. In the examples studied in this paper, finding the minimum gene subsets even allows for extraction of simple diagnostic rules which lead to accurate diagnosis without the need for any classifiers. 2) It simplifies gene expression tests to include only a very small number of genes rather than thousands of genes, which can bring down the cost for cancer testing significantly. 3) It calls for further investigation into the possible biological relationship between these small numbers of genes and cancer development and treatment. Our simple yet very effective method involves two steps. In the first step, we choose some important genes using a feature importance ranking scheme. In the second step, we test the classification capability of all simple combinations of those important genes by using a good classifier. For three "small" and "simple" data sets with two, three, and four cancer (sub)types, our approach obtained very high accuracy with only two or three genes. For a "large" and "complex" data set with 14 cancer types, we divided the whole problem into a group of binary classification problems and applied the 2-step approach to each of these binary classification problems. Through this "divide-and-conquer" approach, we obtained accuracy comparable to previously reported results but with only 28 genes rather than 16,063 genes. In general, our method can significantly reduce the number of genes required for highly reliable diagnosis. PMID:17277412

Wang, Lipo; Chu, Feng; Xie, Wei


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.



Phylogenetic classification of Cordyceps and the clavicipitaceous fungi.  


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 1alpha (tef1), the largest and the second largest subunits of RNA polymerase II (rpb1 and rpb2), beta-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 Clavicipitaceaes. 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 Clavicipitaceaes. 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. PMID:18490993

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



Phylogenetic classification of transporters and other membrane proteins from Saccharomyces cerevisiae  

Microsoft Academic Search

.   On the basis of functional and phylogenetic criteria, we have identified a total of 229 subfamilies and 111 singletons predicted\\u000a to carry out transport or other membrane functions in Saccharomyces cerevisiae. We have extended the Transporter Classification (TC) and created a Membrane Classification (MC) for non-transporter membrane\\u000a proteins. Using the preliminary phylogenetic digits X, Y, Z (for new families,

Benoît De Hertogh; Elvira Carvajal; Emmanuel Talla; Bernard Dujon; Philippe Baret; André Goffeau



Molecular phylogenetics and the classification of honey bee viruses  

Microsoft Academic Search

Summary.  ?We present the phylogenetic relationships of several picorna-like RNA viruses found in honey bees, with respect to 13 additional\\u000a plant and animal positive-strand RNA viruses. Most of the honey bee viruses fall into an unnamed family of insect RNA viruses\\u000a typified by the Drosophila C virus. Different bee viruses are broadly distributed within this group, suggesting either that the ability

J. D. Evans; A. C. Hung



Making Time-Series Classification More Accurate Using Learned Constraints  

Microsoft Academic Search

It has long been known that Dynamic Time Warping (DTW) is superior to Euclidean distance for classification and clustering of time series. However, until lately, most research has utilized Euclidean distance because it is more efficiently calculated. A recently introduced technique that greatly mitigates DTWs demanding CPU time has sparked a flurry of research activity. However, the technique and its

Eamonn J. Keogh



An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV1  

Microsoft Academic Search

Genetically diverse pathogens (such as Human Immunodeficiency virus type 1, HIV-1) are frequently stratified into phylogenetically or immunologically defined subtypes for classification purposes. Computational identification of such subtypes is helpful in surveillance, epidemiological analysis and detection of novel variants, e.g., circulating recombinant forms in HIV-1. A number of conceptually and technically different techniques have been proposed for determining the subtype

Sergei L. Kosakovsky Pond; David Posada; Eric Stawiski; Colombe Chappey; Art F. Y. Poon; Gareth Hughes; Esther Fearnhill; Mike B. Gravenor; Andrew J. Leigh Brown; Simon D. W. Frost



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




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



Phylogenetic classification of transporters and other membrane proteins from Saccharomyces cerevisiae.  


On the basis of functional and phylogenetic criteria, we have identified a total of 229 subfamilies and 111 singletons predicted to carry out transport or other membrane functions in Saccharomyces cerevisiae. We have extended the Transporter Classification (TC) and created a Membrane Classification (MC) for non-transporter membrane proteins. Using the preliminary phylogenetic digits X, Y, Z (for new families, subfamilies, and clusters, respectively), we allocated a five-digit number to 850 proteins predicted to contain more than two transmembrane domains. Compared with a previous TC of the yeast genome, we classified an additional set of 538 membrane proteins (transporters and non-transporters) and identified 111 novel phylogenetic subfamilies. PMID:12192589

De Hertogh, Benoît; Carvajal, Elvira; Talla, Emmanuel; Dujon, Bernard; Baret, Philippe; Goffeau, André



Use of Spoligotyping for Accurate Classification of Recurrent Tuberculosis  

Microsoft Academic Search

The spoligotyping method has become an important tool for the tracking of Mycobacterium tuberculosis strains in different epidemiological settings. In this study, we demonstrate the ability of the spoligotyping technique to accurately determine the pathogenetic mechanism of recurrent disease. This methodology has advantages over conventional restriction fragment length polymorphism methods which may be useful in large- scale intervention studies.

R. M. Warren; E. M. Streicher; S. Charalambous; G. Churchyard; G. D. van der Spuy; A. D. Grant; P. D. van Helden; T. C. Victor



Accurate wet-type centrifugal classification using an almost rigidly rotating flow — classification principle and performance of the batch-type classification  

Microsoft Academic Search

We have proposed a new system for an accurate wet-type centrifugal classification to which an almost rigidly rotating through-flow is applied. This flow can be produced within a highly rotating double-walled container, without any turbulent fluctuation. In the present paper, we have employed the batch-type classification with a cylinder-sphere-shaped container in classification experiments, theoretical and numerical flow analyses, and flow-visualization

Koichi Nakabayashi; Yoichi Tsuchida



The COG database: new developments in phylogenetic classification of proteins from complete genomes  

Microsoft Academic Search

The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of bacteria, archaea and the yeast Saccharomyces cerevisiae (http:\\/\\/\\/COG). In addition, a supplement to the COGs is available, in which proteins encoded in

Roman L. Tatusov; Darren A. Natale; Igor V. Garkavtsev; Tatiana A. Tatusova; Uma T. Shankavaram; Bachoti S. Rao; Boris Kiryutin; Michael Y. Galperin; Natalie D. Fedorova; Eugene V. Koonin



The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.  


Eukaryotes and archaebacteria form the clade neomura and are sisters, as shown decisively by genes fragmented only in archaebacteria and by many sequence trees. This sisterhood refutes all theories that eukaryotes originated by merging an archaebacterium and an alpha-proteobacterium, which also fail to account for numerous features shared specifically by eukaryotes and actinobacteria. I revise the phagotrophy theory of eukaryote origins by arguing that the essentially autogenous origins of most eukaryotic cell properties (phagotrophy, endomembrane system including peroxisomes, cytoskeleton, nucleus, mitosis and sex) partially overlapped and were synergistic with the symbiogenetic origin of mitochondria from an alpha-proteobacterium. These radical innovations occurred in a derivative of the neomuran common ancestor, which itself had evolved immediately prior to the divergence of eukaryotes and archaebacteria by drastic alterations to its eubacterial ancestor, an actinobacterial posibacterium able to make sterols, by replacing murein peptidoglycan by N-linked glycoproteins and a multitude of other shared neomuran novelties. The conversion of the rigid neomuran wall into a flexible surface coat and the associated origin of phagotrophy were instrumental in the evolution of the endomembrane system, cytoskeleton, nuclear organization and division and sexual life-cycles. Cilia evolved not by symbiogenesis but by autogenous specialization of the cytoskeleton. I argue that the ancestral eukaryote was uniciliate with a single centriole (unikont) and a simple centrosomal cone of microtubules, as in the aerobic amoebozoan zooflagellate Phalansterium. I infer the root of the eukaryote tree at the divergence between opisthokonts (animals, Choanozoa, fungi) with a single posterior cilium and all other eukaryotes, designated 'anterokonts' because of the ancestral presence of an anterior cilium. Anterokonts comprise the Amoebozoa, which may be ancestrally unikont, and a vast ancestrally biciliate clade, named 'bikonts'. The apparently conflicting rRNA and protein trees can be reconciled with each other and this ultrastructural interpretation if long-branch distortions, some mechanistically explicable, are allowed for. Bikonts comprise two groups: corticoflagellates, with a younger anterior cilium, no centrosomal cone and ancestrally a semi-rigid cell cortex with a microtubular band on either side of the posterior mature centriole; and Rhizaria [a new infrakingdom comprising Cercozoa (now including Ascetosporea classis nov.), Retaria phylum nov., Heliozoa and Apusozoa phylum nov.], having a centrosomal cone or radiating microtubules and two microtubular roots and a soft surface, frequently with reticulopodia. Corticoflagellates comprise photokaryotes (Plantae and chromalveolates, both ancestrally with cortical alveoli) and Excavata (a new protozoan infrakingdom comprising Loukozoa, Discicristata and Archezoa, ancestrally with three microtubular roots). All basal eukaryotic radiations were of mitochondrial aerobes; hydrogenosomes evolved polyphyletically from mitochondria long afterwards, the persistence of their double envelope long after their genomes disappeared being a striking instance of membrane heredity. I discuss the relationship between the 13 protozoan phyla recognized here and revise higher protozoan classification by updating as subkingdoms Lankester's 1878 division of Protozoa into Corticata (Excavata, Alveolata; with prominent cortical microtubules and ancestrally localized cytostome--the Parabasalia probably secondarily internalized the cytoskeleton) and Gymnomyxa [infrakingdoms Sarcomastigota (Choanozoa, Amoebozoa) and Rhizaria; both ancestrally with a non-cortical cytoskeleton of radiating singlet microtubules and a relatively soft cell surface with diffused feeding]. As the eukaryote root almost certainly lies within Gymnomyxa, probably among the Sarcomastigota, Corticata are derived. Following the single symbiogenetic origin of chloroplasts in a corticoflagellate host with cortical alveoli, this ancestral plant radiated

Cavalier-Smith, T



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.




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.



Classification of Phylogenetic Profiles for Protein Function Prediction: An SVM Approach  

NASA Astrophysics Data System (ADS)

Predicting the function of an uncharacterized protein is a major challenge in post-genomic era due to problems complexity and scale. Having knowledge of protein function is a crucial link in the development of new drugs, better crops, and even the development of biochemicals such as biofuels. Recently numerous high-throughput experimental procedures have been invented to investigate the mechanisms leading to the accomplishment of a protein’s function and Phylogenetic profile is one of them. Phylogenetic profile is a way of representing a protein which encodes evolutionary history of proteins. In this paper we proposed a method for classification of phylogenetic profiles using supervised machine learning method, support vector machine classification along with radial basis function as kernel for identifying functionally linked proteins. We experimentally evaluated the performance of the classifier with the linear kernel, polynomial kernel and compared the results with the existing tree kernel. In our study we have used proteins of the budding yeast saccharomyces cerevisiae genome. We generated the phylogenetic profiles of 2465 yeast genes and for our study we used the functional annotations that are available in the MIPS database. Our experiments show that the performance of the radial basis kernel is similar to polynomial kernel is some functional classes together are better than linear, tree kernel and over all radial basis kernel outperformed the polynomial kernel, linear kernel and tree kernel. In analyzing these results we show that it will be feasible to make use of SVM classifier with radial basis function as kernel to predict the gene functionality using phylogenetic profiles.

Kotaru, Appala Raju; Joshi, Ramesh C.


Machine learning algorithms for accurate flow-based network traffic classification: Evaluation and comparison  

Microsoft Academic Search

The task of network management and monitoring relies on an accurate characterization of network traffic generated by different applications and network protocols. We employ three supervised machine learning (ML) algorithms, Bayesian Networks, Decision Trees and Multilayer Perceptrons for the flow-based classification of six different types of Internet traffic including peer-to-peer (P2P) and content delivery (Akamai) traffic. The dependency of the

Murat Soysal; Ece Guran Schmidt



Molecular phylogenetic evaluation of classification and scenarios of character evolution in calcareous sponges (Porifera, Class Calcarea).  


Calcareous sponges (Phylum Porifera, Class Calcarea) are known to be taxonomically difficult. Previous molecular studies have revealed many discrepancies between classically recognized taxa and the observed relationships at the order, family and genus levels; these inconsistencies question underlying hypotheses regarding the evolution of certain morphological characters. Therefore, we extended the available taxa and character set by sequencing the complete small subunit (SSU) rDNA and the almost complete large subunit (LSU) rDNA of additional key species and complemented this dataset by substantially increasing the length of available LSU sequences. Phylogenetic analyses provided new hypotheses about the relationships of Calcarea and about the evolution of certain morphological characters. We tested our phylogeny against competing phylogenetic hypotheses presented by previous classification systems. Our data reject the current order-level classification by again finding non-monophyletic Leucosolenida, Clathrinida and Murrayonida. In the subclass Calcinea, we recovered a clade that includes all species with a cortex, which is largely consistent with the previously proposed order Leucettida. Other orders that had been rejected in the current system were not found, but could not be rejected in our tests either. We found several additional families and genera polyphyletic: the families Leucascidae and Leucaltidae and the genus Leucetta in Calcinea, and in Calcaronea the family Amphoriscidae and the genus Ute. Our phylogeny also provided support for the vaguely suspected close relationship of several members of Grantiidae with giantortical diactines to members of Heteropiidae. Similarly, our analyses revealed several unexpected affinities, such as a sister group relationship between Leucettusa (Leucaltidae) and Leucettidae and between Leucascandra (Jenkinidae) and Sycon carteri (Sycettidae). According to our results, the taxonomy of Calcarea is in desperate need of a thorough revision, which cannot be achieved by considering morphology alone or relying on a taxon sampling based on the current classification below the subclass level. PMID:22479395

Voigt, Oliver; Wülfing, Eilika; Wörheide, Gert



Cellulose-degrading potentials and phylogenetic classification of carboxymethyl-cellulose decomposing bacteria isolated from soil.  


In a previous study, culturable carboxymethyl-cellulose (CMC) decomposing soil bacteria isolated from different sampling positions across an agricultural encatchment have been classified into 31 pattern groups by digestion of amplified 16S rDNA using a single restriction enzyme (Ulrich and Wirth: Microb. Ecol. 37, 238-247, 1999). In order to reveal relationships between phylogenetic diversity and phenotypic functions, a further differentiation of two selected site-specific pattern groups (I and H) was performed, resulting in a sub-classification of four and three ARDRA groups, respectively. Based on sequencing a representative isolate of each ARDRA group, the isolates were assigned to the genus Streptomyces. The ARDRA groups were dispersed across various clades of the genus with a direct affiliation to species known for cellulolytic activity in one group, only. The isolates differed in potentials to degrade colloidal, native or highly crystalline cellulose derivatives. Out of 39 isolates, 11 were capable of degrading all substrates, 17 were restricted to degrade CMC only, and 11 were active decomposers of exclusively both CMC and colloidal cellulose. In most cases, the genetic classification of the isolates corresponded with groupings based on cellulose degrading capabilities. Thus, isolates of four ARDRA groups were restricted to the degradation of CMC, while two further isolates which efficiently degraded all cellulose derivatives formed two separate ARDRA groups. The major ARDRA group, however; displayed a high variability of degradation capabilities. The study of additional phenotypic features revealed a broad potential to decompose a set of various carbon substrates, which matched the phylogenetic classification in several cases. PMID:12583719

Wirth, Stephan; Ulrich, Andreas



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.



INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences  

PubMed Central

Background Taxonomic classification of metagenomic sequences is the first step in metagenomic analysis. Existing taxonomic classification approaches are of two types, similarity-based and composition-based. Similarity-based approaches, though accurate and specific, are extremely slow. Since, metagenomic projects generate millions of sequences, adopting similarity-based approaches becomes virtually infeasible for research groups having modest computational resources. In this study, we present INDUS - a composition-based approach that incorporates the following novel features. First, INDUS discards the 'one genome-one composition' model adopted by existing compositional approaches. Second, INDUS uses 'compositional distance' information for identifying appropriate assignment levels. Third, INDUS incorporates steps that attempt to reduce biases due to database representation. Results INDUS is able to rapidly classify sequences in both simulated and real metagenomic sequence data sets with classification efficiency significantly higher than existing composition-based approaches. Although the classification efficiency of INDUS is observed to be comparable to those by similarity-based approaches, the binning time (as compared to alignment based approaches) is 23-33 times lower. Conclusion Given it's rapid execution time, and high levels of classification efficiency, INDUS is expected to be of immense interest to researchers working in metagenomics and microbial ecology. Availability A web-server for the INDUS algorithm is available at



Enhanced assessment of the wound-healing process by accurate multiview tissue classification.  


With the widespread use of digital cameras, freehand wound imaging has become common practice in clinical settings. There is however still a demand for a practical tool for accurate wound healing assessment, combining dimensional measurements and tissue classification in a single user-friendly system. We achieved the first part of this objective by computing a 3-D model for wound measurements using uncalibrated vision techniques. We focus here on tissue classification from color and texture region descriptors computed after unsupervised segmentation. Due to perspective distortions, uncontrolled lighting conditions and view points, wound assessments vary significantly between patient examinations. The main contribution of this paper is to overcome this drawback with a multiview strategy for tissue classification, relying on a 3-D model onto which tissue labels are mapped and classification results merged. The experimental classification tests demonstrate that enhanced repeatability and robustness are obtained and that metric assessment is achieved through real area and volume measurements and wound outline extraction. This innovative tool is intended for use not only in therapeutic follow-up in hospitals but also for telemedicine purposes and clinical research, where repeatability and accuracy of wound assessment are critical. PMID:20875969

Wannous, Hazem; Lucas, Yves; Treuillet, Sylvie



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.



Accurate Molecular Classification of Renal Tumors Using MicroRNA Expression  

PubMed Central

Subtypes of renal tumors have different genetic backgrounds, prognoses, and responses to surgical and medical treatment, and their differential diagnosis is a frequent challenge for pathologists. New biomarkers can help improve the diagnosis and hence the management of renal cancer patients. We extracted RNA from 71 formalin-fixed paraffin-embedded (FFPE) renal tumor samples and measured expression of more than 900 microRNAs using custom microarrays. Clustering revealed similarity in microRNA expression between oncocytoma and chromophobe subtypes as well as between conventional (clear-cell) and papillary tumors. By basing a classification algorithm on this structure, we followed inherent biological correlations and could achieve accurate classification using few microRNAs markers. We defined a two-step decision-tree classifier that uses expression levels of six microRNAs: the first step uses expression levels of hsa-miR-210 and hsa-miR-221 to distinguish between the two pairs of subtypes; the second step uses either hsa-miR-200c with hsa-miR-139-5p to identify oncocytoma from chromophobe, or hsa-miR-31 with hsa-miR-126 to identify conventional from papillary tumors. The classifier was tested on an independent set of FFPE tumor samples from 54 additional patients, and identified correctly 93% of the cases. Validation on qRT-PCR platform demonstrated high correlation with microarray results and accurate classification. MicroRNA expression profiling is a very effective molecular bioassay for classification of renal tumors and can offer a quantitative standardized complement to current methods of tumor classification.

Fridman, Eddie; Dotan, Zohar; Barshack, Iris; David, Miriam Ben; Dov, Avital; Tabak, Sarit; Zion, Orit; Benjamin, Sima; Benjamin, Hila; Kuker, Hagit; Avivi, Camila; Rosenblatt, Kinneret; Polak-Charcon, Sylvie; Ramon, Jacob; Rosenfeld, Nitzan; Spector, Yael



Phylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: a case study in graphidaceae (ascomycota).  


Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed. PMID:23251515

Parnmen, Sittiporn; Lücking, Robert; Lumbsch, H Thorsten



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.


A classification of the Chloridoideae (Poaceae) based on multi-gene phylogenetic trees.  


We conducted a molecular phylogenetic study of the subfamily Chloridoideae using six plastid DNA sequences (ndhA intron, ndhF, rps16-trnK, rps16 intron, rps3, and rpl32-trnL) and a single nuclear ITS DNA sequence. Our large original data set includes 246 species (17.3%) representing 95 genera (66%) of the grasses currently placed in the Chloridoideae. The maximum likelihood and Bayesian analysis of DNA sequences provides strong support for the monophyly of the Chloridoideae; followed by, in order of divergence: a Triraphideae clade with Neyraudia sister to Triraphis; an Eragrostideae clade with the Cotteinae (includes Cottea and Enneapogon) sister to the Uniolinae (includes Entoplocamia, Tetrachne, and Uniola), and a terminal Eragrostidinae clade of Ectrosia, Harpachne, and Psammagrostis embedded in a polyphyletic Eragrostis; a Zoysieae clade with Urochondra sister to a Zoysiinae (Zoysia) clade, and a terminal Sporobolinae clade that includes Spartina, Calamovilfa, Pogoneura, and Crypsis embedded in a polyphyletic Sporobolus; and a very large terminal Cynodonteae clade that includes 13 monophyletic subtribes. The Cynodonteae includes, in alphabetical order: Aeluropodinae (Aeluropus); Boutelouinae (Bouteloua); Eleusininae (includes Apochiton, Astrebla with Schoenefeldia embedded, Austrochloris, Brachyachne, Chloris, Cynodon with Brachyachne embedded in part, Eleusine, Enteropogon with Eustachys embedded in part, Eustachys, Chrysochloa, Coelachyrum, Leptochloa with Dinebra embedded, Lepturus, Lintonia, Microchloa, Saugetia, Schoenefeldia, Sclerodactylon, Tetrapogon, and Trichloris); Hilariinae (Hilaria); Monanthochloinae (includes Distichlis, Monanthochloe, and Reederochloa); Muhlenbergiinae (Muhlenbergia with Aegopogon, Bealia, Blepharoneuron, Chaboissaea, Lycurus, Pereilema, Redfieldia, Schaffnerella, and Schedonnardus all embedded); Orcuttiinae (includes Orcuttia and Tuctoria); Pappophorinae (includes Neesiochloa and Pappophorum); Scleropogoninae (includes Blepharidachne, Dasyochloa, Erioneuron, Munroa, Scleropogon, and Swallenia); Traginae (Tragus with Monelytrum, Polevansia, and Willkommia all embedded); Tridentinae (includes Gouinia, Tridens, Triplasis, and Vaseyochloa); Triodiinae (Triodia); and the Tripogoninae (Melanocenchris and Tripogon with Eragrostiella embedded). In our study the Cynodonteae still include 19 genera and the Zoysieae include a single genus that are not yet placed in a subtribe. The tribe Triraphideae and the subtribe Aeluropodinae are newly treated at that rank. We propose a new tribal and subtribal classification for all known genera in the Chloridoideae. The subfamily might have originated in Africa and/or Asia since the basal lineage, the Triraphideae, includes species with African and Asian distribution. PMID:20096795

Peterson, Paul M; Romaschenko, Konstantin; Johnson, Gabriel



Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis  

PubMed Central

Background Sequence-based phylogenetic trees are a well-established tool for characterizing diversity of both macroorganisms and microorganisms. Phylogenetic methods have recently been applied to shotgun metagenomic data from microbial communities, particularly with the aim of classifying reads. But the accuracy of gene-family phylogenies that characterize evolutionary relationships among short, non-overlapping sequencing reads has not been thoroughly evaluated. Results To quantify errors in metagenomic read trees, we developed MetaPASSAGE, a software pipeline to generate in silico bacterial communities, simulate a sample of shotgun reads from a gene family represented in the community, orient or translate reads, and produce a profile-based alignment of the reads from which a gene-family phylogenetic tree can be built. We applied MetaPASSAGE to a variety of RNA and protein-coding gene families, built trees using a range of different phylogenetic methods, and compared the resulting trees using topological and branch-length error metrics. We identified read length as one of the major sources of error. Because phylogenetic methods use a reference database of full-length sequences from the gene family to guide construction of alignments and trees, we found that error can also be substantially reduced through increasing the size and diversity of the reference database. Finally, UniFrac analysis, which compares metagenomic samples based on a summary statistic computed over all branches in a read tree, is very robust to the level of error we observe. Conclusions Bacterial community diversity can be quantified using phylogenetic approaches applied to shotgun metagenomic data. As sequencing reads get longer and more genomes across the bacterial tree of life are sequenced, the accuracy of this approach will continue to improve, opening the door to more applications.



Proceedings towards a natural classification of the worldwide taxa Phellinus s.l. and Inonotus s.l., and phylogenetic relationships of allied genera  

Microsoft Academic Search

The classification of Phellinus s.l., Inonotus s.l. and the phylogenetic relationships of allied gen- era were studied using nuc-lsu rDNA sequence data. The worldwide taxon sampling comprised 107 spe- cies, 99 of them belonging to the Hymenochaetales. The phylogenetic trees were discussed in relation to morphological and anatomical features of the fruit bodies. The Hymenochaetales formed no monophy- letic group

Tobias Wagner


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

Microsoft Academic Search

\\u000a The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics,\\u000a evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequences\\u000a of these rearrangements. However, even simple models lead to NP-hard problems, particularly in the area of phylogenetic analysis.\\u000a Current approaches are limited to small collections of

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



Classification and phylogenetic relationships of African tilapiine fishes inferred from mitochondrial DNA sequences.  


African cichlid fishes are composed of two major lineages, the haplochromines and the tilapiines. Whereas the phylogenetic relationships of the haplochromines have been studied extensively, primarily because of their spectacular adaptive radiations in the Great Lakes of East Africa, little is known about the relationships among the tilapiine species, despite the fact that they have become an important component of African, indeed world, aquaculture. To remedy this situation, molecular phylogenetic analysis of tilapiine fishes was undertaken. A segment of mitochondrial DNA encompassing the terminal part of the tRNA(Pro) gene and the most variable part of the control region was amplified by the polymerase chain reaction with DNA samples isolated from 42 tilapiine species, and the amplification products were subjected to heteroduplex analysis and sequencing. Phylogenetic trees based on 68 sequences revealed the existence of 11 sequence groups and 11 single-sequence branches. The groups, designated Ti1 through Ti11, were distinguished by specific combinations of diagnostic substitutions, formation of monophyletic clusters, and separation by genetic distances in excess of 0.04. Although the relationships among the groups could not be resolved, the sequences separated Oreochromis and Sarotherodon from Tilapia, as defined by Trewavas. The Oreochromis sequences clustered with the Sarotherodon sequences and thus supported the hypothesis that the mouthbrooding behavior of the tilapiine fishes evolved only once from the substrate-spawning behavior. Since on phylogenetic trees the O. alcalicus (sub)species were always separated from O. amphimelas by other Oreochromis species, it was concluded that the adaptation to life in water with a high salt concentration and high pH values evolved independently at least twice in the tilapiine fishes. The tilapiines diverged from the haplochromines more than 8 million years ago; most of the intragroup divergences among the tilapiines took place an estimated 1.1 to 6 million years ago. PMID:11527464

Nagl, S; Tichy, H; Mayer, W E; Samonte, I E; McAndrew, B J; Klein, J



Genomic classification of fish nodaviruses by molecular phylogenetic analysis of the coat protein gene.  

PubMed Central

A molecular phylogenetic analysis of 25 isolates of fish nodaviruses, the causative agents of viral nervous necrosis of marine fish, was performed based on the nucleotide sequences (427 bases) of the coat protein gene. These fish nodaviruses were classified into four clusters: tiger puffer nervous necrosis virus, striped jack nervous necrosis virus, berfin flounder nervous necrosis virus, and red-spotted grouper nervous necrosis virus.

Nishizawa, T; Furuhashi, M; Nagai, T; Nakai, T; Muroga, K



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


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



Toward a Phylogenetic Classification of Primates Based on DNA Evidence Complemented by Fossil Evidence  

Microsoft Academic Search

A highly resolved primate cladogram based on DNA evidence is congruent with extant and fossil osteological evidence. A provisional primate classification based on this cladogram and the time scale provided by fossils and the model of local molecular clocks has all named taxa represent clades and assigns the same taxonomic rank to those clades of roughly equivalent age. Order Primates

Morris Goodman; Calvin A. Porter; John Czelusniak; Scott L. Page; Horacio Schneider; Jeheskel Shoshani; Gregg Gunnell; Colin P. Groves



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

PubMed Central

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 algorithms on FAME data or on 16S rRNA gene data. The knowledge gained from the tree can then be used to evaluate FAME-based classifiers, resulting in a novel framework for bacterial species classification. Results In view of learning in a taxonomic framework, we consider two types of trees. First, a FAME tree is constructed with a supervised divisive clustering algorithm. Subsequently, based on 16S rRNA gene sequence analysis, phylogenetic trees are inferred by the NJ and UPGMA methods. In this second approach, the species classification problem is based on the combination of two different types of data. Herein, 16S rRNA gene sequence data is used for phylogenetic tree inference and the corresponding binary tree splits are learned based on FAME data. We call this learning approach 'phylogenetic learning'. Supervised Random Forest models are developed to train the classification tasks in a stratified cross-validation setting. In this way, better classification results are obtained for species that are typically hard to distinguish by a single or flat multi-class classification model. Conclusions FAME-based bacterial species classification is successfully evaluated in a taxonomic framework. Although the proposed approach does not improve the overall accuracy compared to flat multi-class classification, it has some distinct advantages. First, it has better capabilities for distinguishing species on which flat multi-class classification fails. Secondly, the hierarchical classification structure allows to easily evaluate and visualize the resolution of FAME data for the discrimination of bacterial species. Summarized, by phylogenetic learning we are able to situate and evaluate FAME-based bacterial species classification in a more informative context.



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.



Phylogenetic classification of heterotrophic bacteria associated with filamentous marine cyanobacteria in culture.  


Fifty-one heterotrophic bacterial strains were isolated from the marine cyanobacterial cultures of heterocystous Nodularia harveyana strain Bo53 and non-heterocystous Oscillatoria brevis strain Bo10. Fluorescence in situ hybridisation and fingerprinting methods were used for a preliminary taxonomical classification of 44 of the 51 isolates. The strains obtained from Bo53 were mostly Alphaproteobacteria (10/24), followed by Bacteroidetes (7/24), and Gammaproteobacteria (3/24). The affiliation of the isolates originating from Bo10 was dominated by Alphaproteobacteria (8/20) and Bacteroidetes (7/20), followed by Gammaproteobacteria (3/20). The 16S rRNA genes of four selected isolates were sequenced. A red-coloured bacterium from Bo53 grouped with the alphaproteobacterial genus Porphyrobacter, while the other three strains, obtained from Bo10, belonged to the alphaproteobacterial genera Roseobacter (pink) and Rhodobacter (colourless), and to the genus Muricauda (yellow) of Bacteroidetes. The findings indicated that the aerobic anoxygenic phototroph Porphyrobacter and its relatives only occurred in Bo10 culture, whereas members of the Roseobacter clade and the Bacteroidetes bacterium Muricauda sp. seemed to be more ubiquitous. PMID:19423262

Hube, Annina Elisabeth; Heyduck-Söller, Birgit; Fischer, Ulrich



Phylogenetic analysis and classification of the Brassica rapa SET-domain protein family  

PubMed Central

Background The SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain is an evolutionarily conserved sequence of approximately 130-150 amino acids, and constitutes the catalytic site of lysine methyltransferases (KMTs). KMTs perform many crucial biological functions via histone methylation of chromatin. Histone methylation marks are interpreted differently depending on the histone type (i.e. H3 or H4), the lysine position (e.g. H3K4, H3K9, H3K27, H3K36 or H4K20) and the number of added methyl groups (i.e. me1, me2 or me3). For example, H3K4me3 and H3K36me3 are associated with transcriptional activation, but H3K9me2 and H3K27me3 are associated with gene silencing. The substrate specificity and activity of KMTs are determined by sequences within the SET domain and other regions of the protein. Results Here we identified 49 SET-domain proteins from the recently sequenced Brassica rapa genome. We performed sequence similarity and protein domain organization analysis of these proteins, along with the SET-domain proteins from the dicot Arabidopsis thaliana, the monocots Oryza sativa and Brachypodium distachyon, and the green alga Ostreococcus tauri. We showed that plant SET-domain proteins can be grouped into 6 distinct classes, namely KMT1, KMT2, KMT3, KMT6, KMT7 and S-ET. Apart from the S-ET class, which has an interrupted SET domain and may be involved in methylation of nonhistone proteins, the other classes have characteristics of histone methyltransferases exhibiting different substrate specificities: KMT1 for H3K9, KMT2 for H3K4, KMT3 for H3K36, KMT6 for H3K27 and KMT7 also for H3K4. We also propose a coherent and rational nomenclature for plant SET-domain proteins. Comparisons of sequence similarity and synteny of B. rapa and A. thaliana SET-domain proteins revealed recent gene duplication events for some KMTs. Conclusion This study provides the first characterization of the SET-domain KMT proteins of B. rapa. Phylogenetic analysis data allowed the development of a coherent and rational nomenclature of this important family of proteins in plants, as in animals. The results obtained in this study will provide a base for nomenclature of KMTs in other plant species and facilitate the functional characterization of these important epigenetic regulatory genes in Brassica crops.



