Annotation and Classification of CRISPR-Cas Systems.

Science.gov (United States)

Makarova, Kira S; Koonin, Eugene V

2015-01-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) is a prokaryotic adaptive immune system that is represented in most archaea and many bacteria. Among the currently known prokaryotic defense systems, the CRISPR-Cas genomic loci show unprecedented complexity and diversity. Classification of CRISPR-Cas variants that would capture their evolutionary relationships to the maximum possible extent is essential for comparative genomic and functional characterization of this theoretically and practically important system of adaptive immunity. To this end, a multipronged approach has been developed that combines phylogenetic analysis of the conserved Cas proteins with comparison of gene repertoires and arrangements in CRISPR-Cas loci. This approach led to the current classification of CRISPR-Cas systems into three distinct types and ten subtypes for each of which signature genes have been identified. Comparative genomic analysis of the CRISPR-Cas systems in new archaeal and bacterial genomes performed over the 3 years elapsed since the development of this classification makes it clear that new types and subtypes of CRISPR-Cas need to be introduced. Moreover, this classification system captures only part of the complexity of CRISPR-Cas organization and evolution, due to the intrinsic modularity and evolutionary mobility of these immunity systems, resulting in numerous recombinant variants. Moreover, most of the cas genes evolve rapidly, complicating the family assignment for many Cas proteins and the use of family profiles for the recognition of CRISPR-Cas subtype signatures. Further progress in the comparative analysis of CRISPR-Cas systems requires integration of the most sensitive sequence comparison tools, protein structure comparison, and refined approaches for comparison of gene neighborhoods.

Annotation and Classification of CRISPR-Cas Systems

Science.gov (United States)

Makarova, Kira S.; Koonin, Eugene V.

2018-01-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) is a prokaryotic adaptive immune system that is represented in most archaea and many bacteria. Among the currently known prokaryotic defense systems, the CRISPR-Cas genomic loci show unprecedented complexity and diversity. Classification of CRISPR-Cas variants that would capture their evolutionary relationships to the maximum possible extent is essential for comparative genomic and functional characterization of this theoretically and practically important system of adaptive immunity. To this end, a multipronged approach has been developed that combines phylogenetic analysis of the conserved Cas proteins with comparison of gene repertoires and arrangements in CRISPR-Cas loci. This approach led to the current classification of CRISPR-Cas systems into three distinct types and ten subtypes for each of which signature genes have been identified. Comparative genomic analysis of the CRISPR-Cas systems in new archaeal and bacterial genomes performed over the 3 years elapsed since the development of this classification makes it clear that new types and subtypes of CRISPR-Cas need to be introduced. Moreover, this classification system captures only part of the complexity of CRISPR-Cas organization and evolution, due to the intrinsic modularity and evolutionary mobility of these immunity systems, resulting in numerous recombinant variants. Moreover, most of the cas genes evolve rapidly, complicating the family assignment for many Cas proteins and the use of family profiles for the recognition of CRISPR-Cas subtype signatures. Further progress in the comparative analysis of CRISPR-Cas systems requires integration of the most sensitive sequence comparison tools, protein structure comparison, and refined approaches for comparison of gene neighborhoods. PMID:25981466

Phylogenetic classification of the world's tropical forests

DEFF Research Database (Denmark)

Slik, J. W. Ferry; Franklin, Janet; Arroyo-Rodriguez, Victor

2018-01-01

-Pacific counterparts. We also find indications for the existence of a global dry forest region, with representatives in America, Africa, Madagascar, and India. Additionally, a northern-hemisphere Subtropical forest region was identified with representatives in Asia and America, providing support for a link between......Knowledge about the biogeographic affinities of the world's tropical forests helps to better understand regional differences in forest structure, diversity, composition, and dynamics. Such understanding will enable anticipation of region-specific responses to global environmental change. Modern...... phylogenies, in combination with broad coverage of species inventory data, now allow for global biogeographic analyses that take species evolutionary distance into account. Here we present a classification of the world's tropical forests based on their phylogenetic similarity. We identify five principal...

Awareness and use of Gross Motor Function Classification System ...

African Journals Online (AJOL)

Introduction The degree of disability in children with Cerebral Palsy (CP) can be evaluated with the Gross Motor Function Classification System (GMFCS), a valid tool which was designed for such purposes. However, there appears to be paucity of data on the awareness and use of the GMFCS particularly in the ...

Phylogenetic and functional diversity of metagenomic libraries of phenol degrading sludge from petroleum refinery wastewater treatment system.

Science.gov (United States)

Silva, Cynthia C; Hayden, Helen; Sawbridge, Tim; Mele, Pauline; Kruger, Ricardo H; Rodrigues, Marili Vn; Costa, Gustavo Gl; Vidal, Ramon O; Sousa, Maíra P; Torres, Ana Paula R; Santiago, Vânia Mj; Oliveira, Valéria M

2012-03-27

In petrochemical refinery wastewater treatment plants (WWTP), different concentrations of pollutant compounds are received daily in the influent stream, including significant amounts of phenolic compounds, creating propitious conditions for the development of particular microorganisms that can rapidly adapt to such environment. In the present work, the microbial sludge from a refinery WWTP was enriched for phenol, cloned into fosmid vectors and pyrosequenced. The fosmid libraries yielded 13,200 clones and a comprehensive bioinformatic analysis of the sequence data set revealed a complex and diverse bacterial community in the phenol degrading sludge. The phylogenetic analyses using MEGAN in combination with RDP classifier showed a massive predominance of Proteobacteria, represented mostly by the genera Diaphorobacter, Pseudomonas, Thauera and Comamonas. The functional classification of phenol degrading sludge sequence data set generated by MG-RAST showed the wide metabolic diversity of the microbial sludge, with a high percentage of genes involved in the aerobic and anaerobic degradation of phenol and derivatives. In addition, genes related to the metabolism of many other organic and xenobiotic compounds, such as toluene, biphenyl, naphthalene and benzoate, were found. Results gathered herein demonstrated that the phenol degrading sludge has complex phylogenetic and functional diversities, showing the potential of such community to degrade several pollutant compounds. This microbiota is likely to represent a rich resource of versatile and unknown enzymes which may be exploited for biotechnological processes such as bioremediation.

Developing and validating the Communication Function Classification System for individuals with cerebral palsy

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HIDECKER, MARY JO COOLEY; PANETH, NIGEL; ROSENBAUM, PETER L; KENT, RAYMOND D; LILLIE, JANET; EULENBERG, JOHN B; CHESTER, KEN; JOHNSON, BRENDA; MICHALSEN, LAUREN; EVATT, MORGAN; TAYLOR, KARA

2011-01-01

Aim The purpose of this study was to create and validate a Communication Function Classification System (CFCS) for children with cerebral palsy (CP) that can be used by a wide variety of individuals who are interested in CP. This paper reports the content validity, interrater reliability, and test–retest reliability of the CFCS for children with CP. Method An 11-member development team created comprehensive descriptions of the CFCS levels, and four nominal groups comprising 27 participants critiqued these levels. Within a Delphi survey, 112 participants commented on the clarity and usefulness of the CFCS. Interrater reliability was completed by 61 professionals and 68 parents/relatives who classified 69 children with CP aged 2 to 18 years. Test–retest reliability was completed by 48 professionals who allowed at least 2 weeks between classifications. The participants who assessed the CFCS were all relevant stakeholders: adults with CP, parents of children with CP, educators, occupational therapists, physical therapists, physicians, and speech–language pathologists. Results The interrater reliability of the CFCS was 0.66 between two professionals and 0.49 between a parent and a professional. Professional interrater reliability improved to 0.77 for classification of children older than 4 years. The test–retest reliability was 0.82. Interpretation The CFCS demonstrates content validity and shows very good test–retest reliability, good professional interrater reliability, and moderate parent–professional interrater reliability. Combining the CFCS with the Gross Motor Function Classification System and the Manual Ability Classification System contributes to a functional performance view of daily life for individuals with CP, in accordance with the World Health Organization’s International Classification of Functioning, Disability and Health. PMID:21707596

Towards a formal genealogical classification of the Lezgian languages (North Caucasus: testing various phylogenetic methods on lexical data.

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Alexei Kassian

Full Text Available A lexicostatistical classification is proposed for 20 languages and dialects of the Lezgian group of the North Caucasian family, based on meticulously compiled 110-item wordlists, published as part of the Global Lexicostatistical Database project. The lexical data have been subsequently analyzed with the aid of the principal phylogenetic methods, both distance-based and character-based: Starling neighbor joining (StarlingNJ, Neighbor joining (NJ, Unweighted pair group method with arithmetic mean (UPGMA, Bayesian Markov chain Monte Carlo (MCMC, Unweighted maximum parsimony (UMP. Cognation indexes within the input matrix were marked by two different algorithms: traditional etymological approach and phonetic similarity, i.e., the automatic method of consonant classes (Levenshtein distances. Due to certain reasons (first of all, high lexicographic quality of the wordlists and a consensus about the Lezgian phylogeny among Caucasologists, the Lezgian database is a perfect testing area for appraisal of phylogenetic methods. For the etymology-based input matrix, all the phylogenetic methods, with the possible exception of UMP, have yielded trees that are sufficiently compatible with each other to generate a consensus phylogenetic tree of the Lezgian lects. The obtained consensus tree agrees with the traditional expert classification as well as some of the previously proposed formal classifications of this linguistic group. Contrary to theoretical expectations, the UMP method has suggested the least plausible tree of all. In the case of the phonetic similarity-based input matrix, the distance-based methods (StarlingNJ, NJ, UPGMA have produced the trees that are rather close to the consensus etymology-based tree and the traditional expert classification, whereas the character-based methods (Bayesian MCMC, UMP have yielded less likely topologies.

Towards a formal genealogical classification of the Lezgian languages (North Caucasus): testing various phylogenetic methods on lexical data.

Science.gov (United States)

Kassian, Alexei

2015-01-01

A lexicostatistical classification is proposed for 20 languages and dialects of the Lezgian group of the North Caucasian family, based on meticulously compiled 110-item wordlists, published as part of the Global Lexicostatistical Database project. The lexical data have been subsequently analyzed with the aid of the principal phylogenetic methods, both distance-based and character-based: Starling neighbor joining (StarlingNJ), Neighbor joining (NJ), Unweighted pair group method with arithmetic mean (UPGMA), Bayesian Markov chain Monte Carlo (MCMC), Unweighted maximum parsimony (UMP). Cognation indexes within the input matrix were marked by two different algorithms: traditional etymological approach and phonetic similarity, i.e., the automatic method of consonant classes (Levenshtein distances). Due to certain reasons (first of all, high lexicographic quality of the wordlists and a consensus about the Lezgian phylogeny among Caucasologists), the Lezgian database is a perfect testing area for appraisal of phylogenetic methods. For the etymology-based input matrix, all the phylogenetic methods, with the possible exception of UMP, have yielded trees that are sufficiently compatible with each other to generate a consensus phylogenetic tree of the Lezgian lects. The obtained consensus tree agrees with the traditional expert classification as well as some of the previously proposed formal classifications of this linguistic group. Contrary to theoretical expectations, the UMP method has suggested the least plausible tree of all. In the case of the phonetic similarity-based input matrix, the distance-based methods (StarlingNJ, NJ, UPGMA) have produced the trees that are rather close to the consensus etymology-based tree and the traditional expert classification, whereas the character-based methods (Bayesian MCMC, UMP) have yielded less likely topologies.

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

Directory of Open Access Journals (Sweden)

Oliver Voigt

Full Text Available 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

Promoting consistent use of the communication function classification system (CFCS).

Science.gov (United States)

Cunningham, Barbara Jane; Rosenbaum, Peter; Hidecker, Mary Jo Cooley

2016-01-01

We developed a Knowledge Translation (KT) intervention to standardize the way speech-language pathologists working in Ontario Canada's Preschool Speech and Language Program (PSLP) used the Communication Function Classification System (CFCS). This tool was being used as part of a provincial program evaluation and standardizing its use was critical for establishing reliability and validity within the provincial dataset. Two theoretical foundations - Diffusion of Innovations and the Communication Persuasion Matrix - were used to develop and disseminate the intervention to standardize use of the CFCS among a cohort speech-language pathologists. A descriptive pre-test/post-test study was used to evaluate the intervention. Fifty-two participants completed an electronic pre-test survey, reviewed intervention materials online, and then immediately completed an electronic post-test survey. The intervention improved clinicians' understanding of how the CFCS should be used, their intentions to use the tool in the standardized way, and their abilities to make correct classifications using the tool. Findings from this work will be shared with representatives of the Ontario PSLP. The intervention may be disseminated to all speech-language pathologists working in the program. This study can be used as a model for developing and disseminating KT interventions for clinicians in paediatric rehabilitation. The Communication Function Classification System (CFCS) is a new tool that allows speech-language pathologists to classify children's skills into five meaningful levels of function. There is uncertainty and inconsistent practice in the field about the methods for using this tool. This study used combined two theoretical frameworks to develop an intervention to standardize use of the CFCS among a cohort of speech-language pathologists. The intervention effectively increased clinicians' understanding of the methods for using the CFCS, ability to make correct classifications, and

Assessing the relationships between phylogenetic and functional singularities in sharks (Chondrichthyes).

Science.gov (United States)

Cachera, Marie; Le Loc'h, François

2017-08-01

The relationships between diversity and ecosystem functioning have become a major focus of science. A crucial issue is to estimate functional diversity, as it is intended to impact ecosystem dynamics and stability. However, depending on the ecosystem, it may be challenging or even impossible to directly measure ecological functions and thus functional diversity. Phylogenetic diversity was recently under consideration as a proxy for functional diversity. Phylogenetic diversity is indeed supposed to match functional diversity if functions are conservative traits along evolution. However, in case of adaptive radiation and/or evolutive convergence, a mismatch may appear between species phylogenetic and functional singularities. Using highly threatened taxa, sharks, this study aimed to explore the relationships between phylogenetic and functional diversities and singularities. Different statistical computations were used in order to test both methodological issue (phylogenetic reconstruction) and overall a theoretical questioning: the predictive power of phylogeny for function diversity. Despite these several methodological approaches, a mismatch between phylogeny and function was highlighted. This mismatch revealed that (i) functions are apparently nonconservative in shark species, and (ii) phylogenetic singularity is not a proxy for functional singularity. Functions appeared to be not conservative along the evolution of sharks, raising the conservational challenge to identify and protect both phylogenetic and functional singular species. Facing the current rate of species loss, it is indeed of major importance to target phylogenetically singular species to protect genetic diversity and also functionally singular species in order to maintain particular functions within ecosystem.

Protein clustering and RNA phylogenetic reconstruction of the influenza A [corrected] virus NS1 protein allow an update in classification and identification of motif conservation.

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Sevilla-Reyes, Edgar E; Chavaro-Pérez, David A; Piten-Isidro, Elvira; Gutiérrez-González, Luis H; Santos-Mendoza, Teresa

2013-01-01

The non-structural protein 1 (NS1) of influenza A virus (IAV), coded by its third most diverse gene, interacts with multiple molecules within infected cells. NS1 is involved in host immune response regulation and is a potential contributor to the virus host range. Early phylogenetic analyses using 50 sequences led to the classification of NS1 gene variants into groups (alleles) A and B. We reanalyzed NS1 diversity using 14,716 complete NS IAV sequences, downloaded from public databases, without host bias. Removal of sequence redundancy and further structured clustering at 96.8% amino acid similarity produced 415 clusters that enhanced our capability to detect distinct subgroups and lineages, which were assigned a numerical nomenclature. Maximum likelihood phylogenetic reconstruction using RNA sequences indicated the previously identified deep branching separating group A from group B, with five distinct subgroups within A as well as two and five lineages within the A4 and A5 subgroups, respectively. Our classification model proposes that sequence patterns in thirteen amino acid positions are sufficient to fit >99.9% of all currently available NS1 sequences into the A subgroups/lineages or the B group. This classification reduces host and virus bias through the prioritization of NS1 RNA phylogenetics over host or virus phenetics. We found significant sequence conservation within the subgroups and lineages with characteristic patterns of functional motifs, such as the differential binding of CPSF30 and crk/crkL or the availability of a C-terminal PDZ-binding motif. To understand selection pressures and evolution acting on NS1, it is necessary to organize the available data. This updated classification may help to clarify and organize the study of NS1 interactions and pathogenic differences and allow the drawing of further functional inferences on sequences in each group, subgroup and lineage rather than on a strain-by-strain basis.

The Communication Function Classification System: cultural adaptation, validity, and reliability of the Farsi version for patients with cerebral palsy.

Science.gov (United States)

Soleymani, Zahra; Joveini, Ghodsiye; Baghestani, Ahmad Reza

2015-03-01

This study developed a Farsi language Communication Function Classification System and then tested its reliability and validity. Communication Function Classification System is designed to classify the communication functions of individuals with cerebral palsy. Up until now, there has been no instrument for assessment of this communication function in Iran. The English Communication Function Classification System was translated into Farsi and cross-culturally modified by a panel of experts. Professionals and parents then assessed the content validity of the modified version. A backtranslation of the Farsi version was confirmed by the developer of the English Communication Function Classification System. Face validity was assessed by therapists and parents of 10 patients. The Farsi Communication Function Classification System was administered to 152 individuals with cerebral palsy (age, 2 to 18 years; median age, 10 years; mean age, 9.9 years; standard deviation, 4.3 years). Inter-rater reliability was analyzed between parents, occupational therapists, and speech and language pathologists. The test-retest reliability was assessed for 75 patients with a 14 day interval between tests. The inter-rater reliability of the Communication Function Classification System was 0.81 between speech and language pathologists and occupational therapists, 0.74 between parents and occupational therapists, and 0.88 between parents and speech and language pathologists. The test-retest reliability was 0.96 for occupational therapists, 0.98 for speech and language pathologists, and 0.94 for parents. The findings suggest that the Farsi version of Communication Function Classification System is a reliable and valid measure that can be used in clinical settings to assess communication function in patients with cerebral palsy. Copyright © 2015 Elsevier Inc. All rights reserved.

Phylogenetic classification of the world's tropical forests.

Science.gov (United States)

Slik, J W Ferry; Franklin, Janet; Arroyo-Rodríguez, Víctor; Field, Richard; Aguilar, Salomon; Aguirre, Nikolay; Ahumada, Jorge; Aiba, Shin-Ichiro; Alves, Luciana F; K, Anitha; Avella, Andres; Mora, Francisco; Aymard C, Gerardo A; Báez, Selene; Balvanera, Patricia; Bastian, Meredith L; Bastin, Jean-François; Bellingham, Peter J; van den Berg, Eduardo; da Conceição Bispo, Polyanna; Boeckx, Pascal; Boehning-Gaese, Katrin; Bongers, Frans; Boyle, Brad; Brambach, Fabian; Brearley, Francis Q; Brown, Sandra; Chai, Shauna-Lee; Chazdon, Robin L; Chen, Shengbin; Chhang, Phourin; Chuyong, George; Ewango, Corneille; Coronado, Indiana M; Cristóbal-Azkarate, Jurgi; Culmsee, Heike; Damas, Kipiro; Dattaraja, H S; Davidar, Priya; DeWalt, Saara J; Din, Hazimah; Drake, Donald R; Duque, Alvaro; Durigan, Giselda; Eichhorn, Karl; Eler, Eduardo Schmidt; Enoki, Tsutomu; Ensslin, Andreas; Fandohan, Adandé Belarmain; Farwig, Nina; Feeley, Kenneth J; Fischer, Markus; Forshed, Olle; Garcia, Queila Souza; Garkoti, Satish Chandra; Gillespie, Thomas W; Gillet, Jean-Francois; Gonmadje, Christelle; Granzow-de la Cerda, Iñigo; Griffith, Daniel M; Grogan, James; Hakeem, Khalid Rehman; Harris, David J; Harrison, Rhett D; Hector, Andy; Hemp, Andreas; Homeier, Jürgen; Hussain, M Shah; Ibarra-Manríquez, Guillermo; Hanum, I Faridah; Imai, Nobuo; Jansen, Patrick A; Joly, Carlos Alfredo; Joseph, Shijo; Kartawinata, Kuswata; Kearsley, Elizabeth; Kelly, Daniel L; Kessler, Michael; Killeen, Timothy J; Kooyman, Robert M; Laumonier, Yves; Laurance, Susan G; Laurance, William F; Lawes, Michael J; Letcher, Susan G; Lindsell, Jeremy; Lovett, Jon; Lozada, Jose; Lu, Xinghui; Lykke, Anne Mette; Mahmud, Khairil Bin; Mahayani, Ni Putu Diana; Mansor, Asyraf; Marshall, Andrew R; Martin, Emanuel H; Calderado Leal Matos, Darley; Meave, Jorge A; Melo, Felipe P L; Mendoza, Zhofre Huberto Aguirre; Metali, Faizah; Medjibe, Vincent P; Metzger, Jean Paul; Metzker, Thiago; Mohandass, D; Munguía-Rosas, Miguel A; Muñoz, Rodrigo; Nurtjahy, Eddy; de Oliveira, Eddie Lenza; Onrizal; Parolin, Pia; Parren, Marc; Parthasarathy, N; Paudel, Ekananda; Perez, Rolando; Pérez-García, Eduardo A; Pommer, Ulf; Poorter, Lourens; Qie, Lan; Piedade, Maria Teresa F; Pinto, José Roberto Rodrigues; Poulsen, Axel Dalberg; Poulsen, John R; Powers, Jennifer S; Prasad, Rama Chandra; Puyravaud, Jean-Philippe; Rangel, Orlando; Reitsma, Jan; Rocha, Diogo S B; Rolim, Samir; Rovero, Francesco; Rozak, Andes; Ruokolainen, Kalle; Rutishauser, Ervan; Rutten, Gemma; Mohd Said, Mohd Nizam; Saiter, Felipe Z; Saner, Philippe; Santos, Braulio; Dos Santos, João Roberto; Sarker, Swapan Kumar; Schmitt, Christine B; Schoengart, Jochen; Schulze, Mark; Sheil, Douglas; Sist, Plinio; Souza, Alexandre F; Spironello, Wilson Roberto; Sposito, Tereza; Steinmetz, Robert; Stevart, Tariq; Suganuma, Marcio Seiji; Sukri, Rahayu; Sultana, Aisha; Sukumar, Raman; Sunderland, Terry; Supriyadi; Suresh, H S; Suzuki, Eizi; Tabarelli, Marcelo; Tang, Jianwei; Tanner, Ed V J; Targhetta, Natalia; Theilade, Ida; Thomas, Duncan; Timberlake, Jonathan; de Morisson Valeriano, Márcio; van Valkenburg, Johan; Van Do, Tran; Van Sam, Hoang; Vandermeer, John H; Verbeeck, Hans; Vetaas, Ole Reidar; Adekunle, Victor; Vieira, Simone A; Webb, Campbell O; Webb, Edward L; Whitfeld, Timothy; Wich, Serge; Williams, John; Wiser, Susan; Wittmann, Florian; Yang, Xiaobo; Adou Yao, C Yves; Yap, Sandra L; Zahawi, Rakan A; Zakaria, Rahmad; Zang, Runguo

2018-02-20

Knowledge about the biogeographic affinities of the world's tropical forests helps to better understand regional differences in forest structure, diversity, composition, and dynamics. Such understanding will enable anticipation of region-specific responses to global environmental change. Modern phylogenies, in combination with broad coverage of species inventory data, now allow for global biogeographic analyses that take species evolutionary distance into account. Here we present a classification of the world's tropical forests based on their phylogenetic similarity. We identify five principal floristic regions and their floristic relationships: ( i ) Indo-Pacific, ( ii ) Subtropical, ( iii ) African, ( iv ) American, and ( v ) Dry forests. Our results do not support the traditional neo- versus paleotropical forest division but instead separate the combined American and African forests from their Indo-Pacific counterparts. We also find indications for the existence of a global dry forest region, with representatives in America, Africa, Madagascar, and India. Additionally, a northern-hemisphere Subtropical forest region was identified with representatives in Asia and America, providing support for a link between Asian and American northern-hemisphere forests. Copyright © 2018 the Author(s). Published by PNAS.

Phylogenetic comparative methods complement discriminant function analysis in ecomorphology.

Science.gov (United States)

Barr, W Andrew; Scott, Robert S

2014-04-01

In ecomorphology, Discriminant Function Analysis (DFA) has been used as evidence for the presence of functional links between morphometric variables and ecological categories. Here we conduct simulations of characters containing phylogenetic signal to explore the performance of DFA under a variety of conditions. Characters were simulated using a phylogeny of extant antelope species from known habitats. Characters were modeled with no biomechanical relationship to the habitat category; the only sources of variation were body mass, phylogenetic signal, or random "noise." DFA on the discriminability of habitat categories was performed using subsets of the simulated characters, and Phylogenetic Generalized Least Squares (PGLS) was performed for each character. Analyses were repeated with randomized habitat assignments. When simulated characters lacked phylogenetic signal and/or habitat assignments were random, ecomorphology. Copyright © 2013 Wiley Periodicals, Inc.

Phylogenetic classification of the world’s tropical forests

Science.gov (United States)

Franklin, Janet; Arroyo-Rodríguez, Víctor; Field, Richard; Aguilar, Salomon; Aguirre, Nikolay; Ahumada, Jorge; Aiba, Shin-Ichiro; K, Anitha; Avella, Andres; Mora, Francisco; Aymard C., Gerardo A.; Báez, Selene; Balvanera, Patricia; Bastian, Meredith L.; Bastin, Jean-François; Bellingham, Peter J.; van den Berg, Eduardo; da Conceição Bispo, Polyanna; Boeckx, Pascal; Boehning-Gaese, Katrin; Bongers, Frans; Boyle, Brad; Brearley, Francis Q.; Brown, Sandra; Chai, Shauna-Lee; Chazdon, Robin L.; Chen, Shengbin; Chhang, Phourin; Chuyong, George; Ewango, Corneille; Coronado, Indiana M.; Cristóbal-Azkarate, Jurgi; Culmsee, Heike; Damas, Kipiro; Dattaraja, H. S.; Davidar, Priya; DeWalt, Saara J.; Din, Hazimah; Drake, Donald R.; Durigan, Giselda; Eichhorn, Karl; Eler, Eduardo Schmidt; Enoki, Tsutomu; Ensslin, Andreas; Fandohan, Adandé Belarmain; Farwig, Nina; Feeley, Kenneth J.; Fischer, Markus; Forshed, Olle; Garcia, Queila Souza; Garkoti, Satish Chandra; Gillespie, Thomas W.; Gillet, Jean-Francois; Gonmadje, Christelle; Granzow-de la Cerda, Iñigo; Griffith, Daniel M.; Grogan, James; Hakeem, Khalid Rehman; Harris, David J.; Harrison, Rhett D.; Hector, Andy; Hemp, Andreas; Hussain, M. Shah; Ibarra-Manríquez, Guillermo; Hanum, I. Faridah; Imai, Nobuo; Jansen, Patrick A.; Joly, Carlos Alfredo; Joseph, Shijo; Kartawinata, Kuswata; Kearsley, Elizabeth; Kelly, Daniel L.; Kessler, Michael; Killeen, Timothy J.; Kooyman, Robert M.; Laumonier, Yves; Laurance, William F.; Lawes, Michael J.; Letcher, Susan G.; Lovett, Jon; Lozada, Jose; Lu, Xinghui; Lykke, Anne Mette; Mahmud, Khairil Bin; Mahayani, Ni Putu Diana; Mansor, Asyraf; Marshall, Andrew R.; Martin, Emanuel H.; Calderado Leal Matos, Darley; Meave, Jorge A.; Melo, Felipe P. L.; Mendoza, Zhofre Huberto Aguirre; Metali, Faizah; Medjibe, Vincent P.; Metzger, Jean Paul; Metzker, Thiago; Mohandass, D.; Munguía-Rosas, Miguel A.; Muñoz, Rodrigo; Nurtjahy, Eddy; de Oliveira, Eddie Lenza; Onrizal; Parolin, Pia; Parren, Marc; Parthasarathy, N.; Paudel, Ekananda; Perez, Rolando; Pérez-García, Eduardo A.; Pommer, Ulf; Poorter, Lourens; Qie, Lan; Piedade, Maria Teresa F.; Pinto, José Roberto Rodrigues; Poulsen, Axel Dalberg; Poulsen, John R.; Powers, Jennifer S.; Prasad, Rama Chandra; Puyravaud, Jean-Philippe; Rangel, Orlando; Reitsma, Jan; Rocha, Diogo S. B.; Rolim, Samir; Rovero, Francesco; Ruokolainen, Kalle; Rutishauser, Ervan; Rutten, Gemma; Mohd. Said, Mohd. Nizam; Saiter, Felipe Z.; Saner, Philippe; Santos, Braulio; dos Santos, João Roberto; Sarker, Swapan Kumar; Schoengart, Jochen; Schulze, Mark; Sheil, Douglas; Sist, Plinio; Souza, Alexandre F.; Spironello, Wilson Roberto; Sposito, Tereza; Steinmetz, Robert; Stevart, Tariq; Suganuma, Marcio Seiji; Sukri, Rahayu; Sukumar, Raman; Sunderland, Terry; Supriyadi; Suresh, H. S.; Suzuki, Eizi; Tabarelli, Marcelo; Tang, Jianwei; Tanner, Ed V. J.; Targhetta, Natalia; Theilade, Ida; Thomas, Duncan; Timberlake, Jonathan; de Morisson Valeriano, Márcio; van Valkenburg, Johan; Van Do, Tran; Van Sam, Hoang; Vandermeer, John H.; Verbeeck, Hans; Vetaas, Ole Reidar; Adekunle, Victor; Vieira, Simone A.; Webb, Campbell O.; Webb, Edward L.; Whitfeld, Timothy; Wich, Serge; Williams, John; Wiser, Susan; Wittmann, Florian; Yang, Xiaobo; Adou Yao, C. Yves; Yap, Sandra L.; Zahawi, Rakan A.; Zakaria, Rahmad; Zang, Runguo

2018-01-01

Knowledge about the biogeographic affinities of the world’s tropical forests helps to better understand regional differences in forest structure, diversity, composition, and dynamics. Such understanding will enable anticipation of region-specific responses to global environmental change. Modern phylogenies, in combination with broad coverage of species inventory data, now allow for global biogeographic analyses that take species evolutionary distance into account. Here we present a classification of the world’s tropical forests based on their phylogenetic similarity. We identify five principal floristic regions and their floristic relationships: (i) Indo-Pacific, (ii) Subtropical, (iii) African, (iv) American, and (v) Dry forests. Our results do not support the traditional neo- versus paleotropical forest division but instead separate the combined American and African forests from their Indo-Pacific counterparts. We also find indications for the existence of a global dry forest region, with representatives in America, Africa, Madagascar, and India. Additionally, a northern-hemisphere Subtropical forest region was identified with representatives in Asia and America, providing support for a link between Asian and American northern-hemisphere forests. PMID:29432167

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

Science.gov (United States)

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

2009-01-01

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.

Phylogenetic molecular function annotation

International Nuclear Information System (INIS)

Engelhardt, Barbara E; Jordan, Michael I; Repo, Susanna T; Brenner, Steven E

2009-01-01

It is now easier to discover thousands of protein sequences in a new microbial genome than it is to biochemically characterize the specific activity of a single protein of unknown function. The molecular functions of protein sequences have typically been predicted using homology-based computational methods, which rely on the principle that homologous proteins share a similar function. However, some protein families include groups of proteins with different molecular functions. A phylogenetic approach for predicting molecular function (sometimes called 'phylogenomics') is an effective means to predict protein molecular function. These methods incorporate functional evidence from all members of a family that have functional characterizations using the evolutionary history of the protein family to make robust predictions for the uncharacterized proteins. However, they are often difficult to apply on a genome-wide scale because of the time-consuming step of reconstructing the phylogenies of each protein to be annotated. Our automated approach for function annotation using phylogeny, the SIFTER (Statistical Inference of Function Through Evolutionary Relationships) methodology, uses a statistical graphical model to compute the probabilities of molecular functions for unannotated proteins. Our benchmark tests showed that SIFTER provides accurate functional predictions on various protein families, outperforming other available methods.

Toward mechanistic classification of enzyme functions.

Science.gov (United States)

Almonacid, Daniel E; Babbitt, Patricia C

2011-06-01

Classification of enzyme function should be quantitative, computationally accessible, and informed by sequences and structures to enable use of genomic information for functional inference and other applications. Large-scale studies have established that divergently evolved enzymes share conserved elements of structure and common mechanistic steps and that convergently evolved enzymes often converge to similar mechanisms too, suggesting that reaction mechanisms could be used to develop finer-grained functional descriptions than provided by the Enzyme Commission (EC) system currently in use. Here we describe how evolution informs these structure-function mappings and review the databases that store mechanisms of enzyme reactions along with recent developments to measure ligand and mechanistic similarities. Together, these provide a foundation for new classifications of enzyme function. Copyright © 2011 Elsevier Ltd. All rights reserved.

System diagnostics using qualitative analysis and component functional classification

International Nuclear Information System (INIS)

Reifman, J.; Wei, T.Y.C.

1993-01-01

A method for detecting and identifying faulty component candidates during off-normal operations of nuclear power plants involves the qualitative analysis of macroscopic imbalances in the conservation equations of mass, energy and momentum in thermal-hydraulic control volumes associated with one or more plant components and the functional classification of components. The qualitative analysis of mass and energy is performed through the associated equations of state, while imbalances in momentum are obtained by tracking mass flow rates which are incorporated into a first knowledge base. The plant components are functionally classified, according to their type, as sources or sinks of mass, energy and momentum, depending upon which of the three balance equations is most strongly affected by a faulty component which is incorporated into a second knowledge base. Information describing the connections among the components of the system forms a third knowledge base. The method is particularly adapted for use in a diagnostic expert system to detect and identify faulty component candidates in the presence of component failures and is not limited to use in a nuclear power plant, but may be used with virtually any type of thermal-hydraulic operating system. 5 figures

The development of a classification system for inland aquatic ...

African Journals Online (AJOL)

A classification system is described that was developed for inland aquatic ecosystems in South Africa, including wetlands. The six-tiered classification system is based on a top-down, hierarchical classification of aquatic ecosystems, following the functionally-oriented hydrogeomorphic (HGM) approach to classification but ...

Short notes and reviews Simplifying hydrozoan classification: inappropriateness of the group Hydroidomedusae in a phylogenetic context

OpenAIRE

Marques, Antonio C.

2001-01-01

The systematics of Hydrozoa is considered from the viewpoint of logical consistency between phylogeny and classification. The validity of the nominal taxon Hydroidomedusae (including all groups of Hydrozoa except the Siphonophorae) is discussed with regard to its distinctness and inclusive relationships. In general, phylogenetic systematic evidence suggest that the use of the term Hydroidomedusae is inappropriate given our current level of understanding. It is concluded that no new, or resurr...

Molecular and morphological data supporting phylogenetic reconstruction of the genus Goniothalamus (Annonaceae), including a reassessment of previous infrageneric classifications.

Science.gov (United States)

Tang, Chin Cheung; Thomas, Daniel C; Saunders, Richard M K

2015-09-01

Data is presented in support of a phylogenetic reconstruction of the species-rich early-divergent angiosperm genus Goniothalamus (Annonaceae) (Tang et al., Mol. Phylogenetic Evol., 2015) [1], inferred using chloroplast DNA (cpDNA) sequences. The data includes a list of primers for amplification and sequencing for nine cpDNA regions: atpB-rbcL, matK, ndhF, psbA-trnH, psbM-trnD, rbcL, trnL-F, trnS-G, and ycf1, the voucher information and molecular data (GenBank accession numbers) of 67 ingroup Goniothalamus accessions and 14 outgroup accessions selected from across the tribe Annoneae, and aligned data matrices for each gene region. We also present our Bayesian phylogenetic reconstructions for Goniothalamus, with information on previous infrageneric classifications superimposed to enable an evaluation of monophyly, together with a taxon-character data matrix (with 15 morphological characters scored for 66 Goniothalamus species and seven other species from the tribe Annoneae that are shown to be phylogenetically correlated).

Molecular and morphological data supporting phylogenetic reconstruction of the genus Goniothalamus (Annonaceae, including a reassessment of previous infrageneric classifications

Directory of Open Access Journals (Sweden)

Chin Cheung Tang

2015-09-01

Full Text Available Data is presented in support of a phylogenetic reconstruction of the species-rich early-divergent angiosperm genus Goniothalamus (Annonaceae (Tang et al., Mol. Phylogenetic Evol., 2015 [1], inferred using chloroplast DNA (cpDNA sequences. The data includes a list of primers for amplification and sequencing for nine cpDNA regions: atpB-rbcL, matK, ndhF, psbA-trnH, psbM-trnD, rbcL, trnL-F, trnS-G, and ycf1, the voucher information and molecular data (GenBank accession numbers of 67 ingroup Goniothalamus accessions and 14 outgroup accessions selected from across the tribe Annoneae, and aligned data matrices for each gene region. We also present our Bayesian phylogenetic reconstructions for Goniothalamus, with information on previous infrageneric classifications superimposed to enable an evaluation of monophyly, together with a taxon-character data matrix (with 15 morphological characters scored for 66 Goniothalamus species and seven other species from the tribe Annoneae that are shown to be phylogenetically correlated.

CLASSIFICATION OF LEARNING MANAGEMENT SYSTEMS

Directory of Open Access Journals (Sweden)

Yu. B. Popova

2016-01-01

Full Text Available Using of information technologies and, in particular, learning management systems, increases opportunities of teachers and students in reaching their goals in education. Such systems provide learning content, help organize and monitor training, collect progress statistics and take into account the individual characteristics of each user. Currently, there is a huge inventory of both paid and free systems are physically located both on college servers and in the cloud, offering different features sets of different licensing scheme and the cost. This creates the problem of choosing the best system. This problem is partly due to the lack of comprehensive classification of such systems. Analysis of more than 30 of the most common now automated learning management systems has shown that a classification of such systems should be carried out according to certain criteria, under which the same type of system can be considered. As classification features offered by the author are: cost, functionality, modularity, keeping the customer’s requirements, the integration of content, the physical location of a system, adaptability training. Considering the learning management system within these classifications and taking into account the current trends of their development, it is possible to identify the main requirements to them: functionality, reliability, ease of use, low cost, support for SCORM standard or Tin Can API, modularity and adaptability. According to the requirements at the Software Department of FITR BNTU under the guidance of the author since 2009 take place the development, the use and continuous improvement of their own learning management system.

Application of the International Classification of Functioning, Disability and Health system to symptoms of the Duchenne and Becker muscular dystrophies.

Science.gov (United States)

Conway, Kristin M; Ciafaloni, Emma; Matthews, Dennis; Westfield, Chris; James, Kathy; Paramsothy, Pangaja; Romitti, Paul A

2018-07-01

Duchenne and Becker muscular dystrophies, collectively referred to as dystrophinopathies, are X-linked recessive diseases that affect dystrophin production resulting in compromised muscle function across multiple systems. The International Classification of Functioning, Disability and Health provides a systematic classification scheme from which body functions affected by a dystrophinopathy can be identified and used to examine functional health. The infrastructure of the Muscular Dystrophy Surveillance, Tracking, and Research Network was used to identify commonly affected body functions and link selected functions to clinical surveillance data collected through medical record abstraction. Seventy-one (24 second-, 41 third- and 7 fourth-level) body function categories were selected via clinician review and consensus. Of these, 15 of 24 retained second-level categories were linked to data elements from the Muscular Dystrophy Surveillance, Tracking, and Research Network surveillance database. Our findings support continued development of a core set of body functions from the International Classification of Functioning, Disability and Health system that are representative of disease progression in dystrophinopathies and the incorporation of these functions in standardized evaluations of functional health and implementation of individualized rehabilitation care plans. Implications for Rehabilitation Duchenne and Becker muscular dystrophies, collectively referred to as dystrophinopathies, are X-linked recessive disorders that affect the production of dystrophin resulting in compromised muscle function across multiple systems. The severity and progressive nature of dystrophinopathies can have considerable impact on a patient's participation in activities across multiple life domains. Our findings support continued development of an International Classification of Functioning, Disability and Health core set for childhood-onset dystrophinopathies. A standardized

Developing and Validating the Communication Function Classification System for Individuals with Cerebral Palsy

Science.gov (United States)

Hidecker, Mary Jo Cooley; Paneth, Nigel; Rosenbaum, Peter L.; Kent, Raymond D.; Lillie, Janet; Eulenberg, John B.; Chester, Ken, Jr.; Johnson, Brenda; Michalsen, Lauren; Evatt, Morgan; Taylor, Kara

2011-01-01

Aim: The purpose of this study was to create and validate the Communication Function Classification System (CFCS) for children with cerebral palsy (CP), for use by a wide variety of individuals who are interested in CP. This paper reports the content validity, interrater reliability, and test-retest reliability of the CFCS for children with CP.…

Automated radial basis function neural network based image classification system for diabetic retinopathy detection in retinal images

Science.gov (United States)

Anitha, J.; Vijila, C. Kezi Selva; Hemanth, D. Jude

2010-02-01

Diabetic retinopathy (DR) is a chronic eye disease for which early detection is highly essential to avoid any fatal results. Image processing of retinal images emerge as a feasible tool for this early diagnosis. Digital image processing techniques involve image classification which is a significant technique to detect the abnormality in the eye. Various automated classification systems have been developed in the recent years but most of them lack high classification accuracy. Artificial neural networks are the widely preferred artificial intelligence technique since it yields superior results in terms of classification accuracy. In this work, Radial Basis function (RBF) neural network based bi-level classification system is proposed to differentiate abnormal DR Images and normal retinal images. The results are analyzed in terms of classification accuracy, sensitivity and specificity. A comparative analysis is performed with the results of the probabilistic classifier namely Bayesian classifier to show the superior nature of neural classifier. Experimental results show promising results for the neural classifier in terms of the performance measures.

Light-water reactors reference system classification for the European reliability data system (ERDS)

International Nuclear Information System (INIS)

Melis, M.; Mancini, G.

1982-01-01

The reference system classification represents a basic stage in the organization of the European reliability data system (ERDS) for light-water reactors, a project actually in development at the Joint Research Centre, Ispra. This project is concerned with operational reliability data collection from the various ''national'' data banks, and centralization in a European reliability data system, so improving the significance of the resulting reliability evaluations. In the framework of the ERDS project, the reference system classification provides a LWR functional break-down and represents a plant-unique identification in the process of homogenization of event-data coming from the various ''national'' organizations. The report, after a brief description of the main objectives of the ERDS project, reviews the criteria followed in the elaboration of the reference system classification; then the detailed classification is presented. The nuclear power station is subdivided in about 180 systems. To each system a sheet is associated, containing: a comprehensive description of system-functions and boundaries; a descritpion of the plant operating mode, linked to the various system functions; a list of the main interface system; and finally, a list of the main components, including type and safety classification

Local-scale Partitioning of Functional and Phylogenetic Beta Diversity in a Tropical Tree Assemblage.

Science.gov (United States)

Yang, Jie; Swenson, Nathan G; Zhang, Guocheng; Ci, Xiuqin; Cao, Min; Sha, Liqing; Li, Jie; Ferry Slik, J W; Lin, Luxiang

2015-08-03

The relative degree to which stochastic and deterministic processes underpin community assembly is a central problem in ecology. Quantifying local-scale phylogenetic and functional beta diversity may shed new light on this problem. We used species distribution, soil, trait and phylogenetic data to quantify whether environmental distance, geographic distance or their combination are the strongest predictors of phylogenetic and functional beta diversity on local scales in a 20-ha tropical seasonal rainforest dynamics plot in southwest China. The patterns of phylogenetic and functional beta diversity were generally consistent. The phylogenetic and functional dissimilarity between subplots (10 × 10 m, 20 × 20 m, 50 × 50 m and 100 × 100 m) was often higher than that expected by chance. The turnover of lineages and species function within habitats was generally slower than that across habitats. Partitioning the variation in phylogenetic and functional beta diversity showed that environmental distance was generally a better predictor of beta diversity than geographic distance thereby lending relatively more support for deterministic environmental filtering over stochastic processes. Overall, our results highlight that deterministic processes play a stronger role than stochastic processes in structuring community composition in this diverse assemblage of tropical trees.

Opposing assembly mechanisms in a neotropical dry forest: implications for phylogenetic and functional community ecology.

Science.gov (United States)

Swenson, Nathan G; Enquist, Brian J

2009-08-01

Species diversity is promoted and maintained by ecological and evolutionary processes operating on species attributes through space and time. The degree to which variability in species function regulates distribution and promotes coexistence of species has been debated. Previous work has attempted to quantify the relative importance of species function by using phylogenetic relatedness as a proxy for functional similarity. The key assumption of this approach is that function is phylogenetically conserved. If this assumption is supported, then the phylogenetic dispersion in a community should mirror the functional dispersion. Here we quantify functional trait dispersion along several key axes of tree life-history variation and on multiple spatial scales in a Neotropical dry-forest community. We next compare these results to previously reported patterns of phylogenetic dispersion in this same forest. We find that, at small spatial scales, coexisting species are typically more functionally clustered than expected, but traits related to adult and regeneration niches are overdispersed. This outcome was repeated when the analyses were stratified by size class. Some of the trait dispersion results stand in contrast to the previously reported phylogenetic dispersion results. In order to address this inconsistency we examined the strength of phylogenetic signal in traits at different depths in the phylogeny. We argue that: (1) while phylogenetic relatedness may be a good general multivariate proxy for ecological similarity, it may have a reduced capacity to depict the functional mechanisms behind species coexistence when coexisting species simultaneously converge and diverge in function; and (2) the previously used metric of phylogenetic signal provided erroneous inferences about trait dispersion when married with patterns of phylogenetic dispersion.

Accurate phylogenetic classification of DNA fragments based onsequence composition

Energy Technology Data Exchange (ETDEWEB)

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

2006-05-01

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

A Preliminary Classification of Human Functional Sexual Disorders

Science.gov (United States)

Sharpe, Lawrence; And Others

1976-01-01

A preliminary classification is presented for functional human sexual disorders. This system is based on objective behavior and reports of distress. Five categories of sexual disorders are proposed, including the behavioral, psychological and informational components of sexual functioning in the individual and the couple. (Author)

Phylogenetic and Functional Structure of Wintering Waterbird Communities Associated with Ecological Differences.