Rapid detection, classification and accurate alignment of up to a million or more related protein sequences  

PubMed Central

Motivation: The patterns of sequence similarity and divergence present within functionally diverse, evolutionarily related proteins contain implicit information about corresponding biochemical similarities and differences. A first step toward accessing such information is to statistically analyze these patterns, which, in turn, requires that one first identify and accurately align a very large set of protein sequences. Ideally, the set should include many distantly related, functionally divergent subgroups. Because it is extremely difficult, if not impossible for fully automated methods to align such sequences correctly, researchers often resort to manual curation based on detailed structural and biochemical information. However, multiply-aligning vast numbers of sequences in this way is clearly impractical. Results: This problem is addressed using Multiply-Aligned Profiles for Global Alignment of Protein Sequences (MAPGAPS). The MAPGAPS program uses a set of multiply-aligned profiles both as a query to detect and classify related sequences and as a template to multiply-align the sequences. It relies on Karlin–Altschul statistics for sensitivity and on PSI-BLAST (and other) heuristics for speed. Using as input a carefully curated multiple-profile alignment for P-loop GTPases, MAPGAPS correctly aligned weakly conserved sequence motifs within 33 distantly related GTPases of known structure. By comparison, the sequence- and structurally based alignment methods hmmalign and PROMALS3D misaligned at least 11 and 23 of these regions, respectively. When applied to a dataset of 65 million protein sequences, MAPGAPS identified, classified and aligned (with comparable accuracy) nearly half a million putative P-loop GTPase sequences. Availability: A C++ implementation of MAPGAPS is available at Contact: Supplementary information: Supplementary data are available at Bioinformatics online.

Neuwald, Andrew F.



New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes.  


The Lecanoromycetes includes most of the lichen-forming fungal species (> 13500) and is therefore one of the most diverse class of all Fungi in terms of phenotypic complexity. We report phylogenetic relationships within the Lecanoromycetes resulting from Bayesian and maximum likelihood analyses with complementary posterior probabilities and bootstrap support values based on three combined multilocus datasets using a supermatrix approach. Nine of 10 orders and 43 of 64 families currently recognized in Eriksson's classification of the Lecanoromycetes (Outline of Ascomycota--2006 Myconet 12:1-82) were represented in this sampling. Our analyses strongly support the Acarosporomycetidae and Ostropomycetidae as monophyletic, whereas the delimitation of the largest subclass, the Lecanoromycetidae, remains uncertain. Independent of future delimitation of the Lecanoromycetidae, the Rhizocarpaceae and Umbilicariaceae should be elevated to the ordinal level. This study shows that recent classifications include several nonmonophyletic taxa at different ranks that need to be recircumscribed. Our phylogenies confirm that ascus morphology cannot be applied consistently to shape the classification of lichen-forming fungi. The increasing amount of missing data associated with the progressive addition of taxa resulted in some cases in the expected loss of support, but we also observed an improvement in statistical support for many internodes. We conclude that a phylogenetic synthesis for a chosen taxonomic group should include a comprehensive assessment of phylogenetic confidence based on multiple estimates using different methods and on a progressive taxon sampling with an increasing number of taxa, even if it involves an increasing amount of missing data. PMID:17486983

Miadlikowska, Jolanta; Kauff, Frank; Hofstetter, Valérie; Fraker, Emily; Grube, Martin; Hafellner, Josef; Reeb, Valérie; Hodkinson, Brendan P; Kukwa, Martin; Lücking, Robert; Hestmark, Geir; Otalora, Monica Garcia; Rauhut, Alexandra; Büdel, Burkhard; Scheidegger, Christoph; Timdal, Einar; Stenroos, Soili; Brodo, Irwin; Perlmutter, Gary B; Ertz, Damien; Diederich, Paul; Lendemer, James C; May, Philip; Schoch, Conrad L; Arnold, A Elizabeth; Gueidan, Cécile; Tripp, Erin; Yahr, Rebecca; Robertson, Connie; Lutzoni, François


The use of small training sets containing mixed pixels for accurate hard image classification: Training on mixed spectral responses for classification by a SVM  

Microsoft Academic Search

The accuracy of a supervised image classification is a function of the training data used in its generation. It is, therefore, critical that the training stage of a supervised classification is designed to provide the necessary information. Guidance on the design of the training stage of a classification typically calls for the use of a large sample of randomly selected

Giles M. Foody; Ajay Mathur




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




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.



Comprehensive phylogenetic reconstructions of African swine fever virus: proposal for a new classification and molecular dating of the virus.  


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 18(th) century. PMID:23936068

Michaud, Vincent; Randriamparany, Tantely; Albina, Emmanuel



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



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.



Automatic delineation of sulci and improved partial volume classification for accurate 3D voxel-based cortical thickness estimation from MR.  


Accurate cortical thickness estimation in-vivo is important for the study of many neurodegenerative diseases. When using magnetic resonance images (MRI), accuracy may be hampered by artifacts such as partial volume (PV) as the cortex spans only a few voxels. In zones of opposed sulcal banks (tight sulci) the measurement can be even more difficult. The aim of this work is to propose a voxel-based cortical thickness estimation method from MR by integrating a mechanism for correcting sulci delineation after an improved partial volume classification. First, an efficient and accurate framework was developed to enhance partial volume classification with structural information. Then, the correction of sulci delineation is performed after a homotopic thinning of a cost function image. Integrated to our voxel-based cortical thickness estimation pipeline, the overall method showed a better estimate of thickness and a high reproducibility on real data (R2 > 0.9). A quantitative analysis on clinical data from an Alzheimer's disease study showed significant differences between normal controls and Alzheimer's disease patients. PMID:18979755

Acosta, Oscar; Bourgeat, Pierrick; Fripp, Jurgen; Bonner, Erik; Ourselin, Sébastien; Salvado, Olivier




NSDL National Science Digital Library

Project Overview: Classification is grouping similar objects together. When you go into a grocery store, you see fresh fruits and vegetables, frozen food, cereal, and pet suplies in different aisles. Imagine how difficult life would be if you went into a store, and the aisles were not labeled to tell you where to find the items! You don't have to be a scientist to use classification! You use classification when you group your IPOD music into different genres and when you divide your dark colored clothing from light colors to do laundry. You might even use it to sort Halloween candy into 4 groups: chocolate candy, hard candy, chewy candy, and gum. The science of classification is called taxonomy. Taxonomy classifies organisms based on evolutionary relationships and describes and names organisms with a two-part name: genus and species. Scientists use taxonomy to identify unknown organisms by using books called field guides or by using taxonomic keys (also called dichomotous keys). Project Objective: As a class,you will be previewing and answering some questions about some classification resources to learn how to use a dichotomous key, how to key a specimen, and to help you write your own dichotomous key for school items. Project: Get a sheet of notebook paper and pencil and refer to the websites to find the answers to the questions. One way to classify objects is to create a "tree" to group similar objects together.Open hierarchical classfication of objects to the second page and find the diagram of common household objects. See how all the ...

Ballew, Mrs.



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


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



Exploring the radiation of a diverse reef fish family: phylogenetics of the damselfishes (Pomacentridae), with new classifications based on molecular analyses of all genera.  


The damselfishes (Perciformes, Pomacentridae) are an important family of marine reef fishes that occupy a range of ecological positions in the world's oceans. In order to determine the evolutionary pattern of their radiation, we used multiple methods to examine molecular data from 104 species representing all extant genera. The analysis of 4291 DNA nucleotides (1281bp were parsimony informative) from three nuclear genes (rag-1, rag-2 and bmp-4) and three mitochondrial genes (12s, 16s and nd3), produced well-resolved phylogenies with strong evidence for a monophyletic Pomacentridae, and support for five major damselfish clades. We found that the monotypic subfamily Lepidozyginae evolved early in the pomacentrid radiation. The placement of the genus Altrichthys indicates that brood care has evolved at least twice among the damselfishes. The subfamilies Chrominae and Pomacentrinae, and the genera Abudefduf, Chromis, Chrysiptera, Plectroglyphidodon, and Stegastes, were always found to be polyphyletic, and monophyly was rejected for the genus Amphiprion by almost every analysis. All phylogenetic studies of the Pomacentridae have indicated that their taxonomy is in need of revision at multiple levels. We provide a new classification scheme wherein each subfamily is now monophyletic, and this reorganization is consistent with all previous molecular studies of the damselfishes. The Chrominae are restricted to the genera Chromis and Dascyllus; the Pomacentrinae now represent a lineage of 16 genera that constitute a major, and relatively recent, radiation of coral reef fishes throughout the Indo-West Pacific; we erect the new subfamlies Abudefdufinae and Stegastinae; we relegate the anemonefishes (the Amphiprioninae sensu Allen) to the tribe Amphiprionini within the Pomacentrinae, and synonomize the genus Azurina with Chromis. PMID:19135160

James Cooper, W; Smith, Lydia L; Westneat, Mark W



Molecular phylogenetics of the spider infraorder Mygalomorphae using nuclear rRNA genes (18S and 28S): conflict and agreement with the current system of classification.  


Mygalomorph spiders, which include the tarantulas, trapdoor spiders, and their kin, represent one of three main spider lineages. Mygalomorphs are currently classified into 15 families, comprising roughly 2500 species and 300 genera. The few published phylogenies of mygalomorph relationships are based exclusively on morphological data and reveal areas of both conflict and congruence, suggesting the need for additional phylogenetic research utilizing new character systems. As part of a larger combined evidence study of global mygalomorph relationships, we have gathered approximately 3.7 kb of rRNA data (18S and 28S) for a sample of 80 genera, representing all 15 mygalomorph families. Taxon sampling was particularly intensive across families that are questionable in composition-Cyrtaucheniidae and Nemesiidae. The following primary results are supported by both Bayesian and parsimony analyses of combined matrices representing multiple 28S alignments: (1) the Atypoidea, a clade that includes the families Atypidae, Antrodiaetidae, and Mecicobothriidae, is recovered as a basal lineage sister to all other mygalomorphs, (2) diplurids and hexathelids form a paraphyletic grade at the base of the non-atypoid clade, but neither family is monophyletic in any of our analyses, (3) a clade consisting of all sampled nemesiids, Microstigmata and the cyrtaucheniid genera Kiama, Acontius, and Fufius is consistently recovered, (4) other sampled cyrtaucheniids are fragmented across three separate clades, including a monophyletic North American Euctenizinae and a South African clade, (5) of the Domiothelina, only idiopids are consistently recovered as monophyletic; ctenizids are polyphyletic and migids are only weakly supported. The Domiothelina is not monophyletic. The molecular results we present are consistent with more recent hypotheses of mygalomorph relationship; however, additional work remains before mygalomorph classification can be formally reassessed with confidence-increased taxonomic sampling and the inclusion of additional character systems (more genes and morphology) are required. PMID:16815045

Hedin, Marshal; Bond, Jason E



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



Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors  

Microsoft Academic Search

BACKGROUND: In addition to structural domains, most eukaryotic proteins possess intrinsically disordered (ID) regions. Although ID regions often play important functional roles, their accurate identification is difficult. As human transcription factors (TFs) constitute a typical group of proteins with long ID regions, we regarded them as a model of all proteins and attempted to accurately classify TFs into structural domains

Satoshi Fukuchi; Keiichi Homma; Yoshiaki Minezaki; Takashi Gojobori; Ken Nishikawa



Experimental results on marine targets classification with surveillance HRR by means of non coherent techniques based on hot spots accurate location  

Microsoft Academic Search

In this article, the experimental results are presented of applying a new non coherent and non statistic technique that allows us to endow the coastal surveillance high resolution radars (HRR) with a significant capacity for target classification and identification; making possible the estimation of their size, and also obtaining information about their structure by analyzing the intensity and position of

Felix Perez Martinez; Javier Garcia Fominaya; Jaime Calvo Gallego



Meta-analysis based SVM classification enables accurate detection of Alzheimer's disease across different clinical centers using FDG-PET and MRI.  


The application of support vector machine classification (SVM) to combined information from magnetic resonance imaging (MRI) and [F18]fluorodeoxyglucose positron emission tomography (FDG-PET) has been shown to improve detection and differentiation of Alzheimer's disease dementia (AD) and frontotemporal lobar degeneration. To validate this approach for the most frequent dementia syndrome AD, and to test its applicability to multicenter data, we randomly extracted FDG-PET and MRI data of 28 AD patients and 28 healthy control subjects from the database provided by the Alzheimer's Disease Neuroimaging Initiative (ADNI) and compared them to data of 21 patients with AD and 13 control subjects from our own Leipzig cohort. SVM classification using combined volume-of-interest information from FDG-PET and MRI based on comprehensive quantitative meta-analyses investigating dementia syndromes revealed a higher discrimination accuracy in comparison to single modality classification. For the ADNI dataset accuracy rates of up to 88% and for the Leipzig cohort of up to 100% were obtained. Classifiers trained on the ADNI data discriminated the Leipzig cohorts with an accuracy of 91%. In conclusion, our results suggest SVM classification based on quantitative meta-analyses of multicenter data as a valid method for individual AD diagnosis. Furthermore, combining imaging information from MRI and FDG-PET might substantially improve the accuracy of AD diagnosis. PMID:23149027

Dukart, Juergen; Mueller, Karsten; Barthel, Henryk; Villringer, Arno; Sabri, Osama; Schroeter, Matthias Leopold



ICGA-PSO-ELM Approach for Accurate Multiclass Cancer Classification Resulting in Reduced Gene Sets in Which Genes Encoding Secreted Proteins Are Highly Represented  

Microsoft Academic Search

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

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



Classification of Hepatitis C Viruses Based on Phylogenetic Analysis of the Envelope 1 and Nonstructural 5B Regions and Identification of Five Additional Subtypes  

Microsoft Academic Search

Genotyping of hepatitis C virus-positive sera by means of a line probe assay indicated that <3% of European samples, but up to 30% of Gabonese sera, could not be classified as either 1a, 1b, 2a, 2b, 3a, 3b, 4c, 5a, or 6a. Such samples were analyzed in the 5' untranslated region and in the nonstructural 5 (NS5) region. Classification based

Lieven Stuyver; Wouter van Arnhem; Ann Wyseur; Francisco Hernandez; Eric Delaporte; Geert Maertens



GB Virus C/Hepatitis G Virus Groups and Subgroups: Classification by a Restriction Fragment Length Polymorphism Method Based on Phylogenetic Analysis of the 5? Untranslated Region  

PubMed Central

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 sequencing and subsequent alignment of 21 Argentine GB virus C/hepatitis G virus strains confirmed restriction fragment length polymorphism patterns theoretically predicted. This method may be useful for a rapid screening of samples when either epidemiological or transmission studies of this agent are carried out.

Quarleri, J. F.; Mathet, V. L.; Feld, M.; Ferrario, D.; della Latta, M. P.; Verdun, R.; Sanchez, D. O.; Oubina, J. R.



Automatic Delineation of Sulci and Improved Partial Volume Classification for Accurate 3D Voxel-Based Cortical Thickness Estimation from MR  

Microsoft Academic Search

\\u000a Accurate cortical thickness estimation in-vivo is important for the study of many neurodegenerative diseases. When using magnetic resonance images (MRI), accuracy may be\\u000a hampered by artifacts such as partial volume (PV) as the cortex spans only a few voxels. In zones of opposed sulcal banks\\u000a (tight sulci) the measurement can be even more difficult. The aim of this work is

Oscar Acosta; Pierrick Bourgeat; Jurgen Fripp; Erik Bonner; Sébastien Ourselin; Olivier Salvado



Ensemble of feature sets and classification algorithms for sentiment classification  

Microsoft Academic Search

In this paper, we make a comparative study of the effectiveness of ensemble technique for sentiment classification. The ensemble framework is applied to sentiment classification tasks, with the aim of efficiently integrating different feature sets and classification algorithms to synthesize a more accurate classification procedure. First, two types of feature sets are designed for sentiment classification, namely the part-of-speech based

Rui Xia; Chengqing Zong; Shoushan Li



Construction and annotation of large phylogenetic trees  

Microsoft Academic Search

Broad availability of molecular sequence data allows construction of phylogenetic trees with 1000s or even 10 000s of taxa. This paper reviews methodological, technological and empirical issues raised in phylogenetic inference at this scale. Numerous algorithmic and computational challenges have been identified surrounding the core problem of reconstructing large trees accurately from sequence data, but many other obstacles, both upstream

Michael J. Sanderson


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.



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



Fast and accurate feature selection using hybrid genetic strategies  

Microsoft Academic Search

When dealing with object classification, each object is defined by a set of features (characteristics) that classify the object to a particular class. The problem is how to choose the best subset of characteristics that provide an accurate classification. Previous research has shown that decision tables are as accurate as C4.5 for classification purposes. Two different genetic search techniques, CHC

Cesar Guerra-Salcedo; Stephen Chen; Darrell Whitley; Stephen F. Smith



Biometric speaker classification  

Microsoft Academic Search

We address the problem of classification of speakers based on measurements of features obtained from their speech. The process is an adaption of biometric methods used to identify people. The process for speech differs since speech is not stationary. We therefore propose the classification of speakers b y the statistical distributions of parameters which may be accurately estimated by modern

Douglas J. Nelson; David C. Smith; D. J. Richman; Goffrey Townsend



Phylogenetic taxonomy in Drosophila.  


The genus Drosophila is one of the best-studied model systems in modern biology, with twelve fully sequenced genomes available. In spite of the large number of genetic and genomic resources, little is known concerning the phylogenetic relationships, ecology and evolutionary history of all but a few species. Recent molecular systematic studies have shown that this genus is comprised of at least three independent lineages and that several other genera are actually imbedded within Drosophila. This genus accounts for over 2,000 described, and many more undescribed, species. While some Drosophila researchers are advocating dividing this genus into three or more separate genera, others favor maintaining Drosophila as a single large genus. With the recent sequencing of the genomes of multiple Drosophila species and their expanding use in comparative biology, it is critical that the Drosophila research community understands the taxonomic framework underlying the naming and relationships of these species. The subdivision of this genus has significant biological implications, ranging from the accurate annotation of single genes to understanding how ecological adaptations have occurred over the history of the group. PMID:19556883

O'Grady, Patrick M; Markow, Therese A


Phylogenetic system and zoogeography of the Plecoptera.  


Information about the phylogenetic relationships of Plecoptera is summarized. The few characters supporting monophyly of the order are outlined. Several characters of possible significance for the search for the closest relatives of the stoneflies are discussed, but the sister-group of the order remains unknown. Numerous characters supporting the presently recognized phylogenetic system of Plecoptera are presented, alternative classifications are discussed, and suggestions for future studies are made. Notes on zoogeography are appended. The order as such is old (Permian fossils), but phylogenetic relationships and global distribution patterns suggest that evolution of the extant suborders started with the breakup of Pangaea. There is evidence of extensive recent speciation in all parts of the world. PMID:10761594

Zwick, P



Fast and Accurate Face Recognition Using Support Vector Machines  

Microsoft Academic Search

The challenge of face recognition software is the rapid and accurate identification or classification of a query image, or set of query images, based on a set of known target images. Although Support Vector Machines (SVMs) are known to be accurate for the classification problem they are limited in this application by the time required for training which is dependent

K. E. Gates



Phylogenetic Inference From Conserved sites Alignments  

SciTech Connect

Molecular sequences provide a rich source of data for inferring the phylogenetic relationships among species. However, recent work indicates that even an accurate multiple alignment of a large sequence set may yield an incorrect phylogeny and that the quality of the phylogenetic tree improves when the input consists only of the highly conserved, motif regions of the alignment. This work introduces two methods of producing multiple alignments that include only the conserved regions of the initial alignment. The first method retains conserved motifs, whereas the second retains individual conserved sites in the initial alignment. Using parsimony analysis on a mitochondrial data set containing 19 species among which the phylogenetic relationships are widely accepted, both conserved alignment methods produce better phylogenetic trees than the complete alignment. Unlike any of the 19 inference methods used before to analyze this data, both methods produce trees that are completely consistent with the known phylogeny. The motif-based method employs far fewer alignment sites for comparable error rates. For a larger data set containing mitochondrial sequences from 39 species, the site-based method produces a phylogenetic tree that is largely consistent with known phylogenetic relationships and suggests several novel placements.

grundy, W.N.; Naylor, G.J.P.



High Performance Phylogenetic Inference  

Microsoft Academic Search

Phylogenetic analysis is an integral part of many biological research programs. In essence, it is the study of gene genealogy. It is the study of gene mutation and the generational relationships. Phylogenetic analysis is being used in many diverse areas such as human epidemiology, viral transmission, biogeography, and systematics. Researchers are now commonly generating many DNA sequences from many individuals,

Mark J. Clement; Quinn Snell; Glenn Judd; Michael Whiting



Classification and Evolution  

NSDL National Science Digital Library

This laboratory activity has students first classify 14 living species into genera, families, etc. Then they construct an evolutionary tree of the Caminalcules using an additional 57 fossil species. This illustrates how modern classification schemes attempt to reflect evolutionary history. In the process of doing this exercise, the students are also introduced to concepts such as convergent evolution and vestigial structures. The purpose of this lab is to illustrate the principles of classification and some of the processes of evolution. These exercises are done with artificial organisms so that students will approach the task with no preconceived notion as to how they should be classified. This means that they will have to deal with problems such as convergent evolution just as a taxonomist would. This document contains a cover sheet, the Classification and Evolution Lab handout, pictures of the Caminalcules, instructor notes for both a two- and three-hour lab, and a diagram of the correct phylogenetic tree.

Gendron, Robert


Challenges in prosthesis classification.  


Accurate prosthesis classification is critical for total joint arthroplasty surveillance and assessment of comparative effectiveness. Historically, prosthesis classification was based solely on the names of the prosthesis manufacturers. As a result, prosthesis designs changed without corresponding name changes, and other prostheses' names changed over time without substantial design modifications. As the number of prostheses used in total joint arthroplasty on the market increased, catalog and lot numbers associated with prosthesis descriptions were introduced by manufacturers. Currently, these catalog and lot numbers are not standardized, and there is no consensus on categorization of these numbers into brands or subbrands. Classification of the attributes of a prosthesis also varies, limiting comparisons of prostheses across studies and reports. The development of a universal prosthesis classification system would standardize prosthesis classification and enhance total joint arthroplasty research collaboration worldwide. This is a current area of focus for the International Consortium of Orthopaedic Registries (ICOR). PMID:22262428

Robertsson, Otto; Mendenhall, Stan; Paxton, Elizabeth W; Inacio, Maria C S; Graves, Stephen



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.



Phylogenetics of artificial manuscripts.  


Biological evolution has parallels with the development of natural languages, man-made artifacts, and manuscript texts. As a result, phylogenetic methods developed for evolutionary biology are increasingly being used in linguistics, anthropology, archaeology, and textual criticism. Despite this popularity, there have been few critical tests of their suitability. Here, we apply phylogenetic methods to artificial manuscripts with a known true phylogeny, produced by modern 'scribes'. Although the survival of ancestral forms and multiple descendants from a single ancestor are probably much more common in manuscript evolution than biological evolution, we were able to reconstruct most of the true phylogeny. This is important because phylogenetic methods are influencing the production of critical editions of major written works. We also show that the variation in rates of change at different locations in the text follows a gamma distribution, as is often the case in DNA sequences. PMID:15038985

Spencer, Matthew; Davidson, Elizabeth A; Barbrook, Adrian C; Howe, Christopher J



Tissue destruction classification systems.  


Assessing the level of tissue destruction in wounds can be a confusing challenge. This important task is frequently accompanied by questions and the need for clarification to accurately classify the level of damage seen in wounds. The purpose of this article was to present several known classification systems to help clarify this issue for the clinician. PMID:24149664

Korzendorfer, Holly; Scarborough, Pamela; Hettrick, Heather



A Multichannel Approach to Fingerprint Classification  

Microsoft Academic Search

Fingerprint classification provides an important indexing mechanism in a fingerprint database. An accurate and consistent classification can greatly reduce fingerprint matching time for a large database. We present a fingerprint classification algorithm which is able to achieve an accuracy better than previously reported in the literature. We classify fingerprints into five categories: whorl, right loop, left loop, arch, and tented

Anil K. Jain; Salil Prabhakar; Lin Hong



A Universal Phylogenetic Tree.  

ERIC Educational Resources Information Center

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

Offner, Susan



Fast Phylogenetic DNA Barcoding  

Microsoft Academic Search

We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from

Kasper Munch; Wouter Boomsma; Eske Willerslev; Rasmus Nielsen



Probabilism and Phylogenetic Inference  

Microsoft Academic Search

The maximum likelihood approach to phylogenetics rests on frequency probability theory. This stands in stark contrast to the logical probability of corroboration-based cladistic parsimony. History is particular and cannot be described in terms of universal statements about abstract generalities, the task of the historical sciences being one of explanation, not prediction. Thus, frequency probability methods of estimation are inappropriate for

Mark E. Siddall; Arnold G. Kluge



Refuting phylogenetic relationships  

Microsoft Academic Search

BACKGROUND: Phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. This constitutes an important methodologic dimension not often taken into account. Here we address this dimension in the context of concatenation approaches to phylogeny. RESULTS: We discuss some of the limits of a methodology restricted to verificationism, the philosophy on which gene

James Bucknam; Yan Boucher; Eric Bapteste



Leaf Classification  

NSDL National Science Digital Library

The purpose of this resource is to develop a classification system for a set of objects and learn about hierarchical classification systems. Any set of objects, such as insects or rocks, may be used as well.

The GLOBE Program, University Corporation for Atmospheric Research (UCAR)



Iteratively Refined Guide Trees Help Improving Alignment and Phylogenetic Inference in the Mushroom Family Bolbitiaceae  

PubMed Central

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.

Toth, Annamaria; Hausknecht, Anton; Krisai-Greilhuber, Irmgard; Papp, Tamas; Vagvolgyi, Csaba; Nagy, Laszlo G.



A new classification for fingertip injuries.  


A new classification of fingertip injuries is presented. The PNB classification separates the injury into its effect on the three components of the fingertip: pulp, nail and bone. This provides a three digit number that accurately describes the injury. This new classification can be used to record and document injuries, without having to resort to lengthy description. It could also be used to provide detailed instructions for treatment and indications for referral. Examples of the application of the classification are given. PMID:10763726

Evans, D M; Bernardis, C; Bernadis, C



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



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 ( 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.



Refuting phylogenetic relationships  

PubMed Central

Background Phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. This constitutes an important methodologic dimension not often taken into account. Here we address this dimension in the context of concatenation approaches to phylogeny. Results We discuss some of the limits of a methodology restricted to verificationism, the philosophy on which gene concatenation practices generally rely. As an alternative, we describe a software which identifies and focuses on impossible or refuted relationships, through a simple analysis of bootstrap bipartitions, followed by multivariate statistical analyses. We show how refuting phylogenetic relationships could in principle facilitate systematics. We also apply our method to the study of two complex phylogenies: the phylogeny of the archaea and the phylogeny of the core of genes shared by all life forms. While many groups are rejected, our results left open a possible proximity of N. equitans and the Methanopyrales, of the Archaea and the Cyanobacteria, and as well the possible grouping of the Methanobacteriales/Methanoccocales and Thermosplasmatales, of the Spirochaetes and the Actinobacteria and of the Proteobacteria and firmicutes. Conclusion It is sometimes easier (and preferable) to decide which species do not group together than which ones do. When possible topologies are limited, identifying local relationships that are rejected may be a useful alternative to classical concatenation approaches aiming to find a globally resolved tree on the basis of weak phylogenetic markers. Reviewers This article was reviewed by Mark Ragan, Eugene V Koonin and J Peter Gogarten.

Bucknam, James; Boucher, Yan; Bapteste, Eric




Microsoft Academic Search

Monitoring the Earth using imaging spectrometers has necessitated more accurate analyses and new applications to remote sensing. New algorithms have been developed for hyperspectral data classification lately, but also traditional classification algorithms have often been used. This study compares different classification algorithms for classification of vegetation using imaging spectrometer data. The test area located in southern Finland was imaged by

J. H. Lumme


Tree-Based Algorithms for Protein Classification  

Microsoft Academic Search

The problem of protein sequence classification is one of the crucial tasks in the interpretation of genomic data. Many high-throughput\\u000a systems were developed with the aim of categorizing the proteins based only on their sequences. However, modelling how the\\u000a proteins have evolved can also help in the classification task of sequenced data. Hence the phylo-genetic analysis has gained\\u000a importance in

Róbert Busa-fekete; András Kocsor; Sándor Pongor



Modeling body size evolution in Felidae under alternative phylogenetic hypotheses.  


The use of phylogenetic comparative methods in ecological research has advanced during the last twenty years, mainly due to accurate phylogenetic reconstructions based on molecular data and computational and statistical advances. We used phylogenetic correlograms and phylogenetic eigenvector regression (PVR) to model body size evolution in 35 worldwide Felidae (Mammalia, Carnivora) species using two alternative phylogenies and published body size data. The purpose was not to contrast the phylogenetic hypotheses but to evaluate how analyses of body size evolution patterns can be affected by the phylogeny used for comparative analyses (CA). Both phylogenies produced a strong phylogenetic pattern, with closely related species having similar body sizes and the similarity decreasing with increasing distances in time. The PVR explained 65% to 67% of body size variation and all Moran's I values for the PVR residuals were non-significant, indicating that both these models explained phylogenetic structures in trait variation. Even though our results did not suggest that any phylogeny can be used for CA with the same power, or that "good" phylogenies are unnecessary for the correct interpretation of the evolutionary dynamics of ecological, biogeographical, physiological or behavioral patterns, it does suggest that developments in CA can, and indeed should, proceed without waiting for perfect and fully resolved phylogenies. PMID:21637664

Diniz-Filho, José Alexandre Felizola; Nabout, João Carlos



Modeling body size evolution in Felidae under alternative phylogenetic hypotheses  

PubMed Central

The use of phylogenetic comparative methods in ecological research has advanced during the last twenty years, mainly due to accurate phylogenetic reconstructions based on molecular data and computational and statistical advances. We used phylogenetic correlograms and phylogenetic eigenvector regression (PVR) to model body size evolution in 35 worldwide Felidae (Mammalia, Carnivora) species using two alternative phylogenies and published body size data. The purpose was not to contrast the phylogenetic hypotheses but to evaluate how analyses of body size evolution patterns can be affected by the phylogeny used for comparative analyses (CA). Both phylogenies produced a strong phylogenetic pattern, with closely related species having similar body sizes and the similarity decreasing with increasing distances in time. The PVR explained 65% to 67% of body size variation and all Moran's I values for the PVR residuals were non-significant, indicating that both these models explained phylogenetic structures in trait variation. Even though our results did not suggest that any phylogeny can be used for CA with the same power, or that “good” phylogenies are unnecessary for the correct interpretation of the evolutionary dynamics of ecological, biogeographical, physiological or behavioral patterns, it does suggest that developments in CA can, and indeed should, proceed without waiting for perfect and fully resolved phylogenies.



Entanglement, Invariants, and Phylogenetics  

NASA Astrophysics Data System (ADS)

This thesis develops and expands upon known techniques of mathematical physics relevant to the analysis of the popular Markov model of phylogenetic trees required in biology to reconstruct the evolutionary relationships of taxonomic units from biomolecular sequence data. The techniques of mathematical physics are plethora and have been developed for some time. The Markov model of phylogenetics and its analysis is a relatively new technique where most progress to date has been achieved by using discrete mathematics. This thesis takes a group theoretical approach to the problem by beginning with a remarkable mathematical parallel to the process of scattering in particle physics. This is shown to equate to branching events in the evolutionary history of molecular units. The major technical result of this thesis is the derivation of existence proofs and computational techniques for calculating polynomial group invariant functions on a multi-linear space where the group action is that relevant to a Markovian time evolution. The practical results of this thesis are an extended analysis of the use of invariant functions in distance based methods and the presentation of a new reconstruction technique for quartet trees which is consistent with the most general Markov model of sequence evolution.

Sumner, J. G.



The evolution of HIV: Inferences using phylogenetics  

PubMed Central

Molecular phylogenetics has revolutionized the study of not only evolution but also disparate fields such as genomics, bioinformatics, epidemiology, ecology, microbiology, molecular biology and biochemistry. Particularly significant are its achievements in population genetics as a result of the development of coalescent theory, which have contributed to more accurate model-based parameter estimation and explicit hypothesis testing. The study of the evolution of many microorganisms, and HIV in particular, have benefited from these new methodologies. HIV is well suited for such sophisticated population analyses because of its large population sizes, short generation times, high substitution rates and relatively small genomes. All these factors make HIV an ideal and fascinating model to study molecular evolution in real time. Here we review the significant advances made in HIV evolution through the application of phylogenetic approaches. We first examine the relative roles of mutation and recombination on the molecular evolution of HIV and its adaptive response to drug therapy and tissue allocation. We then review some of the fundamental questions in HIV evolution in relation to its origin and diversification and describe some of the insights gained using phylogenies. Finally, we show how phylogenetic analysis has advanced our knowledge of HIV dynamics (i.e., phylodynamics).

Castro-Nallar, Eduardo; Perez-Losada, Marcos; Burton, Gregory F.; Crandall, Keith A.



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



Fingerprint classification  

Microsoft Academic Search

A fingerprint classification algorithm is presented in this paper. Fingerprints are classified into five categories: arch, tented arch, left loop, right loop and whorl. The algorithm extracts singular points (cores and deltas) in a fingerprint image and performs classification based on the number and locations of the detected singular points. The classifier is invariant to rotation, translation and small amounts

Kalle Karu; Anil K. Jain



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



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



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



Positive, accurate animal identification  

Microsoft Academic Search

Positive, accurate identification of animals and their products would be very helpful in livestock commerce, prevention of theft and fraud and in tracing animals and products to origin. Food safety, animal health, and prevention of epidemics, would be enhanced by combining identification with location. Identification may be by electronic chips, iris or retinal scans, antibody or DNA analysis. A cross

Philip Dziuk



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



Accurate software performance estimation using domain classification and neural networks  

Microsoft Academic Search

For the design of an embedded system, there is a variety of available processors, each one offering a different trade-off concerning factors such as performance and power consumption. High-level performance estimation of the embedded software implemented in a particular architecture is essential for a fast design space exploration, including the choice of the most appropriate processor. However, advanced architectures present

Márcio Seiji Oyamada; Felipe Zschornack; Flávio Rech Wagner



Abacus: Accurate behavioral classification of P2PTV traffic  

Microsoft Academic Search

Peer-to-Peer streaming (P2P-TV) applications offer the capability to watch real time video over the Internet at low cost. Some applications have started to become popular, raising the concern of Network Operators that fear the large amount of traffic they might generate. Unfortunately, most of P2P-TV applications are based on proprietary and unknown protocols, and this makes the detection of such

Paola Bermolen; Marco Mellia; Michela Meo; Dario Rossi; Silvio Valenti



Three Domains, Not Five Kingdoms: A Phylogenetic Classification System.  

ERIC Educational Resources Information Center

|Argues that the Woesian three domain view of life should replace the five kingdom taxonomic scheme presented in most general biology texts and courses. Presents evidence for employing the three domain scheme and a related activity for classroom use. Contains 11 references. (WRM)|

Peirce, Susan K.



A phylogenetic analysis of the myxobacteria: basis for their classification.  


The primary sequence and secondary structural features of the 16S rRNA were compared for 12 different myxobacteria representing all the known cultivated genera. Analysis of these data show the myxobacteria to form a monophyletic grouping consisting of three distinct families, which lies within the delta subdivision of the purple bacterial phylum. The composition of the families is consistent with differences in cell and spore morphology, cell behavior, and pigment and secondary metabolite production but is not correlated with the morphological complexity of the fruiting bodies. The Nannocystis exedens lineage has evolved at an unusually rapid pace and its rRNA shows numerous primary and secondary structural idiosyncrasies. PMID:1384053

Shimkets, L; Woese, C R



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



Mineral Classification  

NSDL National Science Digital Library

This problem set challenges students to determine the chemical classification of minerals based on their chemical formula (provided). For oxygen-bearing minerals, students must also provide the valences of the various cations.


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


Species names in phylogenetic nomenclature.  


Linnaean binomial nomenclature is logically incompatible with the phylogenetic nomenclature of de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449-480): The former is based on the concept of genus, thus making this rank mandatory, while the latter is based on phylogenetic definitions and requires the abandonment of mandatory ranks. Thus, if species are to receive names under phylogenetic nomenclature, a different method must be devised to name them. Here, 13 methods for naming species in the context of phylogenetic nomenclature are contrasted with each other and with Linnaean binomials. A fundamental dichotomy among the proposed methods distinguishes those that retain the entire binomial of a preexisting species name from those that retain only the specific epithet. Other relevant issues include the stability, uniqueness, and ease of pronunciation of species names; their capacity to convey phylogenetic information; and the distinguishability of species names that are governed by a code of phylogenetic nomenclature both from clade names and from species names governed by the current codes. No method is ideal. Each has advantages and drawbacks, and preference for one option over another will be influenced by one's evaluation of the relative importance of the pros and cons for each. Moreover, sometimes the same feature is viewed as an advantage by some and a drawback by others. Nevertheless, all of the proposed methods for naming species in the context of phylogenetic nomenclature provide names that are more stable than Linnaean binomials. PMID:12066299

Cantino, P D; Bryant, H N; de Queiroz, K; Donoghue, M J; Eriksson, T; Hillis, D M; Lee, M S



Entanglement invariants and phylogenetic branching.  


It is possible to consider stochastic models of sequence evolution in phylogenetics in the context of a dynamical tensor description inspired from physics. Approaching the problem in this framework allows for the well developed methods of mathematical physics to be exploited in the biological arena. We present the tensor description of the homogeneous continuous time Markov chain model of phylogenetics with branching events generated by dynamical operations. Standard results from phylogenetics are shown to be derivable from the tensor framework. We summarize a powerful approach to entanglement measures in quantum physics and present its relevance to phylogenetic analysis. Entanglement measures are found to give distance measures that are equivalent to, and expand upon, those already known in phylogenetics. In particular we make the connection between the group invariant functions of phylogenetic data and phylogenetic distance functions. We introduce a new distance measure valid for three taxa based on the group invariant function known in physics as the "tangle". All work is presented for the homogeneous continuous time Markov chain model with arbitrary rate matrices. PMID:15940542

Sumner, J G; Jarvis, P D



Molecular phylogenetics: principles and practice.  


Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection and the demographic changes and migration patterns of species. The advancement of sequencing technologies has taken phylogenetic analysis to a new height. Phylogenies have permeated nearly every branch of biology, and the plethora of phylogenetic methods and software packages that are now available may seem daunting to an experimental biologist. Here, we review the major methods of phylogenetic analysis, including parsimony, distance, likelihood and Bayesian methods. We discuss their strengths and weaknesses and provide guidance for their use. PMID:22456349

Yang, Ziheng; Rannala, Bruce



Explaining Glaciers, Accurately  

NSDL National Science Digital Library

What happens when a geology graduate student and two fourth-grade teachers collaborate on lessons for the classroom? They discover interesting and practical ways to explore geology and other scientific concepts, that's what! Here they share the glacial erosion lessons that grew out of the geologist's frustration at finding glacial erosion labs erroneously showing glaciers eroding by pushing rocks. Their goal was to find a way to show and explain glacial erosion more accurately and in a way that elementary age students could understand.

Tate, Mari; Faw, Mary; Scott, Nancy



Biometric speaker classification  

NASA Astrophysics Data System (ADS)

We address the problem of classification of speakers based on measurements of features obtained from their speech. The process is an adaption of biometric methods used to identify people. The process for speech differs since speech is not stationary. We therefore propose the classification of speakers b y the statistical distributions of parameters which may be accurately estimated by modern signal processing techniques. The intent is to develop a speaker clustering algorithm which is dependent of transmission channel and insensitive to language variations, and which may be re-trained, with minimal data, to include a new speaker. We demonstrate effectiveness on the problem of identification of the speakers gender, and present evidence that the methods may be extended to the general problem of speaker identification.

Nelson, Douglas J.; Smith, David C.; Richman, D. J.; Townsend, Goffrey



Phylogenetic lineages in Pseudocercospora  

PubMed Central

Pseudocercospora is a large cosmopolitan genus of plant pathogenic fungi that are commonly associated with leaf and fruit spots as well as blights on a wide range of plant hosts. They occur in arid as well as wet environments and in a wide range of climates including cool temperate, sub-tropical and tropical regions. Pseudocercospora is now treated as a genus in its own right, although formerly recognised as either an anamorphic state of Mycosphaerella or having mycosphaerella-like teleomorphs. The aim of this study was to sequence the partial 28S nuclear ribosomal RNA gene of a selected set of isolates to resolve phylogenetic generic limits within the Pseudocercospora complex. From these data, 14 clades are recognised, six of which cluster in Mycosphaerellaceae. Pseudocercospora s. str. represents a distinct clade, sister to Passalora eucalypti, and a clade representing the genera Scolecostigmina, Trochophora and Pallidocercospora gen. nov., taxa formerly accommodated in the Mycosphaerella heimii complex and characterised by smooth, pale brown conidia, as well as the formation of red crystals in agar media. Other clades in Mycosphaerellaceae include Sonderhenia, Microcyclosporella, and Paracercospora. Pseudocercosporella resides in a large clade along with Phloeospora, Miuraea, Cercospora and Septoria. Additional clades represent Dissoconiaceae, Teratosphaeriaceae, Cladosporiaceae, and the genera Xenostigmina, Strelitziana, Cyphellophora and Thedgonia. The genus Phaeomycocentrospora is introduced to accommodate Mycocentrospora cantuariensis, primarily distinguished from Pseudocercospora based on its hyaline hyphae, broad conidiogenous loci and hila. Host specificity was considered for 146 species of Pseudocercospora occurring on 115 host genera from 33 countries. Partial nucleotide sequence data for three gene loci, ITS, EF-1?, and ACT suggest that the majority of these species are host specific. Species identified on the basis of host, symptomatology and general morphology, within the same geographic region, frequently differed phylogenetically, indicating that the application of European and American names to Asian taxa, and vice versa, was often not warranted. Taxonomic novelties: New genera - Pallidocercospora Crous, Phaeomycocentrospora Crous, H.D. Shin & U. Braun; New species - Cercospora eucommiae Crous, U. Braun & H.D. Shin, Microcyclospora quercina Crous & Verkley, Pseudocercospora ampelopsis Crous, U. Braun & H.D. Shin, Pseudocercospora cercidicola Crous, U. Braun & C. Nakash., Pseudocercospora crispans G.C. Hunter & Crous, Pseudocercospora crocea Crous, U. Braun, G.C. Hunter & H.D. Shin, Pseudocercospora haiweiensis Crous & X. Zhou, Pseudocercospora humulicola Crous, U. Braun & H.D. Shin, Pseudocercospora marginalis G.C. Hunter, Crous, U. Braun & H.D. Shin, Pseudocercospora ocimi-basilici Crous, M.E. Palm & U. Braun, Pseudocercospora plectranthi G.C. Hunter, Crous, U. Braun & H.D. Shin, Pseudocercospora proteae Crous, Pseudocercospora pseudostigmina-platani Crous, U. Braun & H.D. Shin, Pseudocercospora pyracanthigena Crous, U. Braun & H.D. Shin, Pseudocercospora ravenalicola G.C. Hunter & Crous, Pseudocercospora rhamnellae G.C. Hunter, H.D. Shin, U. Braun & Crous, Pseudocercospora rhododendri-indici Crous, U. Braun & H.D. Shin, Pseudocercospora tibouchinigena Crous & U. Braun, Pseudocercospora xanthocercidis Crous, U. Braun & A. Wood, Pseudocercosporella koreana Crous, U. Braun & H.D. Shin; New combinations - Pallidocercospora acaciigena (Crous & M.J. Wingf.) Crous & M.J. Wingf., Pallidocercospora crystallina (Crous & M.J. Wingf.) Crous & M.J. Wingf., Pallidocercospora heimii (Crous) Crous, Pallidocercospora heimioides (Crous & M.J. Wingf.) Crous & M.J. Wingf., Pallidocercospora holualoana (Crous, Joanne E. Taylor & M.E. Palm) Crous, Pallidocercospora konae (Crous, Joanne E. Taylor & M.E. Palm) Crous, Pallidoocercospora irregulariramosa (Crous & M.J. Wingf.) Crous & M.J. Wingf., Phaeomycocentrospora cantuariensis (E.S. Salmon & Wormald) Crous, H.D. Shin & U. Braun, Pseudocercospora hakeae (U. Braun & Cr

Crous, P.W.; Braun, U.; Hunter, G.C.; Wingfield, M.J.; Verkley, G.J.M.; Shin, H.-D.; Nakashima, C.; Groenewald, J.Z.



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.



Terrain classification  

NASA Astrophysics Data System (ADS)

This work presents methods for terrain classification that support adaptive selection of parameters for Terrain Classification system. Work is also presented for water body detection and we present results from experiments conducted for water detection methods utilizing LADAR, color camera and polarization filter based sensors. Use of multiple sensors can provide better water detection capability. An approach for adaptive terrain classification is shown for existing rule-based classification algorithms. This approach allows us to develop a set of rules for various representative terrain types from various sites and operating conditions (light level, humidity, season, etc.) and exploit the onboard vehicle situational knowledge to select the most suitable set of rules for operation. An important element of this work requires use of data collected for different seasons and locations or terrain types in order to provide sensitivity measures. Existing terrain classification algorithms can utilize input from multiple sensors such as: Color, LADAR, FLIR and Multi-Spectral imagery. The performance of these algorithms is expected to improve as we acquire an increasing number of additional data sets that includes features of interest taken under various conditions of terrain-types types, illumination, temperature, humidity etc. and allow us to build a database of terrain knowledge. Environmental nformation and ground-truth is also collected along with the sensor data data. A Geographical Information System (GIS) interface is utilized along with related public-domain tools. Such tools are integrated to our system and used to provide data-management, spatial-modeling, and visualization.

Sarwal, Alok; Simon, David; Rajagopalan, Venkat



[Classification and phylogeny of pathogenic fungi].  


The clinical isolates are traditionally classified based on morphology, but in recent years a polyphasic taxonomy that combines morphological, physiologic and molecular phylogenetic analyses is used to characterize them. Numerous common pathogenic species, traditionally considered homogeneous, are indeed polyphyletic. Classifications of Candida albicans, Cryptococcus neoformans and Aspergillus fumigatus and relatives based on molecular phylogenetic analyses have been developed. The strains of C. albicans group are divided into 5 genotypes by PCR method. The strains of Cr. neoformans are divided into 3 varieties (var. grubii, var. neoformans, var. gattii) and into 5 serotypes. The strains of A.fumigatus and relative are divided into 5 clades based on DNA sequence analysis. PMID:19069089

Yaguchi, Takashi; Tanaka, Reiko



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



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.



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



HIV classification using coalescent theory  

SciTech Connect

Algorithms for subtype classification and breakpoint detection of HIV-I sequences are based on a classification system of HIV-l. Hence, their quality highly depend on this system. Due to the history of creation of the current HIV-I nomenclature, the current one contains inconsistencies like: The phylogenetic distance between the subtype B and D is remarkably small compared with other pairs of subtypes. In fact, it is more like the distance of a pair of subsubtypes Robertson et al. (2000); Subtypes E and I do not exist any more since they were discovered to be composed of recombinants Robertson et al. (2000); It is currently discussed whether -- instead of CRF02 being a recombinant of subtype A and G -- subtype G should be designated as a circulating recombination form (CRF) nd CRF02 as a subtype Abecasis et al. (2007); There are 8 complete and over 400 partial HIV genomes in the LANL-database which belong neither to a subtype nor to a CRF (denoted by U). Moreover, the current classification system is somehow arbitrary like all complex classification systems that were created manually. To this end, it is desirable to deduce the classification system of HIV systematically by an algorithm. Of course, this problem is not restricted to HIV, but applies to all fast mutating and recombining viruses. Our work addresses the simpler subproblem to score classifications of given input sequences of some virus species (classification denotes a partition of the input sequences in several subtypes and CRFs). To this end, we reconstruct ancestral recombination graphs (ARG) of the input sequences under restrictions determined by the given classification. These restritions are imposed in order to ensure that the reconstructed ARGs do not contradict the classification under consideration. Then, we find the ARG with maximal probability by means of Markov Chain Monte Carlo methods. The probability of the most probable ARG is interpreted as a score for the classification. To our knowledge, this particular problem was not addressed up to now. The software package Lamarc Kuhner et al. (2000) allows for sampling ARGs, but it assumes that recombination events only involve one breakpoint. However, in HIV recombinants usually have more than one breakpoint. Moreover, Lamarc does not perform an explicit breakpoint detection, but tries to find them by chance. Although this approach is suitable for most situations, it will not lead to satisfying results in case of highly recombining viruses with multiple breakpoints.

Zhang, Ming [Los Alamos National Laboratory; Letiner, Thomas K [Los Alamos National Laboratory; Korber, Bette T [Los Alamos National Laboratory



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.



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

Microsoft Academic Search

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

Kyanne R Reidenbach; Shelley Cook; Matthew A Bertone; Ralph E Harbach; Brian M Wiegmann; Nora J Besansky



Accurate Optical Reference Catalogs  

NASA Astrophysics Data System (ADS)

Current and near future all-sky astrometric catalogs on the ICRF are reviewed with the emphasis on reference star data at optical wavelengths for user applications. The standard error of a Hipparcos Catalogue star position is now about 15 mas per coordinate. For the Tycho-2 data it is typically 20 to 100 mas, depending on magnitude. The USNO CCD Astrograph Catalog (UCAC) observing program was completed in 2004 and reductions toward the final UCAC3 release are in progress. This all-sky reference catalogue will have positional errors of 15 to 70 mas for stars in the 10 to 16 mag range, with a high degree of completeness. Proper motions for the about 60 million UCAC stars will be derived by combining UCAC astrometry with available early epoch data, including yet unpublished scans of the complete set of AGK2, Hamburg Zone astrograph and USNO Black Birch programs. Accurate positional and proper motion data are combined in the Naval Observatory Merged Astrometric Dataset (NOMAD) which includes Hipparcos, Tycho-2, UCAC2, USNO-B1, NPM+SPM plate scan data for astrometry, and is supplemented by multi-band optical photometry as well as 2MASS near infrared photometry. The Milli-Arcsecond Pathfinder Survey (MAPS) mission is currently being planned at USNO. This is a micro-satellite to obtain 1 mas positions, parallaxes, and 1 mas/yr proper motions for all bright stars down to about 15th magnitude. This program will be supplemented by a ground-based program to reach 18th magnitude on the 5 mas level.

Zacharias, N.



Lumbar degenerative classification study.  


The purpose of this study was to develop and validate a classification of indications for fusion in lumbar degenerative disease. Nineteen spine surgeons reviewed a series of 32 case histories and selected the indication for fusion based on an outlined classification system. To determine the degree of interrater variability, K coefficients were calculated (K for all 32 cases, 0.63). Results from this study show the significant difficulty in classifying the indication for fusion in lumbar degenerative disease. The level of the 19 surgeons' agreement regarding surgical indication was only moderate, despite a study design that eliminated controversial issues of patient and procedure selection. To a significant extent, the difficulty in classifying indication for fusion underlines the importance of the process. If we cannot agree on why a specific patient is selected for fusion, it is then impossible to accurately compare outcomes for a given disease process or surgical technique. For this reason, an ongoing effort to refine nomenclature and classification is necessary. PMID:16689515

Glassman, Steven D; Carreon, Leah Y; Dimar, John R; Campbell, Mitchell J; Johnson, John R; Puno, Rolando M



Neuromuscular disease classification system  

NASA Astrophysics Data System (ADS)

Diagnosis of neuromuscular diseases is based on subjective visual assessment of biopsies from patients by the pathologist specialist. A system for objective analysis and classification of muscular dystrophies and neurogenic atrophies through muscle biopsy images of fluorescence microscopy is presented. The procedure starts with an accurate segmentation of the muscle fibers using mathematical morphology and a watershed transform. A feature extraction step is carried out in two parts: 24 features that pathologists take into account to diagnose the diseases and 58 structural features that the human eye cannot see, based on the assumption that the biopsy is considered as a graph, where the nodes are represented by each fiber, and two nodes are connected if two fibers are adjacent. A feature selection using sequential forward selection and sequential backward selection methods, a classification using a Fuzzy ARTMAP neural network, and a study of grading the severity are performed on these two sets of features. A database consisting of 91 images was used: 71 images for the training step and 20 as the test. A classification error of 0% was obtained. It is concluded that the addition of features undetectable by the human visual inspection improves the categorization of atrophic patterns.

Sáez, Aurora; Acha, Begoña; Montero-Sánchez, Adoración; Rivas, Eloy; Escudero, Luis M.; Serrano, Carmen



Human phylogenetic relationships according to the D1S80 locus  

Microsoft Academic Search

By analyzing the allelic frequencies at the D1S80 locus in 43 human populations, we show that the locus is polymorphic globally and that it can be used to discriminate between major racial groups and subpopulations through phylogenetic analysis. Although the use of informative multiple loci generally provides more accurate phylogenetic relationships, in instances where time and\\/or target DNA availability is

George Duncan; Emmanuel Thomas; Juan C. Gallol; Lynn S. Baird; Jennifer Garrison; Rene J. Herrera



Classification of the Human Papilloma Viruses  

Microsoft Academic Search

\\u000a In this study we present a whole-genome phylogenetic classification of the human papilloma viruse (HPV) family. We found that\\u000a the high risk of carcinogenicity taxa are clustered together. The most likely insertion and deletion (indel) scenarios of\\u000a HPV nucleotides were computed. We also searched for relationships between the number of indels which occurred during the evolution\\u000a of the HPV family

Abdoulaye Baniré Diallo; Dunarel Badescu; Mathieu Blanchette; Vladimir Makarenkov


Detection of genomic idiosyncrasies using fuzzy phylogenetic profiles.  


Phylogenetic profiles express the presence or absence of genes and their homologs across a number of reference genomes. They have emerged as an elegant representation framework for comparative genomics and have been used for the genome-wide inference and discovery of functionally linked genes or metabolic pathways. As the number of reference genomes grows, there is an acute need for faster and more accurate methods for phylogenetic profile analysis with increased performance in speed and quality. We propose a novel, efficient method for the detection of genomic idiosyncrasies, i.e. sets of genes found in a specific genome with peculiar phylogenetic properties, such as intra-genome correlations or inter-genome relationships. Our algorithm is a four-step process where genome profiles are first defined as fuzzy vectors, then discretized to binary vectors, followed by a de-noising step, and finally a comparison step to generate intra- and inter-genome distances for each gene profile. The method is validated with a carefully selected benchmark set of five reference genomes, using a range of approaches regarding similarity metrics and pre-processing stages for noise reduction. We demonstrate that the fuzzy profile method consistently identifies the actual phylogenetic relationship and origin of the genes under consideration for the majority of the cases, while the detected outliers are found to be particular genes with peculiar phylogenetic patterns. The proposed method provides a time-efficient and highly scalable approach for phylogenetic stratification, with the detected groups of genes being either similar to their own genome profile or different from it, thus revealing atypical evolutionary histories. PMID:23341912

Psomopoulos, Fotis E; Mitkas, Pericles A; Ouzounis, Christos A



Alignment-Free Phylogenetic Reconstruction  

NASA Astrophysics Data System (ADS)

We introduce the first polynomial-time phylogenetic reconstruction algorithm under a model of sequence evolution allowing insertions and deletions (or indels). Given appropriate assumptions, our algorithm requires sequence lengths growing polynomially in the number of leaf taxa. Our techniques are distance-based and largely bypass the problem of multiple alignment.

Daskalakis, Constantinos; Roch, Sebastien


Species Names in Phylogenetic Nomenclature  

Microsoft Academic Search

Linnaean binomial nomenclature is logically incompatible with the phylogenetic nomenclature of de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449-480): The former is based on the concept of genus, thus making this rank mandatory, while the latter is based on phylo- genetic definitions and requires the abandonment of mandatory ranks. Thus, if species are to re- ceive names under




Phylogenetic signals in morphometric data  

Microsoft Academic Search

Although many of the goals and concepts of qualitative morphological analysis and morphometrics are similar, systematists have largely rejected the use of morphometric methods in phylogenetic analysis on a variety of grounds. This review finds that (1) the concepts of a cladistic character and a morphometric vari- able are essentially identical, (2) morphometric methods can be instrumental in discovering and

Norman MacLeod


Molecular phylogenetics of subtribe Aeridinae (Orchidaceae): insights from plastid matK and nuclear ribosomal ITS sequences  

Microsoft Academic Search

We conducted phylogenetic analyses using two DNA sequence data sets derived from matK, the maturase-coding gene located in an intron of the plastid gene trnK, and the internal transcribed spacer region of 18S–26S nuclear ribosomal DNA to examine relationships in subtribe Aeridinae (Orchidaceae). Specifically, we investigated (1) phylogenetic relationships among genera in the subtribe, (2) the congruence between previous classifications

Hidayat Topik; Tomohisa Yukawa; Motomi Ito



Phylogenetic Properties of RNA Viruses  

PubMed Central

A new word, phylodynamics, was coined to emphasize the interconnection between phylogenetic properties, as observed for instance in a phylogenetic tree, and the epidemic dynamics of viruses, where selection, mediated by the host immune response, and transmission play a crucial role. The challenges faced when investigating the evolution of RNA viruses call for a virtuous loop of data collection, data analysis and modeling. This already resulted both in the collection of massive sequences databases and in the formulation of hypotheses on the main mechanisms driving qualitative differences observed in the (reconstructed) evolutionary patterns of different RNA viruses. Qualitatively, it has been observed that selection driven by the host immune response induces an uneven survival ability among co-existing strains. As a consequence, the imbalance level of the phylogenetic tree is manifestly more pronounced if compared to the case when the interaction with the host immune system does not play a central role in the evolutive dynamics. While many imbalance metrics have been introduced, reliable methods to discriminate in a quantitative way different level of imbalance are still lacking. In our work, we reconstruct and analyze the phylogenetic trees of six RNA viruses, with a special emphasis on the human Influenza A virus, due to its relevance for vaccine preparation as well as for the theoretical challenges it poses due to its peculiar evolutionary dynamics. We focus in particular on topological properties. We point out the limitation featured by standard imbalance metrics, and we introduce a new methodology with which we assign the correct imbalance level of the phylogenetic trees, in agreement with the phylodynamics of the viruses. Our thorough quantitative analysis allows for a deeper understanding of the evolutionary dynamics of the considered RNA viruses, which is crucial in order to provide a valuable framework for a quantitative assessment of theoretical predictions.

Pompei, Simone; Loreto, Vittorio; Tria, Francesca



Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies.  


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 6000bp 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



Familial filicide and filicide classification.  


Filicide is the killing of a child by his or her parent. Despite the disturbing nature of these crimes, a study of filicide classification can provide insight into their causes. Furthermore, a study of filicide classification provides information essential to accurate death certification. We report a rare case of familial filicide in which twin sisters both attempted to kill their respective children. We then suggest a detailed classification of filicide subtypes that provides a framework of motives and precipitating factors leading to filicide. We identify 16 subtypes of filicide, each of which is sufficiently characteristic to warrant a separate category. We describe in some detail the characteristic features of these subtypes. A knowledge of filicide subtypes contributes to interpretation of difficult cases. Furthermore, to protect potential child homicide victims, it is necessary to know how and why they are killed. Epidemiologic studies using filicide subtypes as their basis could provide information leading to strategies for prevention. PMID:10507800

Guileyardo, J M; Prahlow, J A; Barnard, J J



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



Phylogenetics of Saccharomycetales, the ascomycete yeasts.  


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


The neuron classification problem.  


A systematic account of neuron cell types is a basic prerequisite for determining the vertebrate nervous system global wiring diagram. With comprehensive lineage and phylogenetic information unavailable, a general ontology based on structure-function taxonomy is proposed and implemented in a knowledge management system, and a prototype analysis of select regions (including retina, cerebellum, and hypothalamus) presented. The supporting Brain Architecture Knowledge Management System (BAMS) Neuron ontology is online and its user interface allows queries about terms and their definitions, classification criteria based on the original literature and "Petilla Convention" guidelines, hierarchies, and relations-with annotations documenting each ontology entry. Combined with three BAMS modules for neural regions, connections between regions and neuron types, and molecules, the Neuron ontology provides a general framework for physical descriptions and computational modeling of neural systems. The knowledge management system interacts with other web resources, is accessible in both XML and RDF/OWL, is extendible to the whole body, and awaits large-scale data population requiring community participation for timely implementation. PMID:17582506

Bota, Mihail; Swanson, Larry W



When do phylogenetic mixture models mimic other phylogenetic models?  


Phylogenetic mixture models, in which the sites in sequences undergo different substitution processes along the same or different trees, allow the description of heterogeneous evolutionary processes. As data sets consisting of longer sequences become available, it is important to understand such models, for both theoretical insights and use in statistical analyses. Some recent articles have highlighted disturbing "mimicking" behavior in which a distribution from a mixture model is identical to one arising on a different tree or trees. Other works have indicated such problems are unlikely to occur in practice, as they require very special parameter choices. After surveying some of these works on mixture models, we give several new results. In general, if the number of components in a generating mixture is not too large and we disallow zero or infinite branch lengths, then it cannot mimic the behavior of a nonmixture on a different tree. On the other hand, if the mixture model is locally overparameterized, it is possible for a phylogenetic mixture model to mimic distributions of another tree model. Although theoretical questions remain, these sorts of results can serve as a guide to when the use of mixture models in either maximum likelihood or Bayesian frameworks is likely to lead to statistically consistent inference, and when mimicking due to heterogeneity should be considered a realistic possibility. [Phylogenetic mixture models; parameter identifiability; heterogeneous sequence evolution.]. PMID:22798332

Allman, Elizabeth S; Rhodes, John A; Sullivant, Seth



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



On the delineation and higher-level classification of algae  

Microsoft Academic Search

Biological classification has been successively shaped by Neoplatonism, ideas of plenitude and one-dimensional continuity (the Great Chain of Being), two-dimensional continuity (Linnaeus's map), idealized comparative morphology and development and, through phylogenetic theory, Darwinian descent with modification. Concepts of Algae have thus evolved within a succession of very different paradigms. Algae have been imperfect plants; a segment of the Great Chain;

Mark Ragan



Phylogenetic analysis of gene expression.  


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



Phylogenetic Analysis of Metabolic Pathways  

Microsoft Academic Search

.   The information provided by completely sequenced genomes can yield insights into the multi-level organization of organisms\\u000a and their evolution. At the lowest level of molecular organization individual enzymes are formed, often through assembly of\\u000a multiple polypeptides. At a higher level, sets of enzymes group into metabolic networks. Much has been learned about the relationship\\u000a of species from phylogenetic trees

Christian V. Forst; Klaus Schulten



Phylogenetic analysis of AAA proteins  

Microsoft Academic Search

AAA ATPases form a large protein family with manifold cellular roles. They belong to the AAA+ superfamily of ringshaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. Phylogenetic analyses have suggested the existence of five major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, and the MSP1\\/katanin\\/spastin

Tancred Frickey; Andrei N Lupas



Phylogenetic methods in drug discovery.  


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



Phylogenetic analysis of AAA proteins.  


AAA ATPases form a large protein family with manifold cellular roles. They belong to the AAA+ superfamily of ringshaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. Phylogenetic analyses have suggested the existence of five major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, and the MSP1/katanin/spastin group), as well as a number of deeply branching minor clades. These analyses however have been characterized by a lack of consistency in defining the boundaries of the AAA family. We have used cluster analysis to delineate unambiguously the group of AAA sequences within the AAA+ superfamily. Phylogenetic and cluster analysis of this sequence set revealed the existence of a sixth major AAA clade, comprising the mitochondrial, membrane-bound protein BCS1 and its homologues. In addition, we identified several deep branches consisting mainly of hypothetical proteins resulting from genomic projects. Analysis of the AAA N-domains provided direct support for the obtained phylogeny for most branches, but revealed some deep splits that had not been apparent from phylogenetic analysis and some unexpected similarities between distant clades. It also revealed highly degenerate D1 domains in plant MSP1 sequences and in at least one deeply branching group of hypothetical proteins (YC46), showing that AAA proteins with two ATPase domains arose at least three times independently. PMID:15037233

Frickey, Tancred; Lupas, Andrei N


Evaluation of feature descriptors for texture classification  

NASA Astrophysics Data System (ADS)

Successful execution of tasks such as image classification, object detection and recognition, and scene classification depends on the definition of a set of features able to describe images effectively. Texture is among the features used by the human visual system. It provides information regarding spatial distribution, changes in brightness, and description regarding the structural arrangement of surfaces. However, although the visual human system is extremely accurate to recognize and describe textures, it is difficult to define a set of textural descriptors to be used in image analysis on different application domains. This work evaluates several texture descriptors and demonstrates that the combination of descriptors can improve the performance of texture classification.

Schwartz, William Robson; Roberti de Siqueira, Fernando; Pedrini, Helio



Caller behaviour classification using computational intelligence methods.  


A classification system that accurately categorizes caller interaction within Interactive Voice Response systems is essential in determining caller behaviour. Field and call performance classifier for pay beneficiary application are developed. Genetic Algorithms, Multi-Layer Perceptron neural network, Radial Basis Function neural network, Fuzzy Inference Systems and Support Vector Machine computational intelligent techniques were considered in this research. Exceptional results were achieved. Classifiers with accuracy values greater than 90% were developed. The preferred models for field 'Say amount', 'Say confirmation' and call performance classification are the ensemble of classifiers. However, the Multi-Layer Perceptron classifiers performed the best in field 'Say account' and 'Select beneficiary' classification. PMID:20180256

Patel, Pretesh B; Marwala, Tshilidzi



Classification Management Tutorial.  

National Technical Information Service (NTIS)

The purpose of this Classification Management tutorial is to provide detailed supplemental guidance to Original Classification Authorities (OCAs) for the development of United States (US) Army security classification guides (SCGs) or guidance. Army Regula...



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



The Number of Replications Needed for Accurate Estimation of the Bootstrap P Value in Phylogenetic Studies  

Microsoft Academic Search

The bootstrap is a statistical method for obtaining a nonparametric estimate of error (Efron 1979, 1982). Felsenstein ( 1985) was the first to apply this method to phylogeny estimation, and his approach is now widely used. Taxa are held constant, and the characters (for sequence data, nucleotide or amino acid sites) are resampled randomly with replacement. A phylogeny is constructed

S. Blair Hedges


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

Microsoft Academic Search

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

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



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



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.



Obesity: criteria and classification.  