Science.gov (United States)

Che, Xianli; Zhang, Min; Zhao, Yanyan; Zhang, Qiang; Quan, Qing; Møller, Anders; Zou, Fasheng

2018-01-19

Ecological differences may be related to community component divisions between Oriental (west) and Sino-Japanese (east) realms, and such differences may result in weak geographical breaks in migratory species that are highly mobile. Here, we conducted comparative phylogenetic and functional structure analyses of wintering waterbird communities in southern China across two realms and subsequently examined possible climate drivers of the observed patterns. An analysis based on such highly migratory species is particularly telling because migration is bound to reduce or completely eliminate any divergence between communities. Phylogenetic and functional structure of eastern communities showed over-dispersion while western communities were clustered. Basal phylogenetic and functional turnover of western communities was significant lower than that of eastern communities. The break between eastern and western communities was masked by these two realms. Geographic patterns were related to mean temperature changes and temperature fluctuations, suggesting that temperature may filter waterbird lineages and traits, thus underlying geographical community divisions. These results suggest phylogenetic and functional divisions in southern China, coinciding with biogeography. This study shows that temperature fluctuations constitute an essential mechanism shaping geographical divisions that have largely gone undetected previously, even under climate change.

On the need for phylogenetic ‘corrections’ in functional trait-based approaches

NARCIS (Netherlands)

de Bello, F.; Berg, M.P.; Dias, A.T.C.; Diniz-Filho, J.A.F.; Götzenberger, L.; Hortal, J.; Ladle, R.J.; Lepš, J.

2015-01-01

There is considerable uncertainty about if, and when, phylogenetic information is needed to answer various ecological questions about trait-based ecological studies. It has been recommended that both functional and phylogenetic information should be combined, and some researchers have even suggested

Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages.

Directory of Open Access Journals (Sweden)

Luis F Aguirre

Full Text Available Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups. Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for

Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages.

Science.gov (United States)

Aguirre, Luis F; Montaño-Centellas, Flavia A; Gavilanez, M Mercedes; Stevens, Richard D

2016-01-01

Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional

Phylogenetics, ancestral state reconstruction, and a new infrafamilial classification of the pantropical Ochnaceae (Medusagynaceae, Ochnaceae s.str., Quiinaceae) based on five DNA regions

NARCIS (Netherlands)

Schneider, J.V.; Bissiengou, P.; Amaral, M.D.; Tahir, A.; Fay, M.F.; Thines, M.; Sosef, M.S.M.; Zizka, G.; Chatrou, L.W.

2014-01-01

Ochnaceae s.str. (Malpighiales) are a pantropical family of about 500 species and 27 genera of almost exclusively woody plants. Infrafamilial classification and relationships have been controversial partially due to the lack of a robust phylogenetic framework. Including all genera except Indosinia

Phylogenetic relationships within and among Brassica species from ...

African Journals Online (AJOL)

Consequently, two potentially susceptible B. napus accessions were identified. The high polymorphic information content (PIC) and number of phylogenetically informative bands established RAPD as a useful tool for phylogenetic reconstruction, quantification of genetic diversity for conservation, cultivar classification and ...

Nuclear power plant systems, structures and components and their safety classification

International Nuclear Information System (INIS)

2000-01-01

The assurance of a nuclear power plant's safety is based on the reliable functioning of the plant as well as on its appropriate maintenance and operation. To ensure the reliability of operation, special attention shall be paid to the design, manufacturing, commissioning and operation of the plant and its components. To control these functions the nuclear power plant is divided into structural and functional entities, i.e. systems. A systems safety class is determined by its safety significance. Safety class specifies the procedures to be employed in plant design, construction, monitoring and operation. The classification document contains all documentation related to the classification of the nuclear power plant. The principles of safety classification and the procedures pertaining to the classification document are presented in this guide. In the Appendix of the guide, examples of systems most typical of each safety class are given to clarify the safety classification principles

Design and implementation based on the classification protection vulnerability scanning system

International Nuclear Information System (INIS)

Wang Chao; Lu Zhigang; Liu Baoxu

2010-01-01

With the application and spread of the classification protection, Network Security Vulnerability Scanning should consider the efficiency and the function expansion. It proposes a kind of a system vulnerability from classification protection, and elaborates the design and implementation of a vulnerability scanning system based on vulnerability classification plug-in technology and oriented classification protection. According to the experiment, the application of classification protection has good adaptability and salability with the system, and it also approves the efficiency of scanning. (authors)

Computational-based structural, functional and phylogenetic analysis of Enterobacter phytases.

Science.gov (United States)

Pramanik, Krishnendu; Kundu, Shreyasi; Banerjee, Sandipan; Ghosh, Pallab Kumar; Maiti, Tushar Kanti

2018-06-01

Myo-inositol hexakisphosphate phosphohydrolases (i.e., phytases) are known to be a very important enzyme responsible for solubilization of insoluble phosphates. In the present study, Enterobacter phytases have characterized by different phylogenetic, structural and functional parameters using some standard bio-computational tools. Results showed that majority of the Enterobacter phytases are acidic in nature as most of the isoelectric points were under 7.0. The aliphatic indices predicted for the selected proteins were below 40 indicating their thermostable nature. The average molecular weight of the proteins was 48 kDa. The lower values of GRAVY of the said proteins implied that they have better interactions with water. Secondary structure prediction revealed that alpha-helical content was highest among the other forms such as sheets, coils, etc. Moreover, the predicted 3D structure of Enterobacter phytases divulged that the proteins consisted of four monomeric polypeptide chains i.e., it was a tetrameric protein. The predicted tertiary model of E. aerogenes (A0A0M3HCJ2) was deposited in Protein Model Database (Acc. No.: PM0080561) for further utilization after a thorough quality check from QMEAN and SAVES server. Functional analysis supported their classification as histidine acid phosphatases. Besides, multiple sequence alignment revealed that "DG-DP-LG" was the most highly conserved residues within the Enterobacter phytases. Thus, the present study will be useful in selecting suitable phytase-producing microbe exclusively for using in the animal food industry as a food additive.

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes

Science.gov (United States)

Fagan, Matthew E.; Willig, Michael R.

2016-01-01

Background Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. Methods We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. Results The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes.

Science.gov (United States)

Cisneros, Laura M; Fagan, Matthew E; Willig, Michael R

2016-01-01

Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition. Variation

Phylogenetic classification of the halichondrids (Porifera, Demospongiae)

NARCIS (Netherlands)

Soest, van R.W.M.; Díaz, Maria Cristina; Pomponi, Shirley A.

1990-01-01

Using a multicharacter approach and numerical cladistic computer programs a phylogenetic analysis is made of a newly defined order Halichondrida (which includes all Halichondrida and parts of the Axinellida sensu Lévi, 1973), with emphasis on the newly defined family Halichondriidae (which includes

Herbicide and fertilizers promote analogous phylogenetic responses but opposite functional responses in plant communities

International Nuclear Information System (INIS)

Pellissier, Loïc; Wisz, Mary S; Strandberg, Beate; Damgaard, Christian

2014-01-01

Throughout the world, herbicides and fertilizers change species composition in agricultural communities, but how do the cumulative effects of these chemicals impact the functional and phylogenetic structure of non-targeted communities when they drift into adjacent semi-natural habitats? Based on long-term experiment we show that fertilizer and herbicides (glyphosate) have contrasting effects on functional structure, but can increase phylogenetic diversity in semi-natural plant communities. We found that an increase in nitrogen promoted an increase in the average specific leaf area and canopy height at the community level, but an increase in glyphosate promoted a decrease in those traits. Phylogenetic diversity of plant communities increased when herbicide and fertilizer were applied together, likely because functional traits facilitating plant success in those conditions were not phylogenetically conserved. Species richness also decreased with increasing levels of nitrogen and glyphosate. Our results suggest that predicting the cumulative effects of agrochemicals is more complex than anticipated due to their distinct selection of traits that may or may not be conserved phylogenetically. Precautionary efforts to mitigate drift of agricultural chemicals into semi-natural habitats are warranted to prevent unforeseeable biodiversity shifts. (paper)

Phylogenetic perspectives on the evolution of functional hermaphroditism in teleost fishes.

Science.gov (United States)

Erisman, Brad E; Petersen, Christopher W; Hastings, Philip A; Warner, Robert R

2013-10-01

Hermaphroditism is taxonomically widespread among teleost fishes and takes on many forms including simultaneous, protogynous, and protandrous hermaphroditism, bidirectional sex change, and androdioecy. The proximate mechanisms that influence the timing, incidence, and forms of hermaphroditism in fishes are supported by numerous theoretical and empirical studies on their mating systems and sexual patterns, but few have examined aspects of sex-allocation theory or the evolution of hermaphroditism for this group within a strict phylogenetic context. Fortunately, species-level phylogenetic reconstructions of the evolutionary history of many lineages of fishes have emerged, providing opportunities for understanding fine-scale evolutionary pathways and transformations of sex allocation. Examinations of several families of fishes with adequate data on phylogeny, patterns of sex allocation, mating systems, and with some form of hermaphroditism reveal that the evolution and expression of protogyny and other forms of sex allocation show little evidence of phylogenetic inertia within specific lineages but rather are associated with particular mating systems in accordance with prevalent theories about sex allocation. Transformations from protogyny to gonochorism in groupers (Epinephelidae), seabasses (Serranidae), and wrasses and parrotfishes (Labridae) are associated with equivalent transformations in the structure of mating groups from spawning of pairs to group spawning and related increases in sperm competition. Similarly, patterns of protandry, androdioecy, simultaneous hermaphroditism, and bidirectional sex change in other lineages (Aulopiformes, Gobiidae, and Pomacentridae) match well with particular mating systems in accordance with sex-allocation theory. Unlike other animals and plants, we did not find evidence that transitions between hermaphroditism and gonochorism required functional intermediates. Two instances in which our general conclusions might not hold

Validity of the Communication Function Classification System for use with preschool children with communication disorders.

Science.gov (United States)

Hidecker, Mary Jo Cooley; Cunningham, Barbara Jane; Thomas-Stonell, Nancy; Oddson, Bruce; Rosenbaum, Peter

2017-05-01

To evaluate construct and predictive validity of the Communication Function Classification System (CFCS) for use with preschool children with a range of speech and language disorders. Seventy-seven preschool children with speech and language disorders (50 males, 27 females; mean 2y 7mo, standard deviation [SD] 1y) participated in this cohort study. Preschool children had speech and language, language-only, or speech-only disorders. Together with parent input, speech-language pathologists (SLPs) completed the CFCS at time 1. Parents and SLPs then independently completed a validated change-detecting functional communication outcome measure, the Focus on the outcomes of Communication Under Six (FOCUS), three times: at assessment (time 1), at the start of treatment (time 2), and at the end of treatment (time 3). There was a significant negative correlation between CFCS classifications and FOCUS scores at all three measurement points for the ratings by both parents and SLPs (correlations ranged from -0.60 to -0.76). As expected, no correlations between CFCS classifications and FOCUS change scores were statistically significant. This study provides evidence of construct and predictive validity of the CFCS, demonstrating its value as a discriminative tool for use with preschool children with a range of speech and language disorders. © 2017 Mac Keith Press.

Herbicide and fertilizers promote analogous phylogenetic responses but opposite functional responses in plant communities

DEFF Research Database (Denmark)

Pellissier, Loïc; Wisz, Mary S.; Strandberg, Beate

2014-01-01

on long-term experiment we show that fertilizer and herbicides (glyphosate) have contrasting effects on functional structure, but can increase phylogenetic diversity in semi-natural plant communities. We found that an increase in nitrogen promoted an increase in the average specific leaf area and canopy...... height at the community level, but an increase in glyphosate promoted a decrease in those traits. Phylogenetic diversity of plant communities increased when herbicide and fertilizer were applied together, likely because functional traits facilitating plant success in those conditions were......Throughout the world, herbicides and fertilizers change species composition in agricultural communities, but how do the cumulative effects of these chemicals impact the functional and phylogenetic structure of non-targeted communities when they drift into adjacent semi-natural habitats? Based...

IR-360 nuclear power plant safety functions and component classification

International Nuclear Information System (INIS)

Yousefpour, F.; Shokri, F.; Soltani, H.

2010-01-01

The IR-360 nuclear power plant as a 2-loop PWR of 360 MWe power generation capacity is under design in MASNA Company. For design of the IR-360 structures, systems and components (SSCs), the codes and standards and their design requirements must be determined. It is a prerequisite to classify the IR-360 safety functions and safety grade of structures, systems and components correctly for selecting and adopting the suitable design codes and standards. This paper refers to the IAEA nuclear safety codes and standards as well as USNRC standard system to determine the IR-360 safety functions and to formulate the principles of the IR-360 component classification in accordance with the safety philosophy and feature of the IR-360. By implementation of defined classification procedures for the IR-360 SSCs, the appropriate design codes and standards are specified. The requirements of specific codes and standards are used in design process of IR-360 SSCs by design engineers of MASNA Company. In this paper, individual determination of the IR-360 safety functions and definition of the classification procedures and roles are presented. Implementation of this work which is described with example ensures the safety and reliability of the IR-360 nuclear power plant.

IR-360 nuclear power plant safety functions and component classification

Energy Technology Data Exchange (ETDEWEB)

Yousefpour, F., E-mail: fyousefpour@snira.co [Management of Nuclear Power Plant Construction Company (MASNA) (Iran, Islamic Republic of); Shokri, F.; Soltani, H. [Management of Nuclear Power Plant Construction Company (MASNA) (Iran, Islamic Republic of)

2010-10-15

The IR-360 nuclear power plant as a 2-loop PWR of 360 MWe power generation capacity is under design in MASNA Company. For design of the IR-360 structures, systems and components (SSCs), the codes and standards and their design requirements must be determined. It is a prerequisite to classify the IR-360 safety functions and safety grade of structures, systems and components correctly for selecting and adopting the suitable design codes and standards. This paper refers to the IAEA nuclear safety codes and standards as well as USNRC standard system to determine the IR-360 safety functions and to formulate the principles of the IR-360 component classification in accordance with the safety philosophy and feature of the IR-360. By implementation of defined classification procedures for the IR-360 SSCs, the appropriate design codes and standards are specified. The requirements of specific codes and standards are used in design process of IR-360 SSCs by design engineers of MASNA Company. In this paper, individual determination of the IR-360 safety functions and definition of the classification procedures and roles are presented. Implementation of this work which is described with example ensures the safety and reliability of the IR-360 nuclear power plant.

Phylogenetic perspectives on reef fish functional traits.

Science.gov (United States)

Floeter, Sergio R; Bender, Mariana G; Siqueira, Alexandre C; Cowman, Peter F

2018-02-01

Functional traits have been fundamental to the evolution and diversification of entire fish lineages on coral reefs. Yet their relationship with the processes promoting speciation, extinction and the filtering of local species pools remains unclear. We review the current literature exploring the evolution of diet, body size, water column use and geographic range size in reef-associated fishes. Using published and new data, we mapped functional traits on to published phylogenetic trees to uncover evolutionary patterns that have led to the current functional diversity of fishes on coral reefs. When examining reconstructed patterns for diet and feeding mode, we found examples of independent transitions to planktivory across different reef fish families. Such transitions and associated morphological alterations may represent cases in which ecological opportunity for the exploitation of different resources drives speciation and adaptation. In terms of body size, reconstructions showed that both large and small sizes appear multiple times within clades of mid-sized fishes and that extreme body sizes have arisen mostly in the last 10 million years (Myr). The reconstruction of range size revealed many cases of disparate range sizes among sister species. Such range size disparity highlights potential vicariant processes through isolation in peripheral locations. When accounting for peripheral speciation processes in sister pairs, we found a significant relationship between labrid range size and lineage age. The diversity and evolution of traits within lineages is influenced by trait-environment interactions as well as by species and trait-trait interactions, where the presence of a given trait may trigger the development of related traits or behaviours. Our effort to assess the evolution of functional diversity across reef fish clades adds to the burgeoning research focusing on the evolutionary and ecological roles of functional traits. We argue that the combination of a

Ontologies vs. Classification Systems

DEFF Research Database (Denmark)

Madsen, Bodil Nistrup; Erdman Thomsen, Hanne

2009-01-01

What is an ontology compared to a classification system? Is a taxonomy a kind of classification system or a kind of ontology? These are questions that we meet when working with people from industry and public authorities, who need methods and tools for concept clarification, for developing meta...... data sets or for obtaining advanced search facilities. In this paper we will present an attempt at answering these questions. We will give a presentation of various types of ontologies and briefly introduce terminological ontologies. Furthermore we will argue that classification systems, e.g. product...... classification systems and meta data taxonomies, should be based on ontologies....

ICF-based classification and measurement of functioning.

Science.gov (United States)

Stucki, G; Kostanjsek, N; Ustün, B; Cieza, A

2008-09-01

If we aim towards a comprehensive understanding of human functioning and the development of comprehensive programs to optimize functioning of individuals and populations we need to develop suitable measures. The approval of the International Classification, Disability and Health (ICF) in 2001 by the 54th World Health Assembly as the first universally shared model and classification of functioning, disability and health marks, therefore an important step in the development of measurement instruments and ultimately for our understanding of functioning, disability and health. The acceptance and use of the ICF as a reference framework and classification has been facilitated by its development in a worldwide, comprehensive consensus process and the increasing evidence regarding its validity. However, the broad acceptance and use of the ICF as a reference framework and classification will also depend on the resolution of conceptual and methodological challenges relevant for the classification and measurement of functioning. This paper therefore describes first how the ICF categories can serve as building blocks for the measurement of functioning and then the current state of the development of ICF based practical tools and international standards such as the ICF Core Sets. Finally it illustrates how to map the world of measures to the ICF and vice versa and the methodological principles relevant for the transformation of information obtained with a clinical test or a patient-oriented instrument to the ICF as well as the development of ICF-based clinical and self-reported measurement instruments.

QA CLASSIFICATION ANALYSIS OF GROUND SUPPORT SYSTEMS

International Nuclear Information System (INIS)

D. W. Gwyn

1996-01-01

The purpose and objective of this analysis is to determine if the permanent function Ground Support Systems (CI: BABEEOOOO) are quality-affecting items and if so, to establish the appropriate Quality Assurance (QA) classification

Common occupational classification system - revision 3

Energy Technology Data Exchange (ETDEWEB)

Stahlman, E.J.; Lewis, R.E.

1996-05-01

Workforce planning has become an increasing concern within the DOE community as the Office of Environmental Restoration and Waste Management (ER/WM or EM) seeks to consolidate and refocus its activities and the Office of Defense Programs (DP) closes production sites. Attempts to manage the growth and skills mix of the EM workforce while retaining the critical skills of the DP workforce have been difficult due to the lack of a consistent set of occupational titles and definitions across the complex. Two reasons for this difficulty may be cited. First, classification systems commonly used in industry often fail to cover in sufficient depth the unique demands of DOE`s nuclear energy and research community. Second, the government practice of contracting the operation of government facilities to the private sector has introduced numerous contractor-specific classification schemes to the DOE complex. As a result, sites/contractors report their workforce needs using unique classification systems. It becomes difficult, therefore, to roll these data up to the national level necessary to support strategic planning and analysis. The Common Occupational Classification System (COCS) is designed to overcome these workforce planning barriers. The COCS is based on earlier workforce planning activities and the input of technical, workforce planning, and human resource managers from across the DOE complex. It provides a set of mutually-exclusive occupation titles and definitions that cover the broad range of activities present in the DOE complex. The COCS is not a required record-keeping or data management guide. Neither is it intended to replace contractor/DOE-specific classification systems. Instead, the system provides a consistent, high- level, functional structure of occupations to which contractors can crosswalk (map) their job titles.

An Improved Binary Differential Evolution Algorithm to Infer Tumor Phylogenetic Trees.

Science.gov (United States)

Liang, Ying; Liao, Bo; Zhu, Wen

2017-01-01

Tumourigenesis is a mutation accumulation process, which is likely to start with a mutated founder cell. The evolutionary nature of tumor development makes phylogenetic models suitable for inferring tumor evolution through genetic variation data. Copy number variation (CNV) is the major genetic marker of the genome with more genes, disease loci, and functional elements involved. Fluorescence in situ hybridization (FISH) accurately measures multiple gene copy number of hundreds of single cells. We propose an improved binary differential evolution algorithm, BDEP, to infer tumor phylogenetic tree based on FISH platform. The topology analysis of tumor progression tree shows that the pathway of tumor subcell expansion varies greatly during different stages of tumor formation. And the classification experiment shows that tree-based features are better than data-based features in distinguishing tumor. The constructed phylogenetic trees have great performance in characterizing tumor development process, which outperforms other similar algorithms.

Molecular phylogenetics and character evolution of morphologically diverse groups, Dendrobium section Dendrobium and allies

Science.gov (United States)

Takamiya, Tomoko; Wongsawad, Pheravut; Sathapattayanon, Apirada; Tajima, Natsuko; Suzuki, Shunichiro; Kitamura, Saki; Shioda, Nao; Handa, Takashi; Kitanaka, Susumu; Iijima, Hiroshi; Yukawa, Tomohisa

2014-01-01

It is always difficult to construct coherent classification systems for plant lineages having diverse morphological characters. The genus Dendrobium, one of the largest genera in the Orchidaceae, includes ∼1100 species, and enormous morphological diversification has hindered the establishment of consistent classification systems covering all major groups of this genus. Given the particular importance of species in Dendrobium section Dendrobium and allied groups as floriculture and crude drug genetic resources, there is an urgent need to establish a stable classification system. To clarify phylogenetic relationships in Dendrobium section Dendrobium and allied groups, we analysed the macromolecular characters of the group. Phylogenetic analyses of 210 taxa of Dendrobium were conducted on DNA sequences of internal transcribed spacer (ITS) regions of 18S–26S nuclear ribosomal DNA and the maturase-coding gene (matK) located in an intron of the plastid gene trnK using maximum parsimony and Bayesian methods. The parsimony and Bayesian analyses revealed 13 distinct clades in the group comprising section Dendrobium and its allied groups. Results also showed paraphyly or polyphyly of sections Amblyanthus, Aporum, Breviflores, Calcarifera, Crumenata, Dendrobium, Densiflora, Distichophyllae, Dolichocentrum, Holochrysa, Oxyglossum and Pedilonum. On the other hand, the monophyly of section Stachyobium was well supported. It was found that many of the morphological characters that have been believed to reflect phylogenetic relationships are, in fact, the result of convergence. As such, many of the sections that have been recognized up to this point were found to not be monophyletic, so recircumscription of sections is required. PMID:25107672

Using a multidisciplinary classification in nursing : The international classification of functioning disability and health

NARCIS (Netherlands)

Van Achterberg, T; Holleman, G; Heijnen-Kaales, Y; Van der Brug, Y; Roodbol, G; Stallinga, HA; Hellema, F; Frederiks, CMA

This paper reports a study to explore systematically the usefulness of the International Classification of Functioning, Disability and Health to nurses giving patient care. The International Classification of Functioning, Disability and Health has a history of more than 20 years. Although this World

Using a multidisciplinary classification in nursing: the International Classification of Functioning Disability and Health

NARCIS (Netherlands)

van Achterberg, Theo; Holleman, Gerda; Heijnen-Kaales, Yvonne; van der Brug, Ype; Roodbol, Gabriël; Stallinga, Hillegonda A.; Hellema, Fokje; Frederiks, Carla M. A.

2005-01-01

This paper reports a study to explore systematically the usefulness of the International Classification of Functioning, Disability and Health to nurses giving patient care. The International Classification of Functioning, Disability and Health has a history of more than 20 years. Although this World

Towards a phylogenetic classification of reef corals: The Indo-Pacific genera Merulina, Goniastrea and Scapophyllia (Scleractinia, Merulinidae)

KAUST Repository

Huang, Danwei

2014-06-03

Recent advances in scleractinian systematics and taxonomy have been achieved through the integration of molecular and morphological data, as well as rigorous analysis using phylogenetic methods. In this study, we continue in our pursuit of a phylogenetic classification by examining the evolutionary relationships between the closely related reef coral genera Merulina, Goniastrea, Paraclavarina and Scapophyllia (Merulinidae). In particular, we address the extreme polyphyly of Favites and Goniastrea that was discovered a decade ago. We sampled 145 specimens belonging to 16 species from a wide geographic range in the Indo-Pacific, focusing especially on type localities, including the Red Sea, western Indian Ocean and central Pacific. Tree reconstructions based on both nuclear and mitochondrial markers reveal a novel lineage composed of three species previously placed in Favites and Goniastrea. Morphological analyses indicate that this clade, Paragoniastrea Huang, Benzoni & Budd, gen. n., has a unique combination of corallite and subcorallite features observable with scanning electron microscopy and thin sections. Molecular and morphological evidence furthermore indicates that the monotypic genus Paraclavarina is nested within Merulina, and the former is therefore synonymised. © 2014 Royal Swedish Academy of Sciences.

Developing a classification system of social communication functioning of preschool children with autism spectrum disorder.

Science.gov (United States)

Di Rezze, Briano; Rosenbaum, Peter; Zwaigenbaum, Lonnie; Hidecker, Mary Jo Cooley; Stratford, Paul; Cousins, Martha; Camden, Chantal; Law, Mary

2016-09-01

Impairments in social communication are the hallmark of autism spectrum disorder (ASD). Operationalizing 'severity' in ASD has been challenging; thus, stratifying by functioning has not been possible. The purpose of this study is to describe the development of the Autism Classification System of Functioning: Social Communication (ACSF:SC) and to evaluate its consistency within and between parent and professional ratings. (1) ACSF:SC development based on focus groups and surveys involving parents, educators, and clinicians familiar with preschoolers with ASD; and (2) evaluation of the intra- and interrater agreement of the ACSF:SC using weighted kappa (кw ). Seventy-six participants were involved in the development process. Core characteristics of social communication were ascertained: communicative intent; communicative skills and reciprocity; and impact of environment. Five ACSF:SC levels were created and content-validated across participants. Best capacity and typical performance agreement ratings varied as follows: intrarater agreement on 41 children was кw =0.61 to 0.69 for parents, and кw =0.71 to 0.95 for professionals; interrater agreement between professionals was кw =0.47 to 0.61, and between parents and professionals was кw =0.33 to 0.53. Perspectives from parents and professionals informed ACSF:SC development, providing common descriptions of the levels of everyday communicative abilities of children with ASD to complement the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition. Rater agreement demonstrates that the ACSF:SC can be used with acceptable consistency compared with other functional classification systems. © 2016 Mac Keith Press.

Intelligent Computer Vision System for Automated Classification

International Nuclear Information System (INIS)

Jordanov, Ivan; Georgieva, Antoniya

2010-01-01

In this paper we investigate an Intelligent Computer Vision System applied for recognition and classification of commercially available cork tiles. The system is capable of acquiring and processing gray images using several feature generation and analysis techniques. Its functionality includes image acquisition, feature extraction and preprocessing, and feature classification with neural networks (NN). We also discuss system test and validation results from the recognition and classification tasks. The system investigation also includes statistical feature processing (features number and dimensionality reduction techniques) and classifier design (NN architecture, target coding, learning complexity and performance, and training with our own metaheuristic optimization method). The NNs trained with our genetic low-discrepancy search method (GLPτS) for global optimisation demonstrated very good generalisation abilities. In our view, the reported testing success rate of up to 95% is due to several factors: combination of feature generation techniques; application of Analysis of Variance (ANOVA) and Principal Component Analysis (PCA), which appeared to be very efficient for preprocessing the data; and use of suitable NN design and learning method.

Functions in Biological Kind Classification

Science.gov (United States)

Lombrozo, Tania; Rehder, Bob

2012-01-01

Biological traits that serve functions, such as a zebra's coloration (for camouflage) or a kangaroo's tail (for balance), seem to have a special role in conceptual representations for biological kinds. In five experiments, we investigate whether and why functional features are privileged in biological kind classification. Experiment 1…

Introduction of the gross motor function classification system in Venezuela--a model for knowledge dissemination.

Science.gov (United States)

Löwing, Kristina; Arredondo, Ynes C; Tedroff, Marika; Tedroff, Kristina

2015-09-04

A current worldwide common goal is to optimize the health and well-being of children with cerebral palsy (CP). In order to reach that goal, for this heterogeneous group, a common language and classification systems are required to predict development and offer evidence based interventions. In most countries in Africa, South America, Asia and Eastern Europe the classification systems for CP are unfamiliar and rarely used. Education and implementation are required. The specific aims of this study were to examine a model in order to introduce the Gross Motor Function Classification System (GMFCS-E&R) in Venezuela, and to examine the validity and the reliability. Children with CP, registered at a National child rehabilitation centre in Venezuela, were invited to participate. The Spanish version of GMFCS-E&R was used. The Wilson mobility scale was translated and used to examine the concurrent validity. A structured questionnaire, comprising aspects of mobility and gross motor function, was constructed. In addition, each child was filmed. A paediatrician in Venezuela received supervised self-education in GMFCS-E&R and the Wilson mobility scale. A Swedish student was educated in GMFCS-E&R and the Wilson mobility scale prior to visiting Venezuela. In Venezuela, all children were classified and scored by the paediatrician and student independently. An experienced paediatric physiotherapist (PT) in Sweden made independent GMFCS-E&R classifications and Wilson mobility scale scorings, accomplished through merging data from the structured questionnaire with observations of the films. Descriptive statistics were used and reliability was presented with weighted Kappa (Kw). Spearman's correlation coefficient was calculated to explore the concurrent validity between GMFCS-E&R and Wilson mobility scale. Eighty-eight children (56 boys), mean age 10 years (3-18), with CP participated. The inter-rater reliability of GMFCS-E&R between; the paediatrician and the PT was Kw = 0.85 (95% CI

Classification in childhood disability: focusing on function in the 21st century.

Science.gov (United States)

Rosenbaum, Peter; Eliasson, Ann-Christin; Hidecker, Mary Jo Cooley; Palisano, Robert J

2014-08-01

Classification systems in health care are usually based on current understanding of the condition. They are often derived empirically and adopted applying sound principles of measurement science to assess whether they are reliable (consistent) and valid (true) for the purposes to which they are applied. In the past 15 years, the authors have developed and validated classification systems for specific aspects of everyday function in people with cerebral palsy--gross motor function, manual abilities, and communicative function. This article describes the approaches used to conceptualize each aspect of function, develop the tools, and assess their reliability and validity. We report on the utility of each system with respect to clinical applicability, use of these tools for research, and the uptake and impact that they have had around the world. We hope that readers will find these accounts interesting, relevant, and applicable to their daily work with children and youth with disabilities. © The Author(s) 2014.

The Impact of Media, Phylogenetic Classification, and E. coli Pathotypes on Biofilm Formation in Extraintestinal and Commensal E. coli From Humans and Animals.

Science.gov (United States)

Nielsen, Daniel W; Klimavicz, James S; Cavender, Tia; Wannemuehler, Yvonne; Barbieri, Nicolle L; Nolan, Lisa K; Logue, Catherine M

2018-01-01

Extraintestinal pathogenic Escherichia coli (ExPEC) include avian pathogenic E. coli (APEC), neonatal meningitis E. coli (NMEC), and uropathogenic E. coli (UPEC) and are responsible for significant animal and human morbidity and mortality. This study sought to investigate if biofilm formation by ExPEC likely contributes to these losses since biofilms are associated with recurrent urinary tract infections, antibiotic resistance, and bacterial exchange of genetic material. Therefore, the goal of this study was to examine differences in biofilm formation among a collection of ExPEC and to ascertain if there is a relationship between their ability to produce biofilms and their assignment to phylogenetic groups in three media types - M63, diluted TSB, and BHI. Our results suggest that ExPEC produce relatively different levels of biofilm formation in the media tested as APEC (70.4%, p = 0.0064) and NMEC (84.4%, p = 0.0093) isolates were poor biofilm formers in minimal medium M63 while UPEC isolates produced significantly higher ODs under nutrient-limited conditions with 25% of strains producing strong biofilms in diluted TSB ( p = 0.0204). Additionally, E. coli phylogenetic assignment using Clermont's original and revised typing scheme demonstrated significant differences among the phylogenetic groups in the different media. When the original phylogenetic group isolates previously typed as group D were phylogenetically typed under the revised scheme and examined, they showed substantial variation in their ability to form biofilms, which may explain the significant values of revised phylogenetic groups E and F in M63 ( p = 0.0291, p = 0.0024). Our data indicates that biofilm formation is correlated with phylogenetic classification and subpathotype or commensal grouping of E. coli strains.

[New International Classification of Chronic Pancreatitis (M-ANNHEIM multifactor classification system, 2007): principles, merits, and demerits].

Science.gov (United States)

Tsimmerman, Ia S

2008-01-01

The new International Classification of Chronic Pancreatitis (designated as M-ANNHEIM) proposed by a group of German specialists in late 2007 is reviewed. All its sections are subjected to analysis (risk group categories, clinical stages and phases, variants of clinical course, diagnostic criteria for "established" and "suspected" pancreatitis, instrumental methods and functional tests used in the diagnosis, evaluation of the severity of the disease using a scoring system, stages of elimination of pain syndrome). The new classification is compared with the earlier classification proposed by the author. Its merits and demerits are discussed.

Functional and phylogenetic structure of island bird communities.

Science.gov (United States)

Si, Xingfeng; Cadotte, Marc W; Zeng, Di; Baselga, Andrés; Zhao, Yuhao; Li, Jiaqi; Wu, Yiru; Wang, Siyu; Ding, Ping

2017-05-01

Biodiversity change in anthropogenically transformed habitats is often nonrandom, yet the nature and importance of the different mechanisms shaping community structure are unclear. Here, we extend the classic Theory of Island Biogeography (TIB) to account for nonrandom processes by incorporating species traits and phylogenetic relationships into a study of faunal relaxation following habitat loss and fragmentation. Two possible mechanisms can create nonrandom community patterns on fragment islands. First, small and isolated islands might consist of similar or closely related species because they are environmentally homogeneous or select for certain shared traits, such as dispersal ability. Alternatively, communities on small islands might contain more dissimilar or distantly related species than on large islands because limited space and resource availability result in greater competitive exclusion among species with high niche overlap. Breeding birds were surveyed on 36 islands and two mainland sites annually from 2010 to 2014 in the Thousand Island Lake region, China. We assessed community structure of breeding birds on these subtropical land-bridge islands by integrating species' trait and evolutionary distances. We additionally analysed habitat heterogeneity and variance in size ratios to distinguish biotic and abiotic processes of community assembly. Results showed that functional-phylogenetic diversity increased with island area, and decreased with isolation. Bird communities on the mainland were more diverse and generally less clustered than island bird communities and not different than randomly assembled communities. Bird communities on islands tend to be functionally similar and phylogenetically clustered, especially on small and isolated islands. The nonrandom decline in species diversity and change in bird community structure with island area and isolation, along with the relatively homogeneous habitats on small islands, support the environmental

A Proposed Functional Abilities Classification Tool for Developmental Disorders Affecting Learning and Behaviour

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Benjamin Klein

2018-02-01

Full Text Available Children with developmental disorders affecting learning and behaviour (DDALB (e.g., attention, social communication, language, and learning disabilities, etc. require individualized support across multiple environments to promote participation, quality of life, and developmental outcomes. Support to enhance participation is based largely on individual profiles of functioning (e.g., communication, cognitive, social skills, executive functioning, etc., which are highly heterogeneous within medical diagnoses. Currently educators, clinicians, and parents encounter widespread difficulties in meeting children’s needs as there is lack of universal classification of functioning and disability for use in school environments. Objective: a practical tool for functional classification broadly applicable for children with DDALB could facilitate the collaboration, identification of points of entry of support, individual program planning, and reassessment in a transparent, equitable process based on functional need and context. We propose such a tool, the Functional Abilities Classification Tool (FACT based on the concepts of the ICF (International Classification of Functioning, Disability and Health. FACT is intended to provide ability and participation classification that is complementary to medical diagnosis. For children presenting with difficulties, the proposed tool initially classifies participation over several environments. Then, functional abilities are classified and personal factors and environment are described. Points of entry for support are identified given an analysis of functional ability profile, personal factors, environmental features, and pattern of participation. Conclusion: case examples, use of the tool and implications for children, agencies, and the system are described.

Optimization of Neuro-Fuzzy System Using Genetic Algorithm for Chromosome Classification

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M. Sarosa

2013-09-01

Full Text Available Neuro-fuzzy system has been shown to provide a good performance on chromosome classification but does not offer a simple method to obtain the accurate parameter values required to yield the best recognition rate. This paper presents a neuro-fuzzy system where its parameters can be automatically adjusted using genetic algorithms. The approach combines the advantages of fuzzy logic theory, neural networks, and genetic algorithms. The structure consists of a four layer feed-forward neural network that uses a GBell membership function as the output function. The proposed methodology has been applied and tested on banded chromosome classification from the Copenhagen Chromosome Database. Simulation result showed that the proposed neuro-fuzzy system optimized by genetic algorithms offers advantages in setting the parameter values, improves the recognition rate significantly and decreases the training/testing time which makes genetic neuro-fuzzy system suitable for chromosome classification.

Catchment Classification: Connecting Climate, Structure and Function

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Sawicz, K. A.; Wagener, T.; Sivapalan, M.; Troch, P. A.; Carrillo, G. A.

2010-12-01

Hydrology does not yet possess a generally accepted catchment classification framework. Such a classification framework needs to: [1] give names to things, i.e. the main classification step, [2] permit transfer of information, i.e. regionalization of information, [3] permit development of generalizations, i.e. to develop new theory, and [4] provide a first order environmental change impact assessment, i.e., the hydrologic implications of climate, land use and land cover change. One strategy is to create a catchment classification framework based on the notion of catchment functions (partitioning, storage, and release). Results of an empirical study presented here connects climate and structure to catchment function (in the form of select hydrologic signatures), based on analyzing over 300 US catchments. Initial results indicate a wide assortment of signature relationships with properties of climate, geology, and vegetation. The uncertainty in the different regionalized signatures varies widely, and therefore there is variability in the robustness of classifying ungauged basins. This research provides insight into the controls of hydrologic behavior of a catchment, and enables a classification framework applicable to gauged and ungauged across the study domain. This study sheds light on what we can expect to achieve in mapping climate, structure and function in a top-down manner. Results of this study complement work done using a bottom-up physically-based modeling framework to generalize this approach (Carrillo et al., this session).

Phylogenetic Distribution of Leaf Spectra and Optically Derived Functional Traits in the American Oaks

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Cavender-Bares, J.; Meireles, J. E.; Couture, J. J.; Kaproth, M.; Townsend, P. A.

2015-12-01

Detecting functional traits of species, genotypes and phylogenetic lineages is critical in monitoring functional biodiversity remotely. We examined the phylogenetic distribution of leaf spectra across the American Oaks for 35 species under greenhouse conditions as well as genetic variation in leaf spectra across Central American populations of a single species grown in common gardens in Honduras. We found significant phylogenetic signal in the leaf spectra (Blomberg's K > 1.0), indicating similarity in spectra among close relatives. Across species, full range leaf spectra were used in a Partial Least Squares Discriminant Analysis (PLS-DA) that allowed species calibration (kappa statistic = 0.55). Validation of the model used to detect species (kappa statistic = 0.4) indicated reasonably good detection of individual species within the same the genus. Among four populations from Belize, Costa Rica, Honduras, and Mexico within a single species (Quercus oleoides), leaf spectra were also able to differentiate populations. Ordination of population-level data using dissimilarities of predicted foliar traits, including leaf mass per area (LMA), lignin content, fiber content, chlorophyll a+b, and C:N ratio in genotypes in either watered or unwatered conditions showed significant differentiation among populations and treatments. These results provide promise for remote detection and differentiation of plant functional traits among plant phylogenetic lineages and genotypes, even among closely related populations and species.

The Impact of Media, Phylogenetic Classification, and E. coli Pathotypes on Biofilm Formation in Extraintestinal and Commensal E. coli From Humans and Animals

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Daniel W. Nielsen

2018-05-01

Full Text Available Extraintestinal pathogenic Escherichia coli (ExPEC include avian pathogenic E. coli (APEC, neonatal meningitis E. coli (NMEC, and uropathogenic E. coli (UPEC and are responsible for significant animal and human morbidity and mortality. This study sought to investigate if biofilm formation by ExPEC likely contributes to these losses since biofilms are associated with recurrent urinary tract infections, antibiotic resistance, and bacterial exchange of genetic material. Therefore, the goal of this study was to examine differences in biofilm formation among a collection of ExPEC and to ascertain if there is a relationship between their ability to produce biofilms and their assignment to phylogenetic groups in three media types – M63, diluted TSB, and BHI. Our results suggest that ExPEC produce relatively different levels of biofilm formation in the media tested as APEC (70.4%, p = 0.0064 and NMEC (84.4%, p = 0.0093 isolates were poor biofilm formers in minimal medium M63 while UPEC isolates produced significantly higher ODs under nutrient-limited conditions with 25% of strains producing strong biofilms in diluted TSB (p = 0.0204. Additionally, E. coli phylogenetic assignment using Clermont’s original and revised typing scheme demonstrated significant differences among the phylogenetic groups in the different media. When the original phylogenetic group isolates previously typed as group D were phylogenetically typed under the revised scheme and examined, they showed substantial variation in their ability to form biofilms, which may explain the significant values of revised phylogenetic groups E and F in M63 (p = 0.0291, p = 0.0024. Our data indicates that biofilm formation is correlated with phylogenetic classification and subpathotype or commensal grouping of E. coli strains.

Classification of huminite-ICCP System 1994

Energy Technology Data Exchange (ETDEWEB)

Sykorova, I. [Institute of Rock Structure and Mechanics, Academy of Science of the Czech Republic, V Holesovicka 41, 182 09 Prague 8 (Czech Republic); Pickel, W. [Coal and Organic Petrology Services Pty Ltd, 23/80 Box Road, Taren Point, NSW 2229 (Australia); Christanis, K. [Department of Geology, University of Patras, 26500 Rio-Patras (Greece); Wolf, M. [Mergelskull 29, 47802 Krefeld (Germany); Taylor, G.H. [15 Hawkesbury Cres, Farrer Act 2607 (Australia); Flores, D. [Departamento de Geologia, Faculdade de Ciencias do Porto, Praca de Gomes Teixeira, 4099-002 Porto (Portugal)

2005-04-12

In the new classification (ICCP System 1994), the maceral group huminite has been revised from the previous classification (ICCP, 1971. Int. Handbook Coal Petr., suppl. to 2nd ed.) to accommodate the nomenclature to changes in the other maceral groups, especially the changes in the vitrinite classification (ICCP, 1998. The new vitrinite classification (ICCP System 1994). Fuel 77, 349-358.). The vitrinite and huminite systems have been correlated so that down to the level of sub-maceral groups, the two systems can be used in parallel. At the level of macerals and for finer classifications, the analyst now has, according to the nature of the coal and the purpose of the analysis, a choice of using either of the two classification systems for huminite and vitrinite. This is in accordance with the new ISO Coal Classification that covers low rank coals as well and allows for the simultaneous use of the huminite and vitrinite nomenclature for low rank coals.

Data for constructing insect genome content matrices for phylogenetic analysis and functional annotation

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Jeffrey Rosenfeld

2016-03-01

Full Text Available Twenty one fully sequenced and well annotated insect genomes were used to construct genome content matrices for phylogenetic analysis and functional annotation of insect genomes. To examine the role of e-value cutoff in ortholog determination we used scaled e-value cutoffs and a single linkage clustering approach.. The present communication includes (1 a list of the genomes used to construct the genome content phylogenetic matrices, (2 a nexus file with the data matrices used in phylogenetic analysis, (3 a nexus file with the Newick trees generated by phylogenetic analysis, (4 an excel file listing the Core (CORE genes and Unique (UNI genes found in five insect groups, and (5 a figure showing a plot of consistency index (CI versus percent of unannotated genes that are apomorphies in the data set for gene losses and gains and bar plots of gains and losses for four consistency index (CI cutoffs.

Phylogenetic classification of the world’s tropical forests

OpenAIRE

Slik, J. W. Ferry; Franklin, Janet; Arroyo-Rodríguez, Víctor; Field, Richard; Aguilar, Salomon; Aguirre, Nikolay; Ahumada, Jorge; Aiba, Shin-Ichiro; Alves, Luciana F.; K, Anitha; Avella, Andres; Mora, Francisco; Aymard C., Gerardo A.; Báez, Selene; Balvanera, Patricia

2018-01-01

Identifying and explaining regional differences in tropical forest dynamics, structure, diversity, and composition are critical for anticipating region-specific responses to global environmental change. Floristic classifications are of fundamental importance for these efforts. Here we provide a global tropical forest classification that is explicitly based on community evolutionary similarity, resulting in identification of five major tropical forest regions and their relationships: (i) Indo-...

Gynecomastia Classification for Surgical Management: A Systematic Review and Novel Classification System.

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Waltho, Daniel; Hatchell, Alexandra; Thoma, Achilleas

2017-03-01

Gynecomastia is a common deformity of the male breast, where certain cases warrant surgical management. There are several surgical options, which vary depending on the breast characteristics. To guide surgical management, several classification systems for gynecomastia have been proposed. A systematic review was performed to (1) identify all classification systems for the surgical management of gynecomastia, and (2) determine the adequacy of these classification systems to appropriately categorize the condition for surgical decision-making. The search yielded 1012 articles, and 11 articles were included in the review. Eleven classification systems in total were ascertained, and a total of 10 unique features were identified: (1) breast size, (2) skin redundancy, (3) breast ptosis, (4) tissue predominance, (5) upper abdominal laxity, (6) breast tuberosity, (7) nipple malposition, (8) chest shape, (9) absence of sternal notch, and (10) breast skin elasticity. On average, classification systems included two or three of these features. Breast size and ptosis were the most commonly included features. Based on their review of the current classification systems, the authors believe the ideal classification system should be universal and cater to all causes of gynecomastia; be surgically useful and easy to use; and should include a comprehensive set of clinically appropriate patient-related features, such as breast size, breast ptosis, tissue predominance, and skin redundancy. None of the current classification systems appears to fulfill these criteria.