Obesity is defined as an excess accumulation of body fat. To measure fat in the body accurately is difficult, and no method is easily available for routine clinical use. Traditionally, overweight and obesity have been evaluated by anthropometric measurement of weight-for-height. More recently, BMI has been used. The normal range is 19-24.9 kg/m2, overweight is 25-29.9 kg/m2, and obesity >/= 30 kg/m2. Not only is the total amount of fat an individual carries important, but also where the fat is distributed in the body. Fat in a central or upper body (android) distribution is most related to health risk. The most accurate way to measure central obesity is by magnetic resonance imaging or computer-assisted tomography scanning, but this approach is too expensive for routine use. Simple anthropometric measurements can be used, such as waist circumference. A waist circumference of greater than 1020 mm in men and 880 mm in women is a risk factor for insulin resistance, diabetes mellitus and cardiovascular disease. There is a clear genetic predisposition for obesity. The genetic contribution to obesity is between 25 and 40 % of the individual differences in BMI. For the overwhelming majority of individuals, the genetic predisposition will not be defined by one gene, but by multiple genes. Eventually, classification of obesity may be done by genetic means, but this approach will require more knowledge. PMID:11115784

Pi-Sunyer, F X



Automated Waste Classification Software (WasteCat) (for Microcomputers).  

National Technical Information Service (NTIS)

The State of California has recently developed a computer automated system to help generators, the regulated community, and the various regulatory agencies accurately determine the proper classification of potentially hazardous waste which may be subject ...



TreeFam: a curated database of phylogenetic trees of animal gene families  

Microsoft Academic Search

TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary his- 20 tory of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively, based on seed align- ments and trees in a similar fashion to Pfam.

Heng Li; Avril Coghlan; Jue Ruan; Lachlan James M. Coin; Jean-karim Hériché; Lara Osmotherly; Ruiqiang Li; Tao Liu; Zhang Zhang; Lars Bolund; Gane Ka-shu Wong; Wei-mou Zheng; Paramvir Dehal; Jun Wang; Richard Durbin



Music Genre Classification Based on Multiple Classifier Fusion  

Microsoft Academic Search

Although researchers have made great progresses on music genre classification in recent years, the need for more accurate system is still not satisfied. In this paper, we propose a method for further reducing the classification error rate based on multiple classifier fusion. First of all, MFCCs and four features from MPEG-7 audio descriptor are extracted in every short time frame,

Lei Wang; Shen Huang; Shijin Wang; Jiaen Liang; Bo Xu



Improving Web Spam Classification using Rank-time Features  

Microsoft Academic Search

In this paper, we study the classification of web spam. Web spam refers to pages that use techniques to mislead search engines into assigning them higher rank, thus increasing their site traffic. Our contributions are two fold. First, we find that the method of dataset construction is crucial for accurate spam classification and we note that this problem occurs generally

Krysta Marie Svore; Qiang Wu; Chris J. C. Burges; Aaswath Raman



Terrain classification for a UGV  

NASA Astrophysics Data System (ADS)

This work addresses the issue of Terrain Classification that can be applied for path planning for an Unmanned Ground Vehicle (UGV) platform. We are interested in classification of features such as rocks, bushes, trees and dirt roads. Currently, the data is acquired from a color camera mounted on the UGV as we can add range data from a second sensor in the future. The classification is accomplished by first, coarse segmenting a frame and then refining the initial segmentations through a convenient user interface. After the first frame, temporal information is exploited to improve the quality of the image segmentation and help classification adapt to changes due to ambient lighting, shadows, and scene changes as the platform moves. The Mean Shift Classifier algorithm provides segmentation of the current frame data. We have tested the above algorithms with four sequence of frames acquired in an environment with terrain representative of the type we expect to see in the field. A comparison of the results from this algorithm was done with accurate manually-segmented (ground-truth) data, for each frame in the sequence.

Sarwal, Alok; Baker, Chris; Rosenblum, Mark



Internet traffic classification using bayesian analysis techniques  

Microsoft Academic Search

Accurate traffic classification is of fundamental importance to numerous other network activities, from security monitoring to accounting, and from Quality of Service to providing operators with useful forecasts for long-term provisioning. We apply a Naïve Bayes estimator to categorize traffic by application. Uniquely, our work capitalizes on hand-classified network data, using it as input to a supervised Naïve Bayes estimator.

A. W. Moore; Denis Zuev



Nucleic acids in the classification of campylobacters  

Microsoft Academic Search

The importance of campylobacters in human disease has stimulated improvements in the methods for identification of strains from hospitals and the environment, Reliable and accurate identification depends on a sound classification for which nucleic acid analyses provide fundamental information about species relationships. Studies on the genusCampylobacter show that the genome DNA of species have base compositions of 29 to 38

R. J. Owen



Randomized Clustering Forests for Image Classification  

Microsoft Academic Search

This paper introduces three new contributions to the problems of image classification and image search. First, we propose a new image patch quantization algorithm. Other competitive approaches require a large code book and the sampling of many local regions for accurate image description, at the expense of a prohibitive processing time. We introduce Extremely Randomized Clustering Forests—ensembles of randomly created

Frank Moosmann; Eric Nowak; Frédéric Jurie



A parallel learning algorithm for text classification  

Microsoft Academic Search

Text classification is the process of classifying documents into predefined categories based on their content. Existing supervised learning algorithms to automatically classify text need sufficient labeled documents to learn accurately. Applying the Expectation-Maximization (EM) algorithm to this problem is an alternative approach that utilizes a large pool of unlabeled documents to augment the available labeled documents. Unfortunately, the time needed

Canasai Kruengkrai; Chuleerat Jaruskulchai



Making sense of arson through classification  

Microsoft Academic Search

Arson classification efforts are an attempt to make sense of a complex whole. To a greater or lesser extent typologies offered to date have relied on assumed motive. More recently, systems that combine information about offender characteristics and\\/or offence features have become increasingly popular. The ability to categorise arsonists accurately has significant implications for both mental health professionals and fire

Rebekah Doley



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



Structure feature selection for chemical compound classification  

Microsoft Academic Search

With the development of highly efficient chemin- formatics data collection technology, classification of chemical structure data emerges as an important topic in cheminfor- matics. Towards building highly accurate predictive models for chemical data, here we present an efficient feature selection method. In our method, we first represent a chemical structure by its 2D connectivity map. We then use frequent subgraph

Hongliang Fei; Jun Huan



More accurate time from the Heathkit most accurate clock  

Microsoft Academic Search

The addition of an auxiliary circuit to the Heathkit GC-1000 clock is described. The circuit, which consists of two integrated circuits, two resistors, and three capacitors, will supply a more accurate timing pulse to the computer. The circuit contains two input signals and produces one output; the inputs are multiplexed seven-digit displays (two digits for hour, minute, and second, and

M. V. Tollefson; R. H. Bloomer Jr.



Molecular phylogenetic relationships of China Seas groupers based on cytochrome b gene fragment sequences  

Microsoft Academic Search

The classification and evolutionary relationships are important issues in the study of the groupers. Cytochrome b gene fragment of twenty-eight grouper species within six genera of subfamily Epinephelinae was amplified using PCR techniques\\u000a and the sequences were analyzed to derive the phylogenetic relationships of the groupers from the China Seas. Genetic information\\u000a indexes, including Kimura-2 parameter genetic distance and T

Shaoxiong Ding; Xuan Zhuang; Feng Guo; Jun Wang; Yongquan Su; Qiyong Zhang; Qifu Li



A second species of Oculogryphus (Coleoptera, Lampyridae), with notes on the phylogenetic affinities of the genus.  


A second species of the enigmatic lampyrid genus Oculogryphus is described and figured as Oculogryphus bicolorsp. n. from Vietnam. The definition of the genus is slightly modified with consideration of newly detected morphological variation from this species. According to a comprehensive phylogenetic analysis including nearly 80% of documented lampyrid genera, Oculogryphus is the putative sister group to Stenocladius s. str. within the paraphyletic group of Ototretinae-Ototretadrilinae.The classification of Stenocladius is briefly discussed in this context. PMID:21594065

Jeng, Ming-Luen; Branham, Marc A; Engel, Michael S



Propionibacterium acnes Types I and II Represent Phylogenetically Distinct Groups  

PubMed Central

Although two phenotypes of the opportunistic pathogen Propionibacterium acnes (types I and II) have been described, epidemiological investigations of their roles in different infections have not been widely reported. Using immunofluorescence microscopy with monoclonal antibodies (MAbs) QUBPa1 and QUBPa2, specific for types I and II, respectively, we investigated the prevalences of the two types among 132 P. acnes isolates. Analysis of isolates from failed prosthetic hip implants (n = 40) revealed approximately equal numbers of type I and II organisms. Isolates from failed prosthetic hip-associated bone (n = 6) and tissue (n = 38) samples, as well as isolates from acne (n = 22), dental infections (n = 8), and skin removed during surgical incision (n = 18) were predominately of type I. A total of 11 (8%) isolates showed atypical MAb labeling and could not be conclusively identified. Phylogenetic analysis of P. acnes by nucleotide sequencing revealed the 16S rRNA gene to be highly conserved between types I and II. In contrast, sequence analysis of recA and a putative hemolysin gene (tly) revealed significantly greater type-specific polymorphisms that corresponded to phylogenetically distinct cluster groups. All 11 isolates with atypical MAb labeling were identified as type I by sequencing. Within the recA and tly phylogenetic trees, nine of these isolates formed a cluster distinct from other type I organisms, suggesting a further phylogenetic subdivision within type I. Our study therefore demonstrates that the phenotypic differences between P. acnes types I and II reflect deeper differences in their phylogeny. Furthermore, nucleotide sequencing provides an accurate method for identifying the type status of P. acnes isolates.

McDowell, Andrew; Valanne, Susanna; Ramage, Gordon; Tunney, Michael M.; Glenn, Josephine V.; McLorinan, Gregory C.; Bhatia, Ajay; Maisonneuve, Jean-Francois; Lodes, Michael; Persing, David H.; Patrick, Sheila



Accurate measurements in volume data  

Microsoft Academic Search

An algorithm for very accurate visualization of an iso- surface in a 3D medical dataset has been developed in the past few years. This technique is extended in this paper to several kinds of measurements in which exact geometric information of a selected iso-surface is used to derive volume, length, curvature, connectivity and similar geometric information from an object of

Javier Olivan; Marco K. Bosma; Jaap Smit; S. K. Mun



Method of accurizing rail guns  

Microsoft Academic Search

In space, projectiles with hypervelocity can deliver large amounts of energy to the target. Long range and high accuracy are essential. This report presents a method of improving the accuracy of hypervelocity vehicles by measuring the output velocity and correcting the direction by impulse from a laser beam normal to the projectile flight path. The accurizer is described, trajectory-correction calculations




Accurate, inexpensive, thermal expansion microtranslator  

Microsoft Academic Search

We have developed an accurate, inexpensive translator utilizing the thermal expansion of an electrically heated wire. The resistance of the wire, measured in a Wheatstone bridge, provides a readout of the length of the wire based on its temperature coefficient of resistance.

James J. Snyder



Role of International Classification of Diseases in medical record management.  


The Medical Record is the major source of Health information. Therefore, it is necessary to maintain good patient records by documenting all the required information, e.g. history, physical examination, progress notes, investigations, treatment including surgical procedures, complete diagnosis and end result, etc., as per the guidelines stated in the International Classification of Diseases published by World Health Organisation. If the documentation is accurate and complete, the health care information could be obtained and classified accurately and completely according to International Classification of Diseases published by WHO. Hence, International Classification of Diseases plays an important role in managing good medical records. PMID:10177052

Mogli, G D



Inter-rater reliability of the EPUAP pressure ulcer classification system using photographs  

Microsoft Academic Search

BACKGROUND: Many classification systems for grading pressure ulcers are discussed in the literature. Correct identification and classification of a pressure ulcer is important for accurate reporting of the magnitude of the problem, and for timely prevention. The reliability of pressure ulcer classification systems has rarely been tested. AIMS AND OBJECTIVES: The purpose of this paper is to examine the inter-rater

Tom Defloor; Lisette Schoonhoven



Traversability classification for UGV navigation: a comparison of patch and superpixel representations  

Microsoft Academic Search

Abstract—Robot navigation in complex outdoor terrain can benefit from accurate traversability classification. Appearancebased traversability estimation can provide a long-range sensing capability which complements the traditional use of stereo or LIDAR ranging. In the standard approach to traversability classification, each image frame is decomposed into patches or pixels for further analysis. However, classification at the pixel level is prone to noise

Dongshin Kim; Sang Min Oh; James M. Rehg



Phylogenetic clustering increases with elevation for microbes.  


Although phylogenetic approaches are useful for providing insights into the processes underlying biodiversity patterns, the studies of microbial phylogenetic relatedness are rare, especially for elevational gradients. Using high-throughput pyrosequencing, we examined the biodiversity patterns for biofilm bacterial communities that were scraped from stream stones along an elevational gradient from 1820 to 4050?m in China. The patterns of bacterial species richness and phylogenetic diversity were hollow towards higher elevations. The bacterial communities consisted of closer relatives than expected and displayed increasing terminal phylogenetic clustering towards mountain top. The increasing phylogenetic clustering with elevation contrasts reports for macroorganisms that revealed phylogenetic overdispersion at low or intermediate elevations. Because water temperature showed the strongest correlation with phylogenetic relatedness (r(2) ?=?0.516), the elevational pattern in the bacterial phylogenetic structure indicated that environmental filtering possibly due to lower temperature or more frequent temperature fluctuations increased towards higher elevations. Evidence supporting the environmental filtering on bacteria was also reflected by the orderly succession in the relative abundance of different bacterial phyla along the elevational gradient and in the high evenness of bacterial taxa at higher elevations. Overall, our results indicated that ecological processes possibly related to temperature may play a dominant role in structuring bacterial biodiversity along the elevational gradient. PMID:23757276

Wang, Jianjun; Soininen, Janne; He, Jizheng; Shen, Ji



Discovering Frequent Agreement Subtrees from Phylogenetic Data  

Microsoft Academic Search

We study a new data mining problem concerning the discovery of frequent agreement subtrees (FASTs) from a set of phylogenetic trees. A phylogenetic tree, or phylogeny, is an unordered tree in which the order among siblings is unimportant. Furthermore, each leaf in the tree has a label representing a taxon (species or organism) name, whereas internal nodes are unlabeled. The

Sen Zhang; Jason Tsong-li Wang



Relating Geographic Pattern to Phylogenetic Process  

Microsoft Academic Search

Observed patterns of within-species geographic variation may reflect phylogenetic history or ecogenetic adaptation, and it is frequently desirable to evaluate their relative contributions. Phylogenetic information can be recovered from relatively neutrally evolving molecular markers, but to what extent are they useful in understanding the causes of observed geographic patterns within species? In the lacertid lizard Gallotia galloti (Western Canary islands),

R. S. Thorpe; A. Malhotra; H. Black; J. C. Daltry; W. Wuster



Phylogenetic Trees: An Information Visualisation Perspective  

Microsoft Academic Search

The development of powerful visualisation tools is a major challenge in bioinformatics. Phylogenetics, a field with a growing impact on a variety of life science areas, is experiencing an increasing but poorly met requirement for software supporting the advanced visualisation of phylogenetic trees. Visualisation problems within the domain are commonly experienced by its researchers, but are poorly documented. Furthermore, the

Savrina F. Carrizo



Phylogenetic Interrelationships of Ginglymodian Fishes (Actinopterygii: Neopterygii)  

Microsoft Academic Search

The Ginglymodi is one of the most common, though poorly understood groups of neopterygians, which includes gars, macrosemiiforms, and “semionotiforms.” In particular, the phylogenetic relationships between the widely distributed “semionotiforms,” and between them and other ginglymodians have been enigmatic. Here, the phylogenetic relationships between eight of the 11 “semionotiform” genera, five genera of living and fossil gars and three macrosemiid

Adriana López-Arbarello



Selecting Species Traits for Biomonitoring Applications in light of Phylogenetic Relationships among Lotic Insects  

NASA Astrophysics Data System (ADS)

The use of species traits as indicators of environmental disturbance is being considered for biomonitoring programs globally. As such, methods to select relevant and informative traits for inclusion in biometrics need to be developed. In this research, we identified 20 traits of aquatic insects within six trait groups: morphology, mobility, life-history strategy, thermal tolerance, feeding guild and ecology (e.g., habitat preference). We constructed phylogenetic trees for 1) all lotic insect species of North America and 2) all Ephemeroptera, Plecoptera and Trichoptera species based on morphology- and molecular-based analyses and classifications. We then measured variability (i.e., plasticity) of the 20 traits and six trait groups across the two phylogenetic trees. Traits with higher degrees of plasticity indicated traits that were less phylogenetically constrained, and were considered informative for biomonitoring purposes. Thermal tolerance, rheophily, body size at maturity and feeding guild showed the highest plasticity across both phylogenetic trees. Two mobility traits, occurrence in drift and adult dispersal distance, showed moderate plasticity. By contrast, adult exiting ability, degree of attachment, adult lifespan and body shape showed low variability and were thus less informative. Plastic species traits that are less phylogenetically constrained may be most useful in detecting community change along environmental gradients.

Poff, N.; Vieira, N. K.; Simmons, M. P.; Olden, J. D.; Kondratieff, B. C.; Finn, D. S.



The phylogenetic relationships and generic limits of finches (Fringillidae).  


Phylogenetic relationships among the true finches (Fringillidae) have been confounded by the recurrence of similar plumage patterns and use of similar feeding niches. Using a dense taxon sampling and a combination of nuclear and mitochondrial sequences we reconstructed a well resolved and strongly supported phylogenetic hypothesis for this family. We identified three well supported, subfamily level clades: the Holoarctic genus Fringilla (subfamly Fringillinae), the Neotropical Euphonia and Chlorophonia (subfamily Euphoniinae), and the more widespread subfamily Carduelinae for the remaining taxa. Although usually separated in a different family-group taxon (Drepanidinae), the Hawaiian honeycreepers are deeply nested within the Carduelinae and sister to a group of Asian Carpodacus. Other new relationships recovered by this analysis include the placement of the extinct Chaunoproctus ferreorostris as sister to some Asian Carpodacus, a clade combining greenfinches (Carduelis chloris and allies), Rhodospiza and Rhynchostruthus, and a well-supported clade with the aberrant Callacanthis and Pyrrhoplectes together with Carpodacus rubescens. Although part of the large Carduelis-Serinus complex, the poorly known Serinus estherae forms a distinct lineage without close relatives. The traditionally delimited genera Carduelis, Serinus, Carpodacus, Pinicola and Euphonia are polyphyletic or paraphyletic. Based on our results we propose a revised generic classification of finches and describe a new monotypic genus for Carpodacus rubescens. PMID:22023825

Zuccon, Dario; Pr?s-Jones, Robert; Rasmussen, Pamela C; Ericson, Per G P



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


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



Multisensor data fusion for supervised land-cover classification using Bayesian and geostatistical techniques  

Microsoft Academic Search

We propose a geostatistical approach incorporated to the Bayesian data fusion technique for supervised classification of multi-sensor\\u000a remote sensing data. The classification based only on the traditional spectral approach cannot preserve the accurate spatial\\u000a information and can result in unrealistic classification results. To obtain accurate spatial\\/contextual information, the indicator\\u000a kriging that allows one to estimate the probability of occurrence of

No-Wook Park; Wooil M. Moon; Kwang-Hoon Chi; Byung-Doo Kwon



Accurate Accident Reconstruction in VANET  

Microsoft Academic Search

\\u000a We propose a forensic VANET application to aid an accurate accident reconstruction. Our application provides a new source\\u000a of objective real-time data impossible to collect using existing methods. By leveraging inter-vehicle communications, we compile\\u000a digital evidence describing events before, during, and after an accident in its entirety. In addition to sensors data and\\u000a major components’ status, we provide relative positions

Yuliya Kopylova; Csilla Farkas; Wenyuan Xu


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.



Phylogenetic systematics of the colorful, cyanide-producing millipedes of Appalachia (Polydesmida, Xystodesmidae, Apheloriini) using a total evidence Bayesian approach.  


Here, we provide an exemplar-approach phylogeny of the xystodesmid millipede tribe Apheloriini with a focus on genus-group relationships-particularly of the genus Brachoria. Exemplars for the phylogenetic analysis were chosen to represent the maximum breadth of morphological diversity within all nominal genera in the tribe Apheloriini, and to broadly sample the genus Brachoria. In addition, three closely related tribes were used (Rhysodesmini, Nannariini, and Pachydesmini). Morphological and DNA sequence data were scored for Bayesian inference of phylogeny. Phylogenetic analysis resulted in polyphyletic genera Brachoria and Sigmoria, a monophyletic Apheloriini, and a "southern clade" that contains most of the tribal species diversity. We used this phylogeny to track morphological character histories and reconstruct ancestral states using stochastic character mapping. Based on the findings from the character mapping study, the diagnostic feature of the genus Brachoria, the cingulum, evolved independently in two lineages. We compared our phylogeny against prior classifications using Bayes factor hypothesis-testing and found that our phylogenetic hypothesis is inconsistent with the previous hypotheses underlying the most recent classification. With our preferred total-evidence phylogeny as a framework for taxonomic modifications, we describe a new genus, Appalachioria; supply phylogenetic diagnoses of monophyletic taxa; and provide a phylogeny-based classification for the tribe Apheloriini. PMID:16876439

Marek, Paul E; Bond, Jason E



More accurate time from the Heathkit most accurate clock  

NASA Astrophysics Data System (ADS)

The addition of an auxiliary circuit to the Heathkit GC-1000 clock is described. The circuit, which consists of two integrated circuits, two resistors, and three capacitors, will supply a more accurate timing pulse to the computer. The circuit contains two input signals and produces one output; the inputs are multiplexed seven-digit displays (two digits for hour, minute, and second, and one for tenths of a second) and the output appears as a string of about 10 low-going pulses about 1.25 ms in duration. Low pass filters (R1 and C1) are utilized to eliminate extraneous pulses. The materials and procedures for attaching the circuit to the clock are examined. The software for the data set ready signal, and the method for accurate timing of data collection are discussed. The accuracy of the clock is evaluated and it is observed that the circuit improves the correct time provided by the clock from + or - 29 ms to + or - 5 ms.

Tollefson, M. V.; Bloomer, R. H., Jr.



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.



Classification Using Growth Curves  

Microsoft Academic Search

Classification using the growth curve model is analyzed according to whether the covariance matrix structure is known to be compound symmetric. A new classification procedure appropriate for classification in the case of models with means that follow a Potthoff and Roy [Potthoff, R. F., Roy, S. N. (1964). A generalized multivariate analysis of variance model useful especially for growth curve

Graciela B. Mentz; Anant M. Kshirsagar



Government Classification: An Overview.  

ERIC Educational Resources Information Center

Classification of government documents (confidential, secret, top secret) is a system used by the executive branch to, in part, protect national security and foreign policy interests. The systematic use of classification markings with precise definitions was established during World War I, and since 1936 major changes in classification have…

Brown, Karen M.


38 CFR 4.46 - Accurate measurement.  

Code of Federal Regulations, 2013 CFR

...RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement...examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be accurately measured and reported....



Accurate prediction of scorpion toxin functional properties from primary structures.  


Scorpion toxins are common experimental tools for studies of biochemical and pharmacological properties of ion channels. The number of functionally annotated scorpion toxins is steadily growing, but the number of identified toxin sequences is increasing at much faster pace. With an estimated 100,000 different variants, bioinformatic analysis of scorpion toxins is becoming a necessary tool for their systematic functional analysis. Here, we report a bioinformatics-driven system involving scorpion toxin structural classification, functional annotation, database technology, sequence comparison, nearest neighbour analysis, and decision rules which produces highly accurate predictions of scorpion toxin functional properties. PMID:15950506

Tan, Paul T J; Srinivasan, K N; Seah, Seng Hong; Koh, Judice L Y; Tan, Tin Wee; Ranganathan, Shoba; Brusic, Vladimir



Prostate segmentation by sparse representation based classification  

PubMed Central

Purpose: The segmentation of prostate in CT images is of essential importance to external beam radiotherapy, which is one of the major treatments for prostate cancer nowadays. During the radiotherapy, the prostate is radiated by high-energy x rays from different directions. In order to maximize the dose to the cancer and minimize the dose to the surrounding healthy tissues (e.g., bladder and rectum), the prostate in the new treatment image needs to be accurately localized. Therefore, the effectiveness and efficiency of external beam radiotherapy highly depend on the accurate localization of the prostate. However, due to the low contrast of the prostate with its surrounding tissues (e.g., bladder), the unpredicted prostate motion, and the large appearance variations across different treatment days, it is challenging to segment the prostate in CT images. In this paper, the authors present a novel classification based segmentation method to address these problems. Methods: To segment the prostate, the proposed method first uses sparse representation based classification (SRC) to enhance the prostate in CT images by pixel-wise classification, in order to overcome the limitation of poor contrast of the prostate images. Then, based on the classification results, previous segmented prostates of the same patient are used as patient-specific atlases to align onto the current treatment image and the majority voting strategy is finally adopted to segment the prostate. In order to address the limitations of the traditional SRC in pixel-wise classification, especially for the purpose of segmentation, the authors extend SRC from the following four aspects: (1) A discriminant subdictionary learning method is proposed to learn a discriminant and compact representation of training samples for each class so that the discriminant power of SRC can be increased and also SRC can be applied to the large-scale pixel-wise classification. (2) The L1 regularized sparse coding is replaced by the elastic net in order to obtain a smooth and clear prostate boundary in the classification result. (3) Residue-based linear regression is incorporated to improve the classification performance and to extend SRC from hard classification to soft classification. (4) Iterative SRC is proposed by using context information to iteratively refine the classification results. Results: The proposed method has been comprehensively evaluated on a dataset consisting of 330 CT images from 24 patients. The effectiveness of the extended SRC has been validated by comparing it with the traditional SRC based on the proposed four extensions. The experimental results show that our extended SRC can obtain not only more accurate classification results but also smoother and clearer prostate boundary than the traditional SRC. Besides, the comparison with other five state-of-the-art prostate segmentation methods indicates that our method can achieve better performance than other methods under comparison. Conclusions: The authors have proposed a novel prostate segmentation method based on the sparse representation based classification, which can achieve considerably accurate segmentation results in CT prostate segmentation.

Gao, Yaozong; Liao, Shu; Shen, Dinggang



Ribosomal ITS sequences and plant phylogenetic inference  

Microsoft Academic Search

One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the internal transcribed spacer (ITS) region of the 18S–5.8S–26S nuclear ribosomal cistron. The prominence of this source of nuclear DNA sequence data is underscored by a survey of phylogenetic publications involving comparisons at the genus level or below, which reveals that of

I. Álvarez; J. F. Wendel



Phylogenetic position of Boodlea vanbosseae (Siphonocladales, Chlorophyta)  

Microsoft Academic Search

The marine green alga Boodlea vanbosseae is widely distributed in the tropical Indo-West Pacific region. The phylogenetic position of this somewhat unusual member of the genus is assessed based on morphological examination and phylogenetic analysis of nuclear-encoded partial large subunit rDNA sequences. Boodlea vanbosseae differs from other species of the genus by its coarse, irregularly branching filaments, the typical rhizoids




Phylogenetic diversity measures based on Hill numbers  

PubMed Central

We propose a parametric class of phylogenetic diversity (PD) measures that are sensitive to both species abundance and species taxonomic or phylogenetic distances. This work extends the conventional parametric species-neutral approach (based on ‘effective number of species’ or Hill numbers) to take into account species relatedness, and also generalizes the traditional phylogenetic approach (based on ‘total phylogenetic length’) to incorporate species abundances. The proposed measure quantifies ‘the mean effective number of species’ over any time interval of interest, or the ‘effective number of maximally distinct lineages’ over that time interval. The product of the measure and the interval length quantifies the ‘branch diversity’ of the phylogenetic tree during that interval. The new measures generalize and unify many existing measures and lead to a natural definition of taxonomic diversity as a special case. The replication principle (or doubling property), an important requirement for species-neutral diversity, is generalized to PD. The widely used Rao's quadratic entropy and the phylogenetic entropy do not satisfy this essential property, but a simple transformation converts each to our measures, which do satisfy the property. The proposed approach is applied to forest data for interpreting the effects of thinning.

Chao, Anne; Chiu, Chun-Huo; Jost, Lou



Phylogenetic niche conservatism in C4 grasses.  


Photosynthetic pathway is used widely to discriminate plant functional types in studies of global change. However, independent evolutionary lineages of C(4) grasses with different variants of C(4) photosynthesis show different biogeographical relationships with mean annual precipitation, suggesting phylogenetic niche conservatism (PNC). To investigate how phylogeny and photosynthetic type differentiate C(4) grasses, we compiled a dataset of morphological and habitat information of 185 genera belonging to two monophyletic subfamilies, Chloridoideae and Panicoideae, which together account for 90 % of the world's C(4) grass species. We evaluated evolutionary variance and covariance of morphological and habitat traits. Strong phylogenetic signals were found in both morphological and habitat traits, arising mainly from the divergence of the two subfamilies. Genera in Chloridoideae had significantly smaller culm heights, leaf widths, 1,000-seed weights and stomata; they also appeared more in dry, open or saline habitats than those of Panicoideae. Controlling for phylogenetic structure showed significant covariation among morphological traits, supporting the hypothesis of phylogenetically independent scaling effects. However, associations between morphological and habitat traits showed limited phylogenetic covariance. Subfamily was a better explanation than photosynthetic type for the variance in most morphological traits. Morphology, habitat water availability, shading, and productivity are therefore all involved in the PNC of C(4) grass lineages. This study emphasized the importance of phylogenetic history in the ecology and biogeography of C(4) grasses, suggesting that divergent lineages need to be considered to fully understand the impacts of global change on plant distributions. PMID:22569558

Liu, Hui; Edwards, Erika J; Freckleton, Robert P; Osborne, Colin P



Phylogenetic approaches to natural product structure prediction.  


Phylogenetics is the study of the evolutionary relatedness among groups of organisms. Molecular phylogenetics uses sequence data to infer these relationships for both organisms and the genes they maintain. With the large amount of publicly available sequence data, phylogenetic inference has become increasingly important in all fields of biology. In the case of natural product research, phylogenetic relationships are proving to be highly informative in terms of delineating the architecture and function of the genes involved in secondary metabolite biosynthesis. Polyketide synthases and nonribosomal peptide synthetases provide model examples in which individual domain phylogenies display different predictive capacities, resolving features ranging from substrate specificity to structural motifs associated with the final metabolic product. This chapter provides examples in which phylogeny has proven effective in terms of predicting functional or structural aspects of secondary metabolism. The basics of how to build a reliable phylogenetic tree are explained along with information about programs and tools that can be used for this purpose. Furthermore, it introduces the Natural Product Domain Seeker, a recently developed Web tool that employs phylogenetic logic to classify ketosynthase and condensation domains based on established enzyme architecture and biochemical function. PMID:23084938

Ziemert, Nadine; Jensen, Paul R



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.



A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction  

PubMed Central

Recent sequencing and computing advances have enabled phylogenetic analyses to expand to both entire genomes and large clades, thus requiring more efficient and accurate methods designed specifically for the phylogenomic context. Here, we present SPIMAP, an efficient Bayesian method for reconstructing gene trees in the presence of a known species tree. We observe many improvements in reconstruction accuracy, achieved by modeling multiple aspects of evolution, including gene duplication and loss (DL) rates, speciation times, and correlated substitution rate variation across both species and loci. We have implemented and applied this method on two clades of fully sequenced species, 12 Drosophila and 16 fungal genomes as well as simulated phylogenies and find dramatic improvements in reconstruction accuracy as compared with the most popular existing methods, including those that take the species tree into account. We find that reconstruction inaccuracies of traditional phylogenetic methods overestimate the number of DL events by as much as 2–3-fold, whereas our method achieves significantly higher accuracy. We feel that the results and methods presented here will have many important implications for future investigations of gene evolution.

Rasmussen, Matthew D.; Kellis, Manolis



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




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.



Sequence length bounds for resolving a deep phylogenetic divergence.  


In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary relationship accurately depends on the model of sequence evolution, the substitution rate, divergence times and the method used to infer phylogenetic history. A particularly challenging problem for phylogenetic methods arises when a rapid divergence event occurred in the distant past. We analyse an idealised form of this problem in which the terminal edges of a symmetric four-taxon tree are some factor (lambda) times the length of the interior edge. We determine an order lambda(2) lower bound on the growth rate for the sequence length required to resolve the tree (independent of any particular branch length). We also show that this rate of sequence length growth can be achieved by existing methods (including the simple 'maximum parsimony' method), and compare these order lambda(2) bounds with an order lambda growth rate for a model that describes low-homoplasy evolution. In the final section, we provide a generic bound on the sequence length requirement for a more general class of Markov processes. PMID:18955066

Fischer, Mareike; Steel, Mike



Phylogenetic mixture models for proteins.  


Standard protein substitution models use a single amino acid replacement rate matrix that summarizes the biological, chemical and physical properties of amino acids. However, site evolution is highly heterogeneous and depends on many factors: genetic code; solvent exposure; secondary and tertiary structure; protein function; etc. These impact the substitution pattern and, in most cases, a single replacement matrix is not enough to represent all the complexity of the evolutionary processes. This paper explores in maximum-likelihood framework phylogenetic mixture models that combine several amino acid replacement matrices to better fit protein evolution.We learn these mixture models from a large alignment database extracted from HSSP, and test the performance using independent alignments from TREEBASE.We compare unsupervised learning approaches, where the site categories are unknown, to supervised ones, where in estimations we use the known category of each site, based on its exposure or its secondary structure. All our models are combined with gamma-distributed rates across sites. Results show that highly significant likelihood gains are obtained when using mixture models compared with the best available single replacement matrices. Mixtures of matrices also improve over mixtures of profiles in the manner of the CAT model. The unsupervised approach tends to be better than the supervised one, but it appears difficult to implement and highly sensitive to the starting values of the parameters, meaning that the supervised approach is still of interest for initialization and model comparison. Using an unsupervised model involving three matrices, the average AIC gain per site with TREEBASE test alignments is 0.31, 0.49 and 0.61 compared with LG (named after Le & Gascuel 2008 Mol. Biol. Evol. 25, 1307-1320), WAG and JTT, respectively. This three-matrix model is significantly better than LG for 34 alignments (among 57), and significantly worse for 1 alignment only. Moreover, tree topologies inferred with our mixture models frequently differ from those obtained with single matrices, indicating that using these mixtures impacts not only the likelihood value but also the output tree. All our models and a PhyML implementation are available from PMID:18852096

Le, Si Quang; Lartillot, Nicolas; Gascuel, Olivier



Image classification supported by digital geomorphology model  

NASA Astrophysics Data System (ADS)

In some complicated terrain area, such a loess plateau of China, it is very difficult to get higher accuracy of landuse classification only depending on the traditional spectral statistics methods, especially the image pixel size is much larger than the geomorphology units. In order to improve the image classification results, large scale relief map has been used to create the digital geomorphology model(DGM). DGM can be used to do the pixel unmixing works, specially reducing the influence of terrain shadow. Applying fuzzy mathematics theory, the DGM has been used to correct the digital image classification result, so as to create more accurate landuse map. In addition, this method is also helpful to find some minor objects in low spatial resolution images.

Zhang, Bing; Li, Xing; Tong, Qingxi; Zheng, Lanfen; Zhang, Xia



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



Euclidean nature of phylogenetic distance matrices.  


Phylogenies are fundamental to comparative biology as they help to identify independent events on which statistical tests rely. Two groups of phylogenetic comparative methods (PCMs) can be distinguished: those that take phylogenies into account by introducing explicit models of evolution and those that only consider phylogenies as a statistical constraint and aim at partitioning trait values into a phylogenetic component (phylogenetic inertia) and one or multiple specific components related to adaptive evolution. The way phylogenetic information is incorporated into the PCMs depends on the method used. For the first group of methods, phylogenies are converted into variance-covariance matrices of traits following a given model of evolution such as Brownian motion (BM). For the second group of methods, phylogenies are converted into distance matrices that are subsequently transformed into Euclidean distances to perform principal coordinate analyses. Here, we show that simply taking the elementwise square root of a distance matrix extracted from a phylogenetic tree ensures having a Euclidean distance matrix. This is true for any type of distances between species (patristic or nodal) and also for trees harboring multifurcating nodes. Moreover, we illustrate that this simple transformation using the square root imposes less geometric distortion than more complex transformations classically used in the literature such as the Cailliez method. Given the Euclidean nature of the elementwise square root of phylogenetic distance matrices, the positive semidefinitiveness of the phylogenetic variance-covariance matrix of a trait following a BM model, or related models of trait evolution, can be established. In that way, we build a bridge between the two groups of statistical methods widely used in comparative analysis. These results should be of great interest for ecologists and evolutionary biologists performing statistical analyses incorporating phylogenies. PMID:21804094

de Vienne, Damien M; Aguileta, Gabriela; Ollier, Sébastien



Phylogenetic Modeling of Heterogeneous Gene-Expression Microarray Data from Cancerous Specimens  

PubMed Central

Abstract The qualitative dimension of gene expression data and its heterogeneous nature in cancerous specimens can be accounted for by phylogenetic modeling that incorporates the directionality of altered gene expressions, complex patterns of expressions among a group of specimens, and data-based rather than specimen-based gene linkage. Our phylogenetic modeling approach is a double algorithmic technique that includes polarity assessment that brings out the qualitative value of the data, followed by maximum parsimony analysis that is most suitable for the data heterogeneity of cancer gene expression. We demonstrate that polarity assessment of expression values into derived and ancestral states, via outgroup comparison, reduces experimental noise; reveals dichotomously expressed asynchronous genes; and allows data pooling as well as comparability of intra- and interplatforms. Parsimony phylogenetic analysis of the polarized values produces a multidimensional classification of specimens into clades that reveal shared derived gene expressions (the synapomorphies); provides better assessment of ontogenic pathways and phyletic relatedness of specimens; efficiently utilizes dichotomously expressed genes; produces highly predictive class recognition; illustrates gene linkage and multiple developmental pathways; provides higher concordance between gene lists; and projects the direction of change among specimens. Further implication of this phylogenetic approach is that it may transform microarray into diagnostic, prognostic, and predictive tool.

Abu-Asab, Mones S.; Chaouchi, Mohamed



A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta  

Microsoft Academic Search

BACKGROUND: There are many advantages to the application of complete mitochondrial (mt) genomes in the accurate reconstruction of phylogenetic relationships in Metazoa. Although over one thousand metazoan genomes have been sequenced, the taxonomic sampling is highly biased, left with many phyla without a single representative of complete mitochondrial genome. Sipuncula (peanut worms or star worms) is a small taxon of

Xin Shen; Xiaoyin Ma; Jianfeng Ren; Fangqing Zhao



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].



How accurate is peer grading?  


Previously we showed that weekly, written, timed, and peer-graded practice exams help increase student performance on written exams and decrease failure rates in an introductory biology course. Here we analyze the accuracy of peer grading, based on a comparison of student scores to those assigned by a professional grader. When students graded practice exams by themselves, they were significantly easier graders than a professional; overall, students awarded ?25% more points than the professional did. This difference represented ?1.33 points on a 10-point exercise, or 0.27 points on each of the five 2-point questions posed. When students graded practice exams as a group of four, the same student-expert difference occurred. The student-professional gap was wider for questions that demanded higher-order versus lower-order cognitive skills. Thus, students not only have a harder time answering questions on the upper levels of Bloom's taxonomy, they have a harder time grading them. Our results suggest that peer grading may be accurate enough for low-risk assessments in introductory biology. Peer grading can help relieve the burden on instructional staff posed by grading written answers-making it possible to add practice opportunities that increase student performance on actual exams. PMID:21123695

Freeman, Scott; Parks, John W



How Accurate Is Peer Grading?  

PubMed Central

Previously we showed that weekly, written, timed, and peer-graded practice exams help increase student performance on written exams and decrease failure rates in an introductory biology course. Here we analyze the accuracy of peer grading, based on a comparison of student scores to those assigned by a professional grader. When students graded practice exams by themselves, they were significantly easier graders than a professional; overall, students awarded ?25% more points than the professional did. This difference represented ?1.33 points on a 10-point exercise, or 0.27 points on each of the five 2-point questions posed. When students graded practice exams as a group of four, the same student-expert difference occurred. The student-professional gap was wider for questions that demanded higher-order versus lower-order cognitive skills. Thus, students not only have a harder time answering questions on the upper levels of Bloom's taxonomy, they have a harder time grading them. Our results suggest that peer grading may be accurate enough for low-risk assessments in introductory biology. Peer grading can help relieve the burden on instructional staff posed by grading written answers—making it possible to add practice opportunities that increase student performance on actual exams.

Parks, John W.



Ultrahighly accurate 3D profilometer  

NASA Astrophysics Data System (ADS)

We have developed an Ultrahigh-Accurate 3-D Profilometer (UA3P), which, using a new, in-house-developed atomic force probe, has an accuracy of 10 nm. It is capable of measuring corners as small as 2 micro meter in radius and can cover an area up to 400 x 400 x 90 (mm), providing a powerful boost to nano-level processing. A commercial product was introduced in 1994. Examples of the key components made possible by this technology include aspherical lenses (used for a Blu-ray Disc device, a next-generation DVD, digital cameras, cellular phones, optical communications), free form lenses (used for frennel lens common to CD and DVD, laser printer lens, multi focus glass lens, cubic phase plate to extend depth of focus), gigabit semiconductor wafers, hard discs, air conditioner scroll vanes, DVC cylinders. The premiere ultra high-precision three-dimensional profilometer delivers superb performance using a variety of micro-measurements for a wide range of applications.

Tsutsumi, Hideki; Yoshizumi, Keiichi; Takeuchi, Hiroyuki



Phylogenetic structure of mammal assemblages at large geographical scales: linking phylogenetic community ecology with macroecology  

PubMed Central

Phylogenetic community ecology seeks to explain the processes involved in the formation of species assemblages by analysing their phylogenetic structure, and to date has focused primarily on local-scale communities. Macroecology, on the other hand, is concerned with the structure of assemblages at large geographical scales, but has remained largely non-phylogenetic. Analysing the phylogenetic structure of large-scale assemblages provides a link between these two research programmes. In this paper, I ask whether we should expect large-scale assemblages to show significant phylogenetic structure, by outlining some of the ecological and macroevolutionary processes that may play a role in assemblage formation. As a case study, I then explore the phylogenetic structure of carnivore assemblages within the terrestrial ecoregions of Africa. Many assemblages at these scales are indeed phylogenetically non-random (either clustered or overdispersed). One interpretation of the observed patterns of phylogenetic structure is that many clades underwent rapid biome-filling radiations, followed by diversification slowdown and competitive sorting as niche space became saturated.

Cardillo, Marcel



Teaching Molecular Phylogenetics through Investigating a Real-World Phylogenetic Problem  

ERIC Educational Resources Information Center

|A phylogenetics exercise is incorporated into the "Introduction to biocomputing" course, a junior-level course at Savannah State University. This exercise is designed to help students learn important concepts and practical skills in molecular phylogenetics through solving a real-world problem. In this application, students are required to…

Zhang, Xiaorong



Automated Manifold Surgery: Constructing Geometrically Accurate and Topologically Correct Models of the Human Cerebral Cortex  

Microsoft Academic Search

Highly accurate surface models of the cerebral cortex are becoming increasingly important as tools in the investigation of the functional organization of the human brain. The construction of such models is difficult using current neuroimaging technology due to the high degree of cortical folding. Even single voxel mis- classifications can result in erroneous connections being created between adjacent banks of

Bruce Fischl; Arthur K. Liu; Anders M. Dale



Privacy-Preserving Sharing of Horizontally-Distributed Private Data for Constructing Accurate Classifiers  

Microsoft Academic Search

Data mining tasks such as supervised classification can often benefit from a large training dataset. However, in many ap- plication domains, privacy concerns can hinder the construc- tion of an accurate classifier by combining datasets from multiple sites. In this work, we propose a novel privacy- preserving distributed data sanitization algorithm that ran- domizes the private data at each site

Vincent Yan Fu Tan; Ng See-kiong



Worldwide phylogenetic relationship of avian poxviruses  

USGS Publications Warehouse

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 Avipoxvirus genus has traditionally relied on one gene region (4b core protein). In this study we have 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.

Gyuranecz, Miklós; Foster, Jeffrey T.; Dán, Ádám; Ip, Hon S.; Egstad, Kristina F.; Parker, Patricia G.; Higashiguchi, Jenni M.; Skinner, Michael A.; Höfle, Ursula; Kreizinger, Zsuzsa; Dorrestein, Gerry M.; Solt, Szabolcs; Sós, Endre; Kim, Young Jun; Uhart, Marcela; Pereda, Ariel; González-Hein, Gisela; Hidalgo, Hector; Blanco, Juan-Manuel; Erdélyi, Károly



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



Worldwide phylogenetic relationship of avian poxviruses.  


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. PMID:23408635

Gyuranecz, Miklós; Foster, Jeffrey T; Dán, Ádám; Ip, Hon S; Egstad, Kristina F; Parker, Patricia G; Higashiguchi, Jenni M; Skinner, Michael A; Höfle, Ursula; Kreizinger, Zsuzsa; Dorrestein, Gerry M; Solt, Szabolcs; Sós, Endre; Kim, Young Jun; Uhart, Marcela; Pereda, Ariel; González-Hein, Gisela; Hidalgo, Hector; Blanco, Juan-Manuel; Erdélyi, Károly



The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists  

Microsoft Academic Search

This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on




Threat diversity will erode mammalian phylogenetic diversity in the near future.  


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. PMID:23029443

Jono, Clémentine M A; Pavoine, Sandrine



Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine  

Microsoft Academic Search

BackgroundVariations in the composition of the human intestinal microbiota are linked to diverse health conditions. High-throughput molecular technologies have recently elucidated microbial community structure at much higher resolution than was previously possible. Here we compare two such methods, pyrosequencing and a phylogenetic array, and evaluate classifications based on two variable 16S rRNA gene regions.Methods and FindingsOver 1.75 million amplicon sequences

Marcus J. Claesson; Orla O'Sullivan; Qiong Wang; Janne Nikkilä; Julian R. Marchesi; Hauke Smidt; Willem M. de Vos; R. Paul Ross; Paul W. O'Toole; Niyaz Ahmed



Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine  

Microsoft Academic Search

BACKGROUND: Variations in the composition of the human intestinal microbiota are linked to diverse health conditions. High-throughput molecular technologies have recently elucidated microbial community structure at much higher resolution than was previously possible. Here we compare two such methods, pyrosequencing and a phylogenetic array, and evaluate classifications based on two variable 16S rRNA gene regions. METHODS AND FINDINGS: Over 1.75

Marcus J. Claesson; Orla O'Sullivan; Qiong Wang; Janne Nikkilä; Julian R. Marchesi; Hauke Smidt; Vos de W. M; R. Paul Ross; Paul W. O'Toole



Phylogenetic conservatism of extinctions in marine bivalves.  


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



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


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


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



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.



New classification criteria for gout: a framework for progress.  


The definitive classification or diagnosis of gout normally relies upon the identification of MSU crystals in SF or from tophi. Where microscopic examination of SF is not available or is impractical, the best approach may differ depending upon the context. For many types of research, clinical classification criteria are necessary. The increasing prevalence of gout, advances in therapeutics and the development of international research collaborations to understand the impact, mechanisms and optimal treatment of this condition emphasize the need for accurate and uniform classification criteria for gout. Five clinical classification criteria for gout currently exist. However, none of the currently available criteria has been adequately validated. An international project is currently under way to develop new validated gout classification criteria. These criteria will be an essential step forward to advance the research agenda in the modern era of gout management. PMID:23611919

Dalbeth, Nicola; Fransen, Jaap; Jansen, Tim L; Neogi, Tuhina; Schumacher, H Ralph; Taylor, William J



Igneous Rock Classification  

NSDL National Science Digital Library

This page presents a classification system used for igneous rocks. The system consists of a matrix which divides rocks on the basis of their texture (in rows) and their chemical composition (in columns). Links are provided to photographs of each rock type, and an explanation of the terms used in the classification.

Celestian, Stan


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



Classification Objectives and Practices  

Microsoft Academic Search

Making correct predictions is only one, and probably not the most important, of the objectives for security classification. In this article, inherent limitations to predictive ability are discussed and four other objectives are emphasized. These objectives are as follows: making classification decisions the right way, making decisions stick, managing decisions, and promoting positive human interaction. The discussion focuses on the

Jack Alexander



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.



Vascular anomalies in pediatric patients: updated classification, imaging, and therapy.  


Recent advances in knowledge regarding histopathology, cause, and treatment of pediatric vascular anomalies have led to substantial changes in classification and terminology. Over the past two decades, various subspecialists have adopted a new classification system proposed by the International Society for the Study of Vascular Anomalies (ISSVA). The ISSVA classification of vascular anomalies divides vascular anomalies into two categories: vascular neoplasms and malformations. It has been widely adopted by various pediatric subspecialists, because it reliably correlates patient presentation and disease progression, with more accurate histology, diagnosis, imaging, and treatment. PMID:23830791

Kollipara, Ramya; Odhav, Ashika; Rentas, Kenny E; Rivard, Douglas C; Lowe, Lisa H; Dinneen, Laura



A Novel Approach for Compressing Phylogenetic Trees  

Microsoft Academic Search

\\u000a Phylogenetic trees are tree structures that depict relationships between organisms. Popular analysis techniques often produce\\u000a large collections of candidate trees, which are expensive to store. We introduce TreeZip, a novel algorithm to compress phylogenetic\\u000a trees based on their shared evolutionary relationships. We evaluate TreeZip’s performance on fourteen tree collections ranging\\u000a from 2,505 trees on 328 taxa to 150,000 trees on

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



Phylogenetic relationships between chlorophytes, chrysophytes, and oomycetes.  

PubMed Central

The phylogenetic relationships among the chlorophyte Chlamydomonas reinhardtii, the chrysophyte Ochromonas danica, and the oomycete Achyla bisexualis were explored by comparing the sequences of their small-subunit ribosomal RNA coding regions. Comparisons of similarity values or inspection of phylogenetic trees constructed by distance matrix methods reveal a very close relationship between oomycetes and chrysophytes. The separation of chrysophytes from chlorophytes is comparable to that of plants from animals, and both separations are far antedated by the divergence of a number of other protist groups.

Gunderson, J H; Elwood, H; Ingold, A; Kindle, K; Sogin, M L



Methodology for hyperspectral image classification using novel neural network  

SciTech Connect

A novel feed forward neural network is used to classify hyperspectral data from the AVIRIS sector. The network applies an alternating direction singular value decomposition technique to achieve rapid training times (few seconds per class). Very few samples (10-12) are required for training. 100% accurate classification is obtained using test data sets. The methodology combines this rapid training neural network together with data reduction and maximal feature separation techniques such as principal component analysis and simultaneous diagonalization of covariance matrices, for rapid and accurate classification of large hyperspectral images. The results are compared to those of standard statistical classifiers. 21 refs., 3 figs., 5 tabs.

Subramanian, S., Gat, N., Sheffield, M., [Opto-Knowledge, Systems, Inc., Manhattan Beach, CA (United States); Barhen, J. [Oak Ridge National Lab., TN (United States); Toomarian, N. [Jet Propulsion Laboratory, Pasadena, CA (United States)



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



Hierarchical Markov random-field modeling for texture classification in chest radiographs  

NASA Astrophysics Data System (ADS)

A hierarchical Markov random field (MRF) modeling approach is presented for the classification of textures in selected regions of interest (ROIs) of chest radiographs. The procedure integrates possible texture classes and their spatial definition with other components present in an image such as noise and background trend. Classification is performed as a maximum a-posteriori (MAP) estimation of texture class and involves an iterative Gibbs- sampling technique. Two cases are studied: classification of lung parenchyma versus bone and classification of normal lung parenchyma versus miliary tuberculosis (MTB). Accurate classification was obtained for all examined cases showing the potential of the proposed modeling approach for texture analysis of radiographic images.

Vargas-Voracek, Rene; Floyd, Carey E.; Nolte, Loren W.; McAdams, Page



CTEP Simplified Disease Classification Overview

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


Phylogenetic study of Catapyrenium s. str. (Verrucariaceae, lichen-forming Ascomycota) and related genus Placidiopsis.  


The current classification of what used to be called Catapyrenium comprises eight genera belonging to distinct lineages in the Verrucariaceae. Previous phylogenetic studies have shown that the redefined genus Catapyrenium (Catapyrenium s. str.) is monophyletic and sister of Placidiopsis within the Staurothele group, but this relationship was based on only two species from each genus. We conducted a phylogenetic study of Catapyrenium and Placidiopsis as currently delimited to evaluate the monophyly of each genus and infer infrageneric relationships. An initial family level phylogenetic analysis based on the nuLSU locus and implementing a backbone constraint tree (with both weighted maximum parsimony and bootstrap maximum likelihood approaches) was performed to infer phylogenetic placements of Catapyrenium and Placidiopsis taxa not included in previous molecular systematic studies. The results of this analysis were used to define the ingroup for a second phylogenetic analysis based on nuITS and nuLSU and centered on Catapyrenium s. str. and Placidiopsis. Placidiopsis was found to be monophyletic, whereas Catapyrenium s. str. was not. Catapyrenium dactylinum was found to be closely related to Placopyrenium caeruleopulvinum and Placopyrenium stanfordii, all of which were closely related to Placocarpus schaereri and Verrucula. In addition we found genus Placopyrenium to be polyphyletic. The resulting trees confirmed that Catapyrenium s. str. (excluding C. dactylinum) and Placidiopsis constitute two sister monophyletic entities. The data do not support Placidiopsis cinerascens and P. tenella as two distinct species because no characters can be used to distinguish them. Thus P. tenella is here reduced to synonymy with P. cinerascens. PMID:20361497

Prieto, María; Martínez, Isabel; Aragón, Gregorio; Otálora, Mónica A G; Lutzoni, François


A Phylogenetic Analysis of the Brassicales Clade Based on an Alignment-Free Sequence Comparison Method  

PubMed Central

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.

Hatje, Klas; Kollmar, Martin



Mitochondrial phylogenetics and evolution of mysticete whales.  


The phylogenetic relationships among baleen whales (Order: Cetacea) remain uncertain despite extensive research in cetacean molecular phylogenetics and a potential morphological sample size of over 2 million animals harvested. Questions remain regarding the number of species and the monophyly of genera, as well as higher order relationships. Here, we approach mysticete phylogeny with complete mitochondrial genome sequence analysis. We determined complete mtDNA sequences of 10 extant Mysticeti species, inferred their phylogenetic relationships, and estimated node divergence times. The mtDNA sequence analysis concurs with previous molecular studies in the ordering of the principal branches, with Balaenidae (right whales) as sister to all other mysticetes base, followed by Neobalaenidae (pygmy right whale), Eschrichtiidae (gray whale), and finally Balaenopteridae (rorquals + humpback whale). The mtDNA analysis further suggests that four lineages exist within the clade of Eschrichtiidae + Balaenopteridae, including a sister relationship between the humpback and fin whales, and a monophyletic group formed by the blue, sei, and Bryde's whales, each of which represents a newly recognized phylogenetic relationship in Mysticeti. We also estimated the divergence times of all extant mysticete species, accounting for evolutionary rate heterogeneity among lineages. When the mtDNA divergence estimates are compared with the mysticete fossil record, several lineages have molecular divergence estimates strikingly older than indicated by paleontological data. We suggest this discrepancy reflects both a large amount of ancestral polymorphism and long generation times of ancestral baleen whale populations. PMID:15805012

Sasaki, Takeshi; Nikaido, Masato; Hamilton, Healy; Goto, Mutsuo; Kato, Hidehiro; Kanda, Naohisa; Pastene, Luis; Cao, Ying; Fordyce, R; Hasegawa, Masami; Okada, Norihiro



Molecular Phylogenetics of Mastodon and Tyrannosaurus rex  

Microsoft Academic Search

We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen alpha1(I) and alpha2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant

Chris L. Organ; Mary H. Schweitzer; Wenxia Zheng; Lisa M. Freimark; Lewis C. Cantley; John M. Asara



Phylogenetic Conservatism of Extinctions in Marine Bivalves  

Microsoft Academic Search

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 ~200 million years show conservatism at multiple levels of evolutionary

Kaustuv Roy; Gene Hunt; David Jablonski



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



Molecular Epidemiology of PRRSV: A Phylogenetic Perspective  

Technology Transfer Automated Retrieval System (TEKTRAN)

Since its first discovery two decades ago, porcine reproductive and respiratory syndrome virus (PRRSV) has been the subject of intensive research due to its huge impact on the worldwide swine industry. Thanks to phylogenetic analyses, much has been learned about the genetic diversity and evolution h...


Phylogenetic Applications of HLA Class II Loci  

Microsoft Academic Search

Human Leukocyte Antigen (HLA) loci widely known for their role in generation of immune responses are often considered to be effective in reconstructing human phylogenies due to high degree of polymorphism and rarity of recombination observed at HLA loci. In the present study, we have made an attempt to substantiate the phylogenetic potential of HLA class II loci by analyzing

Uddalak Bharadwaj; Faisal Khan; Sanjeev Srivastava; Himanshu Goel; Suraksha Agrawal



Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids  

PubMed Central

Background The Vitaceae (grape) is an economically important family of angiosperms whose phylogenetic placement is currently unresolved. Recent phylogenetic analyses based on one to several genes have suggested several alternative placements of this family, including sister to Caryophyllales, asterids, Saxifragales, Dilleniaceae or to rest of rosids, though support for these different results has been weak. There has been a recent interest in using complete chloroplast genome sequences for resolving phylogenetic relationships among angiosperms. These studies have clarified relationships among several major lineages but they have also emphasized the importance of taxon sampling and the effects of different phylogenetic methods for obtaining accurate phylogenies. We sequenced the complete chloroplast genome of Vitis vinifera and used these data to assess relationships among 27 angiosperms, including nine taxa of rosids. Results The Vitis vinifera chloroplast genome is 160,928 bp in length, including a pair of inverted repeats of 26,358 bp that are separated by small and large single copy regions of 19,065 bp and 89,147 bp, respectively. The gene content and order of Vitis is identical to many other unrearranged angiosperm chloroplast genomes, including tobacco. Phylogenetic analyses using maximum parsimony and maximum likelihood were performed on DNA sequences of 61 protein-coding genes for two datasets with 28 or 29 taxa, including eight or nine taxa from four of the seven currently recognized major clades of rosids. Parsimony and likelihood phylogenies of both data sets provide strong support for the placement of Vitaceae as sister to the remaining rosids. However, the position of the Myrtales and support for the monophyly of the eurosid I clade differs between the two data sets and the two methods of analysis. In parsimony analyses, the inclusion of Gossypium is necessary to obtain trees that support the monophyly of the eurosid I clade. However, maximum likelihood analyses place Cucumis as sister to the Myrtales and therefore do not support the monophyly of the eurosid I clade. Conclusion Phylogenies based on DNA sequences from complete chloroplast genome sequences provide strong support for the position of the Vitaceae as the earliest diverging lineage of rosids. Our phylogenetic analyses support recent assertions that inadequate taxon sampling and incorrect model specification for concatenated multi-gene data sets can mislead phylogenetic inferences when using whole chloroplast genomes for phylogeny reconstruction.

Jansen, Robert K; Kaittanis, Charalambos; Saski, Christopher; Lee, Seung-Bum; Tomkins, Jeffrey; Alverson, Andrew J; Daniell, Henry



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.



An improved method for identifying functionally linked proteins using phylogenetic profiles  

PubMed Central

Background Phylogenetic profiles record the occurrence of homologs of genes across fully sequenced organisms. Proteins with similar profiles are typically components of protein complexes or metabolic pathways. Various existing methods measure similarity between two profiles and, hence, the likelihood that the two proteins co-evolve. Some methods ignore phylogenetic relationships between organisms while others account for such with metrics that explicitly model the likelihood of two proteins co-evolving on a tree. The latter methods more sensitively detect co-evolving proteins, but at a significant computational cost. Here we propose a novel heuristic to improve phylogenetic profile analysis that accounts for phylogenetic relationships between genomes in a computationally efficient fashion. We first order the genomes within profiles and then enumerate runs of consecutive matches and accurately compute the probability of observing these. We hypothesize that profiles with many runs are more likely to involve functionally related proteins than profiles in which all the matches are concentrated in one interval of the tree. Results We compared our approach to various previously published methods that both ignore and incorporate the underlying phylogeny between organisms. To evaluate performance, we compare the functional similarity of rank-ordered lists of protein pairs that share similar phylogenetic profiles by assessing significance of overlap in their Gene Ontology annotations. Accounting for runs in phylogenetic profile matches improves our ability to identify functionally related pairs of proteins. Furthermore, the networks that result from our approach tend to have smaller clusters of co-evolving proteins than networks computed using previous approaches and are thus more useful for inferring functional relationships. Finally, we report that our approach is orders of magnitude more computationally efficient than full tree-based methods. Conclusion We have developed an improved method for analyzing phylogenetic profiles. The method allows us to more accurately and efficiently infer functional relationships between proteins based on these profiles than other published approaches. As the number of fully sequenced genomes increases, it becomes more important to account for evolutionary relationships among organisms in comparative analyses. Our approach, therefore, serves as an important example of how these relationships may be accounted for in an efficient manner.

Cokus, Shawn; Mizutani, Sayaka; Pellegrini, Matteo



Cnidarian phylogenetic relationships as revealed by mitogenomics  

PubMed Central

Background Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia?+?Octocorallia) – cnidarians with a reproductive polyp and the absence of a medusa stage – and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) – cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution. Results We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia?+?Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae?+?Coronatae], Acraspeda [Cubozoa?+?Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans. Conclusions Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that the shared morphological characters in these groups are plesiomorphies, originated in the branch leading to Medusozoa. The expansion of mitogenomic data along with improvements in phylogenetic inference methods and use of additional nuclear markers will further enhance our understanding of the phylogenetic relationships and character evolution within Cnidaria.



Phyloclimatic modeling: combining phylogenetics and bioclimatic modeling.  


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



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



EPA Science Inventory

Accurate exposure classification tools are required to link exposure with health effects in epidemiological studies. Although long-term integrated exposure measurements are a critical component of exposure assessment, the ability to include these measurements into epidemiologic...


Classification of Microcalcifications for the Diagnosis of Breast Cancer Using Artificial Neural Networks.  

National Technical Information Service (NTIS)

Early detection of breast cancer depends on the accurate classification of microcalcifications. We have developed a computer vision system that can classify microcalcifications objectively and consistently to aid radiologists in the diagnosis of breast ca...

Y. C. Wu




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...


Online, self-supervised terrain classification via discriminatively trained submodular Markov random fields  

Microsoft Academic Search

The authors present a novel approach to the task of autonomous terrain classification based on structured prediction. We consider the problem of learning a classifier that will accurately segment an image into \\

Paul Vernaza; Ben Taskar; Daniel D. Lee




Technology Transfer Automated Retrieval System (TEKTRAN)

Corn rootworms of the genus Diabrotica (Coleoptera: Chrysomelidae) are the most serious pest of corn in midwestern United States. Despite their economic importance, phylogenetic relationships within the genus remain unclear. Phylogenetic analysis of five Diabrotica was undertaken using DNA sequences...



Technology Transfer Automated Retrieval System (TEKTRAN)

Corn rootworms of the genus Diabrotica (Coleoptera: Chrysomelidae) are the most serious pest of corn in midwestern United States. Despite their economic importance, phylogenetic relationships within the genus remain unclear. Phylogenetic analysis of five Diabrotica was undertaken using DNA sequences...


Minimizing phylogenetic number to find good evolutionary trees.  

National Technical Information Service (NTIS)

Inferring phylogenetic trees is a fundamental problem in computational-biology. We present a new objective criterion, the phylogenetic number, for evaluating evolutionary trees for species defined by biomolecular sequences or other qualitative characters....

L. A. Goldberg P. W. Goldberg C. A. Phillips E. Sweedyk T. Warnow



A general species delimitation method with applications to phylogenetic placements  

PubMed Central

Motivation: Sequence-based methods to delimit species are central to DNA taxonomy, microbial community surveys and DNA metabarcoding studies. Current approaches either rely on simple sequence similarity thresholds (OTU-picking) or on complex and compute-intensive evolutionary models. The OTU-picking methods scale well on large datasets, but the results are highly sensitive to the similarity threshold. Coalescent-based species delimitation approaches often rely on Bayesian statistics and Markov Chain Monte Carlo sampling, and can therefore only be applied to small datasets. Results: We introduce the Poisson tree processes (PTP) model to infer putative species boundaries on a given phylogenetic input tree. We also integrate PTP with our evolutionary placement algorithm (EPA-PTP) to count the number of species in phylogenetic placements. We compare our approaches with popular OTU-picking methods and the General Mixed Yule Coalescent (GMYC) model. For de novo species delimitation, the stand-alone PTP model generally outperforms GYMC as well as OTU-picking methods when evolutionary distances between species are small. PTP neither requires an ultrametric input tree nor a sequence similarity threshold as input. In the open reference species delimitation approach, EPA-PTP yields more accurate results than de novo species delimitation methods. Finally, EPA-PTP scales on large datasets because it relies on the parallel implementations of the EPA and RAxML, thereby allowing to delimit species in high-throughput sequencing data. Availability and implementation: The code is freely available at Contact: Supplementary information: Supplementary data are available at Bioinformatics online.

Zhang, Jiajie; Kapli, Paschalia; Pavlidis, Pavlos; Stamatakis, Alexandros



Delaware Alternative Classifications  

ERIC Educational Resources Information Center

|This article discusses the species designation and taxonomies of Delaware and Algonkian and presents eight classifications of taxa by form, habitat, color, movement, sound, use, relationship, and appearance. Relevant research is also reviewed. (CLK)|

Miller, Jay



Evaluating How Well Your Classification System is Operating: A Practical Approach  

Microsoft Academic Search

With the wide adoption by many states of objective prison classification systems, there has been an associated expectation among prison officials that these new systems would foster improved prison operations and reductions in prison violence. However, this has not always been the case. Failure to realize these expectations can be more accurately traced to improperly designed or implemented classification systems

James Austin



"Bag of words" is not enough for strength of evidence classification.  