Cognitive-motivational deficits in ADHD: development of a classification system.

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Gupta, Rashmi; Kar, Bhoomika R; Srinivasan, Narayanan

2011-01-01

The classification systems developed so far to detect attention deficit/hyperactivity disorder (ADHD) do not have high sensitivity and specificity. We have developed a classification system based on several neuropsychological tests that measure cognitive-motivational functions that are specifically impaired in ADHD children. A total of 240 (120 ADHD children and 120 healthy controls) children in the age range of 6-9 years and 32 Oppositional Defiant Disorder (ODD) children (aged 9 years) participated in the study. Stop-Signal, Task-Switching, Attentional Network, and Choice Delay tests were administered to all the participants. Receiver operating characteristic (ROC) analysis indicated that percentage choice of long-delay reward best classified the ADHD children from healthy controls. Single parameters were not helpful in making a differential classification of ADHD with ODD. Multinominal logistic regression (MLR) was performed with multiple parameters (data fusion) that produced improved overall classification accuracy. A combination of stop-signal reaction time, posterror-slowing, mean delay, switch cost, and percentage choice of long-delay reward produced an overall classification accuracy of 97.8%; with internal validation, the overall accuracy was 92.2%. Combining parameters from different tests of control functions not only enabled us to accurately classify ADHD children from healthy controls but also in making a differential classification with ODD. These results have implications for the theories of ADHD.

Prognostic value of computed tomography classification systems for intra-articular calcaneus fractures.

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Swords, Michael P; Alton, Timothy B; Holt, Sarah; Sangeorzan, Bruce J; Shank, John R; Benirschke, Stephen K

2014-10-01

There are several published computed tomography (CT) classification systems for calcaneus fractures, each validated by a different standard. The goal of this study was to measure which system would best predict clinical outcomes as measured by a widely used and validated musculoskeletal health status questionnaire. Forty-nine patients with isolated intra-articular joint depression calcaneus fractures more than 2 years after treatment were identified. All had preoperative CT studies and were treated with open reduction and plate fixation using a lateral extensile approach. Four different blinded reviewers classified injuries according to the CT classification systems of Crosby and Fitzgibbons, Eastwood, and Sanders. Functional outcomes evaluated with a Musculoskeletal Functional Assessment (MFA). The mean follow-up was 4.3 years. The mean MFA score was 15.7 (SD = 11.6), which is not significantly different from published values for midfoot injuries, hindfoot injuries, or both, 1 year after injury (mean = 22.1, SD = 18.4). The classification systems of Crosby and Fitzgibbons, Eastwood, and Sanders, the number of fragments of the posterior facet, and payer status were not significantly associated with outcome as determined by the MFA. The Sanders classification trended toward significance. Anterior process comminution and surgeon's overall impression of severity were significantly associated with functional outcome. The amount of anterior process comminution was an important determinant of functional outcome with increasing anterior process comminution significantly associated with worsened functional outcome (P = .04). In addition, the surgeon's overall impression of severity of injury was predictive of functional outcome (P = .02), as determined by MFA. Level III, comparative series. © The Author(s) 2014.

Phylogenetic classification and the universal tree.

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Doolittle, W F

1999-06-25

From comparative analyses of the nucleotide sequences of genes encoding ribosomal RNAs and several proteins, molecular phylogeneticists have constructed a "universal tree of life," taking it as the basis for a "natural" hierarchical classification of all living things. Although confidence in some of the tree's early branches has recently been shaken, new approaches could still resolve many methodological uncertainties. More challenging is evidence that most archaeal and bacterial genomes (and the inferred ancestral eukaryotic nuclear genome) contain genes from multiple sources. If "chimerism" or "lateral gene transfer" cannot be dismissed as trivial in extent or limited to special categories of genes, then no hierarchical universal classification can be taken as natural. Molecular phylogeneticists will have failed to find the "true tree," not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree. However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished.

Phylogenetic convolutional neural networks in metagenomics.

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Fioravanti, Diego; Giarratano, Ylenia; Maggio, Valerio; Agostinelli, Claudio; Chierici, Marco; Jurman, Giuseppe; Furlanello, Cesare

2018-03-08

Convolutional Neural Networks can be effectively used only when data are endowed with an intrinsic concept of neighbourhood in the input space, as is the case of pixels in images. We introduce here Ph-CNN, a novel deep learning architecture for the classification of metagenomics data based on the Convolutional Neural Networks, with the patristic distance defined on the phylogenetic tree being used as the proximity measure. The patristic distance between variables is used together with a sparsified version of MultiDimensional Scaling to embed the phylogenetic tree in a Euclidean space. Ph-CNN is tested with a domain adaptation approach on synthetic data and on a metagenomics collection of gut microbiota of 38 healthy subjects and 222 Inflammatory Bowel Disease patients, divided in 6 subclasses. Classification performance is promising when compared to classical algorithms like Support Vector Machines and Random Forest and a baseline fully connected neural network, e.g. the Multi-Layer Perceptron. Ph-CNN represents a novel deep learning approach for the classification of metagenomics data. Operatively, the algorithm has been implemented as a custom Keras layer taking care of passing to the following convolutional layer not only the data but also the ranked list of neighbourhood of each sample, thus mimicking the case of image data, transparently to the user.

Partitioning the regional and local drivers of phylogenetic and functional diversity along temperate elevational gradients on an East Asian peninsula.

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Chun, Jung-Hwa; Lee, Chang-Bae

2018-02-12

Species-centric approaches to biodiversity in ecological research are limited in their ability to reflect the evolutionary history and functional diversity of community assembly. Recently, the introduction of alternative facets of biodiversity, such as phylogenetic and functional diversity, has shed light on this problem and improved our understanding of the processes underlying biodiversity patterns. Here, we investigated the phylogenetic and functional diversity patterns of α, β and γ components in woody plant assemblages along regional and local elevational gradients in South Korea. Although the patterns of phylogenetic and functional diversity varied along regional and local elevational transects, the main drivers were partitioned into two categories: regional area or climate for phylogenetic diversity, depending on whether the transect was at a regional or local scale; and habitat heterogeneity for functional diversity, which was derived in elevational bands. Moreover, environmental distance was more important than was geographic distance for phylogenetic and functional β diversity between paired elevational bands. These results support the hypothesis that niche-based deterministic processes such as environmental filtering and competitive exclusion are fundamental in structuring woody plant assemblages along temperate elevational gradients regardless of scale (regional vs. local) in our study areas.

Factors shaping bacterial phylogenetic and functional diversity in coastal waters of the NW Mediterranean Sea

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Boras, Julia A.; Vaqué, Dolors; Maynou, Francesc; Sà, Elisabet L.; Weinbauer, Markus G.; Sala, Maria Montserrat

2015-03-01

To evaluate the main factors shaping bacterioplankton phylogenetic and functional diversity in marine coastal waters, we carried out a two-year study based on a monthly sampling in Blanes Bay (NW Mediterranean). We expected the key factors driving bacterial diversity to be (1) temperature and nutrient concentration, together with chlorophyll a concentration as an indicator of phytoplankton biomass and, hence, a carbon source for bacteria (here called bottom-up factors), and (2) top-down pressure (virus- and protist-mediated mortality of bacteria). Phylogenetic diversity was analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA. Functional diversity was assessed by using monomeric carbon sources in Biolog EcoPlates and by determining the activity of six extracellular enzymes. Our results indicate that the bacterial phylogenetic and functional diversity in this coastal system is shaped mainly by bottom-up factors. A dendrogram analysis of the DGGE banding patterns revealed three main sample clusters. Two clusters differed significantly in temperature, nitrate and chlorophyll a concentration, and the third was characterized by the highest losses of bacterial production due to viral lysis detected over the whole study period. Protistan grazing had no effect on bacterial functional diversity, since there were no correlations between protist-mediated mortality (PMM) and extracellular enzyme activities, and utilization of only two out of the 31 carbon sources (N-acetyl-D-glucosamine and α-cyclodextrin) was correlated with PMM. In contrast, virus-mediated mortality correlated with changes in the percentage of use of four carbon sources, and also with specific leu-aminopeptidase and β-glucosidase activity. This suggests that viral lysate provides a pool of labile carbon sources, presumably including amino acids and glucose, which may inhibit proteolytic and glucosidic activity. Our results indicate that bottom-up factors play a more important role than

A systematic classification of Plasmodium falciparum P-loop NTPases: structural and functional correlation

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Chauhan Virander S

2009-04-01

Full Text Available Abstract Background The P-loop NTPases constitute one of the largest groups of globular protein domains that play highly diverse functional roles in most of the organisms. Even with the availability of nearly 300 different Hidden Markov Models representing the P-loop NTPase superfamily, not many P-loop NTPases are known in Plasmodium falciparum. A number of characteristic attributes of the genome have resulted into the lack of knowledge about this functionally diverse, but important class of proteins. Method In the study, protein sequences with characteristic motifs of NTPase domain (Walker A and Walker B are computationally extracted from the P. falciparum database. A detailed secondary structure analysis, functional classification, phylogenetic and orthology studies of the NTPase domain of repertoire of 97 P. falciparum P-loop NTPases is carried out. Results Based upon distinct sequence features and secondary structure profile of the P-loop domain of obtained sequences, a cladistic classification is also conceded: nucleotide kinases and GTPases, ABC and SMC family, SF1/2 helicases, AAA+ and AAA protein families. Attempts are made to identify any ortholog(s for each of these proteins in other Plasmodium sp. as well as its vertebrate host, Homo sapiens. A number of P. falciparum P-loop NTPases that have no homologue in the host, as well as those annotated as hypothetical proteins and lack any characteristic functional domain are identified. Conclusion The study suggests a strong correlation between sequence and secondary structure profile of P-loop domains and functional roles of these proteins and thus provides an opportunity to speculate the role of many hypothetical proteins. The study provides a methodical framework for the characterization of biologically diverse NTPases in the P. falciparum genome. The efforts made in the analysis are first of its kind; and the results augment to explore the functional role of many of these proteins from

High-resolution phylogenetic microbial community profiling

Energy Technology Data Exchange (ETDEWEB)

Singer, Esther; Coleman-Derr, Devin; Bowman, Brett; Schwientek, Patrick; Clum, Alicia; Copeland, Alex; Ciobanu, Doina; Cheng, Jan-Fang; Gies, Esther; Hallam, Steve; Tringe, Susannah; Woyke, Tanja

2014-03-17

The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance our knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.

Towards precise classification of cancers based on robust gene functional expression profiles

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Zhu Jing

2005-03-01

Full Text Available Abstract Background Development of robust and efficient methods for analyzing and interpreting high dimension gene expression profiles continues to be a focus in computational biology. The accumulated experiment evidence supports the assumption that genes express and perform their functions in modular fashions in cells. Therefore, there is an open space for development of the timely and relevant computational algorithms that use robust functional expression profiles towards precise classification of complex human diseases at the modular level. Results Inspired by the insight that genes act as a module to carry out a highly integrated cellular function, we thus define a low dimension functional expression profile for data reduction. After annotating each individual gene to functional categories defined in a proper gene function classification system such as Gene Ontology applied in this study, we identify those functional categories enriched with differentially expressed genes. For each functional category or functional module, we compute a summary measure (s for the raw expression values of the annotated genes to capture the overall activity level of the module. In this way, we can treat the gene expressions within a functional module as an integrative data point to replace the multiple values of individual genes. We compare the classification performance of decision trees based on functional expression profiles with the conventional gene expression profiles using four publicly available datasets, which indicates that precise classification of tumour types and improved interpretation can be achieved with the reduced functional expression profiles. Conclusion This modular approach is demonstrated to be a powerful alternative approach to analyzing high dimension microarray data and is robust to high measurement noise and intrinsic biological variance inherent in microarray data. Furthermore, efficient integration with current biological knowledge

Gross Motor Function Classification System Expanded & Revised (GMFCS E & R: reliability between therapists and parents in Brazil

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Daniela B. R. Silva

2013-10-01

Full Text Available BACKGROUND: Several studies have demonstrated the importance of using the Gross Motor Function Classification System (GMFCS to classify gross motor function in children with cerebral palsy, but the reliability of the expanded and revised version has not been examined in Brazil (GMFCS E & R. OBJECTIVE:: To determine the intra- and inter-rater reliability of the Portuguese-Brazil version of the GMFCS E & R applied by therapists and compare to classification provided by parents of children with cerebral palsy. METHOD: Data were obtained from 90 children with cerebral palsy, aged 4 to 18 years old, attending the neurology or rehabilitation service of a Brazilian hospital. Therapists classified the children's motor function using the GMFCS E & R and parents used the Brazilian Portuguese version of the GMFCS Family Report Questionnaire. Intra- and inter-rater reliability was obtained through percentage agreement and Cohen's unweighted Kappa statistics (k. The Chi-square test was used to identify significant differences in the classification of parents and therapists. RESULTS: Almost perfect agreement was reached between the therapists [K=0.90 (95% confidence interval 0.83-0.97] and intra-raters (therapists with K=1.00 [95% confidence interval (1.00-1.00], p<0.001. Agreement between therapists and parents was substantial (k=0.716, confidence interval 0.596-0.836, though parents classify gross motor impairment more severely than therapists (p=0.04. CONCLUSIONS: The Portuguese version of the GMFCS E & R is reliable for use by parents and therapists. Parents tend to classify their children's limitations more severely, because they know their performance in different environments.

14 CFR Section 9 - Functional Classification-Operating Revenues

Science.gov (United States)

2010-01-01

... AIR CARRIERS Profit and Loss Classification Section 9 Functional Classification—Operating Revenues... shall be included in profit and loss classification 8100, Nonoperating Income and Expense-Net, and the... for all air carrier groups and shall include all revenues from the United States Government as direct...

GA Based Optimal Feature Extraction Method for Functional Data Classification

OpenAIRE

Jun Wan; Zehua Chen; Yingwu Chen; Zhidong Bai

2010-01-01

Classification is an interesting problem in functional data analysis (FDA), because many science and application problems end up with classification problems, such as recognition, prediction, control, decision making, management, etc. As the high dimension and high correlation in functional data (FD), it is a key problem to extract features from FD whereas keeping its global characters, which relates to the classification efficiency and precision to heavens. In this paper...

Phylogenetic relationships among species of Lutzomyia, subgenus Lutzomyia (Diptera: Psychodidae).

Science.gov (United States)

Pinto, Israel S; Filho, José D Andrade; Santos, Claudiney B; Falqueto, Aloísio; Leite, Yuri L R

2010-01-01

Lutzomyia França is the largest and most diverse sand fly genus in the New World and contains all the species involved in the transmission of American visceral leishmaniasis (AVL). Morphological characters were used to test the monophyly and to infer phylogenetic relationships among members of the Lutzomyia subgenus. Fifty-two morphological characters from male and female adult specimens belonging to 18 species of Lu. (Lutzomyia) were scored and analyzed. The resulting phylogeny confirms the monophyly of this subgenus and reveals four main internal clades. These four clades, however, do not support the classification of the subgenus in two series, longipalpis and cavernicola, because neither is necessarily monophyletic. Knowledge on phylogenetic relationships among these relevant vectors of AVL should be used as a tool for monitoring target taxa and a first step for establishing an early warning system for disease control.

DIF Trees: Using Classification Trees to Detect Differential Item Functioning

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Vaughn, Brandon K.; Wang, Qiu

2010-01-01

A nonparametric tree classification procedure is used to detect differential item functioning for items that are dichotomously scored. Classification trees are shown to be an alternative procedure to detect differential item functioning other than the use of traditional Mantel-Haenszel and logistic regression analysis. A nonparametric…

Guidance on classification for reproductive toxicity under the globally harmonized system of classification and labelling of chemicals (GHS).

Science.gov (United States)

Moore, Nigel P; Boogaard, Peter J; Bremer, Susanne; Buesen, Roland; Edwards, James; Fraysse, Benoit; Hallmark, Nina; Hemming, Helena; Langrand-Lerche, Carole; McKee, Richard H; Meisters, Marie-Louise; Parsons, Paul; Politano, Valerie; Reader, Stuart; Ridgway, Peter; Hennes, Christa

2013-11-01

The Globally Harmonised System of Classification (GHS) is a framework within which the intrinsic hazards of substances may be determined and communicated. It is not a legislative instrument per se, but is enacted into national legislation with the appropriate legislative instruments. GHS covers many aspects of effects upon health and the environment, including adverse effects upon sexual function and fertility or on development. Classification for these effects is based upon observations in humans or from properly designed experiments in animals, although only the latter is covered herein. The decision to classify a substance based upon experimental data, and the category of classification ascribed, is determined by the level of evidence that is available for an adverse effect on sexual function and fertility or on development that does not arise as a secondary non-specific consequence of other toxic effect. This document offers guidance on the determination of level of concern as a measure of adversity, and the level of evidence to ascribe classification based on data from tests in laboratory animals.

How does cognition evolve? Phylogenetic comparative psychology

Science.gov (United States)

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

2014-01-01

Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution. PMID:21927850

How does cognition evolve? Phylogenetic comparative psychology.

Science.gov (United States)

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

2012-03-01

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

Towards a new classification system for legumes: Progress report from the 6th International Legume Conference

NARCIS (Netherlands)

Pontes Coelho Borges, L.M.; Bruneau, A.; Cardoso, D.; Crisp, M.; Delgado-Salinas, A.; Doyle, J.J.; Egan, A.; Herendeen, P.S.; Hughes, C.; Kenicer, G.; Klitgaard, B.; Koenen, E.; Lavin, M.; Lewis, G.; Luckow, M.; Mackinder, B.; Malecot, V.; Miller, J.T.; Pennington, R.T.; Queiroz, de L.P.; Schrire, B.; Simon, M.F.; Steele, K.; Torke, B.; Wieringa, J.J.; Wojciechowski, M.F.; Boatwright, S.; Estrella, de la M.; Mansano, V.D.; Prado, D.E.; Stirton, C.; Wink, M.

2013-01-01

Legume systematists have been making great progress in understanding evolutionary relationships within the Leguminosae (Fabaceae), the third largest family of flowering plants. As the phylogenetic picture has become clearer, so too has the need for a revised classification of the family. The

Effects of species' similarity and dominance on the functional and phylogenetic structure of a plant meta-community.

Science.gov (United States)

Chalmandrier, L; Münkemüller, T; Lavergne, S; Thuiller, W

2015-01-01

Different assembly processes drive the spatial structure of meta-communities (beta-diversity). Recently, functional and phylogenetic diversities have been suggested as indicators of these assembly processes. Assuming that diversity is a good proxy for niche overlap, high beta-diversity along environmental gradients should be the result of environmental filtering while low beta-diversity should stem from competitive interactions. So far, studies trying to disentangle the relative importance of these assembly processes have provided mixed results. One reason for this may be that these studies often rely on a single measure of diversity and thus implicitly make a choice on how they account for species relative abundances and how species similarities are captured by functional traits or phylogeny. Here, we tested the effect of gradually scaling the importance of dominance (the weight given to dominant vs. rare species) and species similarity (the weight given to small vs. large similarities) on resulting beta-diversity patterns of an alpine plant meta-community. To this end, we combined recent extensions of the Hill numbers framework with Pagel's phylogenetic tree transformation approach. We included functional (based on the leaf-height-seed spectrum) and phylogenetic facets of beta-diversity in our analysis and explicitly accounted for effects of environmental and spatial covariates. We found that functional beta-diversity, was high when the same weight was given to dominant vs. rare species and to large vs. small species' similarities. In contrast, phylogenetic beta-diversity was low when greater weight was given to dominant species and small species' similarities. Those results suggested that different environments along the gradients filtered different species according to their functional traits, while, the same competitive lineages dominated communities across the gradients. Our results highlight that functional vs. phylogenetic facets, presence-absence vs

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

Science.gov (United States)

Allende, Christian; Sohn, Erik; Little, Cedric

2015-12-29

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

On the need for phylogenetic ‘corrections’ in functional trait-based approaches

Czech Academy of Sciences Publication Activity Database

de Bello, Francesco; Berg, M. P.; Dias, A. T. C.; Diniz-Filho, J. A. F.; Götzenberger, Lars; Hortal, J.; Ladle, L. J.; Lepš, Jan

2015-01-01

Roč. 50, č. 4 (2015), 349-357 ISSN 1211-9520 R&D Projects: GA ČR GAP505/12/1296; GA ČR GB14-36079G Institutional support: RVO:67985939 ; RVO:60077344 Keywords : adaptation * functional and phylogenetic diversity * limiting similarity Subject RIV: EH - Ecology, Behaviour Impact factor: 1.433, year: 2015

Pattern classification and recognition of invertebrate functional groups using self-organizing neural networks.

Science.gov (United States)

Zhang, WenJun

2007-07-01

Self-organizing neural networks can be used to mimic non-linear systems. The main objective of this study is to make pattern classification and recognition on sampling information using two self-organizing neural network models. Invertebrate functional groups sampled in the irrigated rice field were classified and recognized using one-dimensional self-organizing map and self-organizing competitive learning neural networks. Comparisons between neural network models, distance (similarity) measures, and number of neurons were conducted. The results showed that self-organizing map and self-organizing competitive learning neural network models were effective in pattern classification and recognition of sampling information. Overall the performance of one-dimensional self-organizing map neural network was better than self-organizing competitive learning neural network. The number of neurons could determine the number of classes in the classification. Different neural network models with various distance (similarity) measures yielded similar classifications. Some differences, dependent upon the specific network structure, would be found. The pattern of an unrecognized functional group was recognized with the self-organizing neural network. A relative consistent classification indicated that the following invertebrate functional groups, terrestrial blood sucker; terrestrial flyer; tourist (nonpredatory species with no known functional role other than as prey in ecosystem); gall former; collector (gather, deposit feeder); predator and parasitoid; leaf miner; idiobiont (acarine ectoparasitoid), were classified into the same group, and the following invertebrate functional groups, external plant feeder; terrestrial crawler, walker, jumper or hunter; neustonic (water surface) swimmer (semi-aquatic), were classified into another group. It was concluded that reliable conclusions could be drawn from comparisons of different neural network models that use different distance

Towards the system-wide implementation of the International Classification of Functioning, Disability and Health in routine practice: Lessons from a pilot study in China.

Science.gov (United States)

Li, Jianan; Prodinger, Birgit; Reinhardt, Jan D; Stucki, Gerold

2016-06-13

In 2011 the Chinese leadership in rehabilitation, in collaboration with the International Classification of Functioning, Disability and Health (ICF) Research Branch, embarked on an effort towards the system-wide implementation of the ICF in the healthcare system in China. We report here on the lessons learned from the pilot phase of testing the ICF Generic Set, a parsimonious set of 7 ICF categories, which have been shown to best describe functioning across the general population and people with various health conditions, for use in routine clinical practice in China. The paper discusses whether classification and measurement are compatible, what number of ICF categories should be included in data collection in routine practice, and the usefulness of a functioning profile and functioning score in clinical practice and health research planning. In addition, the paper reflects on the use of ICF qualifiers in a rating scale and the particularities of certain ICF categories contained in the ICF Generic Set when used as items in the context of Chinese rehabilitation and healthcare. Finally, the steps required to enhance the utility of system-wide implementation of the ICF in rehabilitation and healthcare services are set out.

Cyanobacterial nitrogenases: phylogenetic diversity, regulation and functional predictions

Directory of Open Access Journals (Sweden)

Alberto A. Esteves-Ferreira

2017-03-01

Full Text Available Abstract Cyanobacteria is a remarkable group of prokaryotic photosynthetic microorganisms, with several genera capable of fixing atmospheric nitrogen (N2 and presenting a wide range of morphologies. Although the nitrogenase complex is not present in all cyanobacterial taxa, it is spread across several cyanobacterial strains. The nitrogenase complex has also a high theoretical potential for biofuel production, since H2 is a by-product produced during N2 fixation. In this review we discuss the significance of a relatively wide variety of cell morphologies and metabolic strategies that allow spatial and temporal separation of N2 fixation from photosynthesis in cyanobacteria. Phylogenetic reconstructions based on 16S rRNA and nifD gene sequences shed light on the evolutionary history of the two genes. Our results demonstrated that (i sequences of genes involved in nitrogen fixation (nifD from several morphologically distinct strains of cyanobacteria are grouped in similarity with their morphology classification and phylogeny, and (ii nifD genes from heterocytous strains share a common ancestor. By using this data we also discuss the evolutionary importance of processes such as horizontal gene transfer and genetic duplication for nitrogenase evolution and diversification. Finally, we discuss the importance of H2 synthesis in cyanobacteria, as well as strategies and challenges to improve cyanobacterial H2 production.

Casemix classification systems.

Science.gov (United States)

Fetter, R B

1999-01-01

The idea of using casemix classification to manage hospital services is not new, but has been limited by available technology. It was not until after the introduction of Medicare in the United States in 1965 that serious attempts were made to measure hospital production in order to contain spiralling costs. This resulted in a system of casemix classification known as diagnosis related groups (DRGs). This paper traces the development of DRGs and their evolution from the initial version to the All Patient Refined DRGs developed in 1991.

Relative roles of local disturbance, current climate and palaeoclimate in determining phylogenetic and functional diversity in Chinese forests

DEFF Research Database (Denmark)

Feng, Gang; Mi, Xiangcheng; Bøcher, Peder Klith

2014-01-01

their relative roles in determining woody plant phylogenetic and functional diversity in this important hotspot for woody plant diversity. Local disturbance was the best predictor of functional diversity as represented by maximum canopy height (Hmax), probably reflecting the dominant role of competition...... studied, their relative importance for other aspects of diversity, notably phylogenetic and functional diversity is so far little studied. Here, we link data from large Chinese forest plots to data on current and Last Glacial Maximum (LGM) climate as well as local disturbance regimes to study...

Phylogenetic classification of yeasts and related taxa within Pucciniomycotina.

Science.gov (United States)

Wang, Q-M; Yurkov, A M; Göker, M; Lumbsch, H T; Leavitt, S D; Groenewald, M; Theelen, B; Liu, X-Z; Boekhout, T; Bai, F-Y

2015-06-01

Most small genera containing yeast species in the Pucciniomycotina (Basidiomycota, Fungi) are monophyletic, whereas larger genera including Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces are polyphyletic. With the implementation of the "One Fungus = One Name" nomenclatural principle these polyphyletic genera were revised. Nine genera, namely Bannoa, Cystobasidiopsis, Colacogloea, Kondoa, Erythrobasidium, Rhodotorula, Sporobolomyces, Sakaguchia and Sterigmatomyces, were emended to include anamorphic and teleomorphic species based on the results obtained by a multi-gene phylogenetic analysis, phylogenetic network analyses, branch length-based methods, as well as morphological, physiological and biochemical comparisons. A new class Spiculogloeomycetes is proposed to accommodate the order Spiculogloeales. The new families Buckleyzymaceae with Buckleyzyma gen. nov., Chrysozymaceae with Chrysozyma gen. nov., Microsporomycetaceae with Microsporomyces gen. nov., Ruineniaceae with Ruinenia gen. nov., Symmetrosporaceae with Symmetrospora gen. nov., Colacogloeaceae and Sakaguchiaceae are proposed. The new genera Bannozyma, Buckleyzyma, Fellozyma, Hamamotoa, Hasegawazyma, Jianyunia, Rhodosporidiobolus, Oberwinklerozyma, Phenoliferia, Pseudobensingtonia, Pseudohyphozyma, Sampaiozyma, Slooffia, Spencerozyma, Trigonosporomyces, Udeniozyma, Vonarxula, Yamadamyces and Yunzhangia are proposed to accommodate species segregated from the genera Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces. Ballistosporomyces is emended and reintroduced to include three Sporobolomyces species of the sasicola clade. A total of 111 new combinations are proposed in this study.

Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ∼500 MY

Directory of Open Access Journals (Sweden)

Abhishek Kumar

2015-06-01

Full Text Available The serpin superfamily is characterized by proteins that fold into a conserved tertiary structure and exploits a sophisticated and irreversible suicide-mechanism of inhibition. Vertebrate serpins are classified into six groups (V1–V6, based on three independent biological features—genomic organization, diagnostic amino acid sites and rare indels. However, this classification system was based on the limited number of mammalian genomes available. In this study, several non-mammalian genomes are used to validate this classification system using the powerful Bayesian phylogenetic method. This method supports the intron and indel based vertebrate classification and proves that serpins have been maintained from lampreys to humans for about 500 MY. Lampreys have fewer than 10 serpins, which expand into 36 serpins in humans. The two expanding groups V1 and V2 have SERPINB1/SERPINB6 and SERPINA8/SERPIND1 as the ancestral serpins, respectively. Large clusters of serpins are formed by local duplications of these serpins in tetrapod genomes. Interestingly, the ancestral HCII/SERPIND1 locus (nested within PIK4CA possesses group V4 serpin (A2APL1, homolog of α2-AP/SERPINF2 of lampreys; hence, pointing to the fact that group V4 might have originated from group V2. Additionally in this study, details of the phylogenetic history and genomic characteristics of vertebrate serpins are revisited.

PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis

KAUST Repository

Benavente, Ernest D; Coll, Francesc; Furnham, Nick; McNerney, Ruth; Glynn, Judith R; Campino, Susana; Pain, Arnab; Mohareb, Fady R; Clark, Taane G

2015-01-01

Phylogenetic-based classification of M. tuberculosis and other bacterial genomes is a core analysis for studying evolutionary hypotheses, disease outbreaks and transmission events. Whole genome sequencing is providing new insights

Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae.

Science.gov (United States)

Westneat, Mark W; Alfaro, Michael E; Wainwright, Peter C; Bellwood, David R; Grubich, Justin R; Fessler, Jennifer L; Clements, Kendall D; Smith, Lydia L

2005-05-22

The Labridae is one of the most structurally and functionally diversified fish families on coral and rocky reefs around the world, providing a compelling system for examination of evolutionary patterns of functional change. Labrid fishes have evolved a diverse array of skull forms for feeding on prey ranging from molluscs, crustaceans, plankton, detritus, algae, coral and other fishes. The species richness and diversity of feeding ecology in the Labridae make this group a marine analogue to the cichlid fishes. Despite the importance of labrids to coastal reef ecology, we lack evolutionary analysis of feeding biomechanics among labrids. Here, we combine a molecular phylogeny of the Labridae with the biomechanics of skull function to reveal a broad pattern of repeated convergence in labrid feeding systems. Mechanically fast jaw systems have evolved independently at least 14 times from ancestors with forceful jaws. A repeated phylogenetic pattern of functional divergence in local regions of the labrid tree produces an emergent family-wide pattern of global convergence in jaw function. Divergence of close relatives, convergence among higher clades and several unusual 'breakthroughs' in skull function characterize the evolution of functional complexity in one of the most diverse groups of reef fishes.

Competitive interactions between forest trees are driven by species' trait hierarchy, not phylogenetic or functional similarity: implications for forest community assembly.

Science.gov (United States)

Kunstler, Georges; Lavergne, Sébastien; Courbaud, Benoît; Thuiller, Wilfried; Vieilledent, Ghislain; Zimmermann, Niklaus E; Kattge, Jens; Coomes, David A

2012-08-01

The relative importance of competition vs. environmental filtering in the assembly of communities is commonly inferred from their functional and phylogenetic structure, on the grounds that similar species compete most strongly for resources and are therefore less likely to coexist locally. This approach ignores the possibility that competitive effects can be determined by relative positions of species on a hierarchy of competitive ability. Using growth data, we estimated 275 interaction coefficients between tree species in the French mountains. We show that interaction strengths are mainly driven by trait hierarchy and not by functional or phylogenetic similarity. On the basis of this result, we thus propose that functional and phylogenetic convergence in local tree community might be due to competition-sorting species with different competitive abilities and not only environmental filtering as commonly assumed. We then show a functional and phylogenetic convergence of forest structure with increasing plot age, which supports this view. © 2012 Blackwell Publishing Ltd/CNRS.

Disturbance by an endemic rodent in an arid shrubland is a habitat filter: effects on plant invasion and taxonomical, functional and phylogenetic community structure.

Science.gov (United States)

Escobedo, Víctor M; Rios, Rodrigo S; Salgado-Luarte, Cristian; Stotz, Gisela C; Gianoli, Ernesto

2017-03-01

Disturbance often drives plant invasion and may modify community assembly. However, little is known about how these modifications of community patterns occur in terms of taxonomic, functional and phylogenetic structure. This study evaluated in an arid shrubland the influence of disturbance by an endemic rodent on community functional divergence and phylogenetic structure as well as on plant invasion. It was expected that disturbance would operate as a habitat filter favouring exotic species with short life cycles. Sixteen plots were sampled along a disturbance gradient caused by the endemic fossorial rodent Spalacopus cyanus , measuring community parameters and estimating functional divergence for life history traits (functional dispersion index) and the relative contribution to functional divergence of exotic and native species. The phylogenetic signal (Pagel's lambda) and phylogenetic community structure (mean phylogenetic distance and mean nearest taxon phylogenetic distance) were also estimated. The use of a continuous approach to the disturbance gradient allowed the identification of non-linear relationships between disturbance and community parameters. The relationship between disturbance and both species richness and abundance was positive for exotic species and negative for native species. Disturbance modified community composition, and exotic species were associated with more disturbed sites. Disturbance increased trait convergence, which resulted in phylogenetic clustering because traits showed a significant phylogenetic signal. The relative contribution of exotic species to functional divergence increased, while that of natives decreased, with disturbance. Exotic and native species were not phylogenetically distinct. Disturbance by rodents in this arid shrubland constitutes a habitat filter over phylogeny-dependent life history traits, leading to phylogenetic clustering, and drives invasion by favouring species with short life cycles. Results can be

Introductions do not compensate for functional and phylogenetic losses following extinctions in insular bird assemblages.

Science.gov (United States)

Sobral, Fernando L; Lees, Alexander C; Cianciaruso, Marcus V

2016-09-01

The ratio of species extinctions to introductions has been comparable for many insular assemblages, suggesting that introductions could have 'compensated' for extinctions. However, the capacity for introduced species to replace ecological roles and evolutionary history lost following extinction is unclear. We investigated changes in bird functional and phylogenetic diversity in the wake of extinctions and introductions across a sample of 32 islands worldwide. We found that extinct and introduced species have comparable functional and phylogenetic alpha diversity. However, this was distributed at different positions in functional space and in the phylogeny, indicating a 'false compensation'. Introduced and extinct species did not have equivalent functional roles nor belong to similar lineages. This makes it unlikely that novel island biotas composed of introduced taxa will be able to maintain ecological roles and represent the evolutionary histories of pre-disturbance assemblages and highlights the importance of evaluating changes in alpha and beta diversity concurrently. © 2016 John Wiley & Sons Ltd/CNRS.

A new web-based system for unsupervised classification of satellite images from the Google Maps engine

Science.gov (United States)

Ferrán, Ángel; Bernabé, Sergio; García-Rodríguez, Pablo; Plaza, Antonio

2012-10-01

In this paper, we develop a new web-based system for unsupervised classification of satellite images available from the Google Maps engine. The system has been developed using the Google Maps API and incorporates functionalities such as unsupervised classification of image portions selected by the user (at the desired zoom level). For this purpose, we use a processing chain made up of the well-known ISODATA and k-means algorithms, followed by spatial post-processing based on majority voting. The system is currently hosted on a high performance server which performs the execution of classification algorithms and returns the obtained classification results in a very efficient way. The previous functionalities are necessary to use efficient techniques for the classification of images and the incorporation of content-based image retrieval (CBIR). Several experimental validation types of the classification results with the proposed system are performed by comparing the classification accuracy of the proposed chain by means of techniques available in the well-known Environment for Visualizing Images (ENVI) software package. The server has access to a cluster of commodity graphics processing units (GPUs), hence in future work we plan to perform the processing in parallel by taking advantage of the cluster.

Functional classification of pulmonary hypertension in children: Report from the PVRI pediatric taskforce, Panama 2011.

Science.gov (United States)

Lammers, Astrid E; Adatia, Ian; Cerro, Maria Jesus Del; Diaz, Gabriel; Freudenthal, Alexandra Heath; Freudenthal, Franz; Harikrishnan, S; Ivy, Dunbar; Lopes, Antonio A; Raj, J Usha; Sandoval, Julio; Stenmark, Kurt; Haworth, Sheila G

2011-08-02

The members of the Pediatric Task Force of the Pulmonary Vascular Research Institute (PVRI) were aware of the need to develop a functional classification of pulmonary hypertension in children. The proposed classification follows the same pattern and uses the same criteria as the Dana Point pulmonary hypertension specific classification for adults. Modifications were necessary for children, since age, physical growth and maturation influences the way in which the functional effects of a disease are expressed. It is essential to encapsulate a child's clinical status, to make it possible to review progress with time as he/she grows up, as consistently and as objectively as possible. Particularly in younger children we sought to include objective indicators such as thriving, need for supplemental feeds and the record of school or nursery attendance. This helps monitor the clinical course of events and response to treatment over the years. It also facilitates the development of treatment algorithms for children. We present a consensus paper on a functional classification system for children with pulmonary hypertension, discussed at the Annual Meeting of the PVRI in Panama City, February 2011.

Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction.

Science.gov (United States)

Beiko, Robert G; Ragan, Mark A

2009-01-01

Phylogenomic methods can be used to investigate the tangled evolutionary relationships among genomes. Building 'all the trees of all the genes' can potentially identify common pathways of horizontal gene transfer (HGT) among taxa at varying levels of phylogenetic depth. Phylogenetic affinities can be aggregated and merged with the information about genetic linkage and biochemical function to examine hypotheses of adaptive evolution via HGT. Additionally, the use of many genetic data sets increases the power of statistical tests for phylogenetic artifacts. However, large-scale phylogenetic analyses pose several challenges, including the necessary abandonment of manual validation techniques, the need to translate inferred phylogenetic discordance into inferred HGT events, and the challenges involved in aggregating results from search-based inference methods. In this chapter we describe a tree search procedure to recover the most parsimonious pathways of HGT, and examine some of the assumptions that are made by this method.

Phylogenetic and Functional Diversity of Fleshy-Fruited Plants Are Positively Associated with Seedling Diversity in a Tropical Montane Forest

Directory of Open Access Journals (Sweden)

Marcia C. Muñoz

2017-08-01

Full Text Available Mutualistic interactions between plants and animals can affect both plant and animal communities, and potentially leave imprints on plant demography. Yet, no study has simultaneously tested how trait variation in plant resources shapes the diversity of animal consumers, and how these interactions influence seedling recruitment. Here, we analyzed whether (i phylogenetic diversity and functional diversity of fruiting plants were correlated with the corresponding diversity of frugivorous birds, and (ii whether phylogenetic diversity and functional identity of plant and bird communities influenced the corresponding diversity and identity of seedling communities. We recorded mutualistic interactions between fleshy-fruited plants and frugivorous birds and seedling communities in 10 plots along an elevational gradient in the Colombian Andes. We built a phylogeny for plants/seedlings and birds and measured relevant morphological plant and bird traits that influence plant-bird interactions and seedling recruitment. We found that phylogenetic diversity and functional diversity of frugivorous birds were positively associated with the corresponding diversities of fruiting plants, consistent with a bottom-up effect of plants on birds. Moreover, the phylogenetic diversity of seedlings was related to the phylogenetic diversity of plants, but was unrelated to the phylogenetic diversity of frugivorous birds, suggesting that top-down effects of animals on seedlings were weak. Mean seed mass of seedling communities was positively associated with the mean fruit mass of plants, but was not associated with the mean avian body mass in the frugivore communities. Our study shows that variation in the traits of fleshy-fruited plants was associated with the diversity of frugivorous birds and affected the future trajectory of seedling recruitment, whereas the morphological traits of animal seed dispersers were unrelated to the phylogenetic and functional structure of

Molecular Phylogenetic: Organism Taxonomy Method Based on Evolution History

Directory of Open Access Journals (Sweden)

N.L.P Indi Dharmayanti

2011-03-01

Full Text Available Phylogenetic is described as taxonomy classification of an organism based on its evolution history namely its phylogeny and as a part of systematic science that has objective to determine phylogeny of organism according to its characteristic. Phylogenetic analysis from amino acid and protein usually became important area in sequence analysis. Phylogenetic analysis can be used to follow the rapid change of a species such as virus. The phylogenetic evolution tree is a two dimensional of a species graphic that shows relationship among organisms or particularly among their gene sequences. The sequence separation are referred as taxa (singular taxon that is defined as phylogenetically distinct units on the tree. The tree consists of outer branches or leaves that represents taxa and nodes and branch represent correlation among taxa. When the nucleotide sequence from two different organism are similar, they were inferred to be descended from common ancestor. There were three methods which were used in phylogenetic, namely (1 Maximum parsimony, (2 Distance, and (3 Maximum likehoood. Those methods generally are applied to construct the evolutionary tree or the best tree for determine sequence variation in group. Every method is usually used for different analysis and data.

An Outlyingness Matrix for Multivariate Functional Data Classification

KAUST Repository

Dai, Wenlin

2017-08-25

The classification of multivariate functional data is an important task in scientific research. Unlike point-wise data, functional data are usually classified by their shapes rather than by their scales. We define an outlyingness matrix by extending directional outlyingness, an effective measure of the shape variation of curves that combines the direction of outlyingness with conventional statistical depth. We propose two classifiers based on directional outlyingness and the outlyingness matrix, respectively. Our classifiers provide better performance compared with existing depth-based classifiers when applied on both univariate and multivariate functional data from simulation studies. We also test our methods on two data problems: speech recognition and gesture classification, and obtain results that are consistent with the findings from the simulated data.

The history of female genital tract malformation classifications and proposal of an updated system.

Science.gov (United States)

Acién, Pedro; Acién, Maribel I

2011-01-01

A correct classification of malformations of the female genital tract is essential to prevent unnecessary and inadequate surgical operations and to compare reproductive results. An ideal classification system should be based on aetiopathogenesis and should suggest the appropriate therapeutic strategy. We conducted a systematic review of relevant articles found in PubMed, Scopus, Scirus and ISI webknowledge, and analysis of historical collections of 'female genital malformations' and 'classifications'. Of 124 full-text articles assessed for eligibility, 64 were included because they contained original general, partial or modified classifications. All the existing classifications were analysed and grouped. The unification of terms and concepts was also analysed. Traditionally, malformations of the female genital tract have been catalogued and classified as Müllerian malformations due to agenesis, lack of fusion, the absence of resorption and lack of posterior development of the Müllerian ducts. The American Fertility Society classification of the late 1980s included seven basic groups of malformations also considering the Müllerian development and the relationship of the malformations to fertility. Other classifications are based on different aspects: functional, defects in vertical fusion, embryological or anatomical (Vagina, Cervix, Uterus, Adnex and Associated Malformation: VCUAM classification). However, an embryological-clinical classification system seems to be the most appropriate. Accepting the need for a new classification system of genitourinary malformations that considers the experience gained from the application of the current classification systems, the aetiopathogenesis and that also suggests the appropriate treatment, we proposed an update of our embryological-clinical classification as a new system with six groups of female genitourinary anomalies.

A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference.

Science.gov (United States)

Shen, Xing-Xing; Salichos, Leonidas; Rokas, Antonis

2016-09-02

Molecular phylogenetic inference is inherently dependent on choices in both methodology and data. Many insightful studies have shown how choices in methodology, such as the model of sequence evolution or optimality criterion used, can strongly influence inference. In contrast, much less is known about the impact of choices in the properties of the data, typically genes, on phylogenetic inference. We investigated the relationships between 52 gene properties (24 sequence-based, 19 function-based, and 9 tree-based) with each other and with three measures of phylogenetic signal in two assembled data sets of 2,832 yeast and 2,002 mammalian genes. We found that most gene properties, such as evolutionary rate (measured through the percent average of pairwise identity across taxa) and total tree length, were highly correlated with each other. Similarly, several gene properties, such as gene alignment length, Guanine-Cytosine content, and the proportion of tree distance on internal branches divided by relative composition variability (treeness/RCV), were strongly correlated with phylogenetic signal. Analysis of partial correlations between gene properties and phylogenetic signal in which gene evolutionary rate and alignment length were simultaneously controlled, showed similar patterns of correlations, albeit weaker in strength. Examination of the relative importance of each gene property on phylogenetic signal identified gene alignment length, alongside with number of parsimony-informative sites and variable sites, as the most important predictors. Interestingly, the subsets of gene properties that optimally predicted phylogenetic signal differed considerably across our three phylogenetic measures and two data sets; however, gene alignment length and RCV were consistently included as predictors of all three phylogenetic measures in both yeasts and mammals. These results suggest that a handful of sequence-based gene properties are reliable predictors of phylogenetic signal

The phylogenetic likelihood library.

Science.gov (United States)

Flouri, T; Izquierdo-Carrasco, F; Darriba, D; Aberer, A J; Nguyen, L-T; Minh, B Q; Von Haeseler, A; Stamatakis, A

2015-03-01

We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implementation of the phylogenetic likelihood function and a thorough documentation provide a framework for rapid development of scalable parallel phylogenetic software. By example of two likelihood-based phylogenetic codes we show that the PLL improves the sequential performance of current software by a factor of 2-10 while requiring only 1 month of programming time for integration. We show that, when numerical scaling for preventing floating point underflow is enabled, the double precision likelihood calculations in the PLL are up to 1.9 times faster than those in BEAGLE. On an empirical DNA dataset with 2000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling enabled and required). The PLL is available at http://www.libpll.org under the GNU General Public License (GPL). © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Convergent phylogenetic and functional responses to altered fire regimes in mesic savanna grasslands of North America and South Africa.