Incorporation of evidence from clinical research requires critical appraisal of its quality. Information retrieval systems can facilitate clinicians' judgments by automatically labeling retrieved citations with their strength of evidence categories. Preliminary results of such a text classification experiment involving MEDLINE citations show that a "bag of words" approach is insufficient for accurate classification. PMID:16779318

Lin, Jimmy; Demner-Fushman, Dina



Land cover classification of the North China Plain using MODIS EVI time series  

Microsoft Academic Search

Moderate Resolution Imaging Spectroradiometer (MODIS) data have played an important role in global environmental and resource research. However, its low spatial resolution has been an impediment to researchers pursuing more accurate classification results. In this research, the high temporal resolution of MODIS was employed to improve the accuracy of land cover classification of the North China Plain using MODIS EVI

Zhang Xiaa; Sun Rui; Zhang Bing; Tong Qingxia


A comparison of single date and multitemporal satellite image classifications in a semi-arid grassland  

Microsoft Academic Search

Landsat Thematic Mapper (TM) satellite data were used to produce maps depicting ranges of major vegetation types at the Jornada Experimental Range, New Mexico, U.S.A. Single date and multitemporal classification accuracies were compared using vegetation ground data as references. Single date image classifications were more accurate than multitemporal images for mapping land cover types in this region. Use of single

Susan Kathleen Langley; Heather M. Cheshire; Karen S. Humes



Automatic car model classification  

Microsoft Academic Search

An application is described of dynamic-programming-based matching to car model classification. An edge map is first extracted, and a sequence of pre-processing stages is carried out, culminating in the use of a 2-dimensional circle Hough transform to generate a cued region containing a putative car. Within the cued area a dynamic programming search (edge-based classification) is carried out to classify

Margaret Varga; John Radford



Classification of Wetlands  

Microsoft Academic Search

\\u000a Humans have been classifying and managing wetlands for their ecological services and economic value that are specific to societal\\u000a needs since the dawn of civilization. These classification systems and management strategies evolve as society’s needs change\\u000a both spatially and temporally. In general, most systems of classification can be divided into three broad categories that\\u000a are based on their function (what

Mark M. Brinson


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."


Potato Chip Classification  

NSDL National Science Digital Library

This activity introduces the structure and function of a dichotomous key, in preparation for student identification of plant and animal specimens. It also reinforces the idea that there are many possible answers in science. Students will be able to classify specimens (in this case, potato chips) according to observable characteristics, prepare a key showing their classification system, use their key to identify a specimen, and recognize the validity of classmates' classification systems.



Imbalanced sentiment classification  

Microsoft Academic Search

Sentiment classification has undergone significant development in recent years. However, most existing studies assume the balance between negative and positive samples, which may not be true in reality. In this paper, we investigate imbalanced sentiment classification instead. In particular, a novel clustering-based stratified under-sampling framework and a centroid-directed smoothing strategy are proposed to address the imbalanced class and feature distribution

Shoushan Li; Guodong Zhou; Zhongqing Wang; Sophia Yat Mei Lee; Rangyang Wang



Deterministic Neural Classification  

Microsoft Academic Search

This letter presents a minimum classification error learning formulation for a single-layer feedforward network (SLFN). By approximating the nonlinear counting step function using a quadratic function, the classification error rate is shown to be deterministically solvable. Essentially the derived solution is related to an existing weighted least-squares method with class-specific weights set according to the size of data set. By

Kar-ann Toh



Classification Criteria for APS  

Microsoft Academic Search

\\u000a An international consensus statement on classification criteria for definite APS was published in 1999. A patient with APS\\u000a must meet at least one of the two clinical criteria (vascular thrombosis or pregnancy complications) and at least one of the\\u000a two laboratory criteria (aCL and\\/or LA). Although these criteria have been shown to be specific and sensitive for the classification\\u000a of

Maria Laura Bertolaccini; Oier Ateka-Barrutia; Munther A. Khamashta


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



Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics  

Microsoft Academic Search

We provide a new automated statistical method for DNA barcoding based on a Bayesian phylogenetic analysis. The method is based on automated database sequence retrieval, alignment, and phylogenetic analysis using a custom-built program for Bayesian phylogenetic analysis. We show on real data that the method outperforms Blast searches as a measure of confidence and can help eliminate 80% of all

Kasper Munch; Wouter Boomsma; John Huelsenbeck; Eske Willerslev; Rasmus Nielsen



The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation  

Microsoft Academic Search

Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with the assumption being that as alignments improve, so will phylogenetic reconstructions. Over the last decade or so, new multiple sequence alignment methods have been developed to improve comparative analyses of protein structure, but these new methods have not been typically used in phylogenetic analyses. In this paper,

Li-San Wang; Jim Leebens-Mack; P. Kerr Wall; Kevin Beckmann; Claude W. dePamphilis; Tandy Warnow



iPhy: an integrated phylogenetic workbench for supermatrix analyses  

Microsoft Academic Search

BACKGROUND: The increasing availability of molecular sequence data means that the accuracy of future phylogenetic studies is likely to by limited by systematic bias and taxon choice rather than by data. In order to take advantage of increasing datasets, user-friendly tools are required to facilitate phylogenetic analyses and to reduce duplication of dataset assembly efforts. Current phylogenetic pipelines are dependency-heavy

Martin O. Jones; Georgios D. Koutsovoulos; Mark L. Blaxter



SVM texture classification for tropical vegetation mapping  

NASA Astrophysics Data System (ADS)

Nowadays, remote sensing is an essential science in French Polynesia because of its extended territory and the remoteness of its 120 islands. There is a strong need to study the vegetation cover and its evolution (biodiversity threat, invasive species, etc.). A growing satellite images database has been acquired throughout, giving access to very high resolution optical images such as Quickbird data. These data allow accessing the vegetation canopy spectral and contextual information, texture classification has proved to be an efficient tool to map the complex vegetation found in tropical regions. The main goal of this paper is to propose an optimized SVM multispectral-texture classification method for tropical vegetation mapping. One of the texture computation drawbacks is the window treatment size, which is related to the largest texture element size. In complex tropical vegetation cover, this parameter leads to very small ground truth learning database, inducing a significant degradation of the classifications accuracy. We propose to increase the thumbnail numbers using an under-sampling method, optimizing the size and the number of the thumbnails. The other drawback is the high dimensionality of the problem when dealing with multispectral textures. We thus propose to rank and select the most pertinent textures attributes in order to reduce the dimensionality without reducing the classification accuracy. We first introduce the study context, before exposing preliminary studies on tuning the SVM learning method. The adapted method is then accurately exposed and the interesting experimental results as well as a sample of applications are presented before to conclude.

Chabrier, Sebastien; Stoll, Benoit; Goujon, Jean-Baptiste



Drug classification: science, politics, both or neither?  


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



Randomized clustering forests for image classification.  


Some of the most effective recent methods for content-based image classification work by quantizing image descriptors, and accumulating histograms of the resulting visual word codes. Large numbers of descriptors and large codebooks are required for good results and this becomes slow using k-means. We introduce Extremely Randomized Clustering Forests ensembles of randomly created clustering trees and show that they provide more accurate results, much faster training and testing, and good resistance to background clutter. Second, an efficient image classification method is proposed. It combines ERC-Forests and saliency maps very closely with the extraction of image information. For a given image, a classifier builds a saliency map online and uses it to classify the image. We show in several state-of-the-art image classification tasks that this method can speed up the classification process enormously. Finally, we show that the proposed ERC-Forests can also be used very successfully for learning distance between images. The distance computation algorithm consists of learning the characteristic differences between local descriptors sampled from pairs of same or different objects. These differences are vector quantized by ERC-Forests and the similarity measure is computed from this quantization. The similarity measure has been evaluated on four very different datasets and always outperforms the state-of-the-art competitive approaches. PMID:18617720

Moosmann, Frank; Nowak, Eric; Jurie, Frederic



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 ( 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:



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


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



Phylogenetic analysis reveals the evolution and diversification of cyclins in eukaryotes.  


Cyclins are a family of diverse proteins that play fundamental roles in regulating cell cycle progression in Eukaryotes. Cyclins have been identified from protists to higher Eukaryotes, while its evolution remains vague and the findings turn out controversial. Current classification of cyclins is mainly based on their functions, which may not be appropriate for the systematic evolutionary analysis. In this work, we performed comparative and phylogenetic analysis of cyclins to investigate their classification, origin and evolution. Cyclins originated in early Eukaryotes and evolved from protists to plants, fungi and animals. Based on the phylogenetic tree, cyclins can be divided into three major groups designated as the group I, II and III with different functions and features. Group I plays key roles in cell cycle, group II varied in actions are kingdom (plant, fungi and animal) specific, and group III functions in transcription regulation. Our results showed that the dominating cyclins (group I) diverged from protists to plants, fungi and animals, while divergence of the other cyclins (groups II and III) has occurred in protists. We also discussed the evolutionary relationships between cyclins and cyclin-dependent kinases (CDKs) and found that the cyclins have undergone divergence in protists before the divergence of animal CDKs. This reclassification and evolutionary analysis of cyclins might facilitate understanding eukaryotic cell cycle control. PMID:23261709

Ma, Zhaowu; Wu, Yuliang; Jin, Jialu; Yan, Jun; Kuang, Shuzhen; Zhou, Mi; Zhang, Yuexuan; Guo, An-Yuan



Identifying Early Events of Gene Expression in Breast Cancer with Systems Biology Phylogenetics  

PubMed Central

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.

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



Comparison of Linear and Nonlinear Methods for EEG Signal Classification  

Microsoft Academic Search

The reliable operation of brain-computer inter- faces (BCI's) based on spontaneous electro electroencephalogram (EEG) signals requires accurate classification of multichannel EEG. The design of EEG representations and classifiers for BCI are open research questions whose difficulty stems from the need to extract complex spatial and temporal patterns from noisy mul- tidimensional time series obtained from EEG measurements. It is possible

Deon Garrett; David A. Peterson; Charles W. Anderson; Michael H. Thaut


Evaluation of the Unified Compensation and Classification Plan.  

ERIC Educational Resources Information Center

|The Unified Classification and Compensation Plan of the Dade County (Florida) Public Schools consists of four interdependent activities that include: (1) developing and maintaining accurate job descriptions, (2) conducting evaluations that recommend job worth and grade, (3) developing and maintaining rates of compensation for job values, and (4)…

Dade County Public Schools, Miami, FL. Office of Educational Accountability.


Heart disease classification ensemble optimization using Genetic algorithm  

Microsoft Academic Search

Heart disease diagnosis is considered as one of the complicated tasks in medical field. In order to perform heart disease diagnosis an accurate and efficient automation system can be very helpful. In this research, we propose a classifier ensemble method to improve the decision of the classifiers for heart disease diagnosis. Homogeneous ensemble is applied for heart disease classification and

Benish Fida; Muhammad Nazir; Nawazish Naveed; Sheeraz Akram



Classification of Raman Spectra to Detect Hidden Explosives  

Microsoft Academic Search

Raman spectroscopy is a laser-based vibrational technique that can provide spectral signatures unique to a mul- titude of compounds. The technique is gaining widespread interest as a method for detecting hidden explosives due to its sensitivity and ease of use. In this letter, we present a computationally efficient classification scheme for accurate standoff identification of several common explosives using visible-range

Naveed R. Butt; Mikael Nilsson; Andreas Jakobsson; Markus Nordberg; Anna Pettersson; Sara Wallin; Henric Ostmark



A nonlinear, recurrence-based approach to traffic classification  

Microsoft Academic Search

The ability to accurately classify and identify the network traffic associated with different applications is a central issue for many network operation and research topics including Quality of Service enforcement, traffic engineering, security, monitoring and intrusion-detection. However, traditional classification approaches for traffic to higher-level application mapping, such as those based on port or payload analysis, are highly inaccurate for many

Francesco Palmieri; Ugo Fiore



Preprocessing remotely-sensed data for efficient analysis and classification  

SciTech Connect

Interpreting remotely-sensed data typically requires expensive, specialized computing machinery capable of storing and manipulating large amounts of data quickly. In this paper, we present a method for accurately analyzing and categorizing remotely-sensed data on much smaller, less expensive platforms. Data size is reduced in such a way an efficient, interactive method of data classification.

Kelly, P.M.; White, J.M.



Preprocessing remotely-sensed data for efficient analysis and classification  

SciTech Connect

Interpreting remotely-sensed data typically requires expensive, specialized computing machinery capable of storing and manipulating large amounts of data quickly. In this paper, we present a method for accurately analyzing and categorizing remotely-sensed data on much smaller, less expensive platforms. Data size is reduced in such a way an efficient, interactive method of data classification.

Kelly, P.M.; White, J.M.



Frequency based classification of activities using accelerometer data  

Microsoft Academic Search

This work presents, the classification of user activities such as Rest, Walk and Run, on the basis of frequency component present in the acceleration data in a wireless sensor network environment. As the frequencies of the above mentioned activities differ slightly for different person, so it gives a more accurate result. The algorithm uses just one parameter i.e. the frequency

Annapuma Sharma; Amit Purwar; Young-Dong Lee; Young-Sook Lee; Wan-Young Chung



Neural network system for cloud classification from satellite images  

Microsoft Academic Search

Highly accurate, automated cloud detection and classification methods are essential for processing multispectral meteorological satellite in an operational environment and providing data for meteorological and climatological studies. They help to discover hazardous meteorological phenomena such as hail storms developing on tops of clouds, hurricanes and cyclones. Weather prediction and rainfall estimation systems are enhanced substantially by having access to information

I. S. Torsum; E. Kwiatkowska



Wavelet-Based Feature Extraction for Microarray Data Classification  

Microsoft Academic Search

Microarray data typically have thousands of genes, and thus feature extraction is a critical problem for accurate cancer classification. In this paper, a feature extraction method based on the discrete wavelet transform (DWT) is proposed. The approximation coefficients of DWT, together with some useful features from the high-frequency coefficients selected by the maximum modulus method, are used as features. The

Shutao Li; Chen Liao; James T. Kwok



Rough surface classification using point statistics from photometric stereo  

Microsoft Academic Search

Rough surfaces can be classified by the point statistics of their derivative fields, estimated using photometric stereo. Such a scheme is proposed and found to be more accurate and robust than image-intensity-based classification. It is particularly effective when applied to directional surfaces, even under rotation. The scheme is therefore robust and economic – suitable for many applications and worthy of

Ged Mcgunnigle; Mike J. Chantler



Molecular classification of Pakistani collared dove through DNA barcoding.  


Pakistan is bestowed by a diversified array of wild bird species including collared doves of which the taxonomy has been least studied and reported. DNA barcoding is a geno-taxonomic tool that has been used for characterization of bird species using mitochondrial cytochrome c oxidase I gene (COI). This study aimed to identify taxonomic order of Pakistani collared dove using DNA barcoding. Purposely herein, we present a phylogenetic analysis of Pakistani collared dove based on 650 base pairs of COI gene sequences. Analysis of phylogenetic tree revealed that Pakistani collared dove shared a common clade with Eurasian collared dove (Streptopelia decaocto) and African collared dove (Streptopelia roseogrisea) which indicated a super-species group in Streptopelia genus. This is the first report of molecular classification of Pakistani collared dove using DNA barcoding. PMID:24072655

Awan, Ali Raza; Umar, Emma; Zia Ul Haq, Muhammad; Firyal, Sehrish



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



DNA sequence support for a close phylogenetic relationship between some storks and New World vultures.  

PubMed Central

Nucleotide sequences from the mitochondrial cytochrome b gene were used to address a controversial suggestion that New World vultures are related more closely to storks than to Old World vultures. Phylogenetic analyses of 1-kb sequences from 18 relevant avian species indicate that the similarities in morphology and behavior between New World and Old World vultures probably manifest convergent adaptations associated with carrion-feeding, rather than propinquity of descent. Direct sequence evidence for a close phylogenetic alliance between at least some New World vultures and storks lends support to conclusions reached previously from DNA.DNA hybridization methods and detailed morphology-based appraisals, and it illustrates how mistaken assumptions of homology for organismal adaptations can compromise biological classifications. However, there was a lack of significant resolution for most other branches in the cytochrome b phylogenetic reconstructions. This irresolution is most likely attributable to a close temporal clustering of nodes, rather than to ceiling effects (mutational saturation) producing an inappropriate window of resolution for the cytochrome b sequences. Images

Avise, J C; Nelson, W S; Sibley, C G



Genome-wide identification and phylogenetic analysis of the ERF gene family in cucumbers  

PubMed Central

Members of the ERF transcription-factor family participate in a number of biological processes, viz., responses to hormones, adaptation to biotic and abiotic stress, metabolism regulation, beneficial symbiotic interactions, cell differentiation and developmental processes. So far, no tissue-expression profile of any cucumber ERF protein has been reported in detail. Recent completion of the cucumber full-genome sequence has come to facilitate, not only genome-wide analysis of ERF family members in cucumbers themselves, but also a comparative analysis with those in Arabidopsis and rice. In this study, 103 hypothetical ERF family genes in the cucumber genome were identified, phylogenetic analysis indicating their classification into 10 groups, designated I to X. Motif analysis further indicated that most of the conserved motifs outside the AP2/ERF domain, are selectively distributed among the specific clades in the phylogenetic tree. From chromosomal localization and genome distribution analysis, it appears that tandem-duplication may have contributed to CsERF gene expansion. Intron/exon structure analysis indicated that a few CsERFs still conserved the former intron-position patterns existent in the common ancestor of monocots and eudicots. Expression analysis revealed the widespread distribution of the cucumber ERF gene family within plant tissues, thereby implying the probability of their performing various roles therein. Furthermore, members of some groups presented mutually similar expression patterns that might be related to their phylogenetic groups.

Hu, Lifang; Liu, Shiqiang



Molecular phylogenetics unveils the ancient evolutionary origins of the enigmatic fairy armadillos.  


Fairy armadillos or pichiciegos (Xenarthra, Dasypodidae) are among the most elusive mammals. Due to their subterranean and nocturnal lifestyle, their basic biology and evolutionary history remain virtually unknown. Two distinct species with allopatric distributions are recognized: Chlamyphorus truncatus is restricted to central Argentina, while Calyptophractus retusus occurs in the Gran Chaco of Argentina, Paraguay, and Bolivia. To test their monophyly and resolve their phylogenetic affinities within armadillos, we obtained sequence data from modern and museum specimens for two mitochondrial genes (12S RNA [MT-RNR1] and NADH dehydrogenase 1 [MT-ND1]) and two nuclear exons (breast cancer 1 early onset exon 11 [BRCA1] and von Willebrand factor exon 28 [VWF]). Phylogenetic analyses provided a reference phylogeny and timescale for living xenarthran genera. Our results reveal monophyletic pichiciegos as members of a major armadillo subfamily (Chlamyphorinae). Their strictly fossorial lifestyle probably evolved as a response to the Oligocene aridification that occurred in South America after their divergence from Tolypeutinae around 32 million years ago (Mya). The ancient divergence date (?17Mya) for separation between the two species supports their taxonomic classification into distinct genera. The synchronicity with Middle Miocene marine incursions along the Paraná river basin suggests a vicariant origin for pichiciegos by the disruption of their ancestral range. Their phylogenetic distinctiveness and rarity in the wild argue in favor of high conservation priority. PMID:22122941

Delsuc, Frédéric; Superina, Mariella; Tilak, Marie-Ka; Douzery, Emmanuel J P; Hassanin, Alexandre



Nearest Neighbor Classification by Relearning  

Microsoft Academic Search

Since the k-nearest neighbor (kNN) classification is a simple and effective classification approach, it is well known in the\\u000a data classification. However, improving performance of the classifier is still attractive to cope with the high accuracy processing.\\u000a A tolerant rough set is considered as a basis of the classification of data. The data classification is realized by applying\\u000a the kNN

Naohiro Ishii; Yuta Hoki; Yuki Okada; Yongguang Bao



Optimizing phylogenetic networks for circular split systems.  


We address the problem of realizing a given distance matrix by a planar phylogenetic network with a minimum number of faces. With the help of the popular software SplitsTree4, we start by approximating the distance matrix with a distance metric that is a linear combination of circular splits. The main results of this paper are the necessary and sufficient conditions for the existence of a network with a single face. We show how such a network can be constructed, and we present a heuristic for constructing a network with few faces using the first algorithm as the base case. Experimental results on biological data show that this heuristic algorithm can produce phylogenetic networks with far fewer faces than the ones computed by SplitsTree4, without affecting the approximation of the distance matrix. PMID:21788677

Phipps, Paul; Bereg, Sergey



Molecular phylogenetics of mastodon and Tyrannosaurus rex.  


We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen alpha1(I) and alpha2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for T. rex. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable. PMID:18436782

Organ, Chris L; Schweitzer, Mary H; Zheng, Wenxia; Freimark, Lisa M; Cantley, Lewis C; Asara, John M



Segmentation assisted food classification for dietary assessment  

NASA Astrophysics Data System (ADS)

Accurate methods and tools to assess food and nutrient intake are essential for the association between diet and health. Preliminary studies have indicated that the use of a mobile device with a built-in camera to obtain images of the food consumed may provide a less burdensome and more accurate method for dietary assessment. We are developing methods to identify food items using a single image acquired from the mobile device. Our goal is to automatically determine the regions in an image where a particular food is located (segmentation) and correctly identify the food type based on its features (classification or food labeling). Images of foods are segmented using Normalized Cuts based on intensity and color. Color and texture features are extracted from each segmented food region. Classification decisions for each segmented region are made using support vector machine methods. The segmentation of each food region is refined based on feedback from the output of classifier to provide more accurate estimation of the quantity of food consumed.

Zhu, Fengqing; Bosch, Marc; Schap, Tusarebecca; Khanna, Nitin; Ebert, David S.; Boushey, Carol J.; Delp, Edward J.



Segmentation Assisted Food Classification for Dietary Assessment  

PubMed Central

Accurate methods and tools to assess food and nutrient intake are essential for the association between diet and health. Preliminary studies have indicated that the use of a mobile device with a built-in camera to obtain images of the food consumed may provide a less burdensome and more accurate method for dietary assessment. We are developing methods to identify food items using a single image acquired from the mobile device. Our goal is to automatically determine the regions in an image where a particular food is located (segmentation) and correctly identify the food type based on its features (classification or food labeling). Images of foods are segmented using Normalized Cuts based on intensity and color. Color and texture features are extracted from each segmented food region. Classification decisions for each segmented region are made using support vector machine methods. The segmentation of each food region is refined based on feedback from the output of classifier to provide more accurate estimation of the quantity of food consumed.

Zhu, Fengqing; Bosch, Marc; Schap, TusaRebecca; Khanna, Nitin; Ebert, David S.; Boushey, Carol J.; Delp, Edward J.



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



Phylogenetic analysis of honey bee behavioral evolution  

Microsoft Academic Search

DNA sequences from three mitochondrial (rrnL, cox2, nad2) and one nuclear gene (itpr) from all 9 known honey bee species (Apis), a 10th possible species, Apis dorsata binghami, and three outgroup species (Bombus terrestris, Melipona bicolor and Trigona fimbriata) were used to infer Apis phylogenetic relationships using Bayesian analysis. The dwarf honey bees were confirmed as basal, and the giant

Rika Raffiudin; Ross H. Crozier



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



A comparative test of phylogenetic diversity indices  

Microsoft Academic Search

Traditional measures of biodiversity, such as species richness, usually treat species as being equal. As this is obviously\\u000a not the case, measuring diversity in terms of features accumulated over evolutionary history provides additional value to\\u000a theoretical and applied ecology. Several phylogenetic diversity indices exist, but their behaviour has not yet been tested\\u000a in a comparative framework. We provide a test

Oliver Schweiger; Stefan Klotz; Walter Durka; Ingolf Kühn



Clann: investigating phylogenetic information through supertree analyses  

Microsoft Academic Search

Summary: Clann has been developed in order to provide methods of investigating phylogenetic information through the application of supertrees. Availability: Clann has been precompiled for Linux, Apple Macintosh and Windows operating systems and is avail- able from http:\\/\\/\\/software\\/clann. Source code is available on request from the authors. Supplementary information: Clann has been written in the C programming language. Source code

C. J. Creevey; James O. Mcinerney



Phylogenetic diversity of soda lake alkaliphiles  

Microsoft Academic Search

16S rRNA genes from a range of aerobic chemoorganotrophic, alkaliphilic soda lake Bacteria and Archaea have been sequenced and subjected to phylogenetic analysis. Gram-negative alkaliphiles were found to be confined to the ?3 subdivision of the Proteobacteria, with many isolates related to the Halomonas\\/Deleya group. Gram-positive alkaliphiles were found in both high % G + C and low % G

A. W. Duckworth; W. D. Grant; B. E. Jones; R. van Steenbergen



The prior probabilities of phylogenetic trees  

Microsoft Academic Search

Bayesian methods have become among the most popular methods in phylogenetics, but theoretical opposition to this methodology\\u000a remains. After providing an introduction to Bayesian theory in this context, I attempt to tackle the problem mentioned most\\u000a often in the literature: the “problem of the priors”—how to assign prior probabilities to tree hypotheses. I first argue that\\u000a a recent objection—that an

Joel D. Velasco



Phylogenetic Diversity of Phytopathogenic Mycoplasmalike Organisms  

Microsoft Academic Search

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




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


The New World swallow genus Tachycineta comprises nine species that collectively have a wide geographic distribution and remarkable variation both within- and among-species in ecologically important traits. Existing phylogenetic hypotheses for Tachycineta are based on mitochondrial DNA sequences, thus they provide estimates of a single gene tree. In this study we sequenced multiple individuals from each species at 16 nuclear intron loci. We used gene concatenated approaches (Bayesian and maximum likelihood) as well as coalescent-based species tree inference to reconstruct phylogenetic relationships of the genus. We examined the concordance and conflict between the nuclear and mitochondrial trees and between concatenated and coalescent-based inferences. Our results provide an alternative phylogenetic hypothesis to the existing mitochondrial DNA estimate of phylogeny. This new hypothesis provides a more accurate framework in which to explore trait evolution and examine the evolution of the mitochondrial genome in this group. PMID:22750631

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



Marine turtle mitogenome phylogenetics and evolution.  


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



Phylogenetic conservatism of environmental niches in mammals  

PubMed Central

Phylogenetic niche conservatism is the pattern where close relatives occupy similar niches, whereas distant relatives are more dissimilar. We suggest that niche conservatism will vary across clades in relation to their characteristics. Specifically, we investigate how conservatism of environmental niches varies among mammals according to their latitude, range size, body size and specialization. We use the Brownian rate parameter, ?2, to measure the rate of evolution in key variables related to the ecological niche and define the more conserved group as the one with the slower rate of evolution. We find that tropical, small-ranged and specialized mammals have more conserved thermal niches than temperate, large-ranged or generalized mammals. Partitioning niche conservatism into its spatial and phylogenetic components, we find that spatial effects on niche variables are generally greater than phylogenetic effects. This suggests that recent evolution and dispersal have more influence on species' niches than more distant evolutionary events. These results have implications for our understanding of the role of niche conservatism in species richness patterns and for gauging the potential for species to adapt to global change.

Cooper, Natalie; Freckleton, Rob P.; Jetz, Walter



Topology improves phylogenetic motif functional site predictions.  


Prediction of protein functional sites from sequence-derived data remains an open bioinformatics problem. We have developed a phylogenetic motif (PM) functional site prediction approach that identifies functional sites from alignment fragments that parallel the evolutionary patterns of the family. In our approach, PMs are identified by comparing tree topologies of each alignment fragment to that of the complete phylogeny. Herein, we bypass the phylogenetic reconstruction step and identify PMs directly from distance matrix comparisons. In order to optimize the new algorithm, we consider three different distance matrices and 13 different matrix similarity scores. We assess the performance of the various approaches on a structurally nonredundant data set that includes three types of functional site definitions. Without exception, the predictive power of the original approach outperforms the distance matrix variants. While the distance matrix methods fail to improve upon the original approach, our results are important because they clearly demonstrate that the improved predictive power is based on the topological comparisons. Meaning that phylogenetic trees are a straightforward, yet powerful way to improve functional site prediction accuracy. While complementary studies have shown that topology improves predictions of protein-protein interactions, this report represents the first demonstration that trees improve functional site predictions as well. PMID:21071810

Kc, Dukka B; Livesay, Dennis R


Phylogenetic analysis of cubilin (CUBN) gene  

PubMed Central

Cubilin, (CUBN; also known as intrinsic factor-cobalamin receptor [Homo sapiens Entrez Pubmed ref NM_001081.3; NG_008967.1; GI: 119606627]), located in the epithelium of intestine and kidney acts as a receptor for intrinsic factor – vitamin B12 complexes. Mutations in CUBN may play a role in autosomal recessive megaloblastic anemia. The current study investigated the possible role of CUBN in evolution using phylogenetic testing. A total of 588 BLAST hits were found for the cubilin query sequence and these hits showed putative conserved domain, CUB superfamily (as on 27th Nov 2012). A first-pass phylogenetic tree was constructed to identify the taxa which most often contained the CUBN sequences. Following this, we narrowed down the search by manually deleting sequences which were not CUBN. A repeat phylogenetic analysis of 25 taxa was performed using PhyML, RAxML and TreeDyn softwares to confirm that CUBN is a conserved protein emphasizing its importance as an extracellular domain and being present in proteins mostly known to be involved in development in many chordate taxa but not found in prokaryotes, plants and yeast.. No horizontal gene transfers have been found between different taxa.

Shaik, Abjal Pasha; Alsaeed, Abbas H; Kiranmayee, S; Bammidi, VK; Sultana, Asma



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



An Accurate Method for Measuring Activation Energy  

Microsoft Academic Search

In this letter, we present an accurate method for the measurement of activation energy. This method combined the excitation power dependent photoluminescence and temperature dependent photoluminescence together to obtain activation energy. We found with increasing temperature, there is a step transition from one emission mechanism to another. This step transition gives us an accurate measurement of activation energy. Using this

Xiang-Bai Chen; Jesse Huso; John L. Morrison; Leah Bergman



A molecular phylogeny and classification of Bignoniaceae.  


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



Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling  

PubMed Central

Background Phylogenies are essential to many areas of biology, but phylogenetic methods may give incorrect estimates under some conditions. A potentially common scenario of this type is when few taxa are sampled and terminal branches for the sampled taxa are relatively long. However, the best solution in such cases (i.e., sampling more taxa versus more characters) has been highly controversial. A widespread assumption in this debate is that added taxa must be complete (no missing data) in order to save analyses from the negative impacts of limited taxon sampling. Here, we evaluate whether incomplete taxa can also rescue analyses under these conditions (empirically testing predictions from an earlier simulation study). Methodology/Principal Findings We utilize DNA sequence data from 16 vertebrate species with well-established phylogenetic relationships. In each replicate, we randomly sample 4 species, estimate their phylogeny (using Bayesian, likelihood, and parsimony methods), and then evaluate whether adding in the remaining 12 species (which have 50, 75, or 90% of their data replaced with missing data cells) can improve phylogenetic accuracy relative to analyzing the 4 complete taxa alone. We find that in those cases where sampling few taxa yields an incorrect estimate, adding taxa with 50% or 75% missing data can frequently (>75% of relevant replicates) rescue Bayesian and likelihood analyses, recovering accurate phylogenies for the original 4 taxa. Even taxa with 90% missing data can sometimes be beneficial. Conclusions We show that adding taxa that are highly incomplete can improve phylogenetic accuracy in cases where analyses are misled by limited taxon sampling. These surprising empirical results confirm those from simulations, and show that the benefits of adding taxa may be obtained with unexpectedly small amounts of data. These findings have important implications for the debate on sampling taxa versus characters, and for studies attempting to resolve difficult phylogenetic problems.

Wiens, John J.; Tiu, Jonathan



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.



Multistage approach for clustering and classification of ECG data.  


Accurate and fast approaches for automatic ECG data classification are vital for clinical diagnosis of heart disease. To this end, we propose a novel multistage algorithm that combines various procedures for dimensionality reduction, consensus clustering of randomized samples and fast supervised classification algorithms for processing of the highly dimensional large ECG datasets. We carried out extensive experiments to study the effectiveness of the proposed multistage clustering and classification scheme using precision, recall and F-measure metrics. We evaluated the performance of numerous combinations of various methods for dimensionality reduction, consensus functions and classification algorithms incorporated in our multistage scheme. The results of the experiments demonstrate that the highest precision, recall and F-measure are achieved by the combination of the rank correlation coefficient for dimensionality reduction, HBGF consensus function and the SMO classifier with the polynomial kernel. PMID:24095570

Abawajy, J H; Kelarev, A V; Chowdhury, M



The Banff classification revisited.  


From small beginnings in 1991, the Banff working classification of renal allograft pathology has grown to be a major force for setting standards in renal transplant pathology, and is widely used in international clinical trials of new antirejection agents. The meeting, classification, and consensus process have unique history, and look poised to continue for another several decades as the embodiment of the process for setting global standards in pathology. The Banff meetings have expanded from renal allograft pathology to most other areas of solid organ transplantation, and increasingly incorporate international working groups, so that productive collaborative activity is ongoing, creating an important dynamic process enhancing clinical success in transplantation. On the other hand, despite the successes of the working classifications and ongoing collaborative efforts, there are limitations in this and other pathological classifications, related to potential for sampling error, issues of reproducibility when implemented globally, and lack of formal incorporation of morphometry and molecular and genomics approaches. Some of these problems cannot be overcome within the realm of traditional histopathology, and will only be solved when the classification is able to confidently embrace genomics and molecular medicine parameters for all common diagnoses. The smooth integration of these newer technologies with traditional histopathology is one of the great challenges for the future. PMID:23235566

Solez, Kim; Racusen, Lorraine C



Information gathering for CLP classification.  