Science.gov (United States)

Forrestel, Elisabeth J; Donoghue, Michael J; Smith, Melinda D

2014-08-01

The importance of fire in the creation and maintenance of mesic grassland communities is well recognized. Improved understanding of how grasses--the dominant clade in these important ecosystems--will respond to alterations in fire regimes is needed in the face of anthropogenically driven climate and land-use change. Here, we examined how grass communities shift in response to experimentally manipulated fire regimes at multiple levels of community diversity--taxonomic, phylogenetic and functional--in C4-dominanted mesic savanna grassland sites with similar structure and physiognomy, yet disparate biogeographic histories. We found that the grass communities were similar in their phylogenetic response and aspects of their functional response to high fire frequency. Both sites exhibited phylogenetic clustering of highly abundant species in annually burned plots, driven by species of the Andropogoneae, and a narrow range of functional strategies associated with rapid post-fire regeneration in a high-light, nitrogen-limited environment. By examining multiple facets of diversity in a comparative context, we identified convergent phylogenetic and functional responses to altered fire regimes in two mesic savanna grasslands. Our results highlight the importance of a common filtering process associated with fire that is consistent across grasslands of disparate biogeographic histories and taxonomic representation. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Decoupling phylogenetic and functional diversity to reveal hidden signals in community assembly

Czech Academy of Sciences Publication Activity Database

de Bello, Francesco; Šmilauer, P.; Diniz-Filho, J. A. F.; Carmona, C. P.; Lososová, Z.; Herben, Tomáš; Götzenberger, Lars

2017-01-01

Roč. 8, č. 10 (2017), s. 1200-1211 ISSN 2041-210X R&D Projects: GA ČR(CZ) GA16-15012S; GA ČR GB14-36079G EU Projects: European Commission(XE) 267243 Institutional support: RVO:67985939 Keywords : community ecology * phylogenetic diversity * functional diversity Subject RIV: EH - Ecology, Behaviour OBOR OECD: Ecology Impact factor: 5.708, year: 2016

Classification of parotidectomy: a proposed modification to the European Salivary Gland Society classification system.

Science.gov (United States)

Wong, Wai Keat; Shetty, Subhaschandra

2017-08-01

Parotidectomy remains the mainstay of treatment for both benign and malignant lesions of the parotid gland. There exists a wide range of possible surgical options in parotidectomy in terms of extent of parotid tissue removed. There is increasing need for uniformity of terminology resulting from growing interest in modifications of the conventional parotidectomy. It is, therefore, of paramount importance for a standardized classification system in describing extent of parotidectomy. Recently, the European Salivary Gland Society (ESGS) proposed a novel classification system for parotidectomy. The aim of this study is to evaluate this system. A classification system proposed by the ESGS was critically re-evaluated and modified to increase its accuracy and its acceptability. Modifications mainly focused on subdividing Levels I and II into IA, IB, IIA, and IIB. From June 2006 to June 2016, 126 patients underwent 130 parotidectomies at our hospital. The classification system was tested in that cohort of patient. While the ESGS classification system is comprehensive, it does not cover all possibilities. The addition of Sublevels IA, IB, IIA, and IIB may help to address some of the clinical situations seen and is clinically relevant. We aim to test the modified classification system for partial parotidectomy to address some of the challenges mentioned.

Music Genre Classification Systems - A Computational Approach

DEFF Research Database (Denmark)

Ahrendt, Peter

2006-01-01

Automatic music genre classification is the classification of a piece of music into its corresponding genre (such as jazz or rock) by a computer. It is considered to be a cornerstone of the research area Music Information Retrieval (MIR) and closely linked to the other areas in MIR. It is thought...... that MIR will be a key element in the processing, searching and retrieval of digital music in the near future. This dissertation is concerned with music genre classification systems and in particular systems which use the raw audio signal as input to estimate the corresponding genre. This is in contrast...... to systems which use e.g. a symbolic representation or textual information about the music. The approach to music genre classification systems has here been system-oriented. In other words, all the different aspects of the systems have been considered and it is emphasized that the systems should...

A new gammagraphic and functional-based classification for hyperthyroidism

International Nuclear Information System (INIS)

Sanchez, J.; Lamata, F.; Cerdan, R.; Agilella, V.; Gastaminza, R.; Abusada, R.; Gonzales, M.; Martinez, M.

2000-01-01

The absence of an universal classification for hyperthyroidism's (HT), give rise to inadequate interpretation of series and trials, and prevents decision making. We offer a tentative classification based on gammagraphic and functional findings. Clinical records from patients who underwent thyroidectomy in our Department since 1967 to 1997 were reviewed. Those with functional measurements of hyperthyroidism were considered. All were managed according to the same preestablished guidelines. HT was the surgical indication in 694 (27,1%) of the 2559 thyroidectomy. Based on gammagraphic studies, we classified HTs in: parenchymatous increased-uptake, which could be diffuse, diffuse with cold nodules or diffuse with at least one nodule, and nodular increased-uptake (Autonomous Functioning Thyroid Nodes-AFTN), divided into solitary AFTN or toxic adenoma and multiple AFTN o toxic multi-nodular goiter. This gammagraphic-based classification in useful and has high sensitivity to detect these nodules assessing their activity, allowing us to make therapeutic decision making and, in some cases, to choose surgical technique. (authors)

AOSpine subaxial cervical spine injury classification system

NARCIS (Netherlands)

Vaccaro, Alexander R.; Koerner, John D.; Radcliff, Kris E.; Oner, F. Cumhur; Reinhold, Maximilian; Schnake, Klaus J.; Kandziora, Frank; Fehlings, Michael G.; Dvorak, Marcel F.; Aarabi, Bizhan; Rajasekaran, Shanmuganathan; Schroeder, Gregory D.; Kepler, Christopher K.; Vialle, Luiz R.

2016-01-01

Purpose: This project describes a morphology-based subaxial cervical spine traumatic injury classification system. Using the same approach as the thoracolumbar system, the goal was to develop a comprehensive yet simple classification system with high intra- and interobserver reliability to be used

Oral epithelial dysplasia classification systems

DEFF Research Database (Denmark)

Warnakulasuriya, S; Reibel, J; Bouquot, J

2008-01-01

At a workshop coordinated by the WHO Collaborating Centre for Oral Cancer and Precancer in the United Kingdom issues related to potentially malignant disorders of the oral cavity were discussed by an expert group. The consensus views of the Working Group are presented in a series of papers....... In this report, we review the oral epithelial dysplasia classification systems. The three classification schemes [oral epithelial dysplasia scoring system, squamous intraepithelial neoplasia and Ljubljana classification] were presented and the Working Group recommended epithelial dysplasia grading for routine...... use. Although most oral pathologists possibly recognize and accept the criteria for grading epithelial dysplasia, firstly based on architectural features and then of cytology, there is great variability in their interpretation of the presence, degree and significance of the individual criteria...

Review of international classification systems for uranium resources

International Nuclear Information System (INIS)

Wang Wenyou

2007-01-01

The two primary classification systems for uranium resources in common use in the whole world are described. These uranium resource classification systems were developed under two distinct philosophies, it implies two very different processes, criteria, terms and definitions from which the systems evolved and were implemented. However, the two primary systems are all based on two considerations: the degree of geological confidence and the degree of economic attractiveness based on cost of producing the resource. The uranium resource classification methods currently used in most major uranium producing countries have all a bearing on the two aforesaid classification systems. The disparity exists only in the way or practice of classifying and estimating the uranium resources for reasons of different political and economical systems in various countries. The harmonization of these resource classification systems for uranium can be realized with the economic integration on a global scale. (authors)

The classification of osteonecrosis in patients with cancer: validation of a new radiological classification system

International Nuclear Information System (INIS)

Niinimäki, T.; Niinimäki, J.; Halonen, J.; Hänninen, P.; Harila-Saari, A.; Niinimäki, R.

2015-01-01

Aim: To validate a new, non-joint-specific radiological classification system that is suitable regardless of the site of the osteonecrosis (ON) in patients with cancer. Material and methods: Critical deficiencies in the existing ON classification systems were identified and a new, non-joint-specific radiological classification system was developed. Seventy-two magnetic resonance imaging (MRI) images of patients with cancer and ON lesions were graded, and the validation of the new system was performed by assessing inter- and intra-observer reliability. Results: Intra-observer reliability of ON grading was good or very good, with kappa values of 0.79–0.86. Interobserver agreement was lower but still good, with kappa values of 0.62–0.77. Ninety-eight percent of all intra- or interobserver differences were within one grade. Interobserver reliability of assessing the location of ON was very good, with kappa values of 0.93–0.98. Conclusion: All the available radiological ON classification systems are joint specific. This limitation has spurred the development of multiple systems, which has led to the insufficient use of classifications in ON studies among patients with cancer. The introduced radiological classification system overcomes the problem of joint-specificity, was found to be reliable, and can be used to classify all ON lesions regardless of the affected site. - Highlights: • Patients with cancer may have osteonecrosis lesions at multiple sites. • There is no non-joint-specific osteonecrosis classification available. • We introduced a new non-joint-specific osteonecrosis classification. • The validation was performed by assessing inter- and intra-observer reliability. • The classification was reliable and could be used regardless of the affected site.

Motif-Based Text Mining of Microbial Metagenome Redundancy Profiling Data for Disease Classification.

Science.gov (United States)

Wang, Yin; Li, Rudong; Zhou, Yuhua; Ling, Zongxin; Guo, Xiaokui; Xie, Lu; Liu, Lei

2016-01-01

Text data of 16S rRNA are informative for classifications of microbiota-associated diseases. However, the raw text data need to be systematically processed so that features for classification can be defined/extracted; moreover, the high-dimension feature spaces generated by the text data also pose an additional difficulty. Here we present a Phylogenetic Tree-Based Motif Finding algorithm (PMF) to analyze 16S rRNA text data. By integrating phylogenetic rules and other statistical indexes for classification, we can effectively reduce the dimension of the large feature spaces generated by the text datasets. Using the retrieved motifs in combination with common classification methods, we can discriminate different samples of both pneumonia and dental caries better than other existing methods. We extend the phylogenetic approaches to perform supervised learning on microbiota text data to discriminate the pathological states for pneumonia and dental caries. The results have shown that PMF may enhance the efficiency and reliability in analyzing high-dimension text data.

An evaluation of classification systems for stillbirth

Directory of Open Access Journals (Sweden)

Pattinson Robert

2009-06-01

Full Text Available Abstract Background Audit and classification of stillbirths is an essential part of clinical practice and a crucial step towards stillbirth prevention. Due to the limitations of the ICD system and lack of an international approach to an acceptable solution, numerous disparate classification systems have emerged. We assessed the performance of six contemporary systems to inform the development of an internationally accepted approach. Methods We evaluated the following systems: Amended Aberdeen, Extended Wigglesworth; PSANZ-PDC, ReCoDe, Tulip and CODAC. Nine teams from 7 countries applied the classification systems to cohorts of stillbirths from their regions using 857 stillbirth cases. The main outcome measures were: the ability to retain the important information about the death using the InfoKeep rating; the ease of use according to the Ease rating (both measures used a five-point scale with a score Results InfoKeep scores were significantly different across the classifications (p ≤ 0.01 due to low scores for Wigglesworth and Aberdeen. CODAC received the highest mean (SD score of 3.40 (0.73 followed by PSANZ-PDC, ReCoDe and Tulip [2.77 (1.00, 2.36 (1.21, 1.92 (1.24 respectively]. Wigglesworth and Aberdeen resulted in a high proportion of unexplained stillbirths and CODAC and Tulip the lowest. While Ease scores were different (p ≤ 0.01, all systems received satisfactory scores; CODAC received the highest score. Aberdeen and Wigglesworth showed poor agreement with kappas of 0.35 and 0.25 respectively. Tulip performed best with a kappa of 0.74. The remainder had good to fair agreement. Conclusion The Extended Wigglesworth and Amended Aberdeen systems cannot be recommended for classification of stillbirths. Overall, CODAC performed best with PSANZ-PDC and ReCoDe performing well. Tulip was shown to have the best agreement and a low proportion of unexplained stillbirths. The virtues of these systems need to be considered in the development of an

DNA barcode analysis: a comparison of phylogenetic and statistical classification methods.

Science.gov (United States)

Austerlitz, Frederic; David, Olivier; Schaeffer, Brigitte; Bleakley, Kevin; Olteanu, Madalina; Leblois, Raphael; Veuille, Michel; Laredo, Catherine

2009-11-10

DNA barcoding aims to assign individuals to given species according to their sequence at a small locus, generally part of the CO1 mitochondrial gene. Amongst other issues, this raises the question of how to deal with within-species genetic variability and potential transpecific polymorphism. In this context, we examine several assignation methods belonging to two main categories: (i) phylogenetic methods (neighbour-joining and PhyML) that attempt to account for the genealogical framework of DNA evolution and (ii) supervised classification methods (k-nearest neighbour, CART, random forest and kernel methods). These methods range from basic to elaborate. We investigated the ability of each method to correctly classify query sequences drawn from samples of related species using both simulated and real data. Simulated data sets were generated using coalescent simulations in which we varied the genealogical history, mutation parameter, sample size and number of species. No method was found to be the best in all cases. The simplest method of all, "one nearest neighbour", was found to be the most reliable with respect to changes in the parameters of the data sets. The parameter most influencing the performance of the various methods was molecular diversity of the data. Addition of genetically independent loci--nuclear genes--improved the predictive performance of most methods. The study implies that taxonomists can influence the quality of their analyses either by choosing a method best-adapted to the configuration of their sample, or, given a certain method, increasing the sample size or altering the amount of molecular diversity. This can be achieved either by sequencing more mtDNA or by sequencing additional nuclear genes. In the latter case, they may also have to modify their data analysis method.

DNA barcode analysis: a comparison of phylogenetic and statistical classification methods

Directory of Open Access Journals (Sweden)

Leblois Raphael

2009-11-01

Full Text Available Abstract Background DNA barcoding aims to assign individuals to given species according to their sequence at a small locus, generally part of the CO1 mitochondrial gene. Amongst other issues, this raises the question of how to deal with within-species genetic variability and potential transpecific polymorphism. In this context, we examine several assignation methods belonging to two main categories: (i phylogenetic methods (neighbour-joining and PhyML that attempt to account for the genealogical framework of DNA evolution and (ii supervised classification methods (k-nearest neighbour, CART, random forest and kernel methods. These methods range from basic to elaborate. We investigated the ability of each method to correctly classify query sequences drawn from samples of related species using both simulated and real data. Simulated data sets were generated using coalescent simulations in which we varied the genealogical history, mutation parameter, sample size and number of species. Results No method was found to be the best in all cases. The simplest method of all, "one nearest neighbour", was found to be the most reliable with respect to changes in the parameters of the data sets. The parameter most influencing the performance of the various methods was molecular diversity of the data. Addition of genetically independent loci - nuclear genes - improved the predictive performance of most methods. Conclusion The study implies that taxonomists can influence the quality of their analyses either by choosing a method best-adapted to the configuration of their sample, or, given a certain method, increasing the sample size or altering the amount of molecular diversity. This can be achieved either by sequencing more mtDNA or by sequencing additional nuclear genes. In the latter case, they may also have to modify their data analysis method.

A bayesian hierarchical model for classification with selection of functional predictors.

Science.gov (United States)

Zhu, Hongxiao; Vannucci, Marina; Cox, Dennis D

2010-06-01

In functional data classification, functional observations are often contaminated by various systematic effects, such as random batch effects caused by device artifacts, or fixed effects caused by sample-related factors. These effects may lead to classification bias and thus should not be neglected. Another issue of concern is the selection of functions when predictors consist of multiple functions, some of which may be redundant. The above issues arise in a real data application where we use fluorescence spectroscopy to detect cervical precancer. In this article, we propose a Bayesian hierarchical model that takes into account random batch effects and selects effective functions among multiple functional predictors. Fixed effects or predictors in nonfunctional form are also included in the model. The dimension of the functional data is reduced through orthonormal basis expansion or functional principal components. For posterior sampling, we use a hybrid Metropolis-Hastings/Gibbs sampler, which suffers slow mixing. An evolutionary Monte Carlo algorithm is applied to improve the mixing. Simulation and real data application show that the proposed model provides accurate selection of functional predictors as well as good classification.

REAL-TIME INTELLIGENT MULTILAYER ATTACK CLASSIFICATION SYSTEM

Directory of Open Access Journals (Sweden)

T. Subbhulakshmi

2014-01-01

Full Text Available Intrusion Detection Systems (IDS takes the lion’s share of the current security infrastructure. Detection of intrusions is vital for initiating the defensive procedures. Intrusion detection was done by statistical and distance based methods. A threshold value is used in these methods to indicate the level of normalcy. When the network traffic crosses the level of normalcy then above which it is flagged as anomalous. When there are occurrences of new intrusion events which are increasingly a key part of system security, the statistical techniques cannot detect them. To overcome this issue, learning techniques are used which helps in identifying new intrusion activities in a computer system. The objective of the proposed system designed in this paper is to classify the intrusions using an Intelligent Multi Layered Attack Classification System (IMLACS which helps in detecting and classifying the intrusions with improved classification accuracy. The intelligent multi layered approach contains three intelligent layers. The first layer involves Binary Support Vector Machine classification for detecting the normal and attack. The second layer involves neural network classification to classify the attacks into classes of attacks. The third layer involves fuzzy inference system to classify the attacks into various subclasses. The proposed IMLACS can be able to detect an intrusion behavior of the networks since the system contains a three intelligent layer classification and better set of rules. Feature selection is also used to improve the time of detection. The experimental results show that the IMLACS achieves the Classification Rate of 97.31%.

Systematic analysis of snake neurotoxins' functional classification using a data warehousing approach.

Science.gov (United States)

Siew, Joyce Phui Yee; Khan, Asif M; Tan, Paul T J; Koh, Judice L Y; Seah, Seng Hong; Koo, Chuay Yeng; Chai, Siaw Ching; Armugam, Arunmozhiarasi; Brusic, Vladimir; Jeyaseelan, Kandiah

2004-12-12

Sequence annotations, functional and structural data on snake venom neurotoxins (svNTXs) are scattered across multiple databases and literature sources. Sequence annotations and structural data are available in the public molecular databases, while functional data are almost exclusively available in the published articles. There is a need for a specialized svNTXs database that contains NTX entries, which are organized, well annotated and classified in a systematic manner. We have systematically analyzed svNTXs and classified them using structure-function groups based on their structural, functional and phylogenetic properties. Using conserved motifs in each phylogenetic group, we built an intelligent module for the prediction of structural and functional properties of unknown NTXs. We also developed an annotation tool to aid the functional prediction of newly identified NTXs as an additional resource for the venom research community. We created a searchable online database of NTX proteins sequences (http://research.i2r.a-star.edu.sg/Templar/DB/snake_neurotoxin). This database can also be found under Swiss-Prot Toxin Annotation Project website (http://www.expasy.org/sprot/).

A three-way approach for protein function classification.

Directory of Open Access Journals (Sweden)

Hafeez Ur Rehman

Full Text Available The knowledge of protein functions plays an essential role in understanding biological cells and has a significant impact on human life in areas such as personalized medicine, better crops and improved therapeutic interventions. Due to expense and inherent difficulty of biological experiments, intelligent methods are generally relied upon for automatic assignment of functions to proteins. The technological advancements in the field of biology are improving our understanding of biological processes and are regularly resulting in new features and characteristics that better describe the role of proteins. It is inevitable to neglect and overlook these anticipated features in designing more effective classification techniques. A key issue in this context, that is not being sufficiently addressed, is how to build effective classification models and approaches for protein function prediction by incorporating and taking advantage from the ever evolving biological information. In this article, we propose a three-way decision making approach which provides provisions for seeking and incorporating future information. We considered probabilistic rough sets based models such as Game-Theoretic Rough Sets (GTRS and Information-Theoretic Rough Sets (ITRS for inducing three-way decisions. An architecture of protein functions classification with probabilistic rough sets based three-way decisions is proposed and explained. Experiments are carried out on Saccharomyces cerevisiae species dataset obtained from Uniprot database with the corresponding functional classes extracted from the Gene Ontology (GO database. The results indicate that as the level of biological information increases, the number of deferred cases are reduced while maintaining similar level of accuracy.

Evaluation of classification systems for nonspecific idiopathic orbital inflammation

NARCIS (Netherlands)

Bijlsma, Ward R.; van 't Hullenaar, Fleur C.; Mourits, Maarten P.; Kalmann, Rachel

2012-01-01

To systematically analyze existing classification systems for idiopathic orbital inflammation (IOI) and propose and test a new best practice classification system. A systematic literature search was conducted to find all studies that described and applied a classification system for IOI.

HIV classification using coalescent theory

Energy Technology Data Exchange (ETDEWEB)

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

2008-01-01

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

Extensions to the Speech Disorders Classification System (SDCS)

Science.gov (United States)

Shriberg, Lawrence D.; Fourakis, Marios; Hall, Sheryl D.; Karlsson, Heather B.; Lohmeier, Heather L.; McSweeny, Jane L.; Potter, Nancy L.; Scheer-Cohen, Alison R.; Strand, Edythe A.; Tilkens, Christie M.; Wilson, David L.

2010-01-01

This report describes three extensions to a classification system for paediatric speech sound disorders termed the Speech Disorders Classification System (SDCS). Part I describes a classification extension to the SDCS to differentiate motor speech disorders from speech delay and to differentiate among three sub-types of motor speech disorders.…

A systematic review of definitions and classification systems of adjacent segment pathology.

Science.gov (United States)

Kraemer, Paul; Fehlings, Michael G; Hashimoto, Robin; Lee, Michael J; Anderson, Paul A; Chapman, Jens R; Raich, Annie; Norvell, Daniel C

2012-10-15

Systematic review. To undertake a systematic review to determine how "adjacent segment degeneration," "adjacent segment disease," or clinical pathological processes that serve as surrogates for adjacent segment pathology are classified and defined in the peer-reviewed literature. Adjacent segment degeneration and adjacent segment disease are terms referring to degenerative changes known to occur after reconstructive spine surgery, most commonly at an immediately adjacent functional spinal unit. These can include disc degeneration, instability, spinal stenosis, facet degeneration, and deformity. The true incidence and clinical impact of degenerative changes at the adjacent segment is unclear because there is lack of a universally accepted classification system that rigorously addresses clinical and radiological issues. A systematic review of the English language literature was undertaken and articles were classified using the Grades of Recommendation Assessment, Development, and Evaluation criteria. RESULTS.: Seven classification systems of spinal degeneration, including degeneration at the adjacent segment, were identified. None have been evaluated for reliability or validity specific to patients with degeneration at the adjacent segment. The ways in which terms related to adjacent segment "degeneration" or "disease" are defined in the peer-reviewed literature are highly variable. On the basis of the systematic review presented in this article, no formal classification system for either cervical or thoracolumbar adjacent segment disorders currently exists. No recommendations regarding the use of current classification of degeneration at any segments can be made based on the available literature. A new comprehensive definition for adjacent segment pathology (ASP, the now preferred terminology) has been proposed in this Focus Issue, which reflects the diverse pathology observed at functional spinal units adjacent to previous spinal reconstruction and balances

A Classification Scheme for Production System Processes

DEFF Research Database (Denmark)

Sørensen, Daniel Grud Hellerup; Brunø, Thomas Ditlev; Nielsen, Kjeld

2018-01-01

Manufacturing companies often have difficulties developing production platforms, partly due to the complexity of many production systems and difficulty determining which processes constitute a platform. Understanding production processes is an important step to identifying candidate processes...... for a production platform based on existing production systems. Reviewing a number of existing classifications and taxonomies, a consolidated classification scheme for processes in production of discrete products has been outlined. The classification scheme helps ensure consistency during mapping of existing...

An evaluation of classification systems for stillbirth.

Science.gov (United States)

Flenady, Vicki; Frøen, J Frederik; Pinar, Halit; Torabi, Rozbeh; Saastad, Eli; Guyon, Grace; Russell, Laurie; Charles, Adrian; Harrison, Catherine; Chauke, Lawrence; Pattinson, Robert; Koshy, Rachel; Bahrin, Safiah; Gardener, Glenn; Day, Katie; Petersson, Karin; Gordon, Adrienne; Gilshenan, Kristen

2009-06-19

Audit and classification of stillbirths is an essential part of clinical practice and a crucial step towards stillbirth prevention. Due to the limitations of the ICD system and lack of an international approach to an acceptable solution, numerous disparate classification systems have emerged. We assessed the performance of six contemporary systems to inform the development of an internationally accepted approach. We evaluated the following systems: Amended Aberdeen, Extended Wigglesworth; PSANZ-PDC, ReCoDe, Tulip and CODAC. Nine teams from 7 countries applied the classification systems to cohorts of stillbirths from their regions using 857 stillbirth cases. The main outcome measures were: the ability to retain the important information about the death using the InfoKeep rating; the ease of use according to the Ease rating (both measures used a five-point scale with a score <2 considered unsatisfactory); inter-observer agreement and the proportion of unexplained stillbirths. A randomly selected subset of 100 stillbirths was used to assess inter-observer agreement. InfoKeep scores were significantly different across the classifications (p < or = 0.01) due to low scores for Wigglesworth and Aberdeen. CODAC received the highest mean (SD) score of 3.40 (0.73) followed by PSANZ-PDC, ReCoDe and Tulip [2.77 (1.00), 2.36 (1.21), 1.92 (1.24) respectively]. Wigglesworth and Aberdeen resulted in a high proportion of unexplained stillbirths and CODAC and Tulip the lowest. While Ease scores were different (p < or = 0.01), all systems received satisfactory scores; CODAC received the highest score. Aberdeen and Wigglesworth showed poor agreement with kappas of 0.35 and 0.25 respectively. Tulip performed best with a kappa of 0.74. The remainder had good to fair agreement. The Extended Wigglesworth and Amended Aberdeen systems cannot be recommended for classification of stillbirths. Overall, CODAC performed best with PSANZ-PDC and ReCoDe performing well. Tulip was shown to have the

Host specificity and phylogenetic relationships of chicken and turkey parvoviruses

Science.gov (United States)

Previous reports indicate that the newly discovered chicken parvoviruses (ChPV) and turkey parvoviruses (TuPV) are very similar to each other, yet they represent different species within a new genus of Parvoviridae. Currently, strain classification is based on the phylogenetic analysis of a 561 bas...

Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa.

Science.gov (United States)

Corbelli, Julian Martin; Zurita, Gustavo Andres; Filloy, Julieta; Galvis, Juan Pablo; Vespa, Natalia Isabel; Bellocq, Isabel

2015-01-01

The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD), functional (FBD) and phylogenetic (PBD) facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools) and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants) from two contrasting biomes (subtropical forest and grassland) and land uses (tree plantations and cropfields) in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland), and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation.

Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa

Science.gov (United States)

Corbelli, Julian Martin; Zurita, Gustavo Andres; Filloy, Julieta; Galvis, Juan Pablo; Vespa, Natalia Isabel; Bellocq, Isabel

2015-01-01

The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD), functional (FBD) and phylogenetic (PBD) facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools) and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants) from two contrasting biomes (subtropical forest and grassland) and land uses (tree plantations and cropfields) in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland), and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation. PMID:25978319

Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa.

Directory of Open Access Journals (Sweden)

Julian Martin Corbelli

Full Text Available The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD, functional (FBD and phylogenetic (PBD facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants from two contrasting biomes (subtropical forest and grassland and land uses (tree plantations and cropfields in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland, and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation.

On the integrity of functional brain networks in schizophrenia, Parkinson's disease, and advanced age: Evidence from connectivity-based single-subject classification.

Science.gov (United States)

Pläschke, Rachel N; Cieslik, Edna C; Müller, Veronika I; Hoffstaedter, Felix; Plachti, Anna; Varikuti, Deepthi P; Goosses, Mareike; Latz, Anne; Caspers, Svenja; Jockwitz, Christiane; Moebus, Susanne; Gruber, Oliver; Eickhoff, Claudia R; Reetz, Kathrin; Heller, Julia; Südmeyer, Martin; Mathys, Christian; Caspers, Julian; Grefkes, Christian; Kalenscher, Tobias; Langner, Robert; Eickhoff, Simon B

2017-12-01

Previous whole-brain functional connectivity studies achieved successful classifications of patients and healthy controls but only offered limited specificity as to affected brain systems. Here, we examined whether the connectivity patterns of functional systems affected in schizophrenia (SCZ), Parkinson's disease (PD), or normal aging equally translate into high classification accuracies for these conditions. We compared classification performance between pre-defined networks for each group and, for any given network, between groups. Separate support vector machine classifications of 86 SCZ patients, 80 PD patients, and 95 older adults relative to their matched healthy/young controls, respectively, were performed on functional connectivity in 12 task-based, meta-analytically defined networks using 25 replications of a nested 10-fold cross-validation scheme. Classification performance of the various networks clearly differed between conditions, as those networks that best classified one disease were usually non-informative for the other. For SCZ, but not PD, emotion-processing, empathy, and cognitive action control networks distinguished patients most accurately from controls. For PD, but not SCZ, networks subserving autobiographical or semantic memory, motor execution, and theory-of-mind cognition yielded the best classifications. In contrast, young-old classification was excellent based on all networks and outperformed both clinical classifications. Our pattern-classification approach captured associations between clinical and developmental conditions and functional network integrity with a higher level of specificity than did previous whole-brain analyses. Taken together, our results support resting-state connectivity as a marker of functional dysregulation in specific networks known to be affected by SCZ and PD, while suggesting that aging affects network integrity in a more global way. Hum Brain Mapp 38:5845-5858, 2017. © 2017 Wiley Periodicals, Inc. © 2017

Data Processing And Machine Learning Methods For Multi-Modal Operator State Classification Systems

Science.gov (United States)

Hearn, Tristan A.

2015-01-01

This document is intended as an introduction to a set of common signal processing learning methods that may be used in the software portion of a functional crew state monitoring system. This includes overviews of both the theory of the methods involved, as well as examples of implementation. Practical considerations are discussed for implementing modular, flexible, and scalable processing and classification software for a multi-modal, multi-channel monitoring system. Example source code is also given for all of the discussed processing and classification methods.

A Confidence Paradigm for Classification Systems

Science.gov (United States)

2008-09-01

methodology to determine how much confi- dence one should have in a classifier output. This research proposes a framework to determine the level of...theoretical framework that attempts to unite the viewpoints of the classification system developer (or engineer) and the classification system user (or...operating point. An algorithm is developed that minimizes a “confidence” measure called Binned Error in the Posterior ( BEP ). Then, we prove that training a

Selection of Objective Function For Imbalanced Classification: An Industrial Case Study

DEFF Research Database (Denmark)

Khan, Abdul Rauf; Schiøler, Henrik; Kulahci, Murat

2017-01-01

In this article we discuss the issue of selecting suitable objective function for Genetic Algorithm to solve an imbalanced classification problem. More precisely, first we discuss the need of specialized objective function to solve a real classification problem from our industrial partner and the...... and then we compare the results of our proposed objective function with commonly used candidates to serve this purpose. Our comparison is based on the analysis of real data collected during the quality control stages of the manufacturing process....

A proposed United States resource classification system

International Nuclear Information System (INIS)

Masters, C.D.

1980-01-01

Energy is a world-wide problem calling for world-wide communication to resolve the many supply and distribution problems. Essential to a communication problem are a definition and comparability of elements being communicated. The US Geological Survey, with the co-operation of the US Bureau of Mines and the US Department of Energy, has devised a classification system for all mineral resources, the principles of which, it is felt, offer the possibility of world communication. At present several other systems, extant or under development (Potential Gas Committee of the USA, United Nations Resource Committee, and the American Society of Testing and Materials) are internally consistent and provide easy communication linkage. The system in use by the uranium community in the United States of America, however, ties resource quantities to forward-cost dollar values rendering them inconsistent with other classifications and therefore not comparable. This paper develops the rationale for the new USGS resource classification and notes its benefits relative to a forward-cost classification and its relationship specifically to other current classifications. (author)

Motif-Based Text Mining of Microbial Metagenome Redundancy Profiling Data for Disease Classification

Directory of Open Access Journals (Sweden)

Yin Wang

2016-01-01

Full Text Available Background. Text data of 16S rRNA are informative for classifications of microbiota-associated diseases. However, the raw text data need to be systematically processed so that features for classification can be defined/extracted; moreover, the high-dimension feature spaces generated by the text data also pose an additional difficulty. Results. Here we present a Phylogenetic Tree-Based Motif Finding algorithm (PMF to analyze 16S rRNA text data. By integrating phylogenetic rules and other statistical indexes for classification, we can effectively reduce the dimension of the large feature spaces generated by the text datasets. Using the retrieved motifs in combination with common classification methods, we can discriminate different samples of both pneumonia and dental caries better than other existing methods. Conclusions. We extend the phylogenetic approaches to perform supervised learning on microbiota text data to discriminate the pathological states for pneumonia and dental caries. The results have shown that PMF may enhance the efficiency and reliability in analyzing high-dimension text data.

Classification of ion mobility spectra by functional groups using neural networks

Science.gov (United States)

Bell, S.; Nazarov, E.; Wang, Y. F.; Eiceman, G. A.

1999-01-01

Neural networks were trained using whole ion mobility spectra from a standardized database of 3137 spectra for 204 chemicals at various concentrations. Performance of the network was measured by the success of classification into ten chemical classes. Eleven stages for evaluation of spectra and of spectral pre-processing were employed and minimums established for response thresholds and spectral purity. After optimization of the database, network, and pre-processing routines, the fraction of successful classifications by functional group was 0.91 throughout a range of concentrations. Network classification relied on a combination of features, including drift times, number of peaks, relative intensities, and other factors apparently including peak shape. The network was opportunistic, exploiting different features within different chemical classes. Application of neural networks in a two-tier design where chemicals were first identified by class and then individually eliminated all but one false positive out of 161 test spectra. These findings establish that ion mobility spectra, even with low resolution instrumentation, contain sufficient detail to permit the development of automated identification systems.

DIAGNOSTICS OF DISORDERS AND DISEASES OF MUSCULOSKELETAL SYSTEM IN SCHOOLCHILDREN: APPROACHES, TERMINOLOGY, CLASSIFICATION

Directory of Open Access Journals (Sweden)

N.B. Mirskaya

2009-01-01

Full Text Available This article describes an information system for physicians working in general education institutes, which is named «Detection, correction and prophylaxis of musculoskeletal system disorders in students of general education institutes». This system was created for the purpose of improving diagnostics of initial stages of musculoskeletal system in schoolchildren, detecting of risk factors, and for the provision of timely prophylaxis during school education. The system was based on classification of functional disorders and initial stages of diseases of musculoskeletal system in schoolchildren, developed by authors of present article, and methods of medical examination and organization of this work.Key words: schoolchildren, musculoskeletal system, diagnostics, classification, prophylaxis.(Voprosy sovremennoi pediatrii — Current Pediatrics. 2009;8(3:10-13

Automotive System for Remote Surface Classification.

Science.gov (United States)

Bystrov, Aleksandr; Hoare, Edward; Tran, Thuy-Yung; Clarke, Nigel; Gashinova, Marina; Cherniakov, Mikhail

2017-04-01

In this paper we shall discuss a novel approach to road surface recognition, based on the analysis of backscattered microwave and ultrasonic signals. The novelty of our method is sonar and polarimetric radar data fusion, extraction of features for separate swathes of illuminated surface (segmentation), and using of multi-stage artificial neural network for surface classification. The developed system consists of 24 GHz radar and 40 kHz ultrasonic sensor. The features are extracted from backscattered signals and then the procedures of principal component analysis and supervised classification are applied to feature data. The special attention is paid to multi-stage artificial neural network which allows an overall increase in classification accuracy. The proposed technique was tested for recognition of a large number of real surfaces in different weather conditions with the average accuracy of correct classification of 95%. The obtained results thereby demonstrate that the use of proposed system architecture and statistical methods allow for reliable discrimination of various road surfaces in real conditions.

Discriminant forest classification method and system

Science.gov (United States)

Chen, Barry Y.; Hanley, William G.; Lemmond, Tracy D.; Hiller, Lawrence J.; Knapp, David A.; Mugge, Marshall J.

2012-11-06

A hybrid machine learning methodology and system for classification that combines classical random forest (RF) methodology with discriminant analysis (DA) techniques to provide enhanced classification capability. A DA technique which uses feature measurements of an object to predict its class membership, such as linear discriminant analysis (LDA) or Andersen-Bahadur linear discriminant technique (AB), is used to split the data at each node in each of its classification trees to train and grow the trees and the forest. When training is finished, a set of n DA-based decision trees of a discriminant forest is produced for use in predicting the classification of new samples of unknown class.

Dengue virus type 3 in Brazil: a phylogenetic perspective

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Josélio Maria Galvão de Araújo

2009-05-01

Full Text Available Circulation of a new dengue virus (DENV-3 genotype was recently described in Brazil and Colombia, but the precise classification of this genotype has been controversial. Here we perform phylogenetic and nucleotide-distance analyses of the envelope gene, which support the subdivision of DENV-3 strains into five distinct genotypes (GI to GV and confirm the classification of the new South American genotype as GV. The extremely low genetic distances between Brazilian GV strains and the prototype Philippines/L11423 GV strain isolated in 1956 raise important questions regarding the origin of GV in South America.

Ebolavirus Classification Based on Natural Vectors

Science.gov (United States)

Zheng, Hui; Yin, Changchuan; Hoang, Tung; He, Rong Lucy; Yang, Jie

2015-01-01

According to the WHO, ebolaviruses have resulted in 8818 human deaths in West Africa as of January 2015. To better understand the evolutionary relationship of the ebolaviruses and infer virulence from the relationship, we applied the alignment-free natural vector method to classify the newest ebolaviruses. The dataset includes three new Guinea viruses as well as 99 viruses from Sierra Leone. For the viruses of the family of Filoviridae, both genus label classification and species label classification achieve an accuracy rate of 100%. We represented the relationships among Filoviridae viruses by Unweighted Pair Group Method with Arithmetic Mean (UPGMA) phylogenetic trees and found that the filoviruses can be separated well by three genera. We performed the phylogenetic analysis on the relationship among different species of Ebolavirus by their coding-complete genomes and seven viral protein genes (glycoprotein [GP], nucleoprotein [NP], VP24, VP30, VP35, VP40, and RNA polymerase [L]). The topology of the phylogenetic tree by the viral protein VP24 shows consistency with the variations of virulence of ebolaviruses. The result suggests that VP24 be a pharmaceutical target for treating or preventing ebolaviruses. PMID:25803489

EEG classification of emotions using emotion-specific brain functional network.

Science.gov (United States)

Gonuguntla, V; Shafiq, G; Wang, Y; Veluvolu, K C

2015-08-01

The brain functional network perspective forms the basis to relate mechanisms of brain functions. This work analyzes the network mechanisms related to human emotion based on synchronization measure - phase-locking value in EEG to formulate the emotion specific brain functional network. Based on network dissimilarities between emotion and rest tasks, most reactive channel pairs and the reactive band corresponding to emotions are identified. With the identified most reactive pairs, the subject-specific functional network is formed. The identified subject-specific and emotion-specific dynamic network pattern show significant synchrony variation in line with the experiment protocol. The same network pattern are then employed for classification of emotions. With the study conducted on the 4 subjects, an average classification accuracy of 62 % was obtained with the proposed technique.

42 CFR 412.513 - Patient classification system.

Science.gov (United States)

2010-10-01

... LTC-DRG classification system provides a LTC-DRG, and an appropriate weighting factor, for those cases... intermediary decides that a different LTC-DRG should be assigned, the case will be reviewed by the appropriate... 42 Public Health 2 2010-10-01 2010-10-01 false Patient classification system. 412.513 Section 412...

Toward functional classification of neuronal types.

Science.gov (United States)

Sharpee, Tatyana O

2014-09-17

How many types of neurons are there in the brain? This basic neuroscience question remains unsettled despite many decades of research. Classification schemes have been proposed based on anatomical, electrophysiological, or molecular properties. However, different schemes do not always agree with each other. This raises the question of whether one can classify neurons based on their function directly. For example, among sensory neurons, can a classification scheme be devised that is based on their role in encoding sensory stimuli? Here, theoretical arguments are outlined for how this can be achieved using information theory by looking at optimal numbers of cell types and paying attention to two key properties: correlations between inputs and noise in neural responses. This theoretical framework could help to map the hierarchical tree relating different neuronal classes within and across species. Copyright © 2014 Elsevier Inc. All rights reserved.

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes.

Science.gov (United States)

Feuermann, Marc; Gaudet, Pascale; Mi, Huaiyu; Lewis, Suzanna E; Thomas, Paul D

2016-01-01

We previously reported a paradigm for large-scale phylogenomic analysis of gene families that takes advantage of the large corpus of experimentally supported Gene Ontology (GO) annotations. This 'GO Phylogenetic Annotation' approach integrates GO annotations from evolutionarily related genes across ∼100 different organisms in the context of a gene family tree, in which curators build an explicit model of the evolution of gene functions. GO Phylogenetic Annotation models the gain and loss of functions in a gene family tree, which is used to infer the functions of uncharacterized (or incompletely characterized) gene products, even for human proteins that are relatively well studied. Here, we report our results from applying this paradigm to two well-characterized cellular processes, apoptosis and autophagy. This revealed several important observations with respect to GO annotations and how they can be used for function inference. Notably, we applied only a small fraction of the experimentally supported GO annotations to infer function in other family members. The majority of other annotations describe indirect effects, phenotypes or results from high throughput experiments. In addition, we show here how feedback from phylogenetic annotation leads to significant improvements in the PANTHER trees, the GO annotations and GO itself. Thus GO phylogenetic annotation both increases the quantity and improves the accuracy of the GO annotations provided to the research community. We expect these phylogenetically based annotations to be of broad use in gene enrichment analysis as well as other applications of GO annotations.Database URL: http://amigo.geneontology.org/amigo. © The Author(s) 2016. Published by Oxford University Press.

Applicability of the International Classification of Functioning, Disability and Health (ICF for evaluation of children with cerebral palsy: a systematic review

Directory of Open Access Journals (Sweden)

Lílian de Fátima Dornelas

2014-12-01

Full Text Available Objective: To examine and synthesize the knowledge available in the literature on the instruments used in the perspective of functionality in children with cerebral palsy (CP, and to review the literature evaluating the instruments used for the implementation of the International Classification of Functioning, Disability and Health (ICF in children with CP. Method: The search was conducted in the electronic databases Google Scholar, PubMed, Lilacs and Medline, for articles published between January 2006 and December 2012, using the following keywords: cerebral palsy, child and assessment, combined with ICF. Ten articles were selected for analysis according to pre-established criteria. Results: The authors proposed tools that could standardize the assessment for classification of the components “Structure and function of the body”, “Activities and Participation” and “Environmental Factors”, proposing instruments such as Gross Motor Function Measure (GMFM, Pediatric Evaluation of Disability Inventory (PEDI, Goal Attainment Scaling (GAS, Manual Ability Classification System (MACS, Gross Motor Function Classification System (GMFCS, Physicians Rating Scale (PRS, Vineland Adaptive Behavior Scale (VABS, Pediatric Functional Independence Measure (Wee FIM, Gillette Functional Assessment Questionnaire (FAQ, Pediatric Quality of Life Inventory (PedsQL, Pediatric Outcomes Data Collection Instrument (PODCI, Gillette Gait Index (GGI, Energy Expenditure Index (EEI, and Vécu et Santé Perçue de l’Adolescent (VSP-A. Conclusion: The domains “Structure and function of the body” and “Activities and Participation” are often classified according to ICF in children with CP, and they present a variety of instrumentation for applicability of classification.

PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis

KAUST Repository

Benavente, Ernest D

2015-05-13

Background Phylogenetic-based classification of M. tuberculosis and other bacterial genomes is a core analysis for studying evolutionary hypotheses, disease outbreaks and transmission events. Whole genome sequencing is providing new insights into the genomic variation underlying intra- and inter-strain diversity, thereby assisting with the classification and molecular barcoding of the bacteria. One roadblock to strain investigation is the lack of user-interactive solutions to interrogate and visualise variation within a phylogenetic tree setting. Results We have developed a web-based tool called PhyTB (http://pathogenseq.lshtm.ac.uk/phytblive/index.php webcite) to assist phylogenetic tree visualisation and identification of M. tuberculosis clade-informative polymorphism. Variant Call Format files can be uploaded to determine a sample position within the tree. A map view summarises the geographical distribution of alleles and strain-types. The utility of the PhyTB is demonstrated on sequence data from 1,601 M. tuberculosis isolates. Conclusion PhyTB contextualises M. tuberculosis genomic variation within epidemiological, geographical and phylogenic settings. Further tool utility is possible by incorporating large variants and phenotypic data (e.g. drug-resistance profiles), and an assessment of genotype-phenotype associations. Source code is available to develop similar websites for other organisms (http://sourceforge.net/projects/phylotrack webcite).

Molecular and morphological analyses reveal phylogenetic relationships of stingrays focusing on the family Dasyatidae (Myliobatiformes.

Directory of Open Access Journals (Sweden)

Kean Chong Lim

Full Text Available Elucidating the phylogenetic relationships of the current but problematic Dasyatidae (Order Myliobatiformes was the first priority of the current study. Here, we studied three molecular gene markers of 43 species (COI gene, 33 species (ND2 gene and 34 species (RAG1 gene of stingrays to draft out the phylogenetic tree of the order. Nine character states were identified and used to confirm the molecularly constructed phylogenetic trees. Eight or more clades (at different hierarchical level were identified for COI, ND2 and RAG1 genes in the Myliobatiformes including four clades containing members of the present Dasyatidae, thus rendering the latter non-monophyletic. The uncorrected p-distance between these four 'Dasytidae' clades when compared to the distance between formally known families confirmed that these four clades should be elevated to four separate families. We suggest a revision of the present classification, retaining the Dasyatidae (Dasyatis and Taeniurops species but adding three new families namely, Neotrygonidae (Neotrygon and Taeniura species, Himanturidae (Himantura species and Pastinachidae (Pastinachus species. Our result indicated the need to further review the classification of Dasyatis microps. By resolving the non-monophyletic problem, the suite of nine character states enables the natural classification of the Myliobatiformes into at least thirteen families based on morphology.

Phylogenetic diversity and biodiversity indices on phylogenetic networks.