Regulation 1272/2008 includes provisions for two types of classification: harmonised classification and self-classification. The harmonised classification of substances is decided at Community level and a list of harmonised classifications is included in the Annex VI of the classification, labelling and packaging Regulation (CLP). If a chemical substance is not included in the harmonised classification list it must be self-classified, based on available information, according to the requirements of Annex I of the CLP Regulation. CLP appoints that the harmonised classification will be performed for carcinogenic, mutagenic or toxic to reproduction substances (CMR substances) and for respiratory sensitisers category 1 and for other hazard classes on a case-by-case basis. The first step of classification is the gathering of available and relevant information. This paper presents the procedure for gathering information and to obtain data. The data quality is also discussed. PMID:21709381

Marcello, Ida; Giordano, Felice; Costamagna, Francesca Marina



Accurate histological terminology for small intestine carcinoid tumors  

PubMed Central

The recent WHO Classification of Tumours of the Digestive System reflects the views of a Working Group that convened for an Editorial and Consensus Conference at the International Agency for Research on Cancer (IARC), Lyon, 10 December 2009 [1]. In this classification, the “neuroendocrine neoplasms of the small intestine” include neuroendocrine tumor (NET), neuroendocrine carcinoma (NEC), mixed adenoneuroendocrine carcinoma, EC cell, serotonin-producing NET, gangliocytic paraganglioma, gastrinoma, L cell, glucagon-like peptide-producing, PP/PYY-producing NETs, and somostatin-producing NET. “Carcinoid tumor” is the generic term traditionally applied to low-grade malignant neoplasms originating from the diffuse endocrine system exclusive of the pancreas and the thyroid C-cell, a term being progressively replaced by “well-differentiated (neuro)endocrine tumors/carcinomas”. It is now acknowledged that they represent a group of related neoplasms, not single pathologic entity. In the WHO classification, the NET includes NET G1 and NET G2, and the term “carcinoid” is used as a synonym of NET G1. We believed that the term “carcinoid tumor” is generic; consequently, the term should be avoided. We have read with great interest the paper by Lee et al. – “Multiple carcinoid tumor of the small intestine preoperatively diagnosed by double-balloon endoscopy” [2]. In the paper, Lee et al. wrote: “Histologic examination of the biopsy sample obtained by endoscopy confirmed the diagnosis of a carcinoid tumor. The tumor was composed of small uniform epithelial cells, which stained positively for chromogranin A and synaptophysin.” We believe that the histological diagnosis of carcinoid tumor is not correct. The description is typical of NET G1, according to the new WHO classification. The authors wrote: “These small tumors were diagnosed as carcinoid tumors by endoscopic findings, whereas histologic examination could not make this diagnosis… Microscopically, the tumors were composed of small uniform epithelial cells which stained positively for chromogranin A and synaptophysin. Furthermore, the largest tumor had invaded the muscularis propria. MIB-1 index was less than 1%.” It is evident that histological diagnosis was not reported. In conclusion, accurate histological diagnosis is necessary for the evaluation of treatment impact in the management of neuroendocrine tumors of the small intestine.

Pusiol, Teresa; Morini, Alice; Piscioli, Irene; Scialpi, Michele



An efficient code for environmental sound classification  

PubMed Central

An efficient code for classifying environmental sounds is described that exploits a recent significant advance in signal processing known as compressed sensing (CS) [cf.Donoho, D. (2006). IEEE Trans. Inf. Theory 52, 1289–1306]. CS involves a novel approach to sampling in which the salient information in signals is recovered from the projection onto a small set of random basis functions. The advantage of the random basis over traditional Fourier or wavelet representations is that it allows accurate classification at low target-to-interference ratios based on few samples and little or no prior information about signals.

Arora, Raman; Lutfi, Robert A.



Using minimum DNA marker loci for accurate population classification in rice ( Oryza sativa L.)  

Microsoft Academic Search

Because of the rich diversity among rice accessions grown around the world in distinct environments, traditional methods using\\u000a morphology, cross compatibility and geography for classifying rice accessions according to different sub-populations have\\u000a given way to use of molecular markers. Having a few robust markers that can quickly assign population structure to germplasm\\u000a will facilitate making more informed choices about genetic

Hesham A. AgramaAnna; Anna M. McClung; WenGui Yan


Classification of mental disorders*  

PubMed Central

One of the fundamental difficulties in devising a classification of mental disorders is the lack of agreement among psychiatrists regarding the concepts upon which it should be based: diagnoses can rarely be verified objectively and the same or similar conditions are described under a confusing variety of names. This situation militates against the ready exchange of ideas and experiences and hampers progress. As a first step towards remedying this state of affairs, the author of the article below has undertaken a critical survey of existing classifications. He shows how some of the difficulties created by lack of knowledge regarding pathology and etiology may be overcome by the use of “operational definitions” and outlines the basic principles on which he believes a generally acceptable international classification might be constructed. If this can be done it should lead to a greater measure of agreement regarding the value of specific treatments for mental disorders and greatly facilitate a broad epidemiological approach to psychiatric research.

Stengel, E.



Commission 45: Spectral Classification  

NASA Astrophysics Data System (ADS)

This report gives an update of developments (since the last General Assembly at Prague) in the areas that are of relevance to the commission. In addition to numerous papers, a new monograph entitled Stellar Spectral Classification with Richard Gray and Chris Corbally as leading authors will be published by Princeton University Press as part of their Princeton Series in Astrophysics in April 2009. This book is an up-to-date and encyclopedic review of stellar spectral classification across the H-R diagram, including the traditional MK system in the blue-violet, recent extensions into the ultraviolet and infrared, the newly defined L-type and T-type spectral classes, as well as spectral classification of carbon stars, S-type stars, white dwarfs, novae, supernovae and Wolf-Rayet stars.

Giridhar, Sunetra; Gray, Richard O.; Corbally, Christopher J.; Bailer-Jones, Coryn A. L.; Eyer, Laurent; Irwin, Michael J.; Kirkpatrick, J. Davy; Majewski, Steven; Minniti, Dante; Nordström, Birgitta


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


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




Technology Transfer Automated Retrieval System (TEKTRAN)

The phylogenetic relationships and generic assignments of ‘Finlaya’ and related taxa of uncertain taxonomic position in the classification of Aedini proposed by Reinert et al. (2004) are explored using 232 characters from eggs, fourth-instar larvae, pupae, adults and immature habitat coded for 116 e...


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.



Statistical Analysis of Microspectroscopy Signals for Algae Classification and Phylogenetic Comparison  

Microsoft Academic Search

We performed microspectroscopic evaluation of the pigment composition of the photosynthetic compartments of algae belonging\\u000a to different taxonomic divisions and higher plants. In [11], a supervised Gaussian bands decompositions was performed for\\u000a the pigment spectra, the algae spectrum was modelled as the linear mixture, with unknown coefficients, of the pigment spectra,\\u000a and a user-guided fitting algorithm was employed. The method

Anna Tonazzini; Primo Coltelli; Paolo Gualtieri



Functional Classification of Amino Acid Decarboxylases from the Alanine Racemase Structural Family by Phylogenetic Studies  

Microsoft Academic Search

Arginine decarboxylase (ADC) and ornithine decarboxylase (ODC) are involved in the biosynthesis of putrescine, which is the precursor of other polyamines in animals, plants, and bacteria. These pyridoxal-5#-phosphate-dependent decarbox- ylases belong to the alanine racemase (AR) structural family together with diaminopimelate decarboxylase (DapDC), which catalyzes the final step of lysine biosynthesis in bacteria. We have constructed a multiple-sequence alignment of

Heidi Kidron; Susanna Repo; Mark S. Johnson; Tiina A. Salminen



Accurate and robust extraction of brain regions using a deformable model based on radial basis functions  

Microsoft Academic Search

Brain extraction from head magnetic resonance (MR) images is a classification problem of segmenting image volumes into brain and non-brain regions. It is a difficult task due to the convoluted brain surface and the inapparent brain\\/non-brain boundaries in images. This paper presents an automated, robust, and accurate brain extraction method which utilizes a new implicit deformable model to well represent

Jia-Xiu Liu; Yong-Sheng Chen; Li-Fen Chen



Neurophysiological classification of myoclonus.  


Myoclonus can be diagnosed and classified mainly based on clinical features. Neurophysiologic studies help confirm clinical diagnosis and classification, and understand underlying physiological mechanisms. The neurophysiologic classification of myoclonus is mainly based on surface EMG (individual EMG patterns, muscle spatial distribution and time sequence of muscle activation), EEG, EEG/EMG relationships (jerk-locked back-averaging, cortico-muscular coherence), somatosensory evoked potentials, and long-loop reflexes. Paired stimulation evoked response/long loop reflex and jerk-locked evoked responses evaluate the excitability changes of the primary somatosensory cortex. Transcranial magnetic stimulation can evaluate the excitability state of the primary motor cortex. PMID:17336770

Shibasaki, H



28 CFR 524.73 - Classification procedures.  

Code of Federal Regulations, 2013 CFR

...OF PRISONS, DEPARTMENT OF JUSTICE INMATE ADMISSION, CLASSIFICATION, AND TRANSFER CLASSIFICATION OF INMATES Central Inmate Monitoring (CIM) System § 524.73 Classification procedures. (a) Initial assignment....




Technology Transfer Automated Retrieval System (TEKTRAN)

The insect pathogenic fungus Beauveria is one the leading fungi used in biological control of insects throughout the world. This chapter reviews the history of classification of these fungi, how species are defined, their genetics, and reviews recent progress in understanding their evolutionary rel...


Constraint Classification: A Generalization of Multiclass Classification and Category Ranking  

Microsoft Academic Search

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

Sariel Har-Peled; Dan Roth; Dav Zimak


Phylogenetic Interrelationships of Ginglymodian Fishes (Actinopterygii: Neopterygii)  

PubMed Central

The Ginglymodi is one of the most common, though poorly understood groups of neopterygians, which includes gars, macrosemiiforms, and “semionotiforms.” In particular, the phylogenetic relationships between the widely distributed “semionotiforms,” and between them and other ginglymodians have been enigmatic. Here, the phylogenetic relationships between eight of the 11 “semionotiform” genera, five genera of living and fossil gars and three macrosemiid genera, are analysed through cladistic analysis, based on 90 morphological characters and 37 taxa, including 7 out-group taxa. The results of the analysis show that the Ginglymodi includes two main lineages: Lepisosteiformes and †Semionotiformes. The genera †Pliodetes, †Araripelepidotes, †Lepidotes, †Scheenstia, and †Isanichthys are lepisosteiforms, and not semionotiforms, as previously thought, and these taxa extend the stratigraphic range of the lineage leading to gars back up to the Early Jurassic. A monophyletic †Lepidotes is restricted to the Early Jurassic species, whereas the strongly tritoral species previously referred to †Lepidotes are referred to †Scheenstia. Other species previously referred to †Lepidotes represent other genera or new taxa. The macrosemiids are well nested within semionotiforms, together with †Semionotidae, here restricted to †Semionotus, and a new family including †Callipurbeckia n. gen. minor (previously referred to †Lepidotes), †Macrosemimimus, †Tlayuamichin, †Paralepidotus, and †Semiolepis. Due to the numerous taxonomic changes needed according to the phylogenetic analysis, this article also includes formal taxonomic definitions and diagnoses for all generic and higher taxa, which are new or modified. The study of Mesozoic ginglymodians led to confirm Patterson’s observation that these fishes show morphological affinities with both halecomorphs and teleosts. Therefore, the compilation of large data sets including the Mesozoic ginglymodians and the re-evaluation of several hypotheses of homology are essential to test the hypotheses of the Halecostomi vs. the Holostei, which is one of the major topics in the evolution of Mesozoic vertebrates and the origin of modern fish faunas.

Lopez-Arbarello, Adriana



78 FR 54970 - Cotton Futures Classification: Optional Classification Procedure  

Federal Register 2010, 2011, 2012, 2013

...AMS-CN-13-0043] RIN 0581-AD33 Cotton Futures Classification: Optional Classification...allow for the addition of an optional cotton futures classification ``registration'' by the U.S. cotton industry and the Intercontinental...



Molecular phylogenetic analysis of tropical freshwater mussels (Mollusca: Bivalvia: Unionoida) resolves the position of Coelatura and supports a monophyletic Unionidae.  


In previous molecular phylogenetic analyses of the freshwater mussel family Unionidae (Bivalvia: Unionoida), the Afrotropical genus Coelatura had been recovered in various positions, generally indicating a paraphyletic Unionidae. However that result was typically poorly supported and in conflict with morphology-based analyses. We set out to test the phylogenetic position of Coelatura by sampling tropical lineages omitted from previous studies. Forty-one partial 28S nuclear rDNA and partial COI mtDNA sequences (1130 total aligned nucleotides) were analyzed separately and in combination under both maximum parsimony and likelihood, as well as Bayesian inference. There was significant phylogenetic incongruence between the character sets (partition homogeneity test, p<0.01), but a novel heuristic for comparing bootstrap values among character sets analyzed separately and in combination illustrated that the observed conflict was due to homoplasy rather than separate gene histories. Phylogenetic analyses robustly supported a monophyletic Unionidae, with Coelatura recovered as part of a well-supported Africa-India clade (=Parreysiinae). The implications of this result are discussed in the context of Afrotropical freshwater mussel evolution and the classification of the family Unionidae. PMID:21827862

Whelan, Nathan V; Geneva, Anthony J; Graf, Daniel L



Equipment/product classification  

SciTech Connect

This is a buyer`s guide for various equipment, software, SCADA systems and other allied products and services used in constructing, operating and maintaining pipeline systems around the world. The products are arranged alphabetically and by product item or component classification for easy use and reference.




Waste classification sampling plan.  

National Technical Information Service (NTIS)

The purpose of this sampling is to explain the method used to collect and analyze data necessary to verify and/or determine the radionuclide content of the B-Cell decontamination and decommissioning waste stream so that the correct waste classification fo...

S. D. Landsman



Bricks: Properties and Classifications  

Microsoft Academic Search

Studies the various contemporary standard brick products that are available and examines in detail their inherent properties and classifications which ensures that British bricks conform to the requirements of British Standards Specifications. These properties are significant and the engineer and architect must give them due consideration, for it is their responsibility to ensure they specify correctly for particular applications, and

G. C. J. Lynch



Constituent Parsing by Classification  

Microsoft Academic Search

Ordinary classification techniques can drive a conceptually simple constituent parser that achieves near state-of-the-art accuracy on standard test sets. Here we present such a parser, which avoids some of the limitations of other discriminative parsers. In particular, it does not place any restrictions upon which types of fea- tures are allowed. We also present sev- eral innovations for faster training

Joseph Turian; I. Dan Melamed


Shark Teeth Classification  

ERIC Educational Resources Information Center

|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…

Brown, Tom; Creel, Sally; Lee, Velda



Carbohydrate terminology and classification  

Microsoft Academic Search

Dietary carbohydrates are a group of chemically defined substances with a range of physical and physiological properties and health benefits. As with other macronutrients, the primary classification of dietary carbohydrate is based on chemistry, that is character of individual monomers, degree of polymerization (DP) and type of linkage (? or ?), as agreed at the Food and Agriculture Organization\\/World Health

J H Cummings; A M Stephen



Soil Classification and Treatment.  

ERIC Educational Resources Information Center

This instructional unit was designed to enable students, primarily at the secondary level, to (1) classify soils according to current capability classifications of the Soil Conservation Service, (2) select treatments needed for a given soil class according to current recommendations provided by the Soil Conservation Service, and (3) interpret a…

Clemson Univ., SC. Vocational Education Media Center.


Benchmarking beat classification algorithms  

Microsoft Academic Search

This study compares the accuracy of a range of advanced and classical pattern recognition algorithms for beat and arrhythmia classification from ECG using a principled statistical framework. These are to be used in an application where no patient-specific adaptation of the features or of the model is possible, which means that models must be able to generalise across subjects. Our

I. T. Nabney; D. J. Evans; J. Tenner; L. Gamlyn



Classification of pancreatitis  

Microsoft Academic Search

An international group of doctors interested in pancreatic disease met in Cambridge in March 1983, under the auspices of the Pancreatic Society of Great Britain and Ireland, to discuss the classification of pancreatitis in the light of developments that have taken place in the 20 years since the crucial conference in Marseille.

M Sarner; P B Cotton



Classification of Malabsorption Syndromes  

Microsoft Academic Search

Malabsorption syndrome is usually defined as the complex of symptoms secondary to maldigestion and\\/or malabsorption, realizing when the extension of the disease exceeds the ability of intestine compensation. Several conditions have been recognized as being responsible for this syndrome. Up to now, different criteria have been used to order them, but a definitive classification is still not available because of

Massimo Montalto; Luca Santoro; Ferruccio D’Onofrio; Valentina Curigliano; Dina Visca; Antonella Gallo; Giovanni Cammarota; Antonio Gasbarrini; Giovanni Gasbarrini



Shark Teeth Classification  

Microsoft Academic Search

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

Tom Brown; Sally Creel; Velda Lee



Radar clutter classification  

Microsoft Academic Search

The problem of classifying radar clutter as found on air traffic control radar systems is studied, and an algorithm is developed to carry out this classification automatically. The basis for the algorithm is Bayes decision theory and the parametric maximum a posteriori probability (MAP) classifier. This classifier employs a quadratic discriminant function and is optimum for feature vectors that are

Wolfgang Stehwien



Radar clutter classification  

Microsoft Academic Search

The problem of classifying radar clutter as found on air traffic control radar systems is studied. An algorithm based on Bayes decision theory and the parametric maximum a posteriori probability classifier is developed to perform this classification automatically. This classifier employs a quadratic discriminant function and is optimum for feature vectors that are distributed according to the multivariate normal density.

Wolfgang Stehwien




EPA Science Inventory

Purposes and need for ecological classification will be discussed. Some brief examples will highlight regional and watershed approaches, general issues of extrapolation and classification helpful to monitoring/assessment design for larger aquatic systems, and some specific concep...


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...



Work Classification in Ancient Times.  

ERIC Educational Resources Information Center

The divisions of labor and the classifications of work in ancient times are described, and an early four-part classification based on the "Bhagavad Gita" is compared with that of the present "Dictionary of Occupational Titles." (Author)

Hopke, William



Horny sponges and their affairs: on the phylogenetic relationships of keratose sponges.  


The demosponge orders Dictyoceratida and Dendroceratida are historically assigned to the keratose (or "horny") sponges, which are mostly devoid of primary skeletal elements, but possess an elaborate skeleton of organic fibres instead. This paucity of complex mineral skeletal elements makes their unambiguous classification and phylogenetic reconstruction based on morphological features difficult. Here we present the most comprehensive molecular phylogeny to date for the Dendroceratida, Dictyoceratida, and also other sponge orders that largely lack a mineral skeleton or skeletal elements at all (i.e. Verongida, Halisarcida, Chondrosida), based on independent mitochondrial and nuclear markers. We used molecular data to validate the coherence of all recognised orders, families and subfamilies that are currently defined using morphological characteristics. We discussed the significance of morphological and chemotaxonomic characters for keratose sponges, and suggested adapted definitions for the classification of dendroceratid, dictyoceratid, and verongid higher taxa. Also, we found that chondrosid sponges are non-monophyletic with respect to Halisarcida. Verongida and Dendroceratida were monophyletic, however most of their classically recognised families were not recovered. This indicated that the current distinction between dendritic and mesh-like fibre skeletons is not significant at this level of classification. Dysideidae were found to be the sister-group to the remaining Dictyoceratida. Irciniidae formed a distinct clade, however Thorectidae and Spongiidae could not be separated with the molecular markers used. Finally, we are establishing the name Verongimorpha for the clade combining verongid, chondrosid and halisarcid taxa and readjust the content of its sister-clade Keratosa. PMID:22406528

Erpenbeck, Dirk; Sutcliffe, Patricia; Cook, Steve de C; Dietzel, Andreas; Maldonado, Manuel; van Soest, Rob W M; Hooper, John N A; Wörheide, Gert



Classification-based objective functions  

Microsoft Academic Search

Backpropagation, similar to most learning algorithms that can form complex decision surfaces, is prone to overfitting. This work presents classification-based objective functions, an intuitive approach to training artificial neural networks on classification problems. Classification-based learning attempts to guide the network directly to correct pattern classification rather than using an implicit search of common error minimization heuristics, such as sum-squared-error (SSE)

Michael Rimer; Tony Martinez



Phylogenetic diversity and nature conservation: where are we?  


To date, there is little evidence that phylogenetic diversity has contributed to nature conservation. Here, we discuss the scientific justification of using phylogenetic diversity in conservation and the reasons for its neglect. We show that, apart from valuing the rarity and richness aspect, commonly quoted justifications based on the usage of phylogenetic diversity as a proxy for functional diversity or evolutionary potential are still based on uncertainties. We discuss how a missing guideline through the variety of phylogenetic diversity metrics and their relevance for conservation might be responsible for the hesitation to include phylogenetic diversity in conservation practice. We outline research routes that can help to ease uncertainties and bridge gaps between research and conservation with respect to phylogenetic diversity. PMID:23218499

Winter, Marten; Devictor, Vincent; Schweiger, Oliver



Phylogenetic analysis of Group I marine archaeal rRNA sequences emphasizes the hidden diversity within the primary group Archaea  

PubMed Central

Archaea form one of the three primary groups of extant life and are commonly associated with the extreme environments which many of their members inhabit. Currently, the Archaea are classified into two kingdoms, Crenarchaeota and Euryarchaeota, based on phylogenetic analysis of ribosomal RNA (rRNA) sequences. Molecular techniques allowing the retrieval and analysis of rRNA sequences from diverse environments are increasing our knowledge of archaeal diversity. This report describes the presence of marine Archaea in north-east Atlantic waters. Quantitative estimates indicated that the marine Archaea constitute 8 per cent of the total prokaryotic rRNA in Irish coastal waters. Phylogenetic analysis of the archaeal rRNA gene sequences revealed sufficient genetic diversity within Archaea to indicate that the current two-kingdom classification of Crenarchaeota and Euryarchaeota is restrictive.

McInerney, J. O.; Mullarkey, M.; Wernecke, M. E.; Powell, R.



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




Microsoft Academic Search

The present study explores some of the factors that determine how difficult a classification will be to learn or remember. The experiment to be reported was designed primarily to answer two questions: How does the difficulty of learning vary from one type of classification to another? Is something specific learned about the structure of a classification that will transfer positively

Roger N. Shepard; Carl I. Hovland; Herbert M. Jenkins



Probabilistic First-Order Classification  

Microsoft Academic Search

We discuss the problem of classification using the first order hypotheses. This paper proposes an enhancement of classification based on the naive Bayesian scheme that is able to overcome the conditional independence assumption. Several experiments, involving some artificial and real-world, both propositional and relational domains, were conducted. The results indicate that the classification performance of propositional learners is reached when

Uros Pompe; Igor Kononenko



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


Locating evolutionary precursors on a phylogenetic tree.  


Conspicuous innovations in the history of life are often preceded by more cryptic genetic and developmental precursors. In many cases, these appear to be associated with recurring origins of very similar traits in close relatives (parallelisms) or striking convergences separated by deep time (deep homologies). Although the phylogenetic distribution of gain and loss of traits hints strongly at the existence of such precursors, no models of trait evolution currently permit inference about their location on a tree. Here we develop a new stochastic model, which explicitly captures the dependency implied by a precursor and permits estimation of precursor locations. We apply it to the evolution of extrafloral nectaries (EFNs), an ecologically significant trait mediating a widespread mutualism between plants and ants. In legumes, a species-rich clade with morphologically diverse EFNs, the precursor model fits the data on EFN occurrences significantly better than conventional models. The model generates explicit hypotheses about the phylogenetic location of hypothetical precursors, which may help guide future studies of molecular genetic pathways underlying nectary position, development, and function. PMID:23206146

Marazzi, Brigitte; Ané, Cécile; Simon, Marcelo F; Delgado-Salinas, Alfonso; Luckow, Melissa; Sanderson, Michael J



Phylogenetics in the Bioinformatics Culture of Understanding  

PubMed Central

Bioinformatics, as a relatively young discipline, has grown up in a world of high-throughput large volume data that requires automatic analysis to enable us to stay on top of it all. As a response, the bioinformatics discipline has developed strategies to find patterns in a ‘low signal : noise ratio’ environment. While the need to process large amounts of information and extract hypotheses is both laudable and inescapable, the pressures that such requirements have introduced can lead to short cuts and misapprehensions. This is particularly the case with reference to assumptions about the underlying evolutionary theories that are implicitly invoked by the algorithms utilised in the analysis pipelines. The classic example is the misuse of the term ‘homologous’ to mean ‘similar’ or even ‘functionally similar’, rather than the correct definition of ‘having the same evolutionary origin’, which may or may not imply similarity of function. In this review, we outline some of the common phylogenetic questions from a bioinformatics perspective that can be better addressed with a deeper understanding of evolutionary principles and show, with examples from the amidohydrolase and Toll families, that quite different conclusions can be drawn if such approaches are taken. This review focuses on the importance of the underlying evolutionary biology, rather than assessing the merits of different phylogenetic techniques. The relative merits of a priori and a posteriori inclusion of biological information are discussed.

Allaby, Robin G.



Phylogenetically-Informed Priorities for Amphibian Conservation  

PubMed Central

The amphibian decline and extinction crisis demands urgent action to prevent further large numbers of species extinctions. Lists of priority species for conservation, based on a combination of species’ threat status and unique contribution to phylogenetic diversity, are one tool for the direction and catalyzation of conservation action. We describe the construction of a near-complete species-level phylogeny of 5713 amphibian species, which we use to create a list of evolutionarily distinct and globally endangered species (EDGE list) for the entire class Amphibia. We present sensitivity analyses to test the robustness of our priority list to uncertainty in species’ phylogenetic position and threat status. We find that both sources of uncertainty have only minor impacts on our ‘top 100‘ list of priority species, indicating the robustness of the approach. By contrast, our analyses suggest that a large number of Data Deficient species are likely to be high priorities for conservation action from the perspective of their contribution to the evolutionary history.

Isaac, Nick J. B.; Redding, David W.; Meredith, Helen M.; Safi, Kamran



A phylogenetic analysis of the phylum Fibrobacteres.  


Members of the phylum Fibrobacteres are highly efficient cellulolytic bacteria, best known for their role in rumen function and as potential sources of novel enzymes for bioenergy applications. Despite being key members of ruminants and other digestive microbial communities, our knowledge of this phylum remains incomplete, as much of our understanding is focused on two recognized species, Fibrobacter succinogenes and F. intestinalis. As a result, we lack insights regarding the environmental niche, host range, and phylogenetic organization of this phylum. Here, we analyzed over 1000 16S rRNA Fibrobacteres sequences available from public databases to establish a phylogenetic framework for this phylum. We identify both species- and genus-level clades that are suggestive of previously unknown taxonomic relationships between Fibrobacteres in addition to their putative lifestyles as host-associated or free-living. Our results shed light on this poorly understood phylum and will be useful for elucidating the function, distribution, and diversity of these bacteria in their niches. PMID:23759599

Jewell, Kelsea A; Scott, Jarrod J; Adams, Sandra M; Suen, Garret



Phylogenetic analysis of ancient DNA using BEAST.  


Under exceptional circumstances, it is possible to obtain DNA sequences from samples that are up to hundreds of thousands of years old. These data provide an opportunity to look directly at past genetic diversity, to trace the evolutionary process through time, and to infer demographic and phylogeographic trends. Ancient DNA (aDNA) data sets have some degree of intrinsic temporal structure because the sequences have been obtained from samples of different ages. When analyzing these data sets, it is usually necessary to take the sampling times into account. A number of phylogenetic methods have been designed with this purpose in mind. Here I describe the steps involved in Bayesian phylogenetic analysis of aDNA data. I outline a procedure that can be used to co-estimate the genealogical relationships, mutation rate, evolutionary timescale, and demographic history of the study species in a single analytical framework. A number of modifications to the methodology can be made in order to deal with complicating factors such as postmortem damage, sequences from undated samples, and data sets with low information content. PMID:22237538

Ho, Simon Y W



Phylogenetically-informed priorities for amphibian conservation.  


The amphibian decline and extinction crisis demands urgent action to prevent further large numbers of species extinctions. Lists of priority species for conservation, based on a combination of species' threat status and unique contribution to phylogenetic diversity, are one tool for the direction and catalyzation of conservation action. We describe the construction of a near-complete species-level phylogeny of 5713 amphibian species, which we use to create a list of evolutionarily distinct and globally endangered species (EDGE list) for the entire class Amphibia. We present sensitivity analyses to test the robustness of our priority list to uncertainty in species' phylogenetic position and threat status. We find that both sources of uncertainty have only minor impacts on our 'top 100' list of priority species, indicating the robustness of the approach. By contrast, our analyses suggest that a large number of Data Deficient species are likely to be high priorities for conservation action from the perspective of their contribution to the evolutionary history. PMID:22952807

Isaac, Nick J B; Redding, David W; Meredith, Helen M; Safi, Kamran



Phylogenetic analyses of proton-translocating transhydrogenases.  


The proton-translocating nicotinamide nucleotide transhydrogenases (TH) provide a simple model for understanding chemically coupled transmembrane proton translocation. To further our understanding of TH structure-function relationships, we have identified all sequenced homologous of these vectorial enzymes and have conducted sequence comparison studies. The NAD-binding domains of TH are homologous to bacterial alanine dehydrogenases (ADH) and eukaryotic saccharopine dehydrogenases (SDH) as well as N5(carboxyethyl)-L-ornithine synthase of Lactococcus lactis and dipicolinate synthase of Bacillus subtilis. A multiple alignment, a phylogenetic tree, and two signature sequences for this family, designated the TH-ADH-SDH or TAS superfamily, have been derived. Additionally, the TH family has been characterized. Phylogenetic analyses suggested that these proteins have evolved without inter-system shuffling. However, interdomain splicing-fusion events have occurred during the evolution of several of these systems. Analyses of the multiple alignment for the TH family revealed that domain conservation occurs in the order: NADP-binding domain (domain III) > NAD-binding domain (domain I) > proton-translocating transmembrane domain (domain II). A topologic model for the proton-translocating transmembrane domain consistent with published data is presented, and a possible involvement of specific transmembrane alpha-helical segments in channel formation is suggested. PMID:10587945

Studley, W K; Yamaguchi, M; Hatefi, Y; Saier, M H



Polyhedral geometry of phylogenetic rogue taxa.  


It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this "rogue taxon" effect. In this paper we characterize the behavior of balanced minimum evolution (BME) phylogenetics on data sets of this type using tools from polyhedral geometry. First we show that for any distance matrix there exist distances to a "rogue taxon" such that the BME-optimal tree for the data set with the new taxon does not contain any nontrivial splits (bipartitions) of the optimal tree for the original data. Second, we prove a theorem which restricts the topology of BME-optimal trees for data sets of this type, thus showing that a rogue taxon cannot have an arbitrary effect on the optimal tree. Third, we computationally construct polyhedral cones that give complete answers for BME rogue taxon behavior when our original data fits a tree on four, five, and six taxa. We use these cones to derive sufficient conditions for rogue taxon behavior for four taxa, and to understand the frequency of the rogue taxon effect via simulation. PMID:20640527

Cueto, María Angélica; Matsen, Frederick A



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



Anatomical Brain Images Alone Can Accurately Diagnose Chronic Neuropsychiatric Illnesses  

PubMed Central

Objective Diagnoses using imaging-based measures alone offer the hope of improving the accuracy of clinical diagnosis, thereby reducing the costs associated with incorrect treatments. Previous attempts to use brain imaging for diagnosis, however, have had only limited success in diagnosing patients who are independent of the samples used to derive the diagnostic algorithms. We aimed to develop a classification algorithm that can accurately diagnose chronic, well-characterized neuropsychiatric illness in single individuals, given the availability of sufficiently precise delineations of brain regions across several neural systems in anatomical MR images of the brain. Methods We have developed an automated method to diagnose individuals as having one of various neuropsychiatric illnesses using only anatomical MRI scans. The method employs a semi-supervised learning algorithm that discovers natural groupings of brains based on the spatial patterns of variation in the morphology of the cerebral cortex and other brain regions. We used split-half and leave-one-out cross-validation analyses in large MRI datasets to assess the reproducibility and diagnostic accuracy of those groupings. Results In MRI datasets from persons with Attention-Deficit/Hyperactivity Disorder, Schizophrenia, Tourette Syndrome, Bipolar Disorder, or persons at high or low familial risk for Major Depressive Disorder, our method discriminated with high specificity and nearly perfect sensitivity the brains of persons who had one specific neuropsychiatric disorder from the brains of healthy participants and the brains of persons who had a different neuropsychiatric disorder. Conclusions Although the classification algorithm presupposes the availability of precisely delineated brain regions, our findings suggest that patterns of morphological variation across brain surfaces, extracted from MRI scans alone, can successfully diagnose the presence of chronic neuropsychiatric disorders. Extensions of these methods are likely to provide biomarkers that will aid in identifying biological subtypes of those disorders, predicting disease course, and individualizing treatments for a wide range of neuropsychiatric illnesses.

Bansal, Ravi; Staib, Lawrence H.; Laine, Andrew F.; Hao, Xuejun; Xu, Dongrong; Liu, Jun; Weissman, Myrna; Peterson, Bradley S.



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.