Science.gov (United States)

Wicke, Kristina; Fischer, Mareike

2018-04-01

In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species according to their contribution to overall phylogenetic diversity. However, in many cases evolution is not treelike and thus, phylogenetic networks have been developed as a generalization of phylogenetic trees, allowing for the representation of non-treelike evolutionary events, such as hybridization. Here, we extend the concepts of phylogenetic diversity and phylogenetic diversity indices from phylogenetic trees to phylogenetic networks. On the one hand, we consider the treelike content of a phylogenetic network, e.g. the (multi)set of phylogenetic trees displayed by a network and the so-called lowest stable ancestor tree associated with it. On the other hand, we derive the phylogenetic diversity of subsets of taxa and biodiversity indices directly from the internal structure of the network. We consider both approaches that are independent of so-called inheritance probabilities as well as approaches that explicitly incorporate these probabilities. Furthermore, we introduce our software package NetDiversity, which is implemented in Perl and allows for the calculation of all generalized measures of phylogenetic diversity and generalized phylogenetic diversity indices established in this note that are independent of inheritance probabilities. We apply our methods to a phylogenetic network representing the evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by widespread hybridization. Copyright © 2018 Elsevier Inc. All rights reserved.

[Landscape classification: research progress and development trend].

Science.gov (United States)

Liang, Fa-Chao; Liu, Li-Ming

2011-06-01

Landscape classification is the basis of the researches on landscape structure, process, and function, and also, the prerequisite for landscape evaluation, planning, protection, and management, directly affecting the precision and practicability of landscape research. This paper reviewed the research progress on the landscape classification system, theory, and methodology, and summarized the key problems and deficiencies of current researches. Some major landscape classification systems, e. g. , LANMAP and MUFIC, were introduced and discussed. It was suggested that a qualitative and quantitative comprehensive classification based on the ideology of functional structure shape and on the integral consideration of landscape classification utility, landscape function, landscape structure, physiogeographical factors, and human disturbance intensity should be the major research directions in the future. The integration of mapping, 3S technology, quantitative mathematics modeling, computer artificial intelligence, and professional knowledge to enhance the precision of landscape classification would be the key issues and the development trend in the researches of landscape classification.

Revised Soil Classification System for Coarse-Fine Mixtures

KAUST Repository

Park, Junghee; Santamarina, Carlos

2017-01-01

Soil classification systems worldwide capture great physical insight and enable geotechnical engineers to anticipate the properties and behavior of soils by grouping them into similar response categories based on their index properties. Yet gravimetric analysis and data trends summarized from published papers reveal critical limitations in soil group boundaries adopted in current systems. In particular, current classification systems fail to capture the dominant role of fines on the mechanical and hydraulic properties of soils. A revised soil classification system (RSCS) for coarse-fine mixtures is proposed herein. Definitions of classification boundaries use low and high void ratios that gravel, sand, and fines may attain. This research adopts emax and emin for gravels and sands, and three distinctive void ratio values for fines: soft eF|10  kPa and stiff eF|1  MPa for mechanical response (at effective stress 10 kPa and 1 MPa, respectively), and viscous λ⋅eF|LL for fluid flow control, where λ=2log(LL−25) and eF|LL is the void ratio at the liquid limit. For classification purposes, these void ratios can be estimated from index properties such as particle shape, the coefficient of uniformity, and the liquid limit. Analytically computed and data-adjusted boundaries are soil-specific, in contrast with the Unified Soil Classification System (USCS). Threshold fractions for mechanical control and for flow control are quite distinct in the proposed system. Therefore, the RSCS uses a two-name nomenclature whereby the first letters identify the component(s) that controls mechanical properties, followed by a letter (shown in parenthesis) that identifies the component that controls fluid flow. Sample charts in this paper and a Microsoft Excel facilitate the implementation of this revised classification system.

Revised Soil Classification System for Coarse-Fine Mixtures

KAUST Repository

Park, Junghee

2017-04-17

Soil classification systems worldwide capture great physical insight and enable geotechnical engineers to anticipate the properties and behavior of soils by grouping them into similar response categories based on their index properties. Yet gravimetric analysis and data trends summarized from published papers reveal critical limitations in soil group boundaries adopted in current systems. In particular, current classification systems fail to capture the dominant role of fines on the mechanical and hydraulic properties of soils. A revised soil classification system (RSCS) for coarse-fine mixtures is proposed herein. Definitions of classification boundaries use low and high void ratios that gravel, sand, and fines may attain. This research adopts emax and emin for gravels and sands, and three distinctive void ratio values for fines: soft eF|10  kPa and stiff eF|1  MPa for mechanical response (at effective stress 10 kPa and 1 MPa, respectively), and viscous λ⋅eF|LL for fluid flow control, where λ=2log(LL−25) and eF|LL is the void ratio at the liquid limit. For classification purposes, these void ratios can be estimated from index properties such as particle shape, the coefficient of uniformity, and the liquid limit. Analytically computed and data-adjusted boundaries are soil-specific, in contrast with the Unified Soil Classification System (USCS). Threshold fractions for mechanical control and for flow control are quite distinct in the proposed system. Therefore, the RSCS uses a two-name nomenclature whereby the first letters identify the component(s) that controls mechanical properties, followed by a letter (shown in parenthesis) that identifies the component that controls fluid flow. Sample charts in this paper and a Microsoft Excel facilitate the implementation of this revised classification system.

Language and functionality of post-stroke adults: evaluation based on International Classification of Functioning, Disability and Health (ICF).

Science.gov (United States)

Santana, Maria Tereza Maynard; Chun, Regina Yu Shon

2017-03-09

Cerebrovascular accident is an important Public Health problem because of the high rates of mortality and sequelae such as language disorders. The conceptual health changes have led to the incorporation of functional and social aspects in the assessments as proposed by the World Health Organization in the International Classification of Functioning, Disability and Health. The purpose was to evaluate and classify language aspects, functionality and participation of post-stroke individuals based on the concepts of the International Classification of Functioning, Disability and Health and characterize the sociodemographic profile of participants. Data collection was carried out through the application of a clinical instrument to evaluate language, participation and functionality in fifty individuals based on the International Classification of Functioning, Disability and Health. The age of the participants varied between 32 and 88 years, and the majority were elderly men. Among body functions, the participants reported more difficulties in "memory functions". As for activity and participation, more difficulties were reported in "recreation and leisure". As for environmental factors, the component "healthcare professionals" was indicated as a facilitator by the majority of participants. The results show the impact of language difficulties in the lives of post-stroke adults and reinforce the applicability of the International Classification of Functioning, Disability and Health as an important complementary tool for assessing language, functionality and participation in a comprehensive and humane approach, towards the improvement of health assistance in ambulatory care.

A simplified classification system for partially edentulous spaces

Directory of Open Access Journals (Sweden)

Bhandari Aruna J, Bhandari Akshay J

2014-04-01

Full Text Available Background: There is no single universally employed classification system that will specify the exact edentulous situation. Several classification systems exist to group the situation and avoid confusion. Classifications based on edentulous areas, finished restored prostheses, type of direct retainers or fulcrum lines are there. Some are based depending on the placement of the implants. Widely accepted Kennedy Applegate classification does not give any idea about length, span or number of teeth missing. Rule 6 governing the application of Kennedy method states that additional edentulous areas are referred as modification number 1,2 etc. Rule 7 states that extent of the modification is not considered; only the number of edentulous areas is considered. Hence there is a need to modify the Kennedy –Applegate System. Aims: This new classification system is an attempt to modify Kennedy –Applegate System so as to give the exact idea about missing teeth, space, span, side and areas of partially edentulous arches. Methods and Material: This system will provide the information regarding Maxillary or Mandibular partially edentulous arches, Left or Right side, length of the edentulous space, number of teeth missing and whether there will be tooth borne or tooth – tissue borne prosthesis. Conclusions: This classification is easy for application, communication and will also help to design the removable cast partial denture in a better logical and systematic way. Also, this system will give the idea of the edentulous status and the number of missing teeth in fixed, hybrid or implant prosthesis.

Intra- and Interobserver Reliability of Three Classification Systems for Hallux Rigidus.

Science.gov (United States)

Dillard, Sarita; Schilero, Christina; Chiang, Sharon; Pham, Peter

2018-04-18

There are over ten classification systems currently used in the staging of hallux rigidus. This results in confusion and inconsistency with radiographic interpretation and treatment. The reliability of hallux rigidus classification systems has not yet been tested. The purpose of this study was to evaluate intra- and interobserver reliability using three commonly used classifications for hallux rigidus. Twenty-one plain radiograph sets were presented to ten ACFAS board-certified foot and ankle surgeons. Each physician classified each radiograph based on clinical experience and knowledge according to the Regnauld, Roukis, and Hattrup and Johnson classification systems. The two-way mixed single-measure consistency intraclass correlation was used to calculate intra- and interrater reliability. The intrarater reliability of individual sets for the Roukis and Hattrup and Johnson classification systems was "fair to good" (Roukis, 0.62±0.19; Hattrup and Johnson, 0.62±0.28), whereas the intrarater reliability of individual sets for the Regnauld system bordered between "fair to good" and "poor" (0.43±0.24). The interrater reliability of the mean classification was "excellent" for all three classification systems. Conclusions Reliable and reproducible classification systems are essential for treatment and prognostic implications in hallux rigidus. In our study, Roukis classification system had the best intrarater reliability. Although there are various classification systems for hallux rigidus, our results indicate that all three of these classification systems show reliability and reproducibility.

Improved wavelet packet classification algorithm for vibrational intrusions in distributed fiber-optic monitoring systems

Science.gov (United States)

Wang, Bingjie; Pi, Shaohua; Sun, Qi; Jia, Bo

2015-05-01

An improved classification algorithm that considers multiscale wavelet packet Shannon entropy is proposed. Decomposition coefficients at all levels are obtained to build the initial Shannon entropy feature vector. After subtracting the Shannon entropy map of the background signal, components of the strongest discriminating power in the initial feature vector are picked out to rebuild the Shannon entropy feature vector, which is transferred to radial basis function (RBF) neural network for classification. Four types of man-made vibrational intrusion signals are recorded based on a modified Sagnac interferometer. The performance of the improved classification algorithm has been evaluated by the classification experiments via RBF neural network under different diffusion coefficients. An 85% classification accuracy rate is achieved, which is higher than the other common algorithms. The classification results show that this improved classification algorithm can be used to classify vibrational intrusion signals in an automatic real-time monitoring system.

Portugal's special education law: implementing the International Classification of Functioning, Disability and Health in policy and practice.

Science.gov (United States)

Sanches-Ferreira, Manuela; Simeonsson, Rune J; Silveira-Maia, Mónica; Alves, Sílvia; Tavares, Ana; Pinheiro, Sara

2013-05-01

The International Classification of Functioning, Disability and Health (ICF) was introduced in Portuguese education law as the compulsory system to guide eligibility policy and practice in special education. This paper describes the implementation of the ICF and its utility in the assessment process and eligibility determination of students for special education. A study to evaluate the utility of the ICF was commissioned by the Portuguese Ministry of Education and carried out by an external evaluation team. A document analysis was made of the assessment and eligibility processes of 237 students, selected from a nationally representative sample. The results provided support for the use of the ICF in student assessment and in the multidimensional approach of generating student functioning profiles as the basis for determining eligibility. The use of the ICF contributed to the differentiation of eligible and non eligible students based on their functioning profiles. The findings demonstrate the applicability of the ICF framework and classification system for determining eligibility for special education services on the basis of student functioning rather than medical or psychological diagnose. The use of the International Classification of Functioning, Disability and Health (ICF) framework in special education policy is as follows: • The functional perspective of the ICF offers a more comprehensive, holistic assessment of student needs than medical diagnoses. • ICF-based assessment of the nature and severity of functioning can serve as the basis for determining eligibility for special education and habilitation. • Profiles of functioning can support decision making in designing appropriate educational interventions for students.

Formalization of the classification pattern: survey of classification modeling in information systems engineering.

Science.gov (United States)

Partridge, Chris; de Cesare, Sergio; Mitchell, Andrew; Odell, James

2018-01-01

Formalization is becoming more common in all stages of the development of information systems, as a better understanding of its benefits emerges. Classification systems are ubiquitous, no more so than in domain modeling. The classification pattern that underlies these systems provides a good case study of the move toward formalization in part because it illustrates some of the barriers to formalization, including the formal complexity of the pattern and the ontological issues surrounding the "one and the many." Powersets are a way of characterizing the (complex) formal structure of the classification pattern, and their formalization has been extensively studied in mathematics since Cantor's work in the late nineteenth century. One can use this formalization to develop a useful benchmark. There are various communities within information systems engineering (ISE) that are gradually working toward a formalization of the classification pattern. However, for most of these communities, this work is incomplete, in that they have not yet arrived at a solution with the expressiveness of the powerset benchmark. This contrasts with the early smooth adoption of powerset by other information systems communities to, for example, formalize relations. One way of understanding the varying rates of adoption is recognizing that the different communities have different historical baggage. Many conceptual modeling communities emerged from work done on database design, and this creates hurdles to the adoption of the high level of expressiveness of powersets. Another relevant factor is that these communities also often feel, particularly in the case of domain modeling, a responsibility to explain the semantics of whatever formal structures they adopt. This paper aims to make sense of the formalization of the classification pattern in ISE and surveys its history through the literature, starting from the relevant theoretical works of the mathematical literature and gradually shifting focus

Burke-Fahn-Marsden dystonia severity, Gross Motor, Manual Ability, and Communication Function Classification scales in childhood hyperkinetic movement disorders including cerebral palsy: a 'Rosetta Stone' study.

Science.gov (United States)

Elze, Markus C; Gimeno, Hortensia; Tustin, Kylee; Baker, Lesley; Lumsden, Daniel E; Hutton, Jane L; Lin, Jean-Pierre S-M

2016-02-01

Hyperkinetic movement disorders (HMDs) can be assessed using impairment-based scales or functional classifications. The Burke-Fahn-Marsden Dystonia Rating Scale-movement (BFM-M) evaluates dystonia impairment, but may not reflect functional ability. The Gross Motor Function Classification System (GMFCS), Manual Ability Classification System (MACS), and Communication Function Classification System (CFCS) are widely used in the literature on cerebral palsy to classify functional ability, but not in childhood movement disorders. We explore the concordance of these three functional scales in a large sample of paediatric HMDs and the impact of dystonia severity on these scales. Children with HMDs (n=161; median age 10y 3mo, range 2y 6mo-21y) were assessed using the BFM-M, GMFCS, MACS, and CFCS from 2007 to 2013. This cross-sectional study contrasts the information provided by these scales. All four scales were strongly associated (all Spearman's rank correlation coefficient rs >0.72, pdisorders including cerebral palsy can be effectively evaluated using these scales. © 2015 Mac Keith Press.

Quantitative Classification of Quartz by Laser Induced Breakdown Spectroscopy in Conjunction with Discriminant Function Analysis

Directory of Open Access Journals (Sweden)

A. Ali

2016-01-01

Full Text Available A responsive laser induced breakdown spectroscopic system was developed and improved for utilizing it as a sensor for the classification of quartz samples on the basis of trace elements present in the acquired samples. Laser induced breakdown spectroscopy (LIBS in conjunction with discriminant function analysis (DFA was applied for the classification of five different types of quartz samples. The quartz plasmas were produced at ambient pressure using Nd:YAG laser at fundamental harmonic mode (1064 nm. We optimized the detection system by finding the suitable delay time of the laser excitation. This is the first study, where the developed technique (LIBS+DFA was successfully employed to probe and confirm the elemental composition of quartz samples.

A new tree classification system for southern hardwoods

Science.gov (United States)

James S. Meadows; Daniel A. Jr. Skojac

2008-01-01

A new tree classification system for southern hardwoods is described. The new system is based on the Putnam tree classification system, originally developed by Putnam et al., 1960, Management ond inventory of southern hardwoods, Agriculture Handbook 181, US For. Sew., Washington, DC, which consists of four tree classes: (1) preferred growing stock, (2) reserve growing...

An alternative respiratory sounds classification system utilizing artificial neural networks

Directory of Open Access Journals (Sweden)

Rami J Oweis

2015-04-01

Full Text Available Background: Computerized lung sound analysis involves recording lung sound via an electronic device, followed by computer analysis and classification based on specific signal characteristics as non-linearity and nonstationarity caused by air turbulence. An automatic analysis is necessary to avoid dependence on expert skills. Methods: This work revolves around exploiting autocorrelation in the feature extraction stage. All process stages were implemented in MATLAB. The classification process was performed comparatively using both artificial neural networks (ANNs and adaptive neuro-fuzzy inference systems (ANFIS toolboxes. The methods have been applied to 10 different respiratory sounds for classification. Results: The ANN was superior to the ANFIS system and returned superior performance parameters. Its accuracy, specificity, and sensitivity were 98.6%, 100%, and 97.8%, respectively. The obtained parameters showed superiority to many recent approaches. Conclusions: The promising proposed method is an efficient fast tool for the intended purpose as manifested in the performance parameters, specifically, accuracy, specificity, and sensitivity. Furthermore, it may be added that utilizing the autocorrelation function in the feature extraction in such applications results in enhanced performance and avoids undesired computation complexities compared to other techniques.

Safety classification of nuclear power plant systems, structures and components

International Nuclear Information System (INIS)

1992-01-01

The Safety Classification principles used for the systems, structures and components of a nuclear power plant are detailed in the guide. For classification, the nuclear power plant is divided into structural and operational units called systems. Every structure and component under control is included into some system. The Safety Classes are 1, 2 and 3 and the Class EYT (non-nuclear). Instructions how to assign each system, structure and component to an appropriate safety class are given in the guide. The guide applies to new nuclear power plants and to the safety classification of systems, structures and components designed for the refitting of old nuclear power plants. The classification principles and procedures applying to the classification document are also given

phangorn: phylogenetic analysis in R.

Science.gov (United States)

Schliep, Klaus Peter

2011-02-15

phangorn is a package for phylogenetic reconstruction and analysis in the R language. Previously it was only possible to estimate phylogenetic trees with distance methods in R. phangorn, now offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation. Extending the general ML framework, this package provides the possibility of estimating mixture and partition models. Furthermore, phangorn offers several functions for comparing trees, phylogenetic models or splits, simulating character data and performing congruence analyses. phangorn can be obtained through the CRAN homepage http://cran.r-project.org/web/packages/phangorn/index.html. phangorn is licensed under GPL 2.

Pathohistological classification systems in gastric cancer: diagnostic relevance and prognostic value.

Science.gov (United States)

Berlth, Felix; Bollschweiler, Elfriede; Drebber, Uta; Hoelscher, Arnulf H; Moenig, Stefan

2014-05-21

Several pathohistological classification systems exist for the diagnosis of gastric cancer. Many studies have investigated the correlation between the pathohistological characteristics in gastric cancer and patient characteristics, disease specific criteria and overall outcome. It is still controversial as to which classification system imparts the most reliable information, and therefore, the choice of system may vary in clinical routine. In addition to the most common classification systems, such as the Laurén and the World Health Organization (WHO) classifications, other authors have tried to characterize and classify gastric cancer based on the microscopic morphology and in reference to the clinical outcome of the patients. In more than 50 years of systematic classification of the pathohistological characteristics of gastric cancer, there is no sole classification system that is consistently used worldwide in diagnostics and research. However, several national guidelines for the treatment of gastric cancer refer to the Laurén or the WHO classifications regarding therapeutic decision-making, which underlines the importance of a reliable classification system for gastric cancer. The latest results from gastric cancer studies indicate that it might be useful to integrate DNA- and RNA-based features of gastric cancer into the classification systems to establish prognostic relevance. This article reviews the diagnostic relevance and the prognostic value of different pathohistological classification systems in gastric cancer.

From fault classification to fault tolerance for multi-agent systems

CERN Document Server

Potiron, Katia; Taillibert, Patrick

2013-01-01

Faults are a concern for Multi-Agent Systems (MAS) designers, especially if the MAS are built for industrial or military use because there must be some guarantee of dependability. Some fault classification exists for classical systems, and is used to define faults. When dependability is at stake, such fault classification may be used from the beginning of the system's conception to define fault classes and specify which types of faults are expected. Thus, one may want to use fault classification for MAS; however, From Fault Classification to Fault Tolerance for Multi-Agent Systems argues that

Nuclear reactors transients identification and classification system

International Nuclear Information System (INIS)

Bianchi, Paulo Henrique

2008-01-01

This work describes the study and test of a system capable to identify and classify transients in thermo-hydraulic systems, using a neural network technique of the self-organizing maps (SOM) type, with the objective of implanting it on the new generations of nuclear reactors. The technique developed in this work consists on the use of multiple networks to do the classification and identification of the transient states, being each network a specialist at one respective transient of the system, that compete with each other using the quantization error, that is a measure given by this type of neural network. This technique showed very promising characteristics that allow the development of new functionalities in future projects. One of these characteristics consists on the potential of each network, besides responding what transient is in course, could give additional information about that transient. (author)

Classification process in a text document recommender system

Directory of Open Access Journals (Sweden)

Dan MUNTEANU

2005-12-01

Full Text Available This paper presents the classification process in a recommender system used for textual documents taken especially from web. The system uses in the classification process a combination of content filters, event filters and collaborative filters and it uses implicit and explicit feedback for evaluating documents.

AN APPLICATION OF FUNCTIONAL MULTIVARIATE REGRESSION MODEL TO MULTICLASS CLASSIFICATION

OpenAIRE

Krzyśko, Mirosław; Smaga, Łukasz

2017-01-01

In this paper, the scale response functional multivariate regression model is considered. By using the basis functions representation of functional predictors and regression coefficients, this model is rewritten as a multivariate regression model. This representation of the functional multivariate regression model is used for multiclass classification for multivariate functional data. Computational experiments performed on real labelled data sets demonstrate the effectiveness of the proposed ...

Towards a consensus on a hearing preservation classification system.

Science.gov (United States)

Skarzynski, Henryk; van de Heyning, P; Agrawal, S; Arauz, S L; Atlas, M; Baumgartner, W; Caversaccio, M; de Bodt, M; Gavilan, J; Godey, B; Green, K; Gstoettner, W; Hagen, R; Han, D M; Kameswaran, M; Karltorp, E; Kompis, M; Kuzovkov, V; Lassaletta, L; Levevre, F; Li, Y; Manikoth, M; Martin, J; Mlynski, R; Mueller, J; O'Driscoll, M; Parnes, L; Prentiss, S; Pulibalathingal, S; Raine, C H; Rajan, G; Rajeswaran, R; Rivas, J A; Rivas, A; Skarzynski, P H; Sprinzl, G; Staecker, H; Stephan, K; Usami, S; Yanov, Y; Zernotti, M E; Zimmermann, K; Lorens, A; Mertens, G

2013-01-01

The comprehensive Hearing Preservation classification system presented in this paper is suitable for use for all cochlear implant users with measurable pre-operative residual hearing. If adopted as a universal reporting standard, as it was designed to be, it should prove highly beneficial by enabling future studies to quickly and easily compare the results of previous studies and meta-analyze their data. To develop a comprehensive Hearing Preservation classification system suitable for use for all cochlear implant users with measurable pre-operative residual hearing. The HEARRING group discussed and reviewed a number of different propositions of a HP classification systems and reviewed critical appraisals to develop a qualitative system in accordance with the prerequisites. The Hearing Preservation Classification System proposed herein fulfills the following necessary criteria: 1) classification is independent from users' initial hearing, 2) it is appropriate for all cochlear implant users with measurable pre-operative residual hearing, 3) it covers the whole range of pure tone average from 0 to 120 dB; 4) it is easy to use and easy to understand.

Fast breeder reactor reference system classification for the ENEA data bank

International Nuclear Information System (INIS)

Righini, R.

1988-01-01

This report contains the Reference System Classification (RSC) of fast breeder reactors: it provides a functional system breakdown of the reactor. For each system the following important characteristics are reported: the main function, the mode of operation, its location in the reactor, the main interface system, its main components and the component working environment (fluid and/or atmosphere type). The RSC represent a basic step in organizing the ENEA data bank for the registration and processing of reliability data on typical fast reactor components; it provides a functional component breakdown and represent a plant-unique identification in the process of omogenization of event-data coming from different reactors. In this report it was tried to take into account different generations of nuclear power plants, different plant layouts and solutions: in particular loop and pool reactors are separately treated

[Functioning and disability: the International Classification of Functioning, Disability and Health (ICF)].

Science.gov (United States)

Fernández-López, Juan Antonio; Fernández-Fidalgo, María; Geoffrey, Reed; Stucki, Gerold; Cieza, Alarcos

2009-01-01

The World Health Organization's International Classification of Functioning, Disability and Health (ICF) has provided a new foundation for our understanding of health, functioning, and disability. It covers most of the health and health-related domains that make up the human experience, and the most environmental factors that influence that experience of functioning and disability. With the exhaustive ICF, patients' functioning -including its components body functions and structures and activities and participation-, becomes a central perspective in medicine. To implement the ICF in medicine and other fields, practical tools (= ICF Core Sets) have been developed. They are selected sets of categories out of the whole classification which serve as minimal standards for the assessment and reporting of functioning and health for clinical studies and clinical encounters (Brief ICF Core Set) or as standards for multiprofessional comprehensive assessment (Comprehensive ICF Core Set). Different from generic and condition-specific health-status measures, the ICF Core Sets include important body functions and structures and contextual factors. The use of the ICF Core Sets provides an important step towards improved communications between healthcare providers and professionals, and will enable patients and their families to understand and communicate with health professionals about their functioning and treatment goals. Specific applications include multi- and interdisciplinary assessment in clinical settings and in legal expert evaluations and use in disease or functioning-management programs. The ICF has also a potential as a conceptual framework to clarify an interrelated universe of health-related concepts which can be elucidated based on the ICF and therefore will be an ideal tool for teaching students in all medical fields and may open doors to multi-professional learning.

Mapping a classification system to architectural education

DEFF Research Database (Denmark)

Hermund, Anders; Klint, Lars; Rostrup, Nicolai

2015-01-01

This paper examines to what extent a new classification system, Cuneco Classification System, CCS, proves useful in the education of architects, and to what degree the aim of an architectural education, rather based on an arts and crafts approach than a polytechnic approach, benefits from...... the distinct terminology of the classification system. The method used to examine the relationship between education, practice and the CCS bifurcates in a quantitative and a qualitative exploration: Quantitative comparison of the curriculum with the students’ own descriptions of their studies through...... a questionnaire survey among 88 students in graduate school. Qualitative interviews with a handful of practicing architects, to be able to cross check the relevance of the education with the profession. The examination indicates the need of a new definition, in addition to the CCS’s scale, covering the earliest...

A proposed data base system for detection, classification and ...

African Journals Online (AJOL)

A proposed data base system for detection, classification and location of fault on electricity company of Ghana electrical distribution system. Isaac Owusu-Nyarko, Mensah-Ananoo Eugine. Abstract. No Abstract. Keywords: database, classification of fault, power, distribution system, SCADA, ECG. Full Text: EMAIL FULL TEXT ...

Classification of Headache Disorders: Extending to a Multiaxial System.

Science.gov (United States)

Martin, Paul R

2016-11-01

This article argues for extending the International Classification of Headache Disorders to include information that goes beyond diagnosis. The obvious model is a multiaxial system as has been developed for other taxonomies. An axis for recording disability and impact on functioning, and an axis for recording the triggers of headache/migraine, are perhaps the strongest contenders for adding to the system, but there are other possibilities such as lifestyle factors relevant to headache. Extensions such as these would contribute to headache management, provide clear targets for change, and encourage adoption of a biopsychosocial perspective. © 2016 American Headache Society.

Functional classification of the Gauteng provincial road network ...

African Journals Online (AJOL)

The built environment consists of various land uses and activities connected by a road network. The efficiency and effectiveness of the road network directly impacts economic growth and societal movement. This study involved the functional classification of the Gauteng provincial road network using the South African Road ...

Stochastic change detection in uncertain nonlinear systems using reduced-order models: classification

International Nuclear Information System (INIS)

Yun, Hae-Bum; Masri, Sami F

2009-01-01

A reliable structural health monitoring methodology (SHM) is proposed to detect relatively small changes in uncertain nonlinear systems. A total of 4000 physical tests were performed using a complex nonlinear magneto-rheological (MR) damper. With the effective (or 'genuine') changes and uncertainties in the system characteristics of the semi-active MR damper, which were precisely controlled with known means and standard deviation of the input current, the tested MR damper was identified with the restoring force method (RFM), a non-parametric system identification method involving two-dimensional orthogonal polynomials. Using the identified RFM coefficients, both supervised and unsupervised pattern recognition techniques (including support vector classification and k-means clustering) were employed to detect system changes in the MR damper. The classification results showed that the identified coefficients with orthogonal basis function can be used as reliable indicators for detecting (small) changes, interpreting the physical meaning of the detected changes without a priori knowledge of the monitored system and quantifying the uncertainty bounds of the detected changes. The classification errors were analyzed using the standard detection theory to evaluate the performance of the developed SHM methodology. An optimal classifier design procedure was also proposed and evaluated to minimize type II (or 'missed') errors

Phylogenetic placement of two species known only from resting spores

DEFF Research Database (Denmark)

Hajek, Ann E; Gryganskyi, Andrii; Bittner, Tonya

2016-01-01

resting spores, Zoophthora independentia, infecting Tipula (Lunatipula) submaculata in New York State, is now described as a new species and Tarichium porteri, described in 1942, which infects Tipula (Triplicitipula) colei in Tennessee, is transferred to the genus Zoophthora. We have shown that use......Molecular methods were used to determine the generic placement of two species of Entomophthorales known only from resting spores. Historically, these species would belong in the form-genus Tarichium, but this classification provides no information about phylogenetic relationships. Using DNA from...... of molecular methods can assist with determination of the phylogenetic relations of specimens within the form-genus Tarichium for an already described species and a new species for which only resting spores are available....

Extension classification method for low-carbon product cases

Directory of Open Access Journals (Sweden)

Yanwei Zhao

2016-05-01

Full Text Available In product low-carbon design, intelligent decision systems integrated with certain classification algorithms recommend the existing design cases to designers. However, these systems mostly dependent on prior experience, and product designers not only expect to get a satisfactory case from an intelligent system but also hope to achieve assistance in modifying unsatisfactory cases. In this article, we proposed a new categorization method composed of static and dynamic classification based on extension theory. This classification method can be integrated into case-based reasoning system to get accurate classification results and to inform designers of detailed information about unsatisfactory cases. First, we establish the static classification model for cases by dependent function in a hierarchical structure. Then for dynamic classification, we make transformation for cases based on case model, attributes, attribute values, and dependent function, thus cases can take qualitative changes. Finally, the applicability of proposed method is demonstrated through a case study of screw air compressor cases.

On the classification of structures, systems and components of nuclear research and test reactors

International Nuclear Information System (INIS)

Mattar Neto, Miguel

2009-01-01

The classification of structures, systems and components of nuclear reactors is a relevant issue related to their design because it is directly associated with their safety functions. There is an important statement regarding quality standards and records that says Structures, systems, and components important to safety shall be designed, fabricated, erected, and tested to quality standards commensurate with the importance of the safety functions to be performed. The definition of the codes, standards and technical requirements applied to the nuclear reactor design, fabrication, inspection and tests may be seen as the main result from this statement. There are well established guides to classify structures, systems and components for nuclear power reactors such as the Pressurized Water Reactors but one can not say the same for nuclear research and test reactors. The nuclear reactors safety functions are those required to the safe reactor operation, the safe reactor shutdown and continued safe conditions, the response to anticipated transients, the response to potential accidents and the control of radioactive material. So, it is proposed in this paper an approach to develop the classification of structures, systems and components of these reactors based on their intended safety functions in order to define the applicable set of codes, standards and technical requirements. (author)

The family of DOF transcription factors in Brachypodium distachyon: phylogenetic comparison with rice and barley DOFs and expression profiling

Directory of Open Access Journals (Sweden)

Hernando-Amado Sara

2012-11-01

Full Text Available Abstract Background Transcription factors (TFs are proteins that have played a central role both in evolution and in domestication, and are major regulators of development in living organisms. Plant genome sequences reveal that approximately 7% of all genes encode putative TFs. The DOF (DNA binding with One Finger TF family has been associated with vital processes exclusive to higher plants and to their close ancestors (algae, mosses and ferns. These are seed maturation and germination, light-mediated regulation, phytohormone and plant responses to biotic and abiotic stresses, etc. In Hordeum vulgare and Oryza sativa, 26 and 30 different Dof genes, respectively, have been annotated. Brachypodium distachyon has been the first Pooideae grass to be sequenced and, due to its genomic, morphological and physiological characteristics, has emerged as the model system for temperate cereals, such as wheat and barley. Results Through searches in the B. distachyon genome, 27 Dof genes have been identified and a phylogenetic comparison with the Oryza sativa and the Hordeum vulgare DOFs has been performed. To explore the evolutionary relationship among these DOF proteins, a combined phylogenetic tree has been constructed with the Brachypodium DOFs and those from rice and barley. This phylogenetic analysis has classified the DOF proteins into four Major Cluster of Orthologous Groups (MCOGs. Using RT-qPCR analysis the expression profiles of the annotated BdDof genes across four organs (leaves, roots, spikes and seeds has been investigated. These results have led to a classification of the BdDof genes into two groups, according to their expression levels. The genes highly or preferentially expressed in seeds have been subjected to a more detailed expression analysis (maturation, dry stage and germination. Conclusions Comparison of the expression profiles of the Brachypodium Dof genes with the published functions of closely related DOF sequences from the cereal

A new measure to study phylogenetic relations in the brown algal ...

Indian Academy of Sciences (India)

Unknown

our classification with the ones done earlier. [Das S, Chakrabarti J, Ghosh Z, Sahoo S and Mallick B 2005 A new measure to study phylogenetic relations in the brown algal order Ectocarpales: The “codon impact parameter”; J. Biosci. 30 699–709]. 1. Introduction. Algae have grown in importance all over the world. Today.

Phylogenetic study of the oxytocin-like immunoreactive system in invertebrates.

Science.gov (United States)

Mizuno, J; Takeda, N

1988-01-01

1. A phylogenetic study of oxytocin (OXT)-like immunoreactive cells was performed by the PAP method in the central nervous system of invertebrates. 2. The immunoreactivity was detected in the nerve cells of Hydra magnipapillata of the Coelenterata; Neanthes japonica and Pheretima communissima of the Annelida; Oncidium verrucosum, Limax marginatus and Meretrix lamarckii of the Mollusca; and Baratha brassica of the Arthropoda. 3. No immunoreactive cells were found in Bipalium sp. of the Platyhelminthes; Pomacea canaliculata, Aplysia kurodai, Bradybaena similaris and Achatina fulica of the Mollusca; and Gnorimosphaeroma rayi, Procambarus clarkii, Hemigrapsus sanguineus, Helice tridens and Gryllus bimaculatus of the Arthropoda; Asterina pectinifera of the Echinodermata; and Halocynthia roretzi of the Protochordata. 4. These results demonstrate that an OXT-immunoreactive substance is widely present not only in vertebrates but also in invertebrates. 5. OXT seems to have been introduced into these invertebrates at an early stage of their phylogenetic history.

Trends and concepts in fern classification

Science.gov (United States)

Christenhusz, Maarten J. M.; Chase, Mark W.

2014-01-01

Background and Aims Throughout the history of fern classification, familial and generic concepts have been highly labile. Many classifications and evolutionary schemes have been proposed during the last two centuries, reflecting different interpretations of the available evidence. Knowledge of fern structure and life histories has increased through time, providing more evidence on which to base ideas of possible relationships, and classification has changed accordingly. This paper reviews previous classifications of ferns and presents ideas on how to achieve a more stable consensus. Scope An historical overview is provided from the first to the most recent fern classifications, from which conclusions are drawn on past changes and future trends. The problematic concept of family in ferns is discussed, with a particular focus on how this has changed over time. The history of molecular studies and the most recent findings are also presented. Key Results Fern classification generally shows a trend from highly artificial, based on an interpretation of a few extrinsic characters, via natural classifications derived from a multitude of intrinsic characters, towards more evolutionary circumscriptions of groups that do not in general align well with the distribution of these previously used characters. It also shows a progression from a few broad family concepts to systems that recognized many more narrowly and highly controversially circumscribed families; currently, the number of families recognized is stabilizing somewhere between these extremes. Placement of many genera was uncertain until the arrival of molecular phylogenetics, which has rapidly been improving our understanding of fern relationships. As a collective category, the so-called ‘fern allies’ (e.g. Lycopodiales, Psilotaceae, Equisetaceae) were unsurprisingly found to be polyphyletic, and the term should be abandoned. Lycopodiaceae, Selaginellaceae and Isoëtaceae form a clade (the lycopods) that is

Trends and concepts in fern classification.

Science.gov (United States)

Christenhusz, Maarten J M; Chase, Mark W

2014-03-01

Throughout the history of fern classification, familial and generic concepts have been highly labile. Many classifications and evolutionary schemes have been proposed during the last two centuries, reflecting different interpretations of the available evidence. Knowledge of fern structure and life histories has increased through time, providing more evidence on which to base ideas of possible relationships, and classification has changed accordingly. This paper reviews previous classifications of ferns and presents ideas on how to achieve a more stable consensus. An historical overview is provided from the first to the most recent fern classifications, from which conclusions are drawn on past changes and future trends. The problematic concept of family in ferns is discussed, with a particular focus on how this has changed over time. The history of molecular studies and the most recent findings are also presented. Fern classification generally shows a trend from highly artificial, based on an interpretation of a few extrinsic characters, via natural classifications derived from a multitude of intrinsic characters, towards more evolutionary circumscriptions of groups that do not in general align well with the distribution of these previously used characters. It also shows a progression from a few broad family concepts to systems that recognized many more narrowly and highly controversially circumscribed families; currently, the number of families recognized is stabilizing somewhere between these extremes. Placement of many genera was uncertain until the arrival of molecular phylogenetics, which has rapidly been improving our understanding of fern relationships. As a collective category, the so-called 'fern allies' (e.g. Lycopodiales, Psilotaceae, Equisetaceae) were unsurprisingly found to be polyphyletic, and the term should be abandoned. Lycopodiaceae, Selaginellaceae and Isoëtaceae form a clade (the lycopods) that is sister to all other vascular plants, whereas

Change in mobility function and its causes in adults with cerebral palsy by Gross Motor Function Classification System level: A cross-sectional questionnaire study.

Science.gov (United States)

Himuro, Nobuaki; Mishima, Reiko; Seshimo, Takashi; Morishima, Toshibumi; Kosaki, Keisuke; Ibe, Shigeharu; Asagai, Yoshimi; Minematsu, Koji; Kurita, Kazuhiro; Okayasu, Tsutomu; Shimura, Tsukasa; Hoshino, Kotaro; Suzuki, Toshiro; Yanagizono, Taiichiro

2018-04-07

The prognosis for mobility function by Gross Motor Function Classification System (GMFCS) level is vital as a guide to rehabilitation for people with cerebral palsy. This study sought to investigate change in mobility function and its causes in adults with cerebral palsy by GMFCS level. We conducted a cross-sectional questionnaire study. A total of 386 participants (26 y 8 m, SD 5 y 10 m) with cerebral palsy were analyzed. Participant numbers by GMFCS level were: I (53), II (139), III (74) and IV (120). The median age of participants with peak mobility function in GMFCS level III was younger than that in the other levels. 48% had experienced a decline in mobility. A Kaplan-Meier plot showed the risk of mobility decline increased in GMFCS level III; the hazard ratio was 1.97 (95% CI, 1.20-3.23) compared with level I. The frequently reported causes of mobility decline were changes in environment, and illness and injury in GMFCS level III, stiffness and deformity in level IV, and reduced physical activity in level II and III. Peak mobility function and mobility decline occurred at a younger age in GMFCS level III, with the cause of mobility decline differing by GMFCS level.

Classification system for reporting events involving human malfunctions

DEFF Research Database (Denmark)

Rasmussen, Jens; Pedersen, O.M.; Mancini, G.

1981-01-01

The report describes a set of categories for reporting indus-trial incidents and events involving human malfunction. The classification system aims at ensuring information adequate for improvement of human work situations and man-machine interface systems and for attempts to quantify "human error......" rates. The classification system has a multifacetted non-hierarchical struc-ture and its compatibility with Isprals ERDS classification is described. The collection of the information in general and for quantification purposes are discussed. 24 categories, 12 of which being human factors oriented......, are listed with their respective subcategories, and comments are given. Underlying models of human data processes and their typical malfunc-tions and of a human decision sequence are described....

Classification system for reporting events involving human malfunctions

International Nuclear Information System (INIS)

Rasmussen, J.; Pedersen, O.M.; Mancini, G.; Carnino, A.; Griffon, M.; Gagnolet, P.

1981-03-01

The report describes a set of categories for reporting industrial incidents and events involving human malfunction. The classification system aims at ensuring information adequate for improvement of human work situations and man-machine interface systems and for attempts to quantify ''human error'' rates. The classification system has a multifacetted non-hierarchial structure and its compatibility with Ispra's ERDS classification is described. The collection of the information in general and for quantification purposes are discussed. 24 categories, 12 of which being human factors oriented, are listed with their respective subcategories, and comments are given. Underlying models of human data processes and their typical malfunctions and of a human decision sequence are described. (author)

Partitioning the impact of environment and spatial structure on alpha and beta components of taxonomic, functional, and phylogenetic diversity in European ants.

Science.gov (United States)

Arnan, Xavier; Cerdá, Xim; Retana, Javier

2015-01-01

We analyze the relative contribution of environmental and spatial variables to the alpha and beta components of taxonomic (TD), phylogenetic (PD), and functional (FD) diversity in ant communities found along different climate and anthropogenic disturbance gradients across western and central Europe, in order to assess the mechanisms structuring ant biodiversity. To this aim we calculated alpha and beta TD, PD, and FD for 349 ant communities, which included a total of 155 ant species; we examined 10 functional traits and phylogenetic relatedness. Variation partitioning was used to examine how much variation in ant diversity was explained by environmental and spatial variables. Autocorrelation in diversity measures and each trait's phylogenetic signal were also analyzed. We found strong autocorrelation in diversity measures. Both environmental and spatial variables significantly contributed to variation in TD, PD, and FD at both alpha and beta scales; spatial structure had the larger influence. The different facets of diversity showed similar patterns along environmental gradients. Environment explained a much larger percentage of variation in FD than in TD or PD. All traits demonstrated strong phylogenetic signals. Our results indicate that environmental filtering and dispersal limitations structure all types of diversity in ant communities. Strong dispersal limitations appear to have led to clustering of TD, PD, and FD in western and central Europe, probably because different historical and evolutionary processes generated different pools of species. Remarkably, these three facets of diversity showed parallel patterns along environmental gradients. Trait-mediated species sorting and niche conservatism appear to structure ant diversity, as evidenced by the fact that more variation was explained for FD and that all traits had strong phylogenetic signals. Since environmental variables explained much more variation in FD than in PD, functional diversity should be a

Schizophrenia classification using functional network features

Science.gov (United States)

Rish, Irina; Cecchi, Guillermo A.; Heuton, Kyle

2012-03-01

This paper focuses on discovering statistical biomarkers (features) that are predictive of schizophrenia, with a particular focus on topological properties of fMRI functional networks. We consider several network properties, such as node (voxel) strength, clustering coefficients, local efficiency, as well as just a subset of pairwise correlations. While all types of features demonstrate highly significant statistical differences in several brain areas, and close to 80% classification accuracy, the most remarkable results of 93% accuracy are achieved by using a small subset of only a dozen of most-informative (lowest p-value) correlation features. Our results suggest that voxel-level correlations and functional network features derived from them are highly informative about schizophrenia and can be used as statistical biomarkers for the disease.

Implementation of the international classification of functioning, disability and health (ICF) in the Portuguese educational system: Attitudes and training needs of special education teachers’.

OpenAIRE

Saragoça, M.; Candeias, A. A.; Rosário, A.

2013-01-01

Since 2008, the International Classification of Functioning, Disability and Health - ICF (WHO, 2001) is the framework of reference in the assessment and intervention process with students with SEN, in the Portuguese educational system. As a consequence special education teachers’ training needs emerged from it. In this study, we characterize the received training and the special education teachers’ attitudes and training needs towards ICF. The sample consisted of 913 Portuguese special educat...

Multi-Functional Sensing for Swarm Robots Using Time Sequence Classification: HoverBot, an Example

Directory of Open Access Journals (Sweden)

Markus P. Nemitz

2018-05-01

Full Text Available Scaling up robot swarms to collectives of hundreds or even thousands without sacrificing sensing, processing, and locomotion capabilities is a challenging problem. Low-cost robots are potentially scalable, but the majority of existing systems have limited capabilities, and these limitations substantially constrain the type of experiments that could be performed by robotics researchers. Instead of adding functionality by adding more components and therefore increasing the cost, we demonstrate how low-cost hardware can be used beyond its standard functionality. We systematically review 15 swarm robotic systems and analyse their sensing capabilities by applying a general sensor model from the sensing and measurement community. This work is based on the HoverBot system. A HoverBot is a levitating circuit board that manoeuvres by pulling itself towards magnetic anchors that are embedded into the robot arena. We show that HoverBot’s magnetic field readouts from its Hall-effect sensor can be associated to successful movement, robot rotation and collision measurands. We build a time series classifier based on these magnetic field readouts. We modify and apply signal processing techniques to enable the online classification of the time-variant magnetic field measurements on HoverBot’s low-cost microcontroller. We enabled HoverBot with successful movement, rotation, and collision sensing capabilities by utilising its single Hall-effect sensor. We discuss how our classification method could be applied to other sensors to increase a robot’s functionality while retaining its cost.

Phylogenetic trees

OpenAIRE

Baños, Hector; Bushek, Nathaniel; Davidson, Ruth; Gross, Elizabeth; Harris, Pamela E.; Krone, Robert; Long, Colby; Stewart, Allen; Walker, Robert

2016-01-01

We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees can be used to calculate a generating set for a phylogenetic ideal as well as a lower bound for its dimension. Finally, we show how methods within the package can be used to compute a generating set for the join of any two ideals.

Improving the precision of the structure-function relationship by considering phylogenetic context.

Directory of Open Access Journals (Sweden)

2005-06-01

Full Text Available Understanding the relationship between protein structure and function is one of the foremost challenges in post-genomic biology. Higher conservation of structure could, in principle, allow researchers to extend current limitations of annotation. However, despite significant research in the area, a precise and quantitative relationship between biochemical function and protein structure has been elusive. Attempts to draw an unambiguous link have often been complicated by pleiotropy, variable transcriptional control, and adaptations to genomic context, all of which adversely affect simple definitions of function. In this paper, I report that integrating genomic information can be used to clarify the link between protein structure and function. First, I present a novel measure of functional proximity between protein structures (F-score. Then, using F-score and other entirely automatic methods measuring structure and phylogenetic similarity, I present a three-dimensional landscape describing their inter-relationship. The result is a "well-shaped" landscape that demonstrates the added value of considering genomic context in inferring function from structural homology. A generalization of methodology presented in this paper can be used to improve the precision of annotation of genes in current and newly sequenced genomes.

Controlling a human-computer interface system with a novel classification method that uses electrooculography signals.

Science.gov (United States)

Wu, Shang-Lin; Liao, Lun-De; Lu, Shao-Wei; Jiang, Wei-Ling; Chen, Shi-An; Lin, Chin-Teng

2013-08-01

Electrooculography (EOG) signals can be used to control human-computer interface (HCI) systems, if properly classified. The ability to measure and process these signals may help HCI users to overcome many of the physical limitations and inconveniences in daily life. However, there are currently no effective multidirectional classification methods for monitoring eye movements. Here, we describe a classification method used in a wireless EOG-based HCI device for detecting eye movements in eight directions. This device includes wireless EOG signal acquisition components, wet electrodes and an EOG signal classification algorithm. The EOG classification algorithm is based on extracting features from the electrical signals corresponding to eight directions of eye movement (up, down, left, right, up-left, down-left, up-right, and down-right) and blinking. The recognition and processing of these eight different features were achieved in real-life conditions, demonstrating that this device can reliably measure the features of EOG signals. This system and its classification procedure provide an effective method for identifying eye movements. Additionally, it may be applied to study eye functions in real-life conditions in the near future.

Standard practice for classification of computed radiology systems

CERN Document Server

American Society for Testing and Materials. Philadelphia

2005-01-01

1.1 This practice describes the evaluation and classification of a computed radiography (CR) system, a particular phosphor imaging plate (IP), system scanner and software, in combination with specified metal screens for industrial radiography. It is intended to ensure that the evaluation of image quality, as far as this is influenced by the scanner/IP system, meets the needs of users. 1.2 The practice defines system tests to be used to classify the systems of different suppliers and make them comparable for users. 1.3 The CR system performance is described by signal and noise parameters. For film systems, the signal is represented by gradient and the noise by granularity. The signal-to-noise ratio is normalized by the basic spatial resolution of the system and is part of classification. The normalization is given by the scanning aperture of 100 µm diameter for the micro-photometer, which is defined in Test Method E1815 for film system classification. This practice describes how the parameters shall be meas...

42 CFR 412.10 - Changes in the DRG classification system.

Science.gov (United States)

2010-10-01

... 42 Public Health 2 2010-10-01 2010-10-01 false Changes in the DRG classification system. 412.10... § 412.10 Changes in the DRG classification system. (a) General rule. CMS issues changes in the DRG... after the same date the payment rates are effective. (b) Basis for changes in the DRG classification...

A curated database of cyanobacterial strains relevant for modern taxonomy and phylogenetic studies.

Science.gov (United States)

Ramos, Vitor; Morais, João; Vasconcelos, Vitor M

2017-04-25

The dataset herein described lays the groundwork for an online database of relevant cyanobacterial strains, named CyanoType (http://lege.ciimar.up.pt/cyanotype). It is a database that includes categorized cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes, with associated information obtained by means of a literature-based curation. The dataset lists 371 strains and represents the first version of the database (CyanoType v.1). Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to three different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies (including this), and important bibliographic references. The database will be updated periodically, namely by adding new strains meeting the criteria for inclusion and by revising and adding up-to-date metadata for strains already listed. A global 16S rDNA-based phylogeny is provided in order to assist users when choosing the appropriate strains for their studies.

CLASSIFICATION OF THE MGR WASTE EMPLACEMENT/RETRIEVAL SYSTEM

International Nuclear Information System (INIS)

J.A. Ziegler

2000-01-01

The purpose of this analysis is to document the Quality Assurance (QA) classification of the Monitored Geologic Repository (MGR) waste emplacement/retrieved system structures, systems and components (SSCs) performed by the MGR Preclosure Safety and Systems Engineering Section. This analysis also provides the basis for revision of YMP/90-55Q, Q-List (YMP 2000). The Q-List identifies those MGR SSCs subject to the requirements of DOE/RW-0333P, Quality Assurance Requirements and Description (QARD) (DOE 2000). This QA classification incorporates the current MGR design and the results of the ''Design Basis Event Frequency and Dose Calculation for Site Recommendation'' (CRWMS M andO 2000a). The content and technical approach of this analysis is in accordance with the development plan ''QA Classification of MGR Structures, Systems, and Components'' (CRWMS M andO 1999b)

Hydrologic-Process-Based Soil Texture Classifications for Improved Visualization of Landscape Function

Science.gov (United States)

Groenendyk, Derek G.; Ferré, Ty P.A.; Thorp, Kelly R.; Rice, Amy K.

2015-01-01

function, suggest that hydrologic-process-based classifications should be incorporated into environmental process models and can be used to define application-specific maps of hydrologic function. PMID:26121466

Cirse Quality Assurance Document and Standards for Classification of Complications: The Cirse Classification System.

Science.gov (United States)

Filippiadis, D K; Binkert, C; Pellerin, O; Hoffmann, R T; Krajina, A; Pereira, P L

2017-08-01

Interventional radiology provides a wide variety of vascular, nonvascular, musculoskeletal, and oncologic minimally invasive techniques aimed at therapy or palliation of a broad spectrum of pathologic conditions. Outcome data for these techniques are globally evaluated by hospitals, insurance companies, and government agencies targeting in a high-quality health care policy, including reimbursement strategies. To analyze effectively the outcome of a technique, accurate reporting of complications is necessary. Throughout the literature, numerous classification systems for complications grading and classification have been reported. Until now, there has been no method for uniform reporting of complications both in terms of definition and grading. The purpose of this CIRSE guideline is to provide a classification system of complications based on combining outcome and severity of sequelae. The ultimate challenge will be the adoption of this system by practitioners in different countries and health economies within the European Union and beyond.

Classification Systems, their Digitization and Consequences for Data-Driven Decision Making

DEFF Research Database (Denmark)

Stein, Mari-Klara; Newell, Sue; Galliers, Robert D.

2013-01-01

Classification systems are foundational in many standardized software tools. This digitization of classification systems gives them a new ‘materiality’ that, jointly with the social practices of information producers/consumers, has significant consequences on the representational quality of such ...... and the foundational role of representational quality in understanding the success and consequences of data-driven decision-making.......-narration and meta-narration), and three different information production/consumption situations. We contribute to the relational theorization of representational quality and extend classification systems research by drawing explicit attention to the importance of ‘materialization’ of classification systems...

A discrimlnant function approach to ecological site classification in northern New England

Science.gov (United States)

James M. Fincher; Marie-Louise Smith

1994-01-01

Describes one approach to ecologically based classification of upland forest community types of the White and Green Mountain physiographic regions. The classification approach is based on an intensive statistical analysis of the relationship between the communities and soil-site factors. Discriminant functions useful in distinguishing between types based on soil-site...

Validation of potential classification criteria for systemic sclerosis.

NARCIS (Netherlands)

Johnson, S.R.; Fransen, J.; Khanna, D.; Baron, M.; Hoogen, F. van den; Medsger TA, J.r.; Peschken, C.A.; Carreira, P.E.; Riemekasten, G.; Tyndall, A.; Matucci-Cerinic, M.; Pope, J.E.

2012-01-01

OBJECTIVE: Classification criteria for systemic sclerosis (SSc; scleroderma) are being updated jointly by the American College of Rheumatology and European League Against Rheumatism. Potential items for classification were reduced to 23 using Delphi and nominal group techniques. We evaluated the

Link prediction boosted psychiatry disorder classification for functional connectivity network

Science.gov (United States)

Li, Weiwei; Mei, Xue; Wang, Hao; Zhou, Yu; Huang, Jiashuang

2017-02-01

Functional connectivity network (FCN) is an effective tool in psychiatry disorders classification, and represents cross-correlation of the regional blood oxygenation level dependent signal. However, FCN is often incomplete for suffering from missing and spurious edges. To accurate classify psychiatry disorders and health control with the incomplete FCN, we first `repair' the FCN with link prediction, and then exact the clustering coefficients as features to build a weak classifier for every FCN. Finally, we apply a boosting algorithm to combine these weak classifiers for improving classification accuracy. Our method tested by three datasets of psychiatry disorder, including Alzheimer's Disease, Schizophrenia and Attention Deficit Hyperactivity Disorder. The experimental results show our method not only significantly improves the classification accuracy, but also efficiently reconstructs the incomplete FCN.

Turnover of plant lineages shapes herbivore phylogenetic beta diversity along ecological gradients.

Science.gov (United States)

Pellissier, Loïc; Ndiribe, Charlotte; Dubuis, Anne; Pradervand, Jean-Nicolas; Salamin, Nicolas; Guisan, Antoine; Rasmann, Sergio

2013-05-01

Understanding drivers of biodiversity patterns is of prime importance in this era of severe environmental crisis. More diverse plant communities have been postulated to represent a larger functional trait-space, more likely to sustain a diverse assembly of herbivore species. Here, we expand this hypothesis to integrate environmental, functional and phylogenetic variation of plant communities as factors explaining the diversity of lepidopteran assemblages along elevation gradients in the Swiss Western Alps. According to expectations, we found that the association between butterflies and their host plants is highly phylogenetically structured. Multiple regression analyses showed the combined effect of climate, functional traits and phylogenetic diversity in structuring butterfly communities. Furthermore, we provide the first evidence that plant phylogenetic beta diversity is the major driver explaining butterfly phylogenetic beta diversity. Along ecological gradients, the bottom up control of herbivore diversity is thus driven by phylogenetically structured turnover of plant traits as well as environmental variables. © 2013 Blackwell Publishing Ltd/CNRS.

Validation of a systems-actuarial computer process for multidimensional classification of child psychopathology.

Science.gov (United States)

McDermott, P A; Hale, R L

1982-07-01

Tested diagnostic classifications of child psychopathology produced by a computerized technique known as multidimensional actuarial classification (MAC) against the criterion of expert psychological opinion. The MAC program applies series of statistical decision rules to assess the importance of and relationships among several dimensions of classification, i.e., intellectual functioning, academic achievement, adaptive behavior, and social and behavioral adjustment, to perform differential diagnosis of children's mental retardation, specific learning disabilities, behavioral and emotional disturbance, possible communication or perceptual-motor impairment, and academic under- and overachievement in reading and mathematics. Classifications rendered by MAC are compared to those offered by two expert child psychologists for cases of 73 children referred for psychological services. Experts' agreement with MAC was significant for all classification areas, as was MAC's agreement with the experts held as a conjoint reference standard. Whereas the experts' agreement with MAC averaged 86.0% above chance, their agreement with one another averaged 76.5% above chance. Implications of the findings are explored and potential advantages of the systems-actuarial approach are discussed.

Classification system for reporting events involving human malfunctions

International Nuclear Information System (INIS)

Rasmussen, J.; Pedersen, O.M.; Mancini, G.

1981-01-01

The report describes a set of categories for reporting industrial incidents and events involving human malfunction. The classification system aims at ensuring information adequate for improvement of human work situations and man-machine interface systems and for attempts to quantify ''human error'' rates. The classification system has a multifacetted non-hierarchical structure and its compatibility with Ispra's ERDS classification is described. The collection of the information in general and for quantification purposes are discussed. 24 categories, 12 of which being human factors-oriented, are listed with their respective subcategories, and comments are given. Underlying models of human data process and their typical malfuntions and of a human decision sequence are described. The work reported is a joint contribution to the CSNI Group of Experts on Human Error Data and Assessment

Development of a classification system for cup anemometers - CLASSCUP

DEFF Research Database (Denmark)

Friis Pedersen, Troels

2003-01-01

the objectives to quantify the errors associated with the use of cup anemometers, and to determine the requirements for an optimum design of a cup anemometer, and to develop a classification system forquantification of systematic errors of cup anemometers. The present report describes this proposed...... classification system. A classification method for cup anemometers has been developed, which proposes general external operational ranges to be used. Anormal category range connected to ideal sites of the IEC power performance standard was made, and another extended category range for complex terrain...... was proposed. General classification indices were proposed for all types of cup anemometers. As a resultof the classification, the cup anemometer will be assigned to a certain class: 0.5, 1, 2, 3 or 5 with corresponding intrinsic errors (%) as a vector instrument (3D) or as a horizontal instrument (2D...

Safety classification of systems, structures, and components for pool-type research reactors

Energy Technology Data Exchange (ETDEWEB)

Kim, Tae Ryong [KEPCO International Nuclear Graduate School, Ulsan (Korea, Republic of)

2016-08-15

Structures, systems, and components (SSCs) important to safety of nuclear facilities shall be designed, fabricated, erected, and tested to quality standards commensurate with the importance of the safety functions. Although SSC classification guidelines for nuclear power plants have been well established and applied, those for research reactors have been only recently established by the International Atomic Energy Agency (IAEA). Korea has operated a pool-type research reactor (the High Flux Advanced Neutron Application Reactor) and has recently exported another pool-type reactor (Jordan Research and Training Reactor), which is being built in Jordan. Korea also has a plan to build one more pool-type reactor, the Kijang Research Reactor, in Kijang, Busan. The safety classification of SSCs for pool-type research reactors is proposed in this paper based on the IAEA methodology. The proposal recommends that the SSCs of pool-type research reactors be categorized and classified on basis of their safety functions and safety significance. Because the SSCs in pool-type research reactors are not the pressure-retaining components, codes and standards for design of the SSCs following the safety classification can be selected in a graded approach.

Efficient Detection of Repeating Sites to Accelerate Phylogenetic Likelihood Calculations.

Science.gov (United States)

Kobert, K; Stamatakis, A; Flouri, T

2017-03-01

The phylogenetic likelihood function (PLF) is the major computational bottleneck in several applications of evolutionary biology such as phylogenetic inference, species delimitation, model selection, and divergence times estimation. Given the alignment, a tree and the evolutionary model parameters, the likelihood function computes the conditional likelihood vectors for every node of the tree. Vector entries for which all input data are identical result in redundant likelihood operations which, in turn, yield identical conditional values. Such operations can be omitted for improving run-time and, using appropriate data structures, reducing memory usage. We present a fast, novel method for identifying and omitting such redundant operations in phylogenetic likelihood calculations, and assess the performance improvement and memory savings attained by our method. Using empirical and simulated data sets, we show that a prototype implementation of our method yields up to 12-fold speedups and uses up to 78% less memory than one of the fastest and most highly tuned implementations of the PLF currently available. Our method is generic and can seamlessly be integrated into any phylogenetic likelihood implementation. [Algorithms; maximum likelihood; phylogenetic likelihood function; phylogenetics]. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Low-cost real-time automatic wheel classification system

Science.gov (United States)

Shabestari, Behrouz N.; Miller, John W. V.; Wedding, Victoria

1992-11-01

This paper describes the design and implementation of a low-cost machine vision system for identifying various types of automotive wheels which are manufactured in several styles and sizes. In this application, a variety of wheels travel on a conveyor in random order through a number of processing steps. One of these processes requires the identification of the wheel type which was performed manually by an operator. A vision system was designed to provide the required identification. The system consisted of an annular illumination source, a CCD TV camera, frame grabber, and 386-compatible computer. Statistical pattern recognition techniques were used to provide robust classification as well as a simple means for adding new wheel designs to the system. Maintenance of the system can be performed by plant personnel with minimal training. The basic steps for identification include image acquisition, segmentation of the regions of interest, extraction of selected features, and classification. The vision system has been installed in a plant and has proven to be extremely effective. The system properly identifies the wheels correctly up to 30 wheels per minute regardless of rotational orientation in the camera's field of view. Correct classification can even be achieved if a portion of the wheel is blocked off from the camera. Significant cost savings have been achieved by a reduction in scrap associated with incorrect manual classification as well as a reduction of labor in a tedious task.

PyElph - a software tool for gel images analysis and phylogenetics

Directory of Open Access Journals (Sweden)

Pavel Ana Brânduşa

2012-01-01

(Random Amplification of Polymorphic DNA and STR (Short Tandem Repeat. The similarity between the DNA sequences is computed and used to generate phylogenetic trees which are very useful for population genetics studies and taxonomic classification. Conclusions PyElph decreases the effort and time spent processing data from gel images by providing an automatic step-by-step gel image analysis system with a friendly Graphical User Interface. The proposed free software tool is suitable for researchers and students which do not have access to expensive commercial software and image acquisition devices.

Assembly and phylogenetic structure of Neotropical palm communities

DEFF Research Database (Denmark)

Eiserhardt, Wolf L.; Svenning, J.-C.; Balslev, Henrik

Diversity, composition and dynamics of Neotropical palm communities are receiving an increasing amount of attention due to their economic importance, but also because their high species richness and functional diversity render them valuable model systems for overall forest biodiversity. However......, to better understand these palm communities, it is crucial to gain insight into the mechanisms responsible for their assembly. These can be dispersal limitation, environmental filtering, or biotic interactions. If the degree of niche conservatism is known for a group of organisms, patterns of community...... an unspecific assumption of “general niche conservatism”, phylogenetic signal will be analysed for Neotropical palms. Moreover, as an example for evolutionary mechanisms disrupting phylogenetic signal, speciation modes will be examined in selected genera. With the combined results we aim to show the relative...

Capacities and overlap indexes with an application in fuzzy rule-based classification systems

Czech Academy of Sciences Publication Activity Database

Paternain, D.; Bustince, H.; Pagola, M.; Sussner, P.; Kolesárová, A.; Mesiar, Radko

2016-01-01

Roč. 305, č. 1 (2016), s. 70-94 ISSN 0165-0114 Institutional support: RVO:67985556 Keywords : Capacity * Overlap index * Overlap function * Choquet integral * Fuzzy rule-based classification systems Subject RIV: BA - General Mathematics Impact factor: 2.718, year: 2016 http://library.utia.cas.cz/separaty/2016/E/mesiar-0465739.pdf

Resting State fMRI Functional Connectivity-Based Classification Using a Convolutional Neural Network Architecture.

Science.gov (United States)

Meszlényi, Regina J; Buza, Krisztian; Vidnyánszky, Zoltán

2017-01-01

Machine learning techniques have become increasingly popular in the field of resting state fMRI (functional magnetic resonance imaging) network based classification. However, the application of convolutional networks has been proposed only very recently and has remained largely unexplored. In this paper we describe a convolutional neural network architecture for functional connectome classification called connectome-convolutional neural network (CCNN). Our results on simulated datasets and a publicly available dataset for amnestic mild cognitive impairment classification demonstrate that our CCNN model can efficiently distinguish between subject groups. We also show that the connectome-convolutional network is capable to combine information from diverse functional connectivity metrics and that models using a combination of different connectivity descriptors are able to outperform classifiers using only one metric. From this flexibility follows that our proposed CCNN model can be easily adapted to a wide range of connectome based classification or regression tasks, by varying which connectivity descriptor combinations are used to train the network.

Neuromuscular disease classification system

Science.gov (United States)

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

2013-06-01

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.

Inferring Phylogenetic Networks Using PhyloNet.

Science.gov (United States)

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

2018-07-01

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

Basic Hand Gestures Classification Based on Surface Electromyography

Directory of Open Access Journals (Sweden)

Aleksander Palkowski

2016-01-01

Full Text Available This paper presents an innovative classification system for hand gestures using 2-channel surface electromyography analysis. The system developed uses the Support Vector Machine classifier, for which the kernel function and parameter optimisation are conducted additionally by the Cuckoo Search swarm algorithm. The system developed is compared with standard Support Vector Machine classifiers with various kernel functions. The average classification rate of 98.12% has been achieved for the proposed method.

Effects of gross motor function and manual function levels on performance-based ADL motor skills of children with spastic cerebral palsy.

Science.gov (United States)

Park, Myoung-Ok

2017-02-01

[Purpose] The purpose of this study was to determine effects of Gross Motor Function Classification System and Manual Ability Classification System levels on performance-based motor skills of children with spastic cerebral palsy. [Subjects and Methods] Twenty-three children with cerebral palsy were included. The Assessment of Motor and Process Skills was used to evaluate performance-based motor skills in daily life. Gross motor function was assessed using Gross Motor Function Classification Systems, and manual function was measured using the Manual Ability Classification System. [Results] Motor skills in daily activities were significantly different on Gross Motor Function Classification System level and Manual Ability Classification System level. According to the results of multiple regression analysis, children categorized as Gross Motor Function Classification System level III scored lower in terms of performance based motor skills than Gross Motor Function Classification System level I children. Also, when analyzed with respect to Manual Ability Classification System level, level II was lower than level I, and level III was lower than level II in terms of performance based motor skills. [Conclusion] The results of this study indicate that performance-based motor skills differ among children categorized based on Gross Motor Function Classification System and Manual Ability Classification System levels of cerebral palsy.

Orthology prediction at scalable resolution by phylogenetic tree analysis

NARCIS (Netherlands)

Heijden, R.T.J.M. van der; Snel, B.; Noort, V. van; Huynen, M.A.

2007-01-01

BACKGROUND: Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature of phylogenetic

Functional morphology of the bovid astragalus in relation to habitat: controlling phylogenetic signal in ecomorphology.

Science.gov (United States)

Barr, W Andrew

2014-11-01

Bovid astragali are one of the most commonly preserved bones in the fossil record. Accordingly, astragali are an important target for studies seeking to predict the habitat preferences of fossil bovids based on bony anatomy. However, previous work has not tested functional hypotheses linking astragalar morphology with habitat while controlling for body size and phylogenetic signal. This article presents a functional framework relating the morphology of the bovid astragalus to habitat-specific locomotor ecology and tests four hypotheses emanating from this framework. Highly cursorial bovids living in structurally open habitats are hypothesized to differ from their less cursorial closed-habitat dwelling relatives in having (1) relatively short astragali to maintain rotational speed throughout the camming motion of the rotating astragalus, (2) a greater range of angular excursion at the hock, (3) relatively larger joint surface areas, and (4) a more pronounced "spline-and-groove" morphology promoting lateral joint stability. A diverse sample of 181 astragali from 50 extant species was scanned using a Next Engine laser scanner. Species were assigned to one of four habitat categories based on the published ecological literature. A series of 11 linear measurements and three joint surface areas were measured on each astragalus. A geometric mean body size proxy was used to size-correct the measurement data. Phylogenetic generalized least squares (PGLS) was used to test for differences between habitat categories while controlling for body size differences and phylogenetic signal. Statistically significant PGLS results support Hypotheses 1 and 2 (which are not mutually exclusive) as well as Hypothesis 3. No support was found for Hypothesis 4. These findings confirm that the morphology of the bovid astragalus is related to habitat-specific locomotor ecology, and that this relationship is statistically significant after controlling for body size and phylogeny. Thus, this study

Changing patient classification system for hospital reimbursement in Romania.

Science.gov (United States)

Radu, Ciprian-Paul; Chiriac, Delia Nona; Vladescu, Cristian

2010-06-01

To evaluate the effects of the change in the diagnosis-related group (DRG) system on patient morbidity and hospital financial performance in the Romanian public health care system. Three variables were assessed before and after the classification switch in July 2007: clinical outcomes, the case mix index, and hospital budgets, using the database of the National School of Public Health and Health Services Management, which contains data regularly received from hospitals reimbursed through the Romanian DRG scheme (291 in 2009). The lack of a Romanian system for the calculation of cost-weights imposed the necessity to use an imported system, which was criticized by some clinicians for not accurately reflecting resource consumption in Romanian hospitals. The new DRG classification system allowed a more accurate clinical classification. However, it also exposed a lack of physicians' knowledge on diagnosing and coding procedures, which led to incorrect coding. Consequently, the reported hospital morbidity changed after the DRG switch, reflecting an increase in the national case-mix index of 25% in 2009 (compared with 2007). Since hospitals received the same reimbursement over the first two years after the classification switch, the new DRG system led them sometimes to change patients' diagnoses in order to receive more funding. Lack of oversight of hospital coding and reporting to the national reimbursement scheme allowed the increase in the case-mix index. The complexity of the new classification system requires more resources (human and financial), better monitoring and evaluation, and improved legislation in order to achieve better hospital resource allocation and more efficient patient care.

Supervised Classification High-Resolution Remote-Sensing Image Based on Interval Type-2 Fuzzy Membership Function

Directory of Open Access Journals (Sweden)

Chunyan Wang

2018-05-01

Full Text Available Because of the degradation of classification accuracy that is caused by the uncertainty of pixel class and classification decisions of high-resolution remote-sensing images, we proposed a supervised classification method that is based on an interval type-2 fuzzy membership function for high-resolution remote-sensing images. We analyze the data features of a high-resolution remote-sensing image and construct a type-1 membership function model in a homogenous region by supervised sampling in order to characterize the uncertainty of the pixel class. On the basis of the fuzzy membership function model in the homogeneous region and in accordance with the 3σ criterion of normal distribution, we proposed a method for modeling three types of interval type-2 membership functions and analyze the different types of functions to improve the uncertainty of pixel class expressed by the type-1 fuzzy membership function and to enhance the accuracy of classification decision. According to the principle that importance will increase with a decrease in the distance between the original, upper, and lower fuzzy membership of the training data and the corresponding frequency value in the histogram, we use the weighted average sum of three types of fuzzy membership as the new fuzzy membership of the pixel to be classified and then integrated into the neighborhood pixel relations, constructing a classification decision model. We use the proposed method to classify real high-resolution remote-sensing images and synthetic images. Additionally, we qualitatively and quantitatively evaluate the test results. The results show that a higher classification accuracy can be achieved with the proposed algorithm.

Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism.

Science.gov (United States)

Davies, T Jonathan; Kraft, Nathan J B; Salamin, Nicolas; Wolkovich, Elizabeth M

2012-02-01

The tendency for more closely related species to share similar traits and ecological strategies can be explained by their longer shared evolutionary histories and represents phylogenetic conservatism. How strongly species traits co-vary with phylogeny can significantly impact how we analyze cross-species data and can influence our interpretation of assembly rules in the rapidly expanding field of community phylogenetics. Phylogenetic conservatism is typically quantified by analyzing the distribution of species values on the phylogenetic tree that connects them. Many phylogenetic approaches, however, assume a completely sampled phylogeny: while we have good estimates of deeper phylogenetic relationships for many species-rich groups, such as birds and flowering plants, we often lack information on more recent interspecific relationships (i.e., within a genus). A common solution has been to represent these relationships as polytomies on trees using taxonomy as a guide. Here we show that such trees can dramatically inflate estimates of phylogenetic conservatism quantified using S. P. Blomberg et al.'s K statistic. Using simulations, we show that even randomly generated traits can appear to be phylogenetically conserved on poorly resolved trees. We provide a simple rarefaction-based solution that can reliably retrieve unbiased estimates of K, and we illustrate our method using data on first flowering times from Thoreau's woods (Concord, Massachusetts, USA).

The new vitrinite classification (ICCP System 1994)

Energy Technology Data Exchange (ETDEWEB)

NONE

1998-04-01

This paper has been prepared by the International Committee for Coal and Organic Petrology (ICCP). Within the new vitrinite classification (ICCP System 1994) the maceral group vitrinite is divided into three subgroups, telovitrinite, detrovitrinite and gelovitrinite, which are each further sub-divided into two macerals. The dominant parameter for these newly ordered and in part newly defined sub-groups is the degree of destruction (degradation), whereas the macerals can be further distinguished by their morphological characteristics and their degree of gelificiation. The new system is furthermore related more closely to the huminite classification system still in use and a future one to be published by the ICCP. 69 refs., 2 figs., 2 tabs.

Plant traits determine the phylogenetic structure of arbuscular mycorrhizal fungal communities.

Science.gov (United States)

López-García, Álvaro; Varela-Cervero, Sara; Vasar, Martti; Öpik, Maarja; Barea, José M; Azcón-Aguilar, Concepción

2017-12-01

Functional diversity in ecosystems has traditionally been studied using aboveground plant traits. Despite the known effect of plant traits on the microbial community composition, their effects on the microbial functional diversity are only starting to be assessed. In this study, the phylogenetic structure of arbuscular mycorrhizal (AM) fungal communities associated with plant species differing in life cycle and growth form, that is, plant life forms, was determined to unravel the effect of plant traits on the functional diversity of this fungal group. The results of the 454 pyrosequencing showed that the AM fungal community composition differed across plant life forms and this effect was dependent on the soil collection date. Plants with ruderal characteristics tended to associate with phylogenetically clustered AM fungal communities. By contrast, plants with resource-conservative traits associated with phylogenetically overdispersed AM fungal communities. Additionally, the soil collected in different seasons yielded AM fungal communities with different phylogenetic dispersion. In summary, we found that the phylogenetic structure, and hence the functional diversity, of AM fungal communities is dependent on plant traits. This finding adds value to the use of plant traits for the evaluation of belowground ecosystem diversity, functions and processes. © 2017 John Wiley & Sons Ltd.

A Classification System for Hospital-Based Infection Outbreaks

Directory of Open Access Journals (Sweden)

Paul S. Ganney

2010-01-01

Full Text Available Outbreaks of infection within semi-closed environments such as hospitals, whether inherent in the environment (such as Clostridium difficile (C.Diff or Methicillinresistant Staphylococcus aureus (MRSA or imported from the wider community (such as Norwalk-like viruses (NLVs, are difficult to manage. As part of our work on modelling such outbreaks, we have developed a classification system to describe the impact of a particular outbreak upon an organization. This classification system may then be used in comparing appropriate computer models to real outbreaks, as well as in comparing different real outbreaks in, for example, the comparison of differing management and containment techniques and strategies. Data from NLV outbreaks in the Hull and East Yorkshire Hospitals NHS Trust (the Trust over several previous years are analysed and classified, both for infection within staff (where the end of infection date may not be known and within patients (where it generally is known. A classification system consisting of seven elements is described, along with a goodness-of-fit method for comparing a new classification to previously known ones, for use in evaluating a simulation against history and thereby determining how ‘realistic’ (or otherwise it is.

A classification system for hospital-based infection outbreaks.

Science.gov (United States)

Ganney, Paul S; Madeo, Maurice; Phillips, Roger

2010-12-01

Outbreaks of infection within semi-closed environments such as hospitals, whether inherent in the environment (such as Clostridium difficile (C.Diff) or Methicillin-resistant Staphylococcus aureus (MRSA) or imported from the wider community (such as Norwalk-like viruses (NLVs)), are difficult to manage. As part of our work on modelling such outbreaks, we have developed a classification system to describe the impact of a particular outbreak upon an organization. This classification system may then be used in comparing appropriate computer models to real outbreaks, as well as in comparing different real outbreaks in, for example, the comparison of differing management and containment techniques and strategies. Data from NLV outbreaks in the Hull and East Yorkshire Hospitals NHS Trust (the Trust) over several previous years are analysed and classified, both for infection within staff (where the end of infection date may not be known) and within patients (where it generally is known). A classification system consisting of seven elements is described, along with a goodness-of-fit method for comparing a new classification to previously known ones, for use in evaluating a simulation against history and thereby determining how 'realistic' (or otherwise) it is.

A comparison of the International Classification of Functioning, Disability, and Health to the disability tax credit.

Science.gov (United States)

Conti-Becker, Angela; Doralp, Samantha; Fayed, Nora; Kean, Crystal; Lencucha, Raphael; Leyshon, Rhysa; Mersich, Jackie; Robbins, Shawn; Doyle, Phillip C

2007-01-01

The Disability Tax Credit (DTC) Certification is an assessment tool used to provide Canadians with disability tax relief The International Classification of Functioning, Disability and Health (ICF) provides a universal framework for defining disability. The purpose of this study was to evaluate the DTC and familiarize occupational therapists with the process of mapping measures to the ICF classification system. Concepts within the DTC were identified and mapped to appropriate ICF codes (Cieza et al., 2005). The DTC was linked to 45 unique ICF codes (16 Body Functions, 19 Activities and Participation, and 8 Environmental Factors). The DTC encompasses various domains of the ICF; however, there is no consideration of Personal Factors, Body Structures, and key aspects of Activities and Participation. Refining the DTC to address these aspects will provide an opportunity for fair and just determinations for those who experience disability.

Nuclear power plants - Instrumentation and control systems important for safety - Classification (International Electrotechnical Commission Standard Publication 1226:1993)

International Nuclear Information System (INIS)

Stefanik, J.

1996-01-01

This international standard established a method of classification of the information and command functions for nuclear power plants, and the I and C and equipment that provide those functions, into categories that designate the importance for safety of the functions, and the associated systems and equipment. The resulting classification then determines relevant design criteria. The design criteria are the measures of quality by which the adequacy of each functions, and the associated systems and equipment in relation to its importance to plant safety is ensured. In this standard, the criteria are those of functionality, reliability, performance, environmental durability and quality assurance. This standard is applicable to all the information and command functions, and the instrumentation and control systems and equipment that provide those functions. The functions, systems and equipment under consideration provide automated protection, closed or open loop control, and information to the operating staff. They keep the NPP conditions inside the safe operating envelope and provide automatic actions, or enable manual actions, that mitigate accidents or prevent or minimize radioactive releases to the site or wider environment. The functions, and the associated systems and equipment that fulfill these roles safeguard the health and safety of the NPP operators and the public. This standard complements, and does not replace or supersede, the Safety Guides and Codes of Practice published by the International Atomic Energy Agency

Functional Outcome of Anorectal Malformations and Associated Anomalies in Era of Krickenbeck Classification

International Nuclear Information System (INIS)

Qazi, S. H.; Faruque, A. V.; Khan, M. A. M.

2016-01-01

Objective: To describe the management and functional outcome of anorectal malformations and associated anomalies according to Krickenbeck classification. Study Design: Case series. Place and Duration of Study: The Aga Khan University Hospital, Karachi, from January 2002 to December 2012. Methodology: Anorectal anomalies were classified according to Krickenbeck classification. Data was collected and proforma used regarding the primary disease associated anomalies, its management and functional outcome, according to Krickenbeck classification. Cases included were: all those children with imperforate anus managed during the study period. Qualitative variables like gender and functional outcome were reported as frequencies and percentages. Quantitative variables like age were reported as medians with interquartile ranges. Results: There were 84 children in study group. Most common associated anomaly was cardiac (38 percent), followed by urological anomaly (33 percent). All children were treated by Posterior Sagittal Anorectoplasty (PSARP). Fistula was present in 64 out of 84 (76 percent) cases. The most common fistula was rectourethral (33 percent), followed by recto vestibular (31 percent). According to Krickenbeck classification, continence was achieved in 62 percent children; however 27 percent children were constipated, followed by 12 percent children having fecal soiling. Conclusion: Functional outcome of anorectal malformation depends upon severity of disease. A thorough evaluation of all infants with ARM should be done with particular focus on cardiovascular (38 percent) and genitourinary abnormalities (33 percent). (author)

[Biological function of trophology and the pathogenesis of metabolic syndrome--syndrome of overeating. Phylogenetically theory of general pathology, role of leptin and adiponectin].

Science.gov (United States)

Titov, V N

2014-01-01

Metabolic syndrome (overeating) is a phylogenetically-determined succession of symptoms with the same pathogenesis. There is only one etiological factor, namely, increased consumption of physiologically optimal food. Enterocytes and omental fat cells are a phylogenetically early paracrine-regulated cell community that realizes the biological reactions of exo- and endotrophy. Visceral obesity, high levels of unesterified fatty acids (FA), formation of a pool of micellar FA in the blood, integration of these FA into endothelial cell plasma membrane and enlargement of adipocytes are the causes of hydrodynamic pressure elevation. Toll-like receptors recognize the associates between albumin and greater than physiological number of FA as "foreing" and initiate inflammatory response. "Endoplasm stress" develops in lipid-overloaded cells, protein synthesis (folding) in them is impaired and apoptosis-like cell death is activated. Visceral fat is a phylogenetically early depot of FA to fulfill the biological function of homeostasis, trophology, endoecology and adaptation; it is regulated at the level of paracrine communities and is anatomically limited. The subcutaneous fat depot fulfills the phylogenetically late function of locomotion; the depot size is not anatomically limited. Visceral fat cells have no receptors for phylogenetically late insulin (INS); specialized adipocyes bearing INS and GLUT4 receptors are cells that form the subcutaneous depot. These cells are regulated by phylogenetically late humoral factors at the entire body level. Leptin is an initiator of humoral hypothalamic regulation of in vivo number of ontogenetically programmed number of visceral INS-insensitive fat cells. It prevents "endoplasm stress" and apoptosis, being designed to regulate the amount of consumed food. Leptin initiates storage of FA from visceral pool into subcutaneous pool. Adiponectin is a phylogenetically late humoral hypothalamic regulatory factor that controls optimal number of

The National Ecosystem Services Classification System: A Framework for Identifying and Reducing Relevant Uncertainties

Science.gov (United States)

Rhodes, C. R.; Sinha, P.; Amanda, N.

2013-12-01

In recent years the gap between what scientists know and what policymakers should appreciate in environmental decision making has received more attention, as the costs of the disconnect have become more apparent to both groups. Particularly for water-related policies, the EPA's Office of Water has struggled with benefit estimates held low by the inability to quantify ecological and economic effects that theory, modeling, and anecdotal or isolated case evidence suggest may prove to be larger. Better coordination with ecologists and hydrologists is being explored as a solution. The ecosystem services (ES) concept now nearly two decades old links ecosystem functions and processes to the human value system. But there remains no clear mapping of which ecosystem goods and services affect which individual or economic values. The National Ecosystem Services Classification System (NESCS, 'nexus') project brings together ecologists, hydrologists, and social scientists to do this mapping for aquatic and other ecosystem service-generating systems. The objective is to greatly reduce the uncertainty in water-related policy making by mapping and ultimately quantifying the various functions and products of aquatic systems, as well as how changes to aquatic systems impact the human economy and individual levels of non-monetary appreciation for those functions and products. Primary challenges to fostering interaction between scientists, social scientists, and policymakers are lack of a common vocabulary, and the need for a cohesive comprehensive framework that organizes concepts across disciplines and accommodates scientific data from a range of sources. NESCS builds the vocabulary and the framework so both may inform a scalable transdisciplinary policy-making application. This talk presents for discussion the process and progress in developing both this vocabulary and a classifying framework capable of bridging the gap between a newer but existing ecosystem services classification

Understanding the use of standardized nursing terminology and classification systems in published research: A case study using the International Classification for Nursing Practice(®).

Science.gov (United States)

Strudwick, Gillian; Hardiker, Nicholas R

2016-10-01

In the era of evidenced based healthcare, nursing is required to demonstrate that care provided by nurses is associated with optimal patient outcomes, and a high degree of quality and safety. The use of standardized nursing terminologies and classification systems are a way that nursing documentation can be leveraged to generate evidence related to nursing practice. Several widely-reported nursing specific terminologies and classifications systems currently exist including the Clinical Care Classification System, International Classification for Nursing Practice(®), Nursing Intervention Classification, Nursing Outcome Classification, Omaha System, Perioperative Nursing Data Set and NANDA International. However, the influence of these systems on demonstrating the value of nursing and the professions' impact on quality, safety and patient outcomes in published research is relatively unknown. This paper seeks to understand the use of standardized nursing terminology and classification systems in published research, using the International Classification for Nursing Practice(®) as a case study. A systematic review of international published empirical studies on, or using, the International Classification for Nursing Practice(®) were completed using Medline and the Cumulative Index for Nursing and Allied Health Literature. Since 2006, 38 studies have been published on the International Classification for Nursing Practice(®). The main objectives of the published studies have been to validate the appropriateness of the classification system for particular care areas or populations, further develop the classification system, or utilize it to support the generation of new nursing knowledge. To date, most studies have focused on the classification system itself, and a lesser number of studies have used the system to generate information about the outcomes of nursing practice. Based on the published literature that features the International Classification for Nursing

Topological Classification of Morse Functions and Generalisations of Hilbert's 16-th Problem

International Nuclear Information System (INIS)

Arnold, Vladimir I.

2007-01-01

The topological structures of the generic smooth functions on a smooth manifold belong to the small quantity of the most fundamental objects of study both in pure and applied mathematics. The problem of their study has been formulated by A. Cayley in 1868, who required the classification of the possible configurations of the horizontal lines on the topographical maps of mountain regions, and created the first elements of what is called today 'Morse Theory' and 'Catastrophes Theory'. In the paper we describe this problem, and in particular describe the classification of Morse functions on the 2 sphere and on the torus

Molecular identification and phylogenetic study of Demodex caprae.

Science.gov (United States)

Zhao, Ya-E; Cheng, Juan; Hu, Li; Ma, Jun-Xian

2014-10-01

The DNA barcode has been widely used in species identification and phylogenetic analysis since 2003, but there have been no reports in Demodex. In this study, to obtain an appropriate DNA barcode for Demodex, molecular identification of Demodex caprae based on mitochondrial cox1 was conducted. Firstly, individual adults and eggs of D. caprae were obtained for genomic DNA (gDNA) extraction; Secondly, mitochondrial cox1 fragment was amplified, cloned, and sequenced; Thirdly, cox1 fragments of D. caprae were aligned with those of other Demodex retrieved from GenBank; Finally, the intra- and inter-specific divergences were computed and the phylogenetic trees were reconstructed to analyze phylogenetic relationship in Demodex. Results obtained from seven 429-bp fragments of D. caprae showed that sequence identities were above 99.1% among three adults and four eggs. The intraspecific divergences in D. caprae, Demodex folliculorum, Demodex brevis, and Demodex canis were 0.0-0.9, 0.5-0.9, 0.0-0.2, and 0.0-0.5%, respectively, while the interspecific divergences between D. caprae and D. folliculorum, D. canis, and D. brevis were 20.3-20.9, 21.8-23.0, and 25.0-25.3, respectively. The interspecific divergences were 10 times higher than intraspecific ones, indicating considerable barcoding gap. Furthermore, the phylogenetic trees showed that four Demodex species gathered separately, representing independent species; and Demodex folliculorum gathered with canine Demodex, D. caprae, and D. brevis in sequence. In conclusion, the selected 429-bp mitochondrial cox1 gene is an appropriate DNA barcode for molecular classification, identification, and phylogenetic analysis of Demodex. D. caprae is an independent species and D. folliculorum is closer to D. canis than to D. caprae or D. brevis.

Accurate crop classification using hierarchical genetic fuzzy rule-based systems

Science.gov (United States)

Topaloglou, Charalampos A.; Mylonas, Stelios K.; Stavrakoudis, Dimitris G.; Mastorocostas, Paris A.; Theocharis, John B.

2014-10-01

This paper investigates the effectiveness of an advanced classification system for accurate crop classification using very high resolution (VHR) satellite imagery. Specifically, a recently proposed genetic fuzzy rule-based classification system (GFRBCS) is employed, namely, the Hierarchical Rule-based Linguistic Classifier (HiRLiC). HiRLiC's model comprises a small set of simple IF-THEN fuzzy rules, easily interpretable by humans. One of its most important attributes is that its learning algorithm requires minimum user interaction, since the most important learning parameters affecting the classification accuracy are determined by the learning algorithm automatically. HiRLiC is applied in a challenging crop classification task, using a SPOT5 satellite image over an intensively cultivated area in a lake-wetland ecosystem in northern Greece. A rich set of higher-order spectral and textural features is derived from the initial bands of the (pan-sharpened) image, resulting in an input space comprising 119 features. The experimental analysis proves that HiRLiC compares favorably to other interpretable classifiers of the literature, both in terms of structural complexity and classification accuracy. Its testing accuracy was very close to that obtained by complex state-of-the-art classification systems, such as the support vector machines (SVM) and random forest (RF) classifiers. Nevertheless, visual inspection of the derived classification maps shows that HiRLiC is characterized by higher generalization properties, providing more homogeneous classifications that the competitors. Moreover, the runtime requirements for producing the thematic map was orders of magnitude lower than the respective for the competitors.

Measuring participation according to the International Classification of Functioning to

NARCIS (Netherlands)

Perenboom, R.J.M.; Chorus, A.M.J.

2003-01-01

Purpose of this study was to report which existing survey instruments assess participation according to the International Classification of Functioning. Disability and Health (ICF). A literature search for relevant survey instruments was conducted. Subsequently, survey instruments were evaluated of

Volunteer-Based System for classification of traffic in computer networks

DEFF Research Database (Denmark)

Bujlow, Tomasz; Balachandran, Kartheepan; Riaz, M. Tahir

2011-01-01

To overcome the drawbacks of existing methods for traffic classification (by ports, Deep Packet Inspection, statistical classification) a new system was developed, in which the data are collected from client machines. This paper presents design of the system, implementation, initial runs and obta...

Fission--fusion systems: classification and critique

International Nuclear Information System (INIS)

Lidsky, L.M.

1974-01-01

A useful classification scheme for hybrid systems is described and some common features that the scheme makes apparent are pointed out. The early history of fusion-fission systems is reviewed. Some designs are described along with advantages and disadvantages of each. The extension to low and moderate Q devices is noted. (U.S.)

CLASSIFICATION OF THE MGR WASTE HANDLING BUILDING VENTILATION SYSTEM

International Nuclear Information System (INIS)

J.A. Ziegler

2000-01-01

The purpose of this analysis is to document the Quality Assurance (QA) classification of the Monitored Geologic Repository (MGR) waste handling building ventilation system structures, systems and components (SSCs) performed by the MGR Preclosure Safety and Systems Engineering Section. This analysis also provides the basis for revision of YMP/90-55Q, Q-List (YMP 2000). The Q-List identifies those MGR SSCs subject to the requirements of DOE/RW-0333P, ''Quality Assurance Requirements and Description'' (QARD) (DOE 2000). This QA classification incorporates the current MGR design and the results of the ''Design Basis Event Frequency and Dose Calculation for Site Recommendation'' (CRWMS M andO 2000a) and ''Bounding Individual Category 1 Design Basis Event Dose Calculation to Support Quality Assurance Classification'' (Gwyn 2000)

The theory and practice of the Dewey Decimal Classification system

CERN Document Server

Satija, M P

2013-01-01

The Dewey Decimal Classification system (DDC) is the world's most popular library classification system. The 23rd edition of the DDC was published in 2011. This second edition of The Theory and Practice of the Dewey Decimal Classification System examines the history, management and technical aspects of the DDC up to its latest edition. The book places emphasis on explaining the structure and number building techniques in the DDC and reviews all aspects of subject analysis and number building by the most recent version of the DDC. A history of, and introduction to, the DDC is followed by subjec

Approaches to the classification of brands of professional football clubs in the system of sportive marketing

OpenAIRE

Romat, E.; Ostroverh, S.