Phylogeny and classification of the Catantopidae at the tribal level (Orthoptera, Acridoidea)  

PubMed Central

Abstract The grasshopper family Catantopidae is a well-known group, whose members include some of the most notorious agricultural pests. The existing classifications of the family are mostly utilitarian rather than being based on phylogenetic analysis and therefore unable to provide the stability desired for such an economically important group. In the present study, we present the first comprehensive phylogenetic analysis of the family based on morphology. By extensively sampling from the Chinese fauna, we included in the present analysis multiple representatives of each of the previously recognized tribes in the family. In total, we examined 94 genera represented by 240 species and evaluated 116 characters, including 84 for external morphology and 32 for male genitalia. The final matrix consists of 86 ingroup taxa and 88 characters. Our phylogenetic analyses resulted in a high resolution of the basal relationships of the family while showed considerable uncertainty about the relationships among some crown taxa. We further evaluated the usefulness of morphological characters in phylogeny reconstruction of the catantopids by examining character fit to the shortest trees found, and contrary to previous suggestions, our results suggest that genitalia characters are not as informative as external morphology in inferring higher-level relationship. We further suggest that earlier classification systems of grasshoppers in general and Catantopidae in particular most probably consist of many groups that are not natural due the heavy reliance on genitalia features and need to be revised in the light of future phylogenetic studies. Finally, we outlined a tentative classification scheme based on the results of our phylogenetic analysis.

Li, Baoping; Liu, Zhiwei; Zheng, Zhe-Min



Application of molecular methods to classification and identification of bacteria of the genus Bifidobacterium  

Microsoft Academic Search

The molecular methods currently used in the classification and identification of bifidobacteria are reviewed. The sequencing\\u000a of the 16S rRNA gene and some other genes considered to be phylogenetic markers is a universal and effective approach for\\u000a taxonomic characterization of members of the genus Bifidobacterium and to reliable identification of new isolates. Various techniques of obtaining DNA fingerprints (PFGE, RAPD,

A. V. Sidarenka; G. I. Novik; V. N. Akimov



Evolution and Classification of P-loop Kinases and Related Proteins  

Microsoft Academic Search

Sequences and structures of all P-loop-fold proteins were compared with the aim of reconstructing the principal events in the evolution of P-loop-containing kinases. It is shown that kinases and some related proteins comprise a monophyletic assemblage within the P-loop NTPase fold. An evolutionary classification of these proteins was developed using standard phylogenetic methods, analysis of shared sequence and structural signatures,

Detlef D. Leipe; Eugene V. Koonin; L. Aravind



Noise-Tolerant Hyperspectral Signature Classification in Unresolved Object Detection with Adaptive Tabular Nearest Neighbor Encoding  

NASA Astrophysics Data System (ADS)

Accurate spectral signature classification is a crucial step in the nonimaging detection and recognition of spaceborne objects. In classical hyperspectral recognition applications, especially where linear mixing models are employed, signature classification accuracy depends on accurate spectral endmember discrimination. In selected target recognition (ATR) applications, previous non-adaptive techniques for signature classification have yielded class separation and classifier refinement results that tend to be suboptimal. In practice, the number of signatures accurately classified often depends linearly on the number of inputs. This can lead to potentially severe classification errors in the presence of noise or densely interleaved signatures. In this paper, we present an enhancement of an emerging technology for nonimaging spectral signature classification based on a highly accurate, efficient search engine called Tabular Nearest Neighbor Encoding (TNE). Adaptive TNE can optimize its classifier performance to track input nonergodicities and yield measures of confidence or caution for evaluation of classification results. Unlike neural networks, TNE does not have a hidden intermediate data structure (e.g., a neural net weight matrix). Instead, TNE generates and exploits a user-accessible data structure called the agreement map (AM), which can be manipulated by Boolean logic operations to effect accurate classifier refinement through programmable algorithms. The open architecture and programmability of TNE's pattern-space (AM) processing allows a TNE developer to determine the qualitative and quantitative reasons for classification accuracy, as well as characterize in detail the signatures for which TNE does not obtain classification matches, and why such mis-matches occur. In this study AM-based classification has been modified to partially compensate for input statistical changes, in response to performance metrics such as probability of correct classification (Pd) and rate of false detections (Rfa). Adaptive TNE can thus achieve accurate signature classification in the presence of time-varying noise, closely spaced or interleaved signatures, and imaging system optical distortions. We analyze classification accuracy of closely spaced spectral signatures adapted from a NASA database of space material signatures. Additional analysis pertains to computational complexity and noise sensitivity, which are superior to non-adaptive TNE or Bayesian techniques based on classical neural networks.

Schmalz, M.; Key, G.


Accurate force measurement using optical interferometer  

NASA Astrophysics Data System (ADS)

The present status and the future prospects of a method for accurate force measurement, the levitation mass method (LMM), is reviewed. The LMM has been proposed and improved by the authors. In the LMM, the inertial force of a mass levitated using an aero-static linear bearing is used as the reference/known force applied to the objects under test, such as force transducers, materials or structures. The inertial force of the levitated mass is measured using an optical interferometer. Since the force is one of the most major physical quantities, the application of the LMM as the most accurate dynamic force measurement method is very wide.

Fujii, Yusaku



SLC classification: an update.  


The 386 human SLC superfamily members are diverse in sequence, structure, and function. Using sequence similarity, we previously classified the SLC superfamily members and identified relationships among families. With the recent determination of new SLC structures and identification of previously unknown human SLC families, an update of our previous classification is timely. Here, we comprehensively compare the SLC sequences and structures and discuss the applicability of structure-based ligand discovery to key SLC members. PMID:23778706

Schlessinger, A; Yee, S W; Sali, A; Giacomini, K M



Sentiment Classification across Domains  

Microsoft Academic Search

In this paper we consider the problem of building models that have high sentiment classification accuracy without the aid\\u000a of a labeled dataset from the target domain. For that purpose, we present and evaluate a novel method based on level of abstraction\\u000a of nouns. By comparing high-level features (e.g. level of affective words, level of abstraction of nouns) and low-level

Dinko Lambov; Gaël Dias; Veska Noncheva



Koppen Classification Flow Chart  

NSDL National Science Digital Library

This flow chart presents the climate classification system developed in the early 1900s by German climatologist and amateur botanist Wladimir Koppen. The system establishes six climate zones (denoted by letters) described in terms of average monthly temperature and precipitation. The outline also includes examples of locations which are in a particular zone, controlling factors that contribute to the climate in a zone, and distinguishing characteristics.

Kimmel, Troy M.



Vasculitis: Classification and Management  

PubMed Central

Vasculitis, which is pathologically an inflammatory or necrotic state of blood vessels, consists of a diverse group of disesases. The clinical manifestations of vasculitis vary greatly in severity. The simplified classification described in this article is geared toward recognizing the degree of severity of the vasculitic process so that appropriate management can be initiated expeditiously. Emphasis is placed on the vasculitides likely to be encountered in general practice. ImagesFigure 1Figure 2Figure 3Figure 4Figure 5

Anastassiades, T.P.



Classification and audiovisuals.  


The University of Connecticut Health Center Library's substantial investment in audiovisuals has prompted careful examination of its organization of the AV collection and its effectiveness in answering user needs. While an accession number system worked for a small collection, increased size quickly generated access problems, especially because shelves are open to users. With the present collection of over 2,500 audiovisual items, adoption of the NLM classification promises convenient and continued flexibility in the future. PMID:66078

Brantz, M H; Forsman, R



Trichromatic opponent color classification  

Microsoft Academic Search

Stimuli varying in intensity and chromaticity, presented on numerous backgrounds, were classified into red\\/green, blue\\/yellow and white\\/black opponent color categories. These measurements revealed the shapes of the boundaries that separate opponent colors in three-dimensional color space. Opponent color classification boundaries were generally not planar, but their shapes could be summarized by a piecewise linear model in which increment and decrement

E. J. Chichilnisky; Brian A. Wandell



Visualizing Galaxy Zoo Classifications  

NASA Astrophysics Data System (ADS)

Galaxy Zoo is a web-based collaborative effort examining Sloan Digital Sky Survey images. In order to make use of the large volume of data generated by SDSS, the task of morphological classification is distributed amongst numerous volunteers via the Galaxy Zoo website. In addition to single galaxy classification, comparative data is also collected through Galaxy Wars. Galaxy Wars seeks to determine why some galaxies have more prominent spirals or bars than others. To avoid biases that naturally affect these visual comparisons, the sample is divided into groups of similar size, brightness, and distance. Volunteers are then asked to judge which of the two selected galaxies exhibits more prominent spiral or bar features. By means of this process, an aggregate ranking system is created. In this poster, a time series visualization is used to understand the process in which galaxy classifications and feature prominence rankings are constructed. By representing galaxy location in an area-preserving projection, spatial relationships can be linked with both features and morphology. Additionally, the interface allows for exploration of redshift / spectral data and provides details on demand for any of the galaxies within the sample.

Parrish, Michael



Seismic event classification system  


In the computer interpretation of seismic data, the critical first step is to identify the general class of an unknown event. For example, the classification might be: teleseismic, regional, local, vehicular, or noise. Self-organizing neural networks (SONNs) can be used for classifying such events. Both Kohonen and Adaptive Resonance Theory (ART) SONNs are useful for this purpose. Given the detection of a seismic event and the corresponding signal, computation is made of: the time-frequency distribution, its binary representation, and finally a shift-invariant representation, which is the magnitude of the two-dimensional Fourier transform (2-D FFT) of the binary time-frequency distribution. This pre-processed input is fed into the SONNs. These neural networks are able to group events that look similar. The ART SONN has an advantage in classifying the event because the types of cluster groups do not need to be pre-defined. The results from the SONNs together with an expert seismologist's classification are then used to derive event classification probabilities. 21 figures.

Dowla, F.U.; Jarpe, S.P.; Maurer, W.



[Myelodysplastic syndrome classification].  


Myelodysplastic syndromes (MDS) are myeloid disorders with various clinical and biological presentations. The French-American-British (FAB-1982) classification included five categories basing on morphology and bone marrow blast count. Three criteria are taken into account: 1) the percentage of blasts in peripheral blood and bone marrow, 2) the percentage of ringed sideroblasts, and 3) the number of monocytes in peripheral blood. The World Health Organization classification (WHO 2001, 2008) modifies the FAB system by also taking cytogenetic characteristics and molecular biology into consideration. The last classification (WHO-2008) takes into account: 1) the number of peripheral cytopenia, 2) the percentage of blasts in peripheral blood and bone marrow, 3) the percentage of ringed sideroblasts, 4) the possible presence of Auer Rods, and 5) the detection of a cytogenetic abnormality (the isolated 5q deletion). The following subgroups are defined: refractory cytopenia with unilineage dysplasia, refractory anemia with ringed sideroblasts, refractory cytopenia with multilineage dysplasia, refractory anemia with excess blasts, myelodysplastic syndrome unclassifiable and myelodysplastic syndrome with isolated del(5q). PMID:23587576

Ghariani, Ines; Braham, Najia; Hassine, Mohsen; Kortas, Mondher


Multispectral rock-type separation and classification.  

SciTech Connect

This paper explores the possibility of separating and classifying remotely-sensed multispectral data from rocks and minerals onto seven geological rock-type groups. These groups are extracted from the general categories of metamorphic, igneous and sedimentary rocks. The study is performed under ideal conditions for which the data is generated according to laboratory hyperspectral data for the members, which are, in turn, passed through the Multi-spectral Thermal Imager (MTI) filters yielding 15 bands. The main challenge in separability is the small size of the training data sets, which initially did not permit direct application of Bayesian decision theory. To enable Bayseian classification, the original training data is linearly perturbed with the addition minerals, vegetation, soil, water and other valid impurities. As a result, the size of the training data is significantly increased and accurate estimates of the covariance matrices are achieved. In addition, a set of reduced (five) linearly-extracted canonical features that are optimal in providing the most important information about the data is determined. An alternative nonlinear feature-selection method is also employed based on spectral indices comprising a small subset of all possible ratios between bands. By applying three optimization strategies, combinations of two and three ratios are found that provide reliable separability and classification between all seven groups according to the Bhattacharyya distance. To set a benchmark to which the MTI capability in rock classification can be compared, an optimization strategy is performed for the selection of optimal multispectral filters, other than the MTI filters, and an improvement in classification is predicted.

Moya, Mary M.; Fogler, Robert Joseph; Paskaleva, Biliana (University of New Mexico, Albuquerque, NM); Hayat, Majeed M. (University of New Mexico, Albuquerque, NM)



Embedding filtering criteria into a wrapper marker selection method for brain tumor classification: an application on metabolic peak area ratios  

Microsoft Academic Search

The purpose of this study is to identify reliable sets of metabolic markers that provide accurate classification of complex brain tumors and facilitate the process of clinical diagnosis. Several ratios of metabolites are tested alone or in combination with imaging markers. A wrapper feature selection and classification methodology is studied, employing Fisher's criterion for ranking the markers. The set of

M. G. Kounelakis; M. E. Zervakis; G. C. Giakos; G. J. Postma; L. M. C. Buydens; X. Kotsiakis



Hypothesis: Alzheimer's disease is a phylogenetic disease.  


It is hypothesized that Alzheimer's disease is a human phylogenetic disease which has a common multifactorial pathogenesis in sporadic and familial cases and in Down syndrome, related to a genomic character function G(x). Increments in G(x) accompanied the increased gene expression that sustained brain growth and differentiation during hominid evolution, particularly of the regions liable to Alzheimer pathology, and further occur in Down syndrome [suggesting that genes on chromosome 21 are included in G(x)]. If genes which promoted human brain evolution contribute to the value of G(x), a better understanding of the genomic events which promoted this evolution, using molecular biological techniques, should elucidate the genetic basis of Alzheimer's disease, and vice versa. PMID:2528670

Rapoport, S I



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



Phylogenetic and Biochemical Studies on Stomatococcus mucilaginosus.  


The degree of relatedness of nine strains of Stomatococcus mucilaginosus (formerly classified as 'Micrococcus mucilaginosus') was investigated by deoxyribonucleic acid hybridization. We confirm that all strains are highly related. Differences in the peptidoglycan type and the cytochrome pattern between S. mucilaginosus and members of Micrococcus, together with the results of 23 S ribosomal ribonucleic acid cistron similarity studies and the analysis of the 16S ribosomal ribonucleic acid support the exclusion of this species from the genus Micrococcus and justifies its reclassification as a member of a new genus, Stomatococcus (Bergan and Kocur, 1982). Phylogenetically, S. mucilaginosus represents an independent line of descent within a broad group of Gram-positive bacteria that contains arthrobacteria, micrococci, cellulomonads, brevibacteria and microbacteria. PMID:23194594

Stackebrandt, E; Scheuerlein, C; Schleifer, K H



A new balance index for phylogenetic trees.  


Several indices that measure the degree of balance of a rooted phylogenetic tree have been proposed so far in the literature. In this work we define and study a new index of this kind, which we call the total cophenetic index: the sum, over all pairs of different leaves, of the depth of their lowest common ancestor. This index makes sense for arbitrary trees, can be computed in linear time and it has a larger range of values and a greater resolution power than other indices like Colless' or Sackin's. We compute its maximum and minimum values for arbitrary and binary trees, as well as exact formulas for its expected value for binary trees under the Yule and the uniform models of evolution. As a byproduct of this study, we obtain an exact formula for the expected value of the Sackin index under the uniform model, a result that seems to be new in the literature. PMID:23142312

Mir, Arnau; Rosselló, Francesc; Rotger, Luc? A



Inferring phylogenetic networks from gene order data.  


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. PMID:24069602

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



[Phylogenetic reconstruction of DNA polymerase X family].  


Phylogeny within DNA polymerase X family requires a re-examination as the expansion of family members, particularly considering the enter of two entomopoxvirus(EPV) members. A total of 37 DNA polymerase core-domain sequences(SMART domain), which come from numerous species with different evolutional levels, including above two virus members, were analyzed. The result showed that, the phylogenetic relationship within this family basically assorted with the distribution status of used species, of which two virus members and DNA polymerase beta(pol beta) of eukaryote were clustered together into sister group, indicating the likelihood that the two entomopoxviruses originated from eukaryote. The divergence time of subgroups, similarity of gene structure and conservation of syntenic genes were also analyzed, and evidences showed that, DNA polymerase mu (pol mu) is only present in Mammals, and as a recently occured duplication-gene of terminal deoxynucleotidyl transferase(TdT). PMID:14577380

Zhu, Xin-Yu



Fast Structural Search in Phylogenetic Databases  

PubMed Central

As the size of phylogenetic databases grows, the need for efficiently searching these databases arises. Thanks to previous and ongoing research, searching by attribute value and by text has become commonplace in these databases. However, searching by topological or physical structure, especially for large databases and especially for approximate matches, is still an art. We propose structural search techniques that, given a query or pattern tree P and a database of phylogenies D, find trees in D that are sufficiently close to P. The “closeness” is a measure of the topological relationships in P that are found to be the same or similar in a tree D in D. We develop a filtering technique that accelerates searches and present algorithms for rooted and unrooted trees where the trees can be weighted or unweighted. Experimental results on comparing the similarity measure with existing tree metrics and on evaluating the efficiency of the search techniques demonstrate that the proposed approach is promising.

Wang, Jason T. L.; Shan, Huiyuan; Shasha, Dennis; Piel, William H.



Accurate time-frequency-wavenumber analysis to study coda waves  

NASA Astrophysics Data System (ADS)

An accurate method is developed to characterize the seismic coda phases recorded by small-aperture arrays. The coda is modelled as a superposition of several interfering wavelets identified by their arrival time, frequency content, backazimuth and apparent velocity of propagation. The wavelets are caused by the diffraction and refraction of the direct wavefield by heterogeneities of the propagation medium. The deterministic modelling is different from the statistical one generally used to retrieve mean parameters of the medium. As the complexity of the medium increases, separation of interfering wavelets needs an accurate time-frequency-wavenumber decomposition method that consists of detection and characterization of the different coherent wavelets propagating through the array. Detection is realized by mean time-frequency decomposition, based on the ridges algorithm. The MUltiple SIgnal Classification (MUSIC) algorithm, allowing a higher separation of simultaneous wavelets in the wavenumber domain, is then used to characterize the propagation parameters of the detected components. An optimal use of the MUSIC algorithm assumes the knowledge of the number of sources that simultaneously propagate through the array. The new iterative technique presented here allows the automatic determination of this number of sources. This methodology is applied to synthetic signals simulated in a heterogeneous medium. Results obtained show that: (i) the diffracted wavefield may be more energetic than the primary direct one and (ii) the relative energy diffracted by each heterogeneity is strongly dependent on the location of the array within the medium. The well-controlled results obtained for the synthetic examples allow interpretations of the observations made during the Annot experiment in the southern French Alps in 1998, where four small-aperture arrays were deployed, with small distances between each array (~10 km). The time-azimuth-velocity evolutions determined for the earthquakes recorded during this experiment are used to characterize the heterogeneous structures of the medium.

Schisselé, Estelle; Guilbert, Jocelyn; Gaffet, Stéphane; Cansi, Yves



Finding Single Copy Genes Out of Sequenced Genomes for Multilocus Phylogenetics in Non-Model Fungi  

PubMed Central

Historically, fungal multigene phylogenies have been reconstructed based on a small number of commonly used genes. The availability of complete fungal genomes has given rise to a new wave of model organisms that provide large number of genes potentially useful for building robust gene genealogies. Unfortunately, cross-utilization of these resources to study phylogenetic relationships in the vast majority of non-model fungi (i.e. “orphan” species) remains an unexamined question. To address this problem, we developed a method coupled with a program named “PHYLORPH” (PHYLogenetic markers for ORPHans). The method screens fungal genomic databases (107 fungal genomes fully sequenced) for single copy genes that might be easily transferable and well suited for studies at low taxonomic levels (for example, in species complexes) in non-model fungal species. To maximize the chance to target genes with informative regions, PHYLORPH displays a graphical evaluation system based on the estimation of nucleotide divergence relative to substitution type. The usefulness of this approach was tested by developing markers in four non-model groups of fungal pathogens. For each pathogen considered, 7 to 40% of the 10–15 best candidate genes proposed by PHYLORPH yielded sequencing success. Levels of polymorphism of these genes were compared with those obtained for some genes traditionally used to build fungal phylogenies (e.g. nuclear rDNA, ?-tubulin, ?-actin, Elongation factor EF-1?). These genes were ranked among the best-performing ones and resolved accurately taxa relationships in each of the four non-model groups of fungi considered. We envision that PHYLORPH will constitute a useful tool for obtaining new and accurate phylogenetic markers to resolve relationships between closely related non-model fungal species.

Feau, Nicolas; Decourcelle, Thibaut; Husson, Claude; Desprez-Loustau, Marie-Laure; Dutech, Cyril



A phylogenetic approach to mapping cell fate.  


Recent, surprising, and controversial discoveries have challenged conventional concepts regarding the origins and plasticity of stem cells, and their contributions to tissue regeneration, and highlight just how little is known about mammalian development in comparison to simpler model organisms. In the case of the transparent worm, Caenorhabditis elegans, Sulston and colleagues used a microscope to record the birth and death of every cell during its life, and the compilation of this "fate map" represents a milestone achievement of developmental biology. Determining a fate map for mammals or other higher organisms is more complicated because they are opaque, take a long time to mature, and have a tremendous number of cells. Consequently, fate mapping experiments have relied on tagging a progenitor cell with a dye or genetic marker in order to later identify its descendants. This approach, however, extracts little information because it demonstrates that a population of cells, all having inherited the same label, shares a common ancestor, but it does not reveal how cells in that population are related to one another. To avoid that problem, as well as technical limitations of current methods for mapping cell fate, we, and others, have developed a new strategy for retrospectively deriving cell fate maps by using phylogenetics to infer the order in which somatic mutations have arisen in the genomes of individual cells during development in multicellular organisms. DNA replication inevitably introduces mutations, particularly at repetitive sequences, every time a cell divides. It is thus possible to deduce the history of cell divisions by cataloging somatic mutations and phylogenetically reconstructing cell lineage. This approach has the potential to produce a complete mammalian cell fate map that, in principle, could describe the developmental lineage of any cell and help resolve outstanding questions of stem cell biology, tissue repair and maintenance, and aging. PMID:17498550

Salipante, Stephen J; Horwitz, Marshall S



Software Estimation: Developing an Accurate, Reliable Method.  

National Technical Information Service (NTIS)

From a management perspective, it is essential that software estimates used in a TSP launch are as accurate as possible. Significant growth due to estimation inaccuracy can wreak havoc on a team attempting to stay within cost and schedule while executing ...

B. Hodgins B. Sinclair C. Rickets



Fluorine Compatible Apparatus for Accurate Pvt Measurements.  

National Technical Information Service (NTIS)

A fluorine compatible apparatus, incorporating numerous safety features, is described. This apparatus has been used to make accurate determinations of the PVT properties of gaseous and liquid fluorine from 53.5 K (the triple point) to 300 K and to pressur...

G. C. Straty R. Prydz



Accurate hydrocarbon estimates attained with radioactive isotope  

Microsoft Academic Search

To make accurate economic evaluations of new discoveries, an oil company needs to know how much gas and oil a reservoir contains. The porous rocks of these reservoirs are not completely filled with gas or oil, but contain a mixture of gas, oil and water. It is extremely important to know what volume percentage of this water--called connate water--is contained




Mean shift for accurate license plate localization  

Microsoft Academic Search

This paper presents a region-based algorithm for accurate license plate localization, where mean shift is utilized to filter and segment color vehicle images into candidate regions. Three features are extracted in order to decide whether a candidate region represents a real license plate, namely, rectangularity, aspect ratio, and edge density. Then, the Mahalanobis classifier is used with respect to above

Wenjing Jia; Huaifeng Zhang; Xiangjian He; M. Piccardi



Accurate Assessment--Compelling Evidence for Practice  

ERIC Educational Resources Information Center

Childhood overweight and obesity is a public health concern not just because of its growing prevalence but also for its serious and lasting health consequences. Though height and weight measures are easy to obtain and New Hampshire Head Start sites measure height and weight of their enrollees, there are numerous challenges related to accurate

Flynn, Regina T.; Anderson, Ludmila; Martin, Nancy R.



How Accurately can we Calculate Thermal Systems?  

Microsoft Academic Search

I would like to determine how accurately a variety of neutron transport code packages (code and cross section libraries) can calculate simple integral parameters, such as K{sub eff}, for systems that are sensitive to thermal neutron scattering. Since we will only consider theoretical systems, we cannot really determine absolute accuracy compared to any real system. Therefore rather than accuracy, it

D Cullen; R N Blomquist; C Dean; D Heinrichs; M A Kalugin; M Lee; Y Lee; R MacFarlan; Y Nagaya; A Trkov



The Accurate Hose Model for VPN Provisioning  

Microsoft Academic Search

This work considers the problem of VPN provisioning, focusing on the process of dimensioning the links belonging to the route that connects VPN endpoints, according to the specified traffic demands. To accomplish this, we propose a new model, the Accurate Hose, which can take into consideration a complete or partial traffic matrix and supports group based bandwidth requirements, while maintaining

Dênio Mariz; Judith Kelner; Djamel Sadok; Carlos A. Kamienski


Accurate planar area and contour length measurement  

Microsoft Academic Search

This paper describes a technique for accurately estimating the area and contour length of a planar non-polygonal region in the scene. The approach taken is to formulate a continuous model of the boundary of the region in the scene and use the image data to estimate the parameters of the model. The required information is then extracted from the model

R. J. Valkenburg; R. Kakarala



Accurate Assessment--Compelling Evidence for Practice  

ERIC Educational Resources Information Center

|Childhood overweight and obesity is a public health concern not just because of its growing prevalence but also for its serious and lasting health consequences. Though height and weight measures are easy to obtain and New Hampshire Head Start sites measure height and weight of their enrollees, there are numerous challenges related to accurate

Flynn, Regina T.; Anderson, Ludmila; Martin, Nancy R.



Simple accurate expressions for planar spiral inductances  

Microsoft Academic Search

We present several new simple and accurate expressions for the DC inductance of square, hexagonal, octagonal, and circular spiral inductors. We evaluate the accuracy of our expressions, as well as several previously published inductance expressions, in two ways: by comparison with three-dimensional field solver predictions and by comparison with our own measurements, and also previously published measurements. Our simple expression

Sunderarajan S. Mohan; Maria del Mar Hershenson; Stephen P. Boyd; Thomas H. Lee



Accurate Astrometry in the Solar System  

Microsoft Academic Search

The U.S. Naval Observatory Flagstaff Station (NOFS) has been providing highly accurate astrometry to the Solar Systems Dynamics (SSD) group at JPL since 1991, in support of numerous planetary missions and observing efforts. In 2005, NOFS began a new phase of this work by expanding the range of possible targets, investigating the magnitude variability of asteroids observed at NOFS, and

Alice K. B. Monet



An Accurate Analog Ferrite Phase Shifter  

Microsoft Academic Search

An analog ferrite phase shifter has been developed for applications requiring an accurate relationship between phase shift and control current. A prototype unit is described that operates over a 1.3 GHz. range at X-band with VSWR under 1.2:1, loss under 1 dB., hysteresis at ±1 degree, and negligible frequency dispersion of phase shift.

C. R. Boyd




Microsoft Academic Search

Infrared (IR) radiometry is a very useful form of temperature measurement. Its advantages over contact thermometry are that it has quick response times and it does not have to come in contact with the area being measured. One of its major drawbacks is that it not as accurate as contact thermometry. One of the major sources of this uncertainty is

Frank Liebmann


Phylogenetic relationships of the mockingbirds and thrashers (Aves: Mimidae)  

Microsoft Academic Search

The mockingbirds, thrashers and allied birds in the family Mimidae are broadly distributed across the Americas. Many aspects of their phylogenetic history are well established, but there has been no previous phylogenetic study that included all species in this radiation. Our reconstructions based on mitochondrial and nuclear DNA sequence markers show that an early bifurcation separated the Mimidae into two

Irby J. Lovette; Brian S. Arbogast; Robert L. Curry; Robert M. Zink; Carlos A. Botero; John P. Sullivan; Amanda L. Talaba; Rebecca B. Harris; Dustin R. Rubenstein; Robert E. Ricklefs; Eldredge Bermingham


Fuzzy Clustering improves Phylogenetic Relationships Reconstruction from Metabolic Pathways  

Microsoft Academic Search

The interest in reconstructing phy- logenetic relationships from data on structural similarity of metabolic pathways is growing. The similarity notions and the techniques involved in this reconstruction are assessed by building phylogenetic relationships for model sets of organisms from the similarity measures of the same metabolic pathway for all of them, and then the phylogenetic trees ob- tained are compared

Jaume Casasnovas; C. Clemente; Francesc Rossell; Kenji Satou; Gabriel Valiente


Developmental Data and Phylogenetic Systematics: Evolution of the Vertebrate Limb  

Microsoft Academic Search

SYNOPSIS. Among the primary contributions of phylogenetic systematics to the synthesis of developmental biology and evolution are phylogenetic hypotheses. Phy- logenetic hypotheses are critical in interpreting the patterns of evolution of devel- opmental genes and processes, as are morphological data. Using a robust phylog- eny, the evolutionary history of individual morphological or developmental fea- tures can be traced and ancestral

Paula M. Mabee



Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges  

PubMed Central

Biodiversity conservation addresses information challenges through estimations encapsulated in measures of diversity. A quantitative measure of phylogenetic diversity, “PD”, has been defined as the minimum total length of all the phylogenetic branches required to span a given set of taxa on the phylogenetic tree (Faith 1992a). While a recent paper incorrectly characterizes PD as not including information about deeper phylogenetic branches, PD applications over the past decade document the proper incorporation of shared deep branches when assessing the total PD of a set of taxa. Current PD applications to macroinvertebrate taxa in streams of New South Wales, Australia illustrate the practical importance of this definition. Phylogenetic lineages, often corresponding to new, “cryptic”, taxa, are restricted to a small number of stream localities. A recent case of human impact causing loss of taxa in one locality implies a higher PD value for another locality, because it now uniquely represents a deeper branch. This molecular-based phylogenetic pattern supports the use of DNA barcoding programs for biodiversity conservation planning. Here, PD assessments side-step the contentious use of barcoding-based “species” designations. Bio-informatics challenges include combining different phylogenetic evidence, optimization problems for conservation planning, and effective integration of phylogenetic information with environmental and socio-economic data.

Faith, Daniel P.; Baker, Andrew M.



Molecular evolutionary phylogenetic trees based on minimum description length principle  

Microsoft Academic Search

Ever since the discovery of a molecular clock, many methods have been developed to reconstruct the molec- ular evolutionary phylogenetic trees. In this paper, we deal with this problem from the viewpoint of an induc- tive inference and apply Rissanen's minimum descrip- tion length principle to extract the minimum complex- sty phylogenetic tree. OUT method describes the com- plexity of

Fengrong Ren; Hiroshi Tanaka; Noria Fukuda; Takashi Gojobori



Application of COI Sequences in Studies of Phylogenetic Relationships Among 40 Apionidae Species  

PubMed Central

The systematics of the family Apionidae, as well as the superfamily Curculionoidea, is currently in a state of flux. The comparative analyses of COI sequences from our studies shed some light on the systematics of these weevils. To study the relationship among the organisms of the family Apionidae, we determined the COI sequences of representatives of 23 species and 15 genera, i.e., Apion, Betulapion, Catapion, Ceratapion, Cyanapion, Eutrichapion, Exapion, Hemitrichapion, Holotrichapion, Ischnopterapion, Protapion, Pseudoperapion, Psudoprotapion, Pseudostenapion, and Stenopterapion. Then, they were compared with the COI sequences of 19 species and eight genera from GenBank (Aspidapion, Ceratapion, Exapion, Ischnopterapion, Lepidapion, Omphalapion, Oxystoma, and Protapion). The phylogenetic relationships inferred from molecular data are similar to the classification system developed by Alonso-Zarazaga and Lyal (1999), with some exceptions within the tribe Oxystomatini, and genera Ceratapion and Exapion.

Ptaszynska, Aneta A.; Letowski, Jacek; Gnat, Sebastian; Malek, Wanda



Phylogenetic relationships among eighteen neotropical Culicini species.  


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



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


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



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.



Feedback about More Accurate versus Less Accurate Trials: Differential Effects on Self-Confidence and Activation  

ERIC Educational Resources Information Center

|One purpose of the present study was to examine whether self-confidence or anxiety would be differentially affected by feedback from more accurate rather than less accurate trials. The second purpose was to determine whether arousal variations (activation) would predict performance. On Day 1, participants performed a golf putting task under one…

Badami, Rokhsareh; VaezMousavi, Mohammad; Wulf, Gabriele; Namazizadeh, Mahdi



Profiling sensor classification algorithm implementation on an embedded controller  

NASA Astrophysics Data System (ADS)

This paper provides a feasibility analysis and details of implementing a classification algorithm on an embedded controller for use with a profiling sensor. Such a profiling sensor has been shown to be a feasible approach to a low-cost persistent surveillance sensor for classifying moving objects such as humans, animals, or vehicles. The sensor produces data that can be used to generate object profiles as crude images or silhouettes, and/or the data can be subsequently automatically classified. This paper provides a feasibility analysis of a classification algorithm implemented on an embedded controller, which is packaged with a prototype version of a profiling sensor. Implementation of the embedded controller is a necessary extension of previous work for fielded profiling sensors and their appropriate applications. Field data is used to confirm accurate automated classification.

Reynolds, Robert K.; Russomanno, David J.; Chari, Srikant K.; Halford, Carl E.