2014-01-01

This article was told about methods of classification of professional football clubs in the system of sportive marketing in the total commercial conditions of the most popular kind sport, football. Also was told about importance of brand in the professional football club as an active method of increasing trade value multi-functional enterprise in the sport area, which works on business model. The criterions where proposed and also was told about essence of the classification, which is used to...

CLASSIFICATION OF THE MGR MUCK HANDLING SYSTEM

International Nuclear Information System (INIS)

R. Garrett

1999-01-01

The purpose of this analysis is to document the Quality Assurance (QA) classification of the Monitored Geologic Repository (MGR) muck handling system structures, systems and components (SSCs) performed by the MGR Safety Assurance Department. This analysis also provides the basis for revision of YMP/90-55Q, Q-List (YMP 1998). The Q-List identifies those MGR SSCs subject to the requirements of DOE/RW-0333P, ''Quality Assurance Requirements and Description (QARD) (DOE 1998). This QA classification incorporates the current MGR design and the results of the ''Preliminary Preclosure Design Basis Event Calculations for the Monitored Geologic Repository (CRWMS M and O 1998a)

Developing a dementia-specific health state classification system for a new preference-based instrument AD-5D.

Science.gov (United States)

Nguyen, Kim-Huong; Mulhern, Brendan; Kularatna, Sanjeewa; Byrnes, Joshua; Moyle, Wendy; Comans, Tracy

2017-01-25

With an ageing population, the number of people with dementia is rising. The economic impact on the health care system is considerable and new treatment methods and approaches to dementia care must be cost effective. Economic evaluation requires valid patient reported outcome measures, and this study aims to develop a dementia-specific health state classification system based on the Quality of Life for Alzheimer's disease (QOL-AD) instrument (nursing home version). This classification system will subsequently be valued to generate a preference-based measure for use in the economic evaluation of interventions for people with dementia. We assessed the dimensionality of the QOL-AD to develop a new classification system. This was done using exploratory and confirmatory factor analysis and further assessment of the structure of the measure to ensure coverage of the key areas of quality of life. Secondly, we used Rasch analysis to test the psychometric performance of the items, and select item(s) to describe each dimension. This was done on 13 items of the QOL-AD (excluding two general health items) using a sample of 284 residents living in long-term care facilities in Australia who had a diagnosis of dementia. A five dimension classification system is proposed resulting from the three factor structure (defined as 'interpersonal environment', 'physical health' and 'self-functioning') derived from the factor analysis and two factors ('memory' and 'mood') from the accompanying review. For the first three dimensions, Rasch analysis selected three questions of the QOL-AD ('living situation', 'physical health', and 'do fun things') with memory and mood questions representing their own dimensions. The resulting classification system (AD-5D) includes many of the health-related quality of life dimensions considered important to people with dementia, including mood, global function and skill in daily living. The development of the AD-5D classification system is an important step

Modified Mahalanobis Taguchi System for Imbalance Data Classification

Directory of Open Access Journals (Sweden)

Mahmoud El-Banna

2017-01-01

Full Text Available The Mahalanobis Taguchi System (MTS is considered one of the most promising binary classification algorithms to handle imbalance data. Unfortunately, MTS lacks a method for determining an efficient threshold for the binary classification. In this paper, a nonlinear optimization model is formulated based on minimizing the distance between MTS Receiver Operating Characteristics (ROC curve and the theoretical optimal point named Modified Mahalanobis Taguchi System (MMTS. To validate the MMTS classification efficacy, it has been benchmarked with Support Vector Machines (SVMs, Naive Bayes (NB, Probabilistic Mahalanobis Taguchi Systems (PTM, Synthetic Minority Oversampling Technique (SMOTE, Adaptive Conformal Transformation (ACT, Kernel Boundary Alignment (KBA, Hidden Naive Bayes (HNB, and other improved Naive Bayes algorithms. MMTS outperforms the benchmarked algorithms especially when the imbalance ratio is greater than 400. A real life case study on manufacturing sector is used to demonstrate the applicability of the proposed model and to compare its performance with Mahalanobis Genetic Algorithm (MGA.

Modified Mahalanobis Taguchi System for Imbalance Data Classification

Science.gov (United States)

2017-01-01

The Mahalanobis Taguchi System (MTS) is considered one of the most promising binary classification algorithms to handle imbalance data. Unfortunately, MTS lacks a method for determining an efficient threshold for the binary classification. In this paper, a nonlinear optimization model is formulated based on minimizing the distance between MTS Receiver Operating Characteristics (ROC) curve and the theoretical optimal point named Modified Mahalanobis Taguchi System (MMTS). To validate the MMTS classification efficacy, it has been benchmarked with Support Vector Machines (SVMs), Naive Bayes (NB), Probabilistic Mahalanobis Taguchi Systems (PTM), Synthetic Minority Oversampling Technique (SMOTE), Adaptive Conformal Transformation (ACT), Kernel Boundary Alignment (KBA), Hidden Naive Bayes (HNB), and other improved Naive Bayes algorithms. MMTS outperforms the benchmarked algorithms especially when the imbalance ratio is greater than 400. A real life case study on manufacturing sector is used to demonstrate the applicability of the proposed model and to compare its performance with Mahalanobis Genetic Algorithm (MGA). PMID:28811820

An Outlyingness Matrix for Multivariate Functional Data Classification

KAUST Repository

Dai, Wenlin; Genton, Marc G.

2017-01-01

outlyingness with conventional statistical depth. We propose two classifiers based on directional outlyingness and the outlyingness matrix, respectively. Our classifiers provide better performance compared with existing depth-based classifiers when applied on both univariate and multivariate functional data from simulation studies. We also test our methods on two data problems: speech recognition and gesture classification, and obtain results that are consistent with the findings from the simulated data.

An approach for classification of hydrogeological systems at the regional scale based on groundwater hydrographs

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Haaf, Ezra; Barthel, Roland

2016-04-01

When assessing hydrogeological conditions at the regional scale, the analyst is often confronted with uncertainty of structures, inputs and processes while having to base inference on scarce and patchy data. Haaf and Barthel (2015) proposed a concept for handling this predicament by developing a groundwater systems classification framework, where information is transferred from similar, but well-explored and better understood to poorly described systems. The concept is based on the central hypothesis that similar systems react similarly to the same inputs and vice versa. It is conceptually related to PUB (Prediction in ungauged basins) where organization of systems and processes by quantitative methods is intended and used to improve understanding and prediction. Furthermore, using the framework it is expected that regional conceptual and numerical models can be checked or enriched by ensemble generated data from neighborhood-based estimators. In a first step, groundwater hydrographs from a large dataset in Southern Germany are compared in an effort to identify structural similarity in groundwater dynamics. A number of approaches to group hydrographs, mostly based on a similarity measure - which have previously only been used in local-scale studies, can be found in the literature. These are tested alongside different global feature extraction techniques. The resulting classifications are then compared to a visual "expert assessment"-based classification which serves as a reference. A ranking of the classification methods is carried out and differences shown. Selected groups from the classifications are related to geological descriptors. Here we present the most promising results from a comparison of classifications based on series correlation, different series distances and series features, such as the coefficients of the discrete Fourier transform and the intrinsic mode functions of empirical mode decomposition. Additionally, we show examples of classes

Dimensions of biodiversity loss: Spatial mismatch in land-use impacts on species, functional and phylogenetic diversity of European bees.

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De Palma, Adriana; Kuhlmann, Michael; Bugter, Rob; Ferrier, Simon; Hoskins, Andrew J; Potts, Simon G; Roberts, Stuart P M; Schweiger, Oliver; Purvis, Andy

2017-12-01

Agricultural intensification and urbanization are important drivers of biodiversity change in Europe. Different aspects of bee community diversity vary in their sensitivity to these pressures, as well as independently influencing ecosystem service provision (pollination). To obtain a more comprehensive understanding of human impacts on bee diversity across Europe, we assess multiple, complementary indices of diversity. One Thousand four hundred and forty six sites across Europe. We collated data on bee occurrence and abundance from the published literature and supplemented them with the PREDICTS database. Using Rao's Quadratic Entropy, we assessed how species, functional and phylogenetic diversity of 1,446 bee communities respond to land-use characteristics including land-use class, cropland intensity, human population density and distance to roads. We combined these models with statistically downscaled estimates of land use in 2005 to estimate and map-at a scale of approximately 1 km 2 -the losses in diversity relative to semi-natural/natural baseline (the predicted diversity of an uninhabited grid square, consisting only of semi-natural/natural vegetation). We show that-relative to the predicted local diversity in uninhabited semi-natural/natural habitat-half of all EU27 countries have lost over 10% of their average local species diversity and two-thirds of countries have lost over 5% of their average local functional and phylogenetic diversity. All diversity measures were generally lower in pasture and higher-intensity cropland than in semi-natural/natural vegetation, but facets of diversity showed less consistent responses to human population density. These differences have led to marked spatial mismatches in losses: losses in phylogenetic diversity were in some areas almost 20 percentage points (pp.) more severe than losses in species diversity, but in other areas losses were almost 40 pp. less severe. These results highlight the importance of exploring

Social Mating System and Sex-Biased Dispersal in Mammals and Birds: A Phylogenetic Analysis

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Mabry, Karen E.; Shelley, Erin L.; Davis, Katie E.; Blumstein, Daniel T.; Van Vuren, Dirk H.

2013-01-01

The hypothesis that patterns of sex-biased dispersal are related to social mating system in mammals and birds has gained widespread acceptance over the past 30 years. However, two major complications have obscured the relationship between these two behaviors: 1) dispersal frequency and dispersal distance, which measure different aspects of the dispersal process, have often been confounded, and 2) the relationship between mating system and sex-biased dispersal in these vertebrate groups has not been examined using modern phylogenetic comparative methods. Here, we present a phylogenetic analysis of the relationship between mating system and sex-biased dispersal in mammals and birds. Results indicate that the evolution of female-biased dispersal in mammals may be more likely on monogamous branches of the phylogeny, and that females may disperse farther than males in socially monogamous mammalian species. However, we found no support for a relationship between social mating system and sex-biased dispersal in birds when the effects of phylogeny are taken into consideration. We caution that although there are larger-scale behavioral differences in mating system and sex-biased dispersal between mammals and birds, mating system and sex-biased dispersal are far from perfectly associated within these taxa. PMID:23483957

Phylogenetically informed logic relationships improve detection of biological network organization

Science.gov (United States)

2011-01-01

Background A "phylogenetic profile" refers to the presence or absence of a gene across a set of organisms, and it has been proven valuable for understanding gene functional relationships and network organization. Despite this success, few studies have attempted to search beyond just pairwise relationships among genes. Here we search for logic relationships involving three genes, and explore its potential application in gene network analyses. Results Taking advantage of a phylogenetic matrix constructed from the large orthologs database Roundup, we invented a method to create balanced profiles for individual triplets of genes that guarantee equal weight on the different phylogenetic scenarios of coevolution between genes. When we applied this idea to LAPP, the method to search for logic triplets of genes, the balanced profiles resulted in significant performance improvement and the discovery of hundreds of thousands more putative triplets than unadjusted profiles. We found that logic triplets detected biological network organization and identified key proteins and their functions, ranging from neighbouring proteins in local pathways, to well separated proteins in the whole pathway, and to the interactions among different pathways at the system level. Finally, our case study suggested that the directionality in a logic relationship and the profile of a triplet could disclose the connectivity between the triplet and surrounding networks. Conclusion Balanced profiles are superior to the raw profiles employed by traditional methods of phylogenetic profiling in searching for high order gene sets. Gene triplets can provide valuable information in detection of biological network organization and identification of key genes at different levels of cellular interaction. PMID:22172058

[Phylogenetic analysis of closely related Leuconostoc citreum species based on partial housekeeping genes].

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Lv, Qiang; Chen, Ming; Xu, Haiyan; Song, Yuqin; Sun, Zhihong; Dan, Tong; Sun, Tiansong

2013-07-04

Using the 16S rRNA, dnaA, murC and pyrG gene sequences, we identified the phylogenetic relationship among closely related Leuconostoc citreum species. Seven Leu. citreum strains originally isolated from sourdough were characterized by PCR methods to amplify the dnaA, murC and pyrG gene sequences, which were determined to assess the suitability as phylogenetic markers. Then, we estimated the genetic distance and constructed the phylogenetic trees including 16S rRNA and above mentioned three housekeeping genes combining with published corresponding sequences. By comparing the phylogenetic trees, the topology of three housekeeping genes trees were consistent with that of 16S rRNA gene. The homology of closely related Leu. citreum species among dnaA, murC, pyrG and 16S rRNA gene sequences were different, ranged from75.5% to 97.2%, 50.2% to 99.7%, 65.0% to 99.8% and 98.5% 100%, respectively. The phylogenetic relationship of three housekeeping genes sequences were highly consistent with the results of 16S rRNA gene sequence, while the genetic distance of these housekeeping genes were extremely high than 16S rRNA gene. Consequently, the dnaA, murC and pyrG gene are suitable for classification and identification closely related Leu. citreum species.

Clock gene evolution: seasonal timing, phylogenetic signal, or functional constraint?

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Krabbenhoft, Trevor J; Turner, Thomas F

2014-01-01

Genetic determinants of seasonal reproduction are not fully understood but may be important predictors of organism responses to climate change. We used a comparative approach to study the evolution of seasonal timing within a fish community in a natural common garden setting. We tested the hypothesis that allelic length variation in the PolyQ domain of a circadian rhythm gene, Clock1a, corresponded to interspecific differences in seasonal reproductive timing across 5 native and 1 introduced cyprinid fishes (n = 425 individuals) that co-occur in the Rio Grande, NM, USA. Most common allele lengths were longer in native species that initiated reproduction earlier (Spearman's r = -0.70, P = 0.23). Clock1a allele length exhibited strong phylogenetic signal and earlier spawners were evolutionarily derived. Aside from length variation in Clock1a, all other amino acids were identical across native species, suggesting functional constraint over evolutionary time. Interestingly, the endangered Rio Grande silvery minnow (Hybognathus amarus) exhibited less allelic variation in Clock1a and observed heterozygosity was 2- to 6-fold lower than the 5 other (nonimperiled) species. Reduced genetic variation in this functionally important gene may impede this species' capacity to respond to ongoing environmental change.

A phylogenetic analysis of Diurideae (Orchidaceae) based on plastid DNA sequence data.

Science.gov (United States)

Kores, P J; Molvray, M; Weston, P H; Hopper, S D; Brown, A P; Cameron, K M; Chase, M W

2001-10-01

DNA sequence data from plastid matK and trnL-F regions were used in phylogenetic analyses of Diurideae, which indicate that Diurideae are not monophyletic as currently delimited. However, if Chloraeinae and Pterostylidinae are excluded from Diurideae, the remaining subtribes form a well-supported, monophyletic group that is sister to a "spiranthid" clade. Chloraea, Gavilea, and Megastylis pro parte (Chloraeinae) are all placed among the spiranthid orchids and form a grade with Pterostylis leading to a monophyletic Cranichideae. Codonorchis, previously included among Chloraeinae, is sister to Orchideae. Within the more narrowly delimited Diurideae two major lineages are apparent. One includes Diuridinae, Cryptostylidinae, Thelymitrinae, and an expanded Drakaeinae; the other includes Caladeniinae s.s., Prasophyllinae, and Acianthinae. The achlorophyllous subtribe Rhizanthellinae is a member of Diurideae, but its placement is otherwise uncertain. The sequence-based trees indicate that some morphological characters used in previous classifications, such as subterranean storage organs, anther position, growth habit, fungal symbionts, and pollination syndromes have more complex evolutionary histories than previously hypothesized. Treatments based upon these characters have produced conflicting classifications, and molecular data offer a tool for reevaluating these phylogenetic hypotheses.

Comparative morphology of premolar foramen in lagomorphs (Mammalia: Glires and its functional and phylogenetic implications.

Directory of Open Access Journals (Sweden)

Łucja Fostowicz-Frelik

Full Text Available Lagomorphs (a group that consists of pikas, hares, rabbits and allies are notable for their conservative morphology retained for most of their over 50 million years evolutionary history. On the other hand, their remarkable morphological uniformity partly stems from a considerable number of homoplasies in cranial and dental structures that hamper phylogenetic analyses. The premolar foramen, an opening in the palate of lagomorphs, has been characterized as an important synapomorphy of one clade, Ochotonidae (pikas. Within Lagomorpha, however, its phylogenetic distribution is much wider, the foramen being present not only in all ochotonids but also in leporids and stem taxa; its morphology and incidence also varies considerably across the order, even intraspecifically. In this study, we provide a broad survey of the taxonomic distribution of the premolar foramen in extant and fossil Lagomorpha and describe in detail the morphological variation of this character within the group. Micro-computed tomography was used to examine the hard palate and infraorbital groove morphology in Poelagus (Leporidae and Ochotona. Scans revealed the course and contacts of the canal behind the premolar foramen and structural differences between the two crown clades. We propose that the premolar foramen has evolved independently in several lineages of Lagomorpha, and we discuss development and function of this foramen in the lagomorph skull. This study shows the importance of comprehensive studies on phylogenetically informative non-dental characters in Lagomorpha.

The rise of a novel classification system for endometrial carcinoma; integration of molecular subclasses.

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McAlpine, Jessica; Leon-Castillo, Alicia; Bosse, Tjalling

2018-04-01

Endometrial cancer is a clinically heterogeneous disease and it is becoming increasingly clear that this heterogeneity may be a function of the diversity of the underlying molecular alterations. Recent large-scale genomic studies have revealed that endometrial cancer can be divided into at least four distinct molecular subtypes, with well-described underlying genomic aberrations. These subtypes can be reliably delineated and carry significant prognostic as well as predictive information; embracing and incorporating them into clinical practice is thus attractive. The road towards the integration of molecular features into current classification systems is not without obstacles. Collaborative studies engaging research teams from across the world are working to define pragmatic assays, improve risk stratification systems by combining molecular features and traditional clinicopathological parameters, and determine how molecular classification can be optimally utilized to direct patient care. Pathologists and clinicians caring for women with endometrial cancer need to engage with and understand the possibilities and limitations of this new approach, because integration of molecular classification of endometrial cancers is anticipated to become an essential part of gynaecological pathology practice. This review will describe the challenges in current systems of endometrial carcinoma classification, the evolution of new molecular technologies that define prognostically distinct molecular subtypes, and potential applications of molecular classification as a step towards precision medicine and refining care for individuals with the most common gynaecological cancer in the developed world. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Classification systems for causes of stillbirth and neonatal death, 2009-2014: an assessment of alignment with characteristics for an effective global system.

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Leisher, Susannah Hopkins; Teoh, Zheyi; Reinebrant, Hanna; Allanson, Emma; Blencowe, Hannah; Erwich, Jan Jaap; Frøen, J Frederik; Gardosi, Jason; Gordijn, Sanne; Gülmezoglu, A Metin; Heazell, Alexander E P; Korteweg, Fleurisca; Lawn, Joy; McClure, Elizabeth M; Pattinson, Robert; Smith, Gordon C S; Tunçalp, Ӧzge; Wojcieszek, Aleena M; Flenady, Vicki

2016-09-15

To reduce the burden of 5.3 million stillbirths and neonatal deaths annually, an understanding of causes of deaths is critical. A systematic review identified 81 systems for classification of causes of stillbirth (SB) and neonatal death (NND) between 2009 and 2014. The large number of systems hampers efforts to understand and prevent these deaths. This study aimed to assess the alignment of current classification systems with expert-identified characteristics for a globally effective classification system. Eighty-one classification systems were assessed for alignment with 17 characteristics previously identified through expert consensus as necessary for an effective global system. Data were extracted independently by two authors. Systems were assessed against each characteristic and weighted and unweighted scores assigned to each. Subgroup analyses were undertaken by system use, setting, type of death included and type of characteristic. None of the 81 systems were aligned with more than 9 of the 17 characteristics; most (82 %) were aligned with four or fewer. On average, systems were aligned with 19 % of characteristics. The most aligned system (Frøen 2009-Codac) still had an unweighted score of only 9/17. Alignment with individual characteristics ranged from 0 to 49 %. Alignment was somewhat higher for widely used as compared to less used systems (22 % v 17 %), systems used only in high income countries as compared to only in low and middle income countries (20 % vs 16 %), and systems including both SB and NND (23 %) as compared to NND-only (15 %) and SB-only systems (13 %). Alignment was higher with characteristics assessing structure (23 %) than function (15 %). There is an unmet need for a system exhibiting all the characteristics of a globally effective system as defined by experts in the use of systems, as none of the 81 contemporary classification systems assessed was highly aligned with these characteristics. A particular concern in terms of

SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees.

Science.gov (United States)

Beccati, Alan; Gerken, Jan; Quast, Christian; Yilmaz, Pelin; Glöckner, Frank Oliver

2017-09-30

Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA Tree Viewer is based on Web Geographic Information Systems (Web-GIS) technology with a PostgreSQL backend. It enables zoom and pan functionalities similar to Google Maps. The SILVA Tree Viewer enables access to two phylogenetic (guide) trees provided by the SILVA database: the SSU Ref NR99 inferred from high-quality, full-length small subunit sequences, clustered at 99% sequence identity and the LSU Ref inferred from high-quality, full-length large subunit sequences. The Tree Viewer provides tree navigation, search and browse tools as well as an interactive feedback system to collect any kinds of requests ranging from taxonomy to data curation and improving the tool itself.

Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of Pseudo-Response Regulators

Directory of Open Access Journals (Sweden)

Saito Shigeru

2010-05-01

Full Text Available Abstract Background Plant circadian clocks regulate many photoperiodic and diurnal responses that are conserved among plant species. The plant circadian clock system has been uncovered in the model plant, Arabidopsis thaliana, using genetics and systems biology approaches. However, it is still not clear how the clock system had been organized in the evolutionary history of plants. We recently revealed the molecular phylogeny of LHY/CCA1 genes, one of the essential components of the clock system. The aims of this study are to reconstruct the phylogenetic relationships of angiosperm clock-associated PRR genes, the partner of the LHY/CCA1 genes, and to clarify the evolutionary history of the plant clock system in angiosperm lineages. Results In the present study, to investigate the molecular phylogeny of PRR genes, we performed two approaches: reconstruction of phylogenetic trees and examination of syntenic relationships. Phylogenetic analyses revealed that PRR genes had diverged into three clades prior to the speciation of monocots and eudicots. Furthermore, copy numbers of PRR genes have been independently increased in monocots and eudicots as a result of ancient chromosomal duplication events. Conclusions Based on the molecular phylogenies of both PRR genes and LHY/CCA1 genes, we inferred the evolutionary process of the plant clock system in angiosperms. This scenario provides evolutionary information that a common ancestor of monocots and eudicots had retained the basic components required for reconstructing a clock system and that the plant circadian clock may have become a more elaborate mechanism after the speciation of monocots and eudicots because of the gene expansion that resulted from polyploidy events.

Ototoxicity (cochleotoxicity) classifications: A review.

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Crundwell, Gemma; Gomersall, Phil; Baguley, David M

2016-01-01

Drug-mediated ototoxicity, specifically cochleotoxicity, is a concern for patients receiving medications for the treatment of serious illness. A number of classification schemes exist, most of which are based on pure-tone audiometry, in order to assist non-audiological/non-otological specialists in the identification and monitoring of iatrogenic hearing loss. This review identifies the primary classification systems used in cochleototoxicity monitoring. By bringing together classifications published in discipline-specific literature, the paper aims to increase awareness of their relative strengths and limitations in the assessment and monitoring of ototoxic hearing loss and to indicate how future classification systems may improve upon the status-quo. Literature review. PubMed identified 4878 articles containing the search term ototox*. A systematic search identified 13 key classification systems. Cochleotoxicity classification systems can be divided into those which focus on hearing change from a baseline audiogram and those that focus on the functional impact of the hearing loss. Common weaknesses of these grading scales included a lack of sensitivity to small adverse changes in hearing thresholds, a lack of high-frequency audiometry (>8 kHz), and lack of indication of which changes are likely to be clinically significant for communication and quality of life.

A taxonomic, functional, and phylogenetic perspective on the community assembly of passerine birds along an elevational gradient in southwest China.

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He, Xuelian; Luo, Kang; Brown, Calum; Lin, Luxiang

2018-03-01

Integrating multiple facets of biodiversity to describe spatial and temporal distribution patterns is one way of revealing the mechanisms driving community assembly. We assessed the species, functional, and phylogenetic composition and structure of passerine bird communities along an elevational gradient both in wintering and breeding seasons in the Ailao Mountains, southwest China, in order to identify the dominant ecological processes structuring the communities and how these processes change with elevation and season. Our research confirms that the highest taxonomic diversity, and distinct community composition, was found in the moist evergreen broadleaf forest at high elevation in both seasons. Environmental filtering was the dominant force at high elevations with relatively cold and wet climatic conditions, while the observed value of mean pairwise functional and phylogenetic distances of low elevation was constantly higher than expectation in two seasons, suggested interspecific competition could play the key role at low elevations, perhaps because of relative rich resource result from complex vegetation structure and human-induced disturbance. Across all elevations, there was a trend of decreasing intensity of environmental filtering whereas increasing interspecific competition from wintering season to breeding season. This was likely due to the increased resource availability but reproduction-associated competition in the summer months. In general, there is a clear justification for conservation efforts to protect entire elevational gradients in the Ailao Mountains, given the distinct taxonomic, functional, and phylogenetic compositions and also elevational migration pattern in passerine bird communities.

Fascia: a morphological description and classification system based on a literature review

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Kumka, Myroslava; Bonar, Jason

2012-01-01

Fascia is virtually inseparable from all structures in the body and acts to create continuity amongst tissues to enhance function and support. In the past fascia has been difficult to study leading to ambiguities in nomenclature, which have only recently been addressed. Through review of the available literature, advances in fascia research were compiled, and issues related to terminology, descriptions, and clinical relevance of fascia were addressed. Our multimodal search strategy was conducted in Medline and PubMed databases, with other targeted searches in Google Scholar and by hand, utilizing reference lists and conference proceedings. In an effort to organize nomenclature for fascial structures provided by the Federative International Committee on Anatomical Terminology (FICAT), we developed a functional classification system which includes four categories of fascia: i) linking, ii) fascicular, iii) compression, and iv) separating fasciae. Each category was developed from descriptions in the literature on gross anatomy, histology, and biomechanics; the category names reflect the function of the fascia. An up-to-date definition of fascia is provided, as well as descriptions of its function and clinical features. Our classification demonstrates the use of internationally accepted terminology in an ontology which can improve understanding of major terms in each category of fascia. PMID:22997468

Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks.

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Pérez-Valera, Eduardo; Goberna, Marta; Faust, Karoline; Raes, Jeroen; García, Carlos; Verdú, Miguel

2017-01-01

Fire alters ecosystems by changing the composition and community structure of soil microbes. The phylogenetic structure of a community provides clues about its main assembling mechanisms. While environmental filtering tends to reduce the community phylogenetic diversity by selecting for functionally (and hence phylogenetically) similar species, processes like competitive exclusion by limiting similarity tend to increase it by preventing the coexistence of functionally (and phylogenetically) similar species. We used co-occurrence networks to detect co-presence (bacteria that co-occur) or exclusion (bacteria that do not co-occur) links indicative of the ecological interactions structuring the community. We propose that inspecting the phylogenetic structure of co-presence or exclusion links allows to detect the main processes simultaneously assembling the community. We monitored a soil bacterial community after an experimental fire and found that fire altered its composition, richness and phylogenetic diversity. Both co-presence and exclusion links were more phylogenetically related than expected by chance. We interpret such a phylogenetic clustering in co-presence links as a result of environmental filtering, while that in exclusion links reflects competitive exclusion by limiting similarity. This suggests that environmental filtering and limiting similarity operate simultaneously to assemble soil bacterial communities, widening the traditional view that only environmental filtering structures bacterial communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Predicting rates of interspecific interaction from phylogenetic trees.

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Nuismer, Scott L; Harmon, Luke J

2015-01-01

Integrating phylogenetic information can potentially improve our ability to explain species' traits, patterns of community assembly, the network structure of communities, and ecosystem function. In this study, we use mathematical models to explore the ecological and evolutionary factors that modulate the explanatory power of phylogenetic information for communities of species that interact within a single trophic level. We find that phylogenetic relationships among species can influence trait evolution and rates of interaction among species, but only under particular models of species interaction. For example, when interactions within communities are mediated by a mechanism of phenotype matching, phylogenetic trees make specific predictions about trait evolution and rates of interaction. In contrast, if interactions within a community depend on a mechanism of phenotype differences, phylogenetic information has little, if any, predictive power for trait evolution and interaction rate. Together, these results make clear and testable predictions for when and how evolutionary history is expected to influence contemporary rates of species interaction. © 2014 John Wiley & Sons Ltd/CNRS.

Carcinogenesis: alterations in reciprocal interactions of normal functional structure of biologic systems.

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Davydyan, Garri

2015-12-01

The evolution of biologic systems (BS) includes functional mechanisms that in some conditions may lead to the development of cancer. Using mathematical group theory and matrix analysis, previously, it was shown that normally functioning BS are steady functional structures regulated by three basis regulatory components: reciprocal links (RL), negative feedback (NFB) and positive feedback (PFB). Together, they form an integrative unit maintaining system's autonomy and functional stability. It is proposed that phylogenetic development of different species is implemented by the splitting of "rudimentary" characters into two relatively independent functional parts that become encoded in chromosomes. The functional correlate of splitting mechanisms is RL. Inversion of phylogenetic mechanisms during ontogenetic development leads cell differentiation until cells reach mature states. Deterioration of reciprocal structure in the genome during ontogenesis gives rise of pathological conditions characterized by unsteadiness of the system. Uncontrollable cell proliferation and invasive cell growth are the leading features of the functional outcomes of malfunctioning systems. The regulatory element responsible for these changes is RL. In matrix language, pathological regulation is represented by matrices having positive values of diagonal elements ( TrA  > 0) and also positive values of matrix determinant ( detA  > 0). Regulatory structures of that kind can be obtained if the negative entry of the matrix corresponding to RL is replaced with the positive one. To describe not only normal but also pathological states of BS, a unit matrix should be added to the basis matrices representing RL, NFB and PFB. A mathematical structure corresponding to the set of these four basis functional patterns (matrices) is a split quaternion (coquaternion). The structure and specific role of basis elements comprising four-dimensional linear space of split quaternions help to understand what

Function-centered modeling of engineering systems using the goal tree-success tree technique and functional primitives

International Nuclear Information System (INIS)

Modarres, Mohammad; Cheon, Se Woo

1999-01-01

Most of the complex systems are formed through some hierarchical evolution. Therefore, those systems can be best described through hierarchical frameworks. This paper describes some fundamental attributes of complex physical systems and several hierarchies such as functional, behavioral, goal/condition, and event hierarchies, then presents a function-centered approach to system modeling. Based on the function-centered concept, this paper describes the joint goal tree-success tree (GTST) and the master logic diagram (MLD) as a framework for developing models of complex physical systems. A function-based lexicon for classifying the most common elements of engineering systems for use in the GTST-MLD framework has been proposed. The classification is based on the physical conservation laws that govern the engineering systems. Functional descriptions based on conservation laws provide a simple and rich vocabulary for modeling complex engineering systems

Phylogenetic comparative methods on phylogenetic networks with reticulations.

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Bastide, Paul; Solís-Lemus, Claudia; Kriebel, Ricardo; Sparks, K William; Ané, Cécile

2018-04-25

The goal of Phylogenetic Comparative Methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species' traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. One natural extension of the BM is to use a weighted average model for the trait of a hybrid, at a reticulation point. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel's λ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts, and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios, and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a dataset of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.

Evaluation of Urinary Tract Dilation Classification System for Grading Postnatal Hydronephrosis.

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Hodhod, Amr; Capolicchio, John-Paul; Jednak, Roman; El-Sherif, Eid; El-Doray, Abd El-Alim; El-Sherbiny, Mohamed

2016-03-01

We assessed the reliability and validity of the Urinary Tract Dilation classification system as a new grading system for postnatal hydronephrosis. We retrospectively reviewed charts of patients who presented with hydronephrosis from 2008 to 2013. We included patients diagnosed prenatally and those with hydronephrosis discovered incidentally during the first year of life. We excluded cases involving urinary tract infection, neurogenic bladder and chromosomal anomalies, those associated with extraurinary congenital malformations and those with followup of less than 24 months without resolution. Hydronephrosis was graded postnatally using the Society for Fetal Urology system, and then the management protocol was chosen. All units were regraded using the Urinary Tract Dilation classification system and compared to the Society for Fetal Urology system to assess reliability. Univariate and multivariate analyses were performed to assess the validity of the Urinary Tract Dilation classification system in predicting hydronephrosis resolution and surgical intervention. A total of 490 patients (730 renal units) were eligible to participate. The Urinary Tract Dilation classification system was reliable in the assessment of hydronephrosis (parallel forms 0.92). Hydronephrosis resolved in 357 units (49%), and 86 units (12%) were managed by surgical intervention. The remainder of renal units demonstrated stable or improved hydronephrosis. Multivariate analysis revealed that the likelihood of surgical intervention was predicted independently by Urinary Tract Dilation classification system risk group, while Society for Fetal Urology grades were predictive of likelihood of resolution. The Urinary Tract Dilation classification system is reliable for evaluation of postnatal hydronephrosis and is valid in predicting surgical intervention. Copyright © 2016 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

The effects of habitat management on the species, phylogenetic and functional diversity of bees are modified by the environmental context.

Science.gov (United States)

Sydenham, Markus A K; Moe, Stein R; Stanescu-Yadav, Diana N; Totland, Ørjan; Eldegard, Katrine

2016-02-01

Anthropogenic landscape elements, such as roadsides, hedgerows, field edges, and power line clearings, can be managed to provide important habitats for wild bees. However, the effects of habitat improvement schemes in power line clearings on components of diversity are poorly studied. We conducted a large-scale experiment to test the effects of different management practices on the species, phylogenetic, and functional diversity of wild bees in power line clearings (n = 19 sites across southeastern Norway) and explored whether any treatment effects were modified by the environmental context. At each site, we conducted the following treatments: (1) Cut: all trees cut and left to decay in the clearing; (2) Cut + Remove: all trees cut and removed from the plot; and (3) Uncut: uncleared. The site-specific environmental context (i.e., elevation and floral diversity) influenced the species, phylogenetic, and functional diversity within bee species assemblages. The largest number of species was found in the Cut + Remove treatment in plots with a high forb species richness, indicating that the outcome of management practices depends on the environmental context. Clearing of treatment plots with many forb species also appeared to alter the phylogenetic composition of bee species assemblages, that is, more closely related species were found in the Cut and the Cut + Remove plots than in the Uncut plots. Synthesis and applications: Our experimental simulation of management practices in power line clearings influenced the species, phylogenetic, and functional diversity of bee species assemblages. Frequent clearing and removal of the woody debris at low elevations with a high forb species richness can increase the value of power line clearings for solitary bees. It is therefore important for managers to consider the environmental context when designing habitat improvement schemes for solitary bees.

A systematic literature review of automated clinical coding and classification systems.

Science.gov (United States)

Stanfill, Mary H; Williams, Margaret; Fenton, Susan H; Jenders, Robert A; Hersh, William R

2010-01-01

Clinical coding and classification processes transform natural language descriptions in clinical text into data that can subsequently be used for clinical care, research, and other purposes. This systematic literature review examined studies that evaluated all types of automated coding and classification systems to determine the performance of such systems. Studies indexed in Medline or other relevant databases prior to March 2009 were considered. The 113 studies included in this review show that automated tools exist for a variety of coding and classification purposes, focus on various healthcare specialties, and handle a wide variety of clinical document types. Automated coding and classification systems themselves are not generalizable, nor are the results of the studies evaluating them. Published research shows these systems hold promise, but these data must be considered in context, with performance relative to the complexity of the task and the desired outcome.

Interplay of biopharmaceutics, biopharmaceutics drug disposition and salivary excretion classification systems

Science.gov (United States)

Idkaidek, Nasir M.

2013-01-01

The aim of this commentary is to investigate the interplay of Biopharmaceutics Classification System (BCS), Biopharmaceutics Drug Disposition Classification System (BDDCS) and Salivary Excretion Classification System (SECS). BCS first classified drugs based on permeability and solubility for the purpose of predicting oral drug absorption. Then BDDCS linked permeability with hepatic metabolism and classified drugs based on metabolism and solubility for the purpose of predicting oral drug disposition. On the other hand, SECS classified drugs based on permeability and protein binding for the purpose of predicting the salivary excretion of drugs. The role of metabolism, rather than permeability, on salivary excretion is investigated and the results are not in agreement with BDDCS. Conclusion The proposed Salivary Excretion Classification System (SECS) can be used as a guide for drug salivary excretion based on permeability (not metabolism) and protein binding. PMID:24493977

A new classification system for congenital laryngeal cysts.

Science.gov (United States)

Forte, Vito; Fuoco, Gabriel; James, Adrian

2004-06-01

A new classification system for congenital laryngeal cysts based on the extent of the cyst and on the embryologic tissue of origin is proposed. Retrospective chart review. The charts of 20 patients with either congenital or acquired laryngeal cysts that were treated surgically between 1987 and 2002 at the Hospital for Sick Children, Toronto were retrospectively reviewed. Clinical presentation, radiologic findings, surgical management, histopathology, and outcome were recorded. A new classification system is proposed to better appreciate the origin of these cysts and to guide in their successful surgical management. Fourteen of the supraglottic and subglottic simple mucous retention cysts posed no diagnostic or therapeutic challenge and were treated successfully by a single endoscopic excision or marsupialization. The remaining six patients with congenital cysts in the study were deemed more complex, and all required open surgical procedures for cure. On the basis of the analysis of the data of these patients, a new classification of congenital laryngeal cysts is proposed. Type I cysts are confined to the larynx, the cyst wall composed of endodermal elements only, and can be managed endoscopically. Type II cysts extend beyond the confines of the larynx and require an external approach. The Type II cysts are further subclassified histologically on the basis of the embryologic tissue of origin: IIa, composed of endoderm only and IIb, containing endodermal and mesodermal elements (epithelium and cartilage) in the wall of the cyst. A new classification system for congenital laryngeal cysts is proposed on the basis of the extent of the cyst and the embryologic tissue of origin. This classification can help guide the surgeon with initial management and help us better understand the origin of these cysts.

A review on fault classification methodologies in power transmission systems: Part-II

Directory of Open Access Journals (Sweden)

Avagaddi Prasad

2018-05-01

Full Text Available The countless extent of power systems and applications requires the improvement in suitable techniques for the fault classification in power transmission systems, to increase the efficiency of the systems and to avoid major damages. For this purpose, the technical literature proposes a large number of methods. The paper analyzes the technical literature, summarizing the most important methods that can be applied to fault classification methodologies in power transmission systems.The part 2 of the article is named “A review on fault classification methodologies in power transmission systems”. In this part 2 we discussed the advanced technologies developed by various researchers for fault classification in power transmission systems. Keywords: Transmission line protection, Protective relaying, Soft computing techniques

Automated recognition system for ELM classification in JET

International Nuclear Information System (INIS)

Duro, N.; Dormido, R.; Vega, J.; Dormido-Canto, S.; Farias, G.; Sanchez, J.; Vargas, H.; Murari, A.

2009-01-01

Edge localized modes (ELMs) are instabilities occurring in the edge of H-mode plasmas. Considerable efforts are being devoted to understanding the physics behind this non-linear phenomenon. A first characterization of ELMs is usually their identification as type I or type III. An automated pattern recognition system has been developed in JET for off-line ELM recognition and classification. The empirical method presented in this paper analyzes each individual ELM instead of starting from a temporal segment containing many ELM bursts. The ELM recognition and isolation is carried out using three signals: Dα, line integrated electron density and stored diamagnetic energy. A reduced set of characteristics (such as diamagnetic energy drop, ELM period or Dα shape) has been extracted to build supervised and unsupervised learning systems for classification purposes. The former are based on support vector machines (SVM). The latter have been developed with hierarchical and K-means clustering methods. The success rate of the classification systems is about 98% for a database of almost 300 ELMs.

Phylogenetic turnover during subtropical forest succession across environmental and phylogenetic scales.

Science.gov (United States)

Purschke, Oliver; Michalski, Stefan G; Bruelheide, Helge; Durka, Walter

2017-12-01

Although spatial and temporal patterns of phylogenetic community structure during succession are inherently interlinked and assembly processes vary with environmental and phylogenetic scales, successional studies of community assembly have yet to integrate spatial and temporal components of community structure, while accounting for scaling issues. To gain insight into the processes that generate biodiversity after disturbance, we combine analyses of spatial and temporal phylogenetic turnover across phylogenetic scales, accounting for covariation with environmental differences. We compared phylogenetic turnover, at the species- and individual-level, within and between five successional stages, representing woody plant communities in a subtropical forest chronosequence. We decomposed turnover at different phylogenetic depths and assessed its covariation with between-plot abiotic differences. Phylogenetic turnover between stages was low relative to species turnover and was not explained by abiotic differences. However, within the late-successional stages, there was high presence-/absence-based turnover (clustering) that occurred deep in the phylogeny and covaried with environmental differentiation. Our results support a deterministic model of community assembly where (i) phylogenetic composition is constrained through successional time, but (ii) toward late succession, species sorting into preferred habitats according to niche traits that are conserved deep in phylogeny, becomes increasingly important.

A classification system for tableting behaviors of binary powder mixtures

Directory of Open Access Journals (Sweden)

Changquan Calvin Sun

2016-08-01

Full Text Available The ability to predict tableting properties of a powder mixture from individual components is of both fundamental and practical importance to the efficient formulation development of tablet products. A common tableting classification system (TCS of binary powder mixtures facilitates the systematic development of new knowledge in this direction. Based on the dependence of tablet tensile strength on weight fraction in a binary mixture, three main types of tableting behavior are identified. Each type is further divided to arrive at a total of 15 sub-classes. The proposed classification system lays a framework for a better understanding of powder interactions during compaction. Potential applications and limitations of this classification system are discussed.

Multi-Site Diagnostic Classification of Schizophrenia Using Discriminant Deep Learning with Functional Connectivity MRI

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Ling-Li Zeng

2018-04-01

Full Text Available Background: A lack of a sufficiently large sample at single sites causes poor generalizability in automatic diagnosis classification of heterogeneous psychiatric disorders such as schizophrenia based on brain imaging scans. Advanced deep learning methods may be capable of learning subtle hidden patterns from high dimensional imaging data, overcome potential site-related variation, and achieve reproducible cross-site classification. However, deep learning-based cross-site transfer classification, despite less imaging site-specificity and more generalizability of diagnostic models, has not been investigated in schizophrenia. Methods: A large multi-site functional MRI sample (n = 734, including 357 schizophrenic patients from seven imaging resources was collected, and a deep discriminant autoencoder network, aimed at learning imaging site-shared functional connectivity features, was developed to discriminate schizophrenic individuals from healthy controls. Findings: Accuracies of approximately 85·0% and 81·0% were obtained in multi-site pooling classification and leave-site-out transfer classification, respectively. The learned functional connectivity features revealed dysregulation of the cortical-striatal-cerebellar circuit in schizophrenia, and the most discriminating functional connections were primarily located within and across the default, salience, and control networks. Interpretation: The findings imply that dysfunctional integration of the cortical-striatal-cerebellar circuit across the default, salience, and control networks may play an important role in the “disconnectivity” model underlying the pathophysiology of schizophrenia. The proposed discriminant deep learning method may be capable of learning reliable connectome patterns and help in understanding the pathophysiology and achieving accurate prediction of schizophrenia across multiple independent imaging sites. Keywords: Schizophrenia, Deep learning, Connectome, f

Multi-Site Diagnostic Classification of Schizophrenia Using Discriminant Deep Learning with Functional Connectivity MRI.

Science.gov (United States)

Zeng, Ling-Li; Wang, Huaning; Hu, Panpan; Yang, Bo; Pu, Weidan; Shen, Hui; Chen, Xingui; Liu, Zhening; Yin, Hong; Tan, Qingrong; Wang, Kai; Hu, Dewen

2018-04-01

A lack of a sufficiently large sample at single sites causes poor generalizability in automatic diagnosis classification of heterogeneous psychiatric disorders such as schizophrenia based on brain imaging scans. Advanced deep learning methods may be capable of learning subtle hidden patterns from high dimensional imaging data, overcome potential site-related variation, and achieve reproducible cross-site classification. However, deep learning-based cross-site transfer classification, despite less imaging site-specificity and more generalizability of diagnostic models, has not been investigated in schizophrenia. A large multi-site functional MRI sample (n = 734, including 357 schizophrenic patients from seven imaging resources) was collected, and a deep discriminant autoencoder network, aimed at learning imaging site-shared functional connectivity features, was developed to discriminate schizophrenic individuals from healthy controls. Accuracies of approximately 85·0% and 81·0% were obtained in multi-site pooling classification and leave-site-out transfer classification, respectively. The learned functional connectivity features revealed dysregulation of the cortical-striatal-cerebellar circuit in schizophrenia, and the most discriminating functional connections were primarily located within and across the default, salience, and control networks. The findings imply that dysfunctional integration of the cortical-striatal-cerebellar circuit across the default, salience, and control networks may play an important role in the "disconnectivity" model underlying the pathophysiology of schizophrenia. The proposed discriminant deep learning method may be capable of learning reliable connectome patterns and help in understanding the pathophysiology and achieving accurate prediction of schizophrenia across multiple independent imaging sites. Copyright © 2018 German Center for Neurodegenerative Diseases (DZNE). Published by Elsevier B.V. All rights reserved.

Explosives Classifications Tracking System User Manual

Energy Technology Data Exchange (ETDEWEB)

Genoni, R.P.

1993-10-01

The Explosives Classification Tracking System (ECTS) presents information and data for U.S. Department of Energy (DOE) explosives classifications of interest to EM-561, Transportation Management Division, other DOE facilities, and contractors. It is intended to be useful to the scientist, engineer, and transportation professional, who needs to classify or transport explosives. This release of the ECTS reflects upgrading of the software which provides the user with an environment that makes comprehensive retrieval of explosives related information quick and easy. Quarterly updates will be provided to the ECTS throughout its development in FY 1993 and thereafter. The ECTS is a stand alone, single user system that contains unclassified, publicly available information, and administrative information (contractor names, product descriptions, transmittal dates, EX-Numbers, etc.) information from many sources for non-decisional engineering and shipping activities. The data is the most up-to-date and accurate available to the knowledge of the system developer. The system is designed to permit easy revision and updating as new information and data become available. These, additions and corrections are welcomed by the developer. This user manual is intended to help the user install, understand, and operate the system so that the desired information may be readily obtained, reviewed, and reported.

Drug-induced sedation endoscopy (DISE) classification systems: a systematic review and meta-analysis.

Science.gov (United States)

Dijemeni, Esuabom; D'Amone, Gabriele; Gbati, Israel

2017-12-01

Drug-induced sedation endoscopy (DISE) classification systems have been used to assess anatomical findings on upper airway obstruction, and decide and plan surgical treatments and act as a predictor for surgical treatment outcome for obstructive sleep apnoea management. The first objective is to identify if there is a universally accepted DISE grading and classification system for analysing DISE findings. The second objective is to identify if there is one DISE grading and classification treatment planning framework for deciding appropriate surgical treatment for obstructive sleep apnoea (OSA). The third objective is to identify if there is one DISE grading and classification treatment outcome framework for determining the likelihood of success for a given OSA surgical intervention. A systematic review was performed to identify new and significantly modified DISE classification systems: concept, advantages and disadvantages. Fourteen studies proposing a new DISE classification system and three studies proposing a significantly modified DISE classification were identified. None of the studies were based on randomised control trials. DISE is an objective method for visualising upper airway obstruction. The classification and assessment of clinical findings based on DISE is highly subjective due to the increasing number of DISE classification systems. Hence, this creates a growing divergence in surgical treatment planning and treatment outcome. Further research on a universally accepted objective DISE assessment is critically needed.

Fuzzy Expert System based on a Novel Hybrid Stem Cell (HSC) Algorithm for Classification of Micro Array Data.

Science.gov (United States)

Vijay, S Arul Antran; GaneshKumar, P

2018-02-21

In the growing scenario, microarray data is extensively used since it provides a more comprehensive understanding of genetic variants among diseases. As the gene expression samples have high dimensionality it becomes tedious to analyze the samples manually. Hence an automated system is needed to analyze these samples. The fuzzy expert system offers a clear classification when compared to the machine learning and statistical methodologies. In fuzzy classification, knowledge acquisition would be a major concern. Despite several existing approaches for knowledge acquisition much effort is necessary to enhance the learning process. This paper proposes an innovative Hybrid Stem Cell (HSC) algorithm that utilizes Ant Colony optimization and Stem Cell algorithm for designing fuzzy classification system to extract the informative rules to form the membership functions from the microarray dataset. The HSC algorithm uses a novel Adaptive Stem Cell Optimization (ASCO) to improve the points of membership function and Ant Colony Optimization to produce the near optimum rule set. In order to extract the most informative genes from the large microarray dataset a method called Mutual Information is used. The performance results of the proposed technique evaluated using the five microarray datasets are simulated. These results prove that the proposed Hybrid Stem Cell (HSC) algorithm produces a precise fuzzy system than the existing methodologies.

Visualising very large phylogenetic trees in three dimensional hyperbolic space

Directory of Open Access Journals (Sweden)

Liberles David A

2004-04-01

Full Text Available Abstract Background Common existing phylogenetic tree visualisation tools are not able to display readable trees with more than a few thousand nodes. These existing methodologies are based in two dimensional space. Results We introduce the idea of visualising phylogenetic trees in three dimensional hyperbolic space with the Walrus graph visualisation tool and have developed a conversion tool that enables the conversion of standard phylogenetic tree formats to Walrus' format. With Walrus, it becomes possible to visualise and navigate phylogenetic trees with more than 100,000 nodes. Conclusion Walrus enables desktop visualisation of very large phylogenetic trees in 3 dimensional hyperbolic space. This application is potentially useful for visualisation of the tree of life and for functional genomics derivatives, like The Adaptive Evolution Database (TAED.

A molecular phylogenetic appraisal of the acanthostomines Acanthostomum and Timoniella and their position within Cryptogonimidae (Trematoda: Opisthorchioidea).

Science.gov (United States)

Martínez-Aquino, Andrés; Vidal-Martínez, Victor M; Aguirre-Macedo, M Leopoldina

2017-01-01

The phylogenetic position of three taxa from two trematode genera, belonging to the subfamily Acanthostominae (Opisthorchioidea: Cryptogonimidae), were analysed using partial 28S ribosomal DNA (Domains 1-2) and internal transcribed spacers (ITS1-5.8S-ITS2). Bayesian inference and Maximum likelihood analyses of combined 28S rDNA and ITS1 + 5.8S + ITS2 sequences indicated the monophyly of the genus Acanthostomum ( A. cf. americanum and A. burminis ) and paraphyly of the Acanthostominae . These phylogenetic relationships were consistent in analyses of 28S alone and concatenated 28S + ITS1 + 5.8S + ITS2 sequences analyses. Based on molecular phylogenetic analyses, the subfamily Acanthostominae is therefore a paraphyletic taxon, in contrast with previous classifications based on morphological data. Phylogenetic patterns of host specificity inferred from adult stages of other cryptogonimid taxa are also well supported. However, analyses using additional genera and species are necessary to support the phylogenetic inferences from this study. Our molecular phylogenetic reconstruction linked two larval stages of A. cf. americanum cercariae and metacercariae. Here, we present the evolutionary and ecological implications of parasitic infections in freshwater and brackish environments.

A molecular phylogenetic appraisal of the acanthostomines Acanthostomum and Timoniella and their position within Cryptogonimidae (Trematoda: Opisthorchioidea

Directory of Open Access Journals (Sweden)

Andrés Martínez-Aquino

2017-12-01

Full Text Available The phylogenetic position of three taxa from two trematode genera, belonging to the subfamily Acanthostominae (Opisthorchioidea: Cryptogonimidae, were analysed using partial 28S ribosomal DNA (Domains 1–2 and internal transcribed spacers (ITS1–5.8S–ITS2. Bayesian inference and Maximum likelihood analyses of combined 28S rDNA and ITS1 + 5.8S + ITS2 sequences indicated the monophyly of the genus Acanthostomum (A. cf. americanum and A. burminis and paraphyly of the Acanthostominae. These phylogenetic relationships were consistent in analyses of 28S alone and concatenated 28S + ITS1 + 5.8S + ITS2 sequences analyses. Based on molecular phylogenetic analyses, the subfamily Acanthostominae is therefore a paraphyletic taxon, in contrast with previous classifications based on morphological data. Phylogenetic patterns of host specificity inferred from adult stages of other cryptogonimid taxa are also well supported. However, analyses using additional genera and species are necessary to support the phylogenetic inferences from this study. Our molecular phylogenetic reconstruction linked two larval stages of A. cf. americanum cercariae and metacercariae. Here, we present the evolutionary and ecological implications of parasitic infections in freshwater and brackish environments.

Hotel Classification Systems: A Comparison of International Case Studies

Directory of Open Access Journals (Sweden)

Roberta Minazzi,

2010-12-01

Full Text Available Over the last few decades we have witnessed an increasing interest of scholars andespecially operators in service quality in the lodging business. Firstly, it is important to observe thatthe diverseness of the hospitality industry also affects the classification of hotel quality. We canactually find many programmes, classifications and seals of quality promoted by public authoritiesand private companies that create confusion in the consumer perceptions of hotel quality. Moreover,new electronic distribution channels and their ratings are becoming a new way to gather informationabout a hotel and its quality. Secondly, a point that can cause complications is that different countriesand regions can choose differing approaches depending on the features of the classification (numberof levels, symbols used, etc. and the nature of the programme (public, private. Considering theseassumptions and the recent changes in the Italian hotel classification system, this paper aims toanalyse the situation in Italy, underlining both its positive and negative aspects and comparing it withother European and North American cases. Based on a review of literature and tourism laws as wellas personal interviews with public authorities and exponents of the private sectors, we were able toidentify critical issues and trends in hotel classification systems. The comparison of case studiesshows a heterogeneous situation. Points in common are the scale and the symbol used but, if weanalyse the requirements of each category, we discover very different circumstances, also sometimesin the same country. A future European classification system could be possible only after astandardization of minimum requirements and criteria at a national level. In this situation brands andonline consumers’ feedbacks become even more considered by the customers in the hospitalityindustry.

Migraine classification using magnetic resonance imaging resting-state functional connectivity data.

Science.gov (United States)

Chong, Catherine D; Gaw, Nathan; Fu, Yinlin; Li, Jing; Wu, Teresa; Schwedt, Todd J

2017-08-01

Background This study used machine-learning techniques to develop discriminative brain-connectivity biomarkers from resting-state functional magnetic resonance neuroimaging ( rs-fMRI) data that distinguish between individual migraine patients and healthy controls. Methods This study included 58 migraine patients (mean age = 36.3 years; SD = 11.5) and 50 healthy controls (mean age = 35.9 years; SD = 11.0). The functional connections of 33 seeded pain-related regions were used as input for a brain classification algorithm that tested the accuracy of determining whether an individual brain MRI belongs to someone with migraine or to a healthy control. Results The best classification accuracy using a 10-fold cross-validation method was 86.1%. Resting functional connectivity of the right middle temporal, posterior insula, middle cingulate, left ventromedial prefrontal and bilateral amygdala regions best discriminated the migraine brain from that of a healthy control. Migraineurs with longer disease durations were classified more accurately (>14 years; 96.7% accuracy) compared to migraineurs with shorter disease durations (≤14 years; 82.1% accuracy). Conclusions Classification of migraine using rs-fMRI provides insights into pain circuits that are altered in migraine and could potentially contribute to the development of a new, noninvasive migraine biomarker. Migraineurs with longer disease burden were classified more accurately than migraineurs with shorter disease burden, potentially indicating that disease duration leads to reorganization of brain circuitry.

Bosniak Classification system

DEFF Research Database (Denmark)

Graumann, Ole; Osther, Susanne Sloth; Karstoft, Jens

2014-01-01

Background: The Bosniak classification is a diagnostic tool for the differentiation of cystic changes in the kidney. The process of categorizing renal cysts may be challenging, involving a series of decisions that may affect the final diagnosis and clinical outcome such as surgical management....... Purpose: To investigate the inter- and intra-observer agreement among experienced uroradiologists when categorizing complex renal cysts according to the Bosniak classification. Material and Methods: The original categories of 100 cystic renal masses were chosen as “Gold Standard” (GS), established...... to the calculated weighted κ all readers performed “very good” for both inter-observer and intra-observer variation. Most variation was seen in cysts catagorized as Bosniak II, IIF, and III. These results show that radiologists who evaluate complex renal cysts routinely may apply the Bosniak classification...

Feature-Based Classification of Amino Acid Substitutions outside Conserved Functional Protein Domains

Directory of Open Access Journals (Sweden)

Branislava Gemovic

2013-01-01

Full Text Available There are more than 500 amino acid substitutions in each human genome, and bioinformatics tools irreplaceably contribute to determination of their functional effects. We have developed feature-based algorithm for the detection of mutations outside conserved functional domains (CFDs and compared its classification efficacy with the most commonly used phylogeny-based tools, PolyPhen-2 and SIFT. The new algorithm is based on the informational spectrum method (ISM, a feature-based technique, and statistical analysis. Our dataset contained neutral polymorphisms and mutations associated with myeloid malignancies from epigenetic regulators ASXL1, DNMT3A, EZH2, and TET2. PolyPhen-2 and SIFT had significantly lower accuracies in predicting the effects of amino acid substitutions outside CFDs than expected, with especially low sensitivity. On the other hand, only ISM algorithm showed statistically significant classification of these sequences. It outperformed PolyPhen-2 and SIFT by 15% and 13%, respectively. These results suggest that feature-based methods, like ISM, are more suitable for the classification of amino acid substitutions outside CFDs than phylogeny-based tools.

Land Cover - Minnesota Land Cover Classification System

Data.gov (United States)

Minnesota Department of Natural Resources — Land cover data set based on the Minnesota Land Cover Classification System (MLCCS) coding scheme. This data was produced using a combination of aerial photograph...

Development of the standard classification system of technical information in the field of RI-biomics and its application to the web system

International Nuclear Information System (INIS)

Jang, Sol Ah; Kim, Joo Yeon; Park, Tai Jin

2014-01-01

RI-Biomics is a new concept that combines radioisotopes (RI) and Biomics. For efficient collection of information, establishment of database for technical information system and its application to the system, there is an increasing need for constructing the standard classification system of technical information by its systematical classification. In this paper, we have summarized the development process of the standard classification system of technical information in the field of RI-Biomics and its application to the system. Constructing the draft version for the standard classification system of technical information was based on that standard classification one in national science and technology in Korea. The final classification system was then derived through the reconstruction and the feedback process based on the consultation from the 7 experts. These results were applied to the database of technical information system after transforming as standard code. Thus, the standard classification system were composed of 5 large classifications and 20 small classifications, and those classification are expected to establish the foundation of information system by achieving the circular structure of collection-analysis-application of information

A system for heart sounds classification.

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Grzegorz Redlarski

Full Text Available The future of quick and efficient disease diagnosis lays in the development of reliable non-invasive methods. As for the cardiac diseases - one of the major causes of death around the globe - a concept of an electronic stethoscope equipped with an automatic heart tone identification system appears to be the best solution. Thanks to the advancement in technology, the quality of phonocardiography signals is no longer an issue. However, appropriate algorithms for auto-diagnosis systems of heart diseases that could be capable of distinguishing most of known pathological states have not been yet developed. The main issue is non-stationary character of phonocardiography signals as well as a wide range of distinguishable pathological heart sounds. In this paper a new heart sound classification technique, which might find use in medical diagnostic systems, is presented. It is shown that by combining Linear Predictive Coding coefficients, used for future extraction, with a classifier built upon combining Support Vector Machine and Modified Cuckoo Search algorithm, an improvement in performance of the diagnostic system, in terms of accuracy, complexity and range of distinguishable heart sounds, can be made. The developed system achieved accuracy above 93% for all considered cases including simultaneous identification of twelve different heart sound classes. The respective system is compared with four different major classification methods, proving its reliability.

Albinism in phylogenetically and geographically distinct populations of Astyanax cavefish arises through the same loss-of-function Oca2 allele

Science.gov (United States)

Gross, J B; Wilkens, H

2013-01-01

The Mexican tetra, Astyanax mexicanus, comprises 29 populations of cave-adapted fish distributed across a vast karst region in northeastern Mexico. These populations have a complex evolutionary history, having descended from ‘old' and ‘young' ancestral surface-dwelling stocks that invaded the region ∼6.7 and ∼2.8 MYa, respectively. This study investigates a set of captive, pigmented Astyanax cavefish collected from the Micos cave locality in 1970, in which albinism appeared over the past two decades. We combined novel coloration analyses, coding sequence comparisons and mRNA expression level studies to investigate the origin of albinism in captive-bred Micos cavefish. We discovered that albino Micos cavefish harbor two copies of a loss-of-function ocular and cutaneous albinism type II (Oca2) allele previously identified in the geographically distant Pachón cave population. This result suggests that phylogenetically young Micos cavefish and phylogenetically old Pachón cave fish inherited this Oca2 allele from the ancestral surface-dwelling taxon. This likely resulted from the presence of the loss-of-function Oca2 haplotype in the ‘young' ancestral surface-dwelling stock that colonized the Micos cave and also introgressed into the ancient Pachón cave population. The appearance of albinism in captive Micos cavefish, caused by the same loss-of-function allele present in Pachón cavefish, implies that geographically and phylogenetically distinct cave populations can evolve the same troglomorphic phenotype from standing genetic variation present in the ancestral taxon. PMID:23572122

Analysis of Different Classification Techniques for Two-Class Functional Near-Infrared Spectroscopy-Based Brain-Computer Interface

Directory of Open Access Journals (Sweden)

Noman Naseer

2016-01-01

Full Text Available We analyse and compare the classification accuracies of six different classifiers for a two-class mental task (mental arithmetic and rest using functional near-infrared spectroscopy (fNIRS signals. The signals of the mental arithmetic and rest tasks from the prefrontal cortex region of the brain for seven healthy subjects were acquired using a multichannel continuous-wave imaging system. After removal of the physiological noises, six features were extracted from the oxygenated hemoglobin (HbO signals. Two- and three-dimensional combinations of those features were used for classification of mental tasks. In the classification, six different modalities, linear discriminant analysis (LDA, quadratic discriminant analysis (QDA, k-nearest neighbour (kNN, the Naïve Bayes approach, support vector machine (SVM, and artificial neural networks (ANN, were utilized. With these classifiers, the average classification accuracies among the seven subjects for the 2- and 3-dimensional combinations of features were 71.6, 90.0, 69.7, 89.8, 89.5, and 91.4% and 79.6, 95.2, 64.5, 94.8, 95.2, and 96.3%, respectively. ANN showed the maximum classification accuracies: 91.4 and 96.3%. In order to validate the results, a statistical significance test was performed, which confirmed that the p values were statistically significant relative to all of the other classifiers (p < 0.005 using HbO signals.

Bosniak classification system

DEFF Research Database (Denmark)

Graumann, Ole; Osther, Susanne Sloth; Karstoft, Jens

2016-01-01

BACKGROUND: The Bosniak classification was originally based on computed tomographic (CT) findings. Magnetic resonance (MR) and contrast-enhanced ultrasonography (CEUS) imaging may demonstrate findings that are not depicted at CT, and there may not always be a clear correlation between the findings...... at MR and CEUS imaging and those at CT. PURPOSE: To compare diagnostic accuracy of MR, CEUS, and CT when categorizing complex renal cystic masses according to the Bosniak classification. MATERIAL AND METHODS: From February 2011 to June 2012, 46 complex renal cysts were prospectively evaluated by three...... readers. Each mass was categorized according to the Bosniak classification and CT was chosen as gold standard. Kappa was calculated for diagnostic accuracy and data was compared with pathological results. RESULTS: CT images found 27 BII, six BIIF, seven BIII, and six BIV. Forty-three cysts could...

CADASTRAL CLASSIFICATION OF THE LAND PLOTS IN UKRAINE

Directory of Open Access Journals (Sweden)

KIRICHEK Yu. O.

2016-04-01

Full Text Available Summary. Work concerns development of national system of classification of the land plots. The developed classification will allow to solve correctly a number of the corresponding cadastral, land management, estimated and other tasks. The analysis of classifications of lands, improvements and real estate in general is made. The created offers concerning creation of a new classification of the land plots in Ukraine. Today the Ukrainian real estate market has no single system that separates the system property groups, classes and types. This significantly complicates the work and can not fully be aware of the specific situation of real estate market. This task is designed to solve classification properties, it is used to transition from a diversity of individual properties to a limited number of classes of evaluation objects. The classification is different functional purpose (use facilities assessment, which determines the difference in value.

Excitation equilibria in plasmas: a classification

International Nuclear Information System (INIS)

Mullen, J.-J.A.M. van der.

1986-01-01

In this thesis the author presents a classification of plasmas based on the atomic state distribution function. The study is based on the relation between the distribution function and the underlying processes and starts with the proper understanding of thermodynamic equilibrium (TE). Four types of proper balances are relevant: The 'Maxwell balance' of kinetic energy transfer, the 'Boltzmann balance' of excitation/deexcitation, the 'Saha balance' of ionization/recombination and the 'Planck balance' for interaction of atoms with radiation. Special attention is paid to the distribution function of the ionizing excitation saturation balance. The classification theory of the distribution functions in relation with underlying balances is supported by experimental evidence in an ionizing argon plasma. The AR I system provides a pertinent support of the theory. Experimental facts found in the AR II system can be interpreted in global terms. (Auth.)

Measurement of semantic similarity for land use and land cover classification systems

Science.gov (United States)

Deng, Dongpo

2008-12-01

Land use and land cover (LULC) data is essential to environmental and ecological research. However, semantic heterogeneous of land use and land cover classification are often resulted from different data resources, different cultural contexts, and different utilities. Therefore, there is need to develop a method to measure, compare and integrate between land cover categories. To understand the meaning and the use of terminology from different domains, the common ontology approach is used to acquire information regarding the meaning of terms, and to compare two terms to determine how they might be related. Ontology is a formal specification of a shared conceptualization of a domain of interest. LULC classification system is a ontology. The semantic similarity method is used to compare to entities of three LULC classification systems: CORINE (European Environmental Agency), Oregon State, USA), and Taiwan. The semantic properties and relations firstly have been extracted from their definitions of LULC classification systems. Then semantic properties and relations of categories in three LULC classification systems are mutually compared. The visualization of semantic proximity is finally presented to explore the similarity or dissimilarity of data. This study shows the semantic similarity method efficiently detect semantic distance in three LULC classification systems and find out the semantic similar objects.

Evolutionary history determines how plant productivity responds to phylogenetic diversity and species richness

Directory of Open Access Journals (Sweden)

Mark A. Genung

2014-03-01

Full Text Available The relationship between biodiversity and ecosystem function has received a great deal of attention in ecological research and recent results, from re-analyses, suggest that ecosystem function improves with increases in phylogenetic diversity. However, many of these results have been generalized across a range of different species and clades, and plants with different evolutionary histories could display different relationships between biodiversity and ecosystem function. To experimentally test this hypothesis, we manipulated species richness and phylogenetic diversity using 26 species from two subgenera of the genus Eucalyptus (subgenus Eucalyptus and subgenus Symphyomyrtus. We found that plant biomass (a measurement of ecosystem function sometimes, but not always, responded to increases in species richness and phylogenetic diversity. Specifically, Symphyomyrtus plants showed a positive response while no comparable effect was observed for Eucalyptus plants, showing that responses to biodiversity can vary across different phylogenetic groups. Our results show that the impacts of evolutionary history may complicate the relationship between the diversity of plant communities and plant biomass.

CREST--classification resources for environmental sequence tags.

Directory of Open Access Journals (Sweden)

Anders Lanzén

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

A comparison of the Web of Science with publication-level classification systems of science

Energy Technology Data Exchange (ETDEWEB)

Perianes-Rodriguez, A.; Ruiz-Castillo, J.

2016-07-01

In this paper we propose a new criterion for choosing between a pair of classification systems of science that assign publications (or journals) to a set of scientific fields. Consider the standard normalization procedure in which field mean citations are used as normalization factors. We recommend system A over system B whenever the standard normalization procedure based on A performs better than the when it is based on B. Since the evaluation can be made in terms of either system, the performance assessment requires a double test. In addition, since the assessment of two normalization procedures would be generally biased in favor of the one based on the classification system used for evaluation purposes, ideally a pair of classification systems must be compared using a third, independent classification system for evaluation purposes. We illustrate this strategy by comparing a Web of Science journal-level classification system, consisting of 236 journal subject categories, with two publication-level algorithmically constructed classification systems consisting of 1,363 (G6) and 5,119 (G8) clusters. There are two main findings. (1) The G8 system is found to dominate the G6 system. Therefore, when we have a choice between two classification systems at different granularity levels, we should use the system at the higher level because it typically exhibits a better standard normalization performance. (2) The G8 system and the Web of Science (WoS) journal-level system are found to be non-comparable. Nevertheless, the G8-normalization procedure performs better using the WoS system for evaluation purposes than the WoS-normalization procedure using the G8 system for evaluation purposes. Furthermore, when we use the G6 system for evaluation purposes, the G8-normalization procedure performs better than the WoS-normalization procedure. We conclude that algorithmically constructed classification systems constitute a credible alternative to the WoS system and, by extension, to

Comparison of an automated classification system with an empirical classification of circulation patterns over the Pannonian basin, Central Europe

Science.gov (United States)

Maheras, Panagiotis; Tolika, Konstantia; Tegoulias, Ioannis; Anagnostopoulou, Christina; Szpirosz, Klicász; Károssy, Csaba; Makra, László

2018-04-01

The aim of the study is to compare the performance of the two classification methods, based on the atmospheric circulation types over the Pannonian basin in Central Europe. Moreover, relationships including seasonal occurrences and correlation coefficients, as well as comparative diagrams of the seasonal occurrences of the circulation types of the two classification systems are presented. When comparing of the automated (objective) and empirical (subjective) classification methods, it was found that the frequency of the empirical anticyclonic (cyclonic) types is much higher (lower) than that of the automated anticyclonic (cyclonic) types both on an annual and seasonal basis. The highest and statistically significant correlations between the circulation types of the two classification systems, as well as those between the cumulated seasonal anticyclonic and cyclonic types occur in winter for both classifications, since the weather-influencing effect of the atmospheric circulation in this season is the most prevalent. Precipitation amounts in Budapest display a decreasing trend in accordance with the decrease in the occurrence of the automated cyclonic types. In contrast, the occurrence of the empirical cyclonic types displays an increasing trend. There occur types in a given classification that are usually accompanied by high ratios of certain types in the other classification.

Interrater reliability of a Pilates movement-based classification system.

Science.gov (United States)

Yu, Kwan Kenny; Tulloch, Evelyn; Hendrick, Paul

2015-01-01

To determine the interrater reliability for identification of a specific movement pattern using a Pilates Classification system. Videos of 5 subjects performing specific movement tasks were sent to raters trained in the DMA-CP classification system. Ninety-six raters completed the survey. Interrater reliability for the detection of a directional bias was excellent (Pi = 0.92, and K(free) = 0.89). Interrater reliability for classifying an individual into a specific subgroup was moderate (Pi = 0.64, K(free) = 0.55) however raters who had completed levels 1-4 of the DMA-CP training and reported using the assessment daily demonstrated excellent reliability (Pi = 0.89 and K(free) = 0.87). The reliability of the classification system demonstrated almost perfect agreement in determining the existence of a specific movement pattern and classifying into a subgroup for experienced raters. There was a trend for greater reliability associated with increased levels of training and experience of the raters. Copyright © 2014 Elsevier Ltd. All rights reserved.

Phylogenetic relationships in Asarum: Effect of data partitioning and a revised classification.

Science.gov (United States)

Sinn, Brandon T; Kelly, Lawrence M; Freudenstein, John V

2015-05-01

Generic boundaries and infrageneric relationships among the charismatic temperate magnoliid Asarum sensu lato (Aristolochiaceae) have long been uncertain. Previous molecular phylogenetic analyses used either plastid or nuclear loci alone and varied greatly in their taxonomic implications for the genus. We analyzed additional molecular markers from the nuclear and plastid genomes, reevaluated the possibility of a derived loss of autonomous self-pollination, and investigated the topological effects of matrix-partitioning-scheme choice. We sequenced seven plastid regions and the nuclear ITS1-ITS2 region of 58 individuals representing all previously recognized Asarum s.l. segregate genera and the monotypic genus Saruma. Matrices were partitioned using common a priori partitioning schemes and PartitionFinder. Topologies that were recovered using a priori partitioning of matrices differed from those recovered using a PartitionFinder-selected scheme, and by analysis method. We recovered six monophyletic groups that we circumscribed into three subgenera and six sections. Putative fungal mimic characters served as synapomorphies only for subgenus Heterotropa. Subgenus Geotaenium, a new subgenus, was recovered as sister to the remainder of Asarum by ML analyses of highly partitioned datasets. Section Longistylis, also newly named, is sister to section Hexastylis. Our analyses do not unambiguously support a single origin for all fungal-mimicry characters. Topologies recovered through the analysis of PartitionFinder-optimized matrices can differ drastically from those inferred from a priori partitioned matrices, and by analytical method. We recommend that investigators evaluate the topological effects of matrix partitioning using multiple methods of phylogenetic reconstruction. © 2015 Botanical Society of America, Inc.

Evolution and classification of the CRISPR-Cas systems

Science.gov (United States)

S. Makarova, Kira; H. Haft, Daniel; Barrangou, Rodolphe; J. J. Brouns, Stan; Charpentier, Emmanuelle; Horvath, Philippe; Moineau, Sylvain; J. M. Mojica, Francisco; I. Wolf, Yuri; Yakunin, Alexander F.; van der Oost, John; V. Koonin, Eugene

2012-01-01

The CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) modules are adaptive immunity systems that are present in many archaea and bacteria. These defence systems are encoded by operons that have an extraordinarily diverse architecture and a high rate of evolution for both the cas genes and the unique spacer content. Here, we provide an updated analysis of the evolutionary relationships between CRISPR–Cas systems and Cas proteins. Three major types of CRISPR–Cas system are delineated, with a further division into several subtypes and a few chimeric variants. Given the complexity of the genomic architectures and the extremely dynamic evolution of the CRISPR–Cas systems, a unified classification of these systems should be based on multiple criteria. Accordingly, we propose a `polythetic' classification that integrates the phylogenies of the most common cas genes, the sequence and organization of the CRISPR repeats and the architecture of the CRISPR–cas loci. PMID:21552286

Classification system of the mineral reserves and resources of Ukraine

International Nuclear Information System (INIS)

Lovinyukov, V.I.

1998-01-01

This paper describes the system used to classify the resources and reserves of all minerals and fuels in Ukraine. The classification system is part of an official procedure determined by the Ukrainian State Commission on Reserves. Following preparation of resource estimates the results are registered with the State, which maintains an official inventory of all mineral resources. This paper compares the Ukrainian system to, and finds it compatible with the United Nations International Framework of resource classification. The UN system is based on economics of production and mineability. (author)

Classification system of the mineral reserves and resources of Ukraine

International Nuclear Information System (INIS)

Lovyunikov, V.I.

1997-01-01

This paper describes the system used to classify the resources and reserves of all minerals and fuels in Ukraine. The classification system is part of an official procedures determined by the Ukrainian State Commission on Reserves. Following preparation of resource estimates the results are registered with the State, which maintains an official inventory of all mineral resources. This paper compares the Ukrainian system to, and finds it compatible with the United Nations International Framework of resources classification. The UN system is based on economics of production and mineability. (author). 1 tab

Update of the LIPID MAPS comprehensive classification system for lipids

NARCIS (Netherlands)

Fahy, E.; Subramaniam, S.; Murphy, R.C.; Nishijima, M.; Raetz, C.R.H.; Shimizu, T.; Spener, F.; van Meer, G.|info:eu-repo/dai/nl/068570368; Wakelam, M.J.O.; Dennis, E.A.

2009-01-01

In 2005, the International Lipid Classification and Nomenclature Committee under the sponsorship of the LIPID MAPS Consortium developed and established a “Comprehensive Classification System for Lipids” based on well-defined chemical and biochemical principles and using an ontology that is

Calibration of a Plastic Classification System with the Ccw Model

International Nuclear Information System (INIS)

Barcala Riveira, J. M.; Fernandez Marron, J. L.; Alberdi Primicia, J.; Navarrete Marin, J. J.; Oller Gonzalez, J. C.

2003-01-01

This document describes the calibration of a plastic Classification system with the Ccw model (Classification by Quantum's built with Wavelet Coefficients). The method is applied to spectra of plastics usually present in domestic wastes. Obtained results are showed. (Author) 16 refs

Setting a generalized functional linear model (GFLM for the classification of different types of cancer

Directory of Open Access Journals (Sweden)

Miguel Flores

2016-11-01

Full Text Available This work aims to classify the DNA sequences of healthy and malignant cancer respectively. For this, supervised and unsupervised classification methods from a functional context are used; i.e. each strand of DNA is an observation. The observations are discretized, for that reason different ways to represent these observations with functions are evaluated. In addition, an exploratory study is done: estimating the mean and variance of each functional type of cancer. For the unsupervised classification method, hierarchical clustering with different measures of functional distance is used. On the other hand, for the supervised classification method, a functional generalized linear model is used. For this model the first and second derivatives are used which are included as discriminating variables. It has been verified that one of the advantages of working in the functional context is to obtain a model to correctly classify cancers by 100%. For the implementation of the methods it has been used the fda.usc R package that includes all the techniques of functional data analysis used in this work. In addition, some that have been developed in recent decades. For more details of these techniques can be consulted Ramsay, J. O. and Silverman (2005 and Ferraty et al. (2006.

Host Rock Classification (HRC) system for nuclear waste disposal in crystalline bedrock

International Nuclear Information System (INIS)

Hagros, A.

2006-01-01

A new rock mass classification scheme, the Host Rock Classification system (HRC-system) has been developed for evaluating the suitability of volumes of rock mass for the disposal of high-level nuclear waste in Precambrian crystalline bedrock. To support the development of the system, the requirements of host rock to be used for disposal have been studied in detail and the significance of the various rock mass properties have been examined. The HRC-system considers both the long-term safety of the repository and the constructability in the rock mass. The system is specific to the KBS-3V disposal concept and can be used only at sites that have been evaluated to be suitable at the site scale. By using the HRC-system, it is possible to identify potentially suitable volumes within the site at several different scales (repository, tunnel and canister scales). The selection of the classification parameters to be included in the HRC-system is based on an extensive study on the rock mass properties and their various influences on the long-term safety, the constructability and the layout and location of the repository. The parameters proposed for the classification at the repository scale include fracture zones, strength/stress ratio, hydraulic conductivity and the Groundwater Chemistry Index. The parameters proposed for the classification at the tunnel scale include hydraulic conductivity, Q' and fracture zones and the parameters proposed for the classification at the canister scale include hydraulic conductivity, Q', fracture zones, fracture width (aperture + filling) and fracture trace length. The parameter values will be used to determine the suitability classes for the volumes of rock to be classified. The HRC-system includes four suitability classes at the repository and tunnel scales and three suitability classes at the canister scale and the classification process is linked to several important decisions regarding the location and acceptability of many components of

The development of an automatic classification system of nuclear power plant states

International Nuclear Information System (INIS)

Mitomo, Nobuo; Matsuoka, Takeshi

2000-01-01

For the future autonomous plant, automatic control and diagnostics are being incorporated and operators are mainly engaged in the high levels of diagnosis and decision-making in emergencies. Therefore these matters will be performed through the Man-Machine Interface(MMI). Ship Research Institute has been carrying out the research on the MMI system for autonomous power plants. The automatic classification system of plant states is one of the functions of this MMI and the system utilizes COBWEB, which is known as a way of clustering data to acquire concepts. In this paper, many plant states produced by a plant simulator we examined in order to confirm the effectiveness of this system. The system has well classified plant states produced by a plant simulator. (author)

A model to facilitate implementation of the International Classification of Functioning, Disability and Health into prosthetics and orthotics.

Science.gov (United States)

Jarl, Gustav; Ramstrand, Nerrolyn

2017-09-01

The International Classification of Functioning, Disability and Health is a classification of human functioning and disability and is based on a biopsychosocial model of health. As such, International Classification of Functioning, Disability and Health seems suitable as a basis for constructing models defining the clinical P&O process. The aim was to use International Classification of Functioning, Disability and Health to facilitate development of such a model. Proposed model: A model, the Prosthetic and Orthotic Process (POP) model, is proposed. The Prosthetic and Orthotic Process model is based on the concepts of the International Classification of Functioning, Disability and Health and comprises four steps in a cycle: (1) Assessment, including the medical history and physical examination of the patient. (2) Goals, specified on four levels including those related to participation, activity, body functions and structures and technical requirements of the device. (3) Intervention, in which the appropriate course of action is determined based on the specified goal and evidence-based practice. (4) Evaluation of outcomes, where the outcomes are assessed and compared to the corresponding goals. After the evaluation of goal fulfilment, the first cycle in the process is complete, and a broad evaluation is now made including overriding questions about the patient's satisfaction with the outcomes and the process. This evaluation will determine if the process should be ended or if another cycle in the process should be initiated. The Prosthetic and Orthotic Process model can provide a common understanding of the P&O process. Concepts of International Classification of Functioning, Disability and Health have been incorporated into the model to facilitate communication with other rehabilitation professionals and encourage a holistic and patient-centred approach in clinical practice. Clinical relevance The Prosthetic and Orthotic Process model can support the implementation

Multiple kernel learning using single stage function approximation for binary classification problems

Science.gov (United States)

Shiju, S.; Sumitra, S.

2017-12-01

In this paper, the multiple kernel learning (MKL) is formulated as a supervised classification problem. We dealt with binary classification data and hence the data modelling problem involves the computation of two decision boundaries of which one related with that of kernel learning and the other with that of input data. In our approach, they are found with the aid of a single cost function by constructing a global reproducing kernel Hilbert space (RKHS) as the direct sum of the RKHSs corresponding to the decision boundaries of kernel learning and input data and searching that function from the global RKHS, which can be represented as the direct sum of the decision boundaries under consideration. In our experimental analysis, the proposed model had shown superior performance in comparison with that of existing two stage function approximation formulation of MKL, where the decision functions of kernel learning and input data are found separately using two different cost functions. This is due to the fact that single stage representation helps the knowledge transfer between the computation procedures for finding the decision boundaries of kernel learning and input data, which inturn boosts the generalisation capacity of the model.

Road and Street Centerlines - FUNCTIONAL_CLASS_INDOTMODEL_IN: Functional Classification of Roadways in Indiana, 2015 (Indiana Department of Transportation, Line Shapefile)

Data.gov (United States)

NSGIC State | GIS Inventory — FUNCTIONAL_CLASS_INDOTMODEL_IN is a line shapefile that shows the Federal Highway Administration functional classification of roadways from the Road Inventory of the...

A proposal of criteria for the classification of systemic sclerosis.

Science.gov (United States)

Nadashkevich, Oleg; Davis, Paul; Fritzler, Marvin J

2004-11-01

Sensitive and specific criteria for the classification of systemic sclerosis are required by clinicians and investigators to achieve higher quality clinical studies and approaches to therapy. A clinical study of systemic sclerosis patients in Europe and Canada led to a set of criteria that achieve high sensitivity and specificity. Both clinical and laboratory investigations of patients with systemic sclerosis, related conditions and diseases with clinical features that can be mistaken as part of the systemic sclerosis spectrum were undertaken. Laboratory investigations included the detection of autoantibodies to centromere proteins, Scl-70 (topoisomerase I), and fibrillarin (U3-RNP). Based on the investigation of 269 systemic sclerosis patients and 720 patients presenting with related and confounding conditions, the following set of criteria for the classification of systemic sclerosis was proposed: 1) autoantibodies to: centromere proteins, Scl-70 (topo I), fibrillarin; 2) bibasilar pulmonary fibrosis; 3) contractures of the digital joints or prayer sign; 4) dermal thickening proximal to the wrists; 5) calcinosis cutis; 6) Raynaud's phenomenon; 7) esophageal distal hypomotility or reflux-esophagitis; 8) sclerodactyly or non-pitting digital edema; 9) teleangiectasias. The classification of definite SSc requires at least three of the above criteria. Criteria for the classification of systemic sclerosis have been proposed. Preliminary testing has defined the sensitivity and specificity of these criteria as high as 99% and 100%, respectively. Testing and validation of the proposed criteria by other clinical centers is required.

Classification system for acute and chronic radiation treatment sequelae

International Nuclear Information System (INIS)

Seegenschmiedt, M.H.; Sauer, R.

1993-01-01

A classification system in German language is proposed for scoring of acute and chronic treatment sequelae after radiotherapy. It includes all important organs and organ systems. The proposed grading corresponds to the four-scale-system of the WHO and UICC. The system is also compatible to the RTOG and EORTC acute and late radiation morbidity scoring criteria. This facilitates the data transfer for retrospective and prospective analysis of monomodal and multimodal radiotherapy treatment regimes. We recommend to use this scoring system in all German speaking countries for multicentric prospective studies. It is possible, that organ-specific sophistications of the toxicity grading will be developed in the future. These additions should conform with (inter)national standards and apply the same four-scale grading of this classification system. (orig.) [de

Towards automated human gait disease classification using phase space representation of intrinsic mode functions

Science.gov (United States)

Pratiher, Sawon; Patra, Sayantani; Pratiher, Souvik

2017-06-01

A novel analytical methodology for segregating healthy and neurological disorders from gait patterns is proposed by employing a set of oscillating components called intrinsic mode functions (IMF's). These IMF's are generated by the Empirical Mode Decomposition of the gait time series and the Hilbert transformed analytic signal representation forms the complex plane trace of the elliptical shaped analytic IMFs. The area measure and the relative change in the centroid position of the polygon formed by the Convex Hull of these analytic IMF's are taken as the discriminative features. Classification accuracy of 79.31% with Ensemble learning based Adaboost classifier validates the adequacy of the proposed methodology for a computer aided diagnostic (CAD) system for gait pattern identification. Also, the efficacy of several potential biomarkers like Bandwidth of Amplitude Modulation and Frequency Modulation IMF's and it's Mean Frequency from the Fourier-Bessel expansion from each of these analytic IMF's has been discussed for its potency in diagnosis of gait pattern identification and classification.

A Consistent Phylogenetic Backbone for the Fungi

Science.gov (United States)

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

2012-01-01

The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data—a common practice in phylogenomic analyses—introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses. PMID:22114356

Climate-driven extinctions shape the phylogenetic structure of temperate tree floras.

Science.gov (United States)

Eiserhardt, Wolf L; Borchsenius, Finn; Plum, Christoffer M; Ordonez, Alejandro; Svenning, Jens-Christian

2015-03-01

When taxa go extinct, unique evolutionary history is lost. If extinction is selective, and the intrinsic vulnerabilities of taxa show phylogenetic signal, more evolutionary history may be lost than expected under random extinction. Under what conditions this occurs is insufficiently known. We show that late Cenozoic climate change induced phylogenetically selective regional extinction of northern temperate trees because of phylogenetic signal in cold tolerance, leading to significantly and substantially larger than random losses of phylogenetic diversity (PD). The surviving floras in regions that experienced stronger extinction are phylogenetically more clustered, indicating that non-random losses of PD are of increasing concern with increasing extinction severity. Using simulations, we show that a simple threshold model of survival given a physiological trait with phylogenetic signal reproduces our findings. Our results send a strong warning that we may expect future assemblages to be phylogenetically and possibly functionally depauperate if anthropogenic climate change affects taxa similarly. © 2015 John Wiley & Sons Ltd/CNRS.

Language of Czech Medical Reports and Classification Systems in Medicine

Czech Academy of Sciences Publication Activity Database

Přečková, Petra

2010-01-01

Roč. 6, č. 1 (2010), s. 58-65 ISSN 1801-5603 R&D Projects: GA MŠk(CZ) 1M06014 Institutional research plan: CEZ:AV0Z10300504 Keywords : terminology, * synonyms * classification systems * thesaurus * nomenclature * electronic health record * interoperability * semantic interoperability * cardiology * atherosclerosis Subject RIV: IN - Informatics, Computer Science http://www.ejbi.org/en/ejbi/article/53-en-language-of-czech-medical-reports- and -classification-systems-in-medicine.html

Development of a definition, classification system, and model for cultural geology

Science.gov (United States)

Mitchell, Lloyd W., III

The concept for this study is based upon a personal interest by the author, an American Indian, in promoting cultural perspectives in undergraduate college teaching and learning environments. Most academicians recognize that merged fields can enhance undergraduate curricula. However, conflict may occur when instructors attempt to merge social science fields such as history or philosophy with geoscience fields such as mining and geomorphology. For example, ideologies of Earth structures derived from scientific methodologies may conflict with historical and spiritual understandings of Earth structures held by American Indians. Specifically, this study addresses the problem of how to combine cultural studies with the geosciences into a new merged academic discipline called cultural geology. This study further attempts to develop the merged field of cultural geology using an approach consisting of three research foci: a definition, a classification system, and a model. Literature reviews were conducted for all three foci. Additionally, to better understand merged fields, a literature review was conducted specifically for academic fields that merged social and physical sciences. Methodologies concentrated on the three research foci: definition, classification system, and model. The definition was derived via a two-step process. The first step, developing keyword hierarchical ranking structures, was followed by creating and analyzing semantic word meaning lists. The classification system was developed by reviewing 102 classification systems and incorporating selected components into a system framework. The cultural geology model was created also utilizing a two-step process. A literature review of scientific models was conducted. Then, the definition and classification system were incorporated into a model felt to reflect the realm of cultural geology. A course syllabus was then developed that incorporated the resulting definition, classification system, and model. This

Proposal plan of classification faceted for federal universities

Directory of Open Access Journals (Sweden)

Renata Santos Brandão

2017-09-01

Full Text Available This study aims to present a faceted classification plan for the archival management of documents in the federal universities of Brazil. For this, was done a literature review on the archival management in Brazil, the types of classification plans and the theory of the Ranganathan faceted classification, through searches in databases in the areas of Librarianship and Archivology. It was identified the classification plan used in the Federal Institutions of Higher Education to represent the functional facet and created the structural classification plan to represent the structural facet. The two classification plans were inserted into a digital repository management system to give rise to the faceted classification plan. The system used was Tainacan, free software wordpress-based used in digital document management. The developed faceted classification plan allows the user to choose and even combine the way to look for the information that guarantees agreater efficiency in the information retrieval.

Functional Communication Profiles in Children with Cerebral Palsy in Relation to Gross Motor Function and Manual and Intellectual Ability.

Science.gov (United States)

Choi, Ja Young; Park, Jieun; Choi, Yoon Seong; Goh, Yu Ra; Park, Eun Sook

2018-07-01

The aim of the present study was to investigate communication function using classification systems and its association with other functional profiles, including gross motor function, manual ability, intellectual functioning, and brain magnetic resonance imaging (MRI) characteristics in children with cerebral palsy (CP). This study recruited 117 individuals with CP aged from 4 to 16 years. The Communication Function Classification System (CFCS), Viking Speech Scale (VSS), Speech Language Profile Groups (SLPG), Gross Motor Function Classification System (GMFCS), Manual Ability Classification System (MACS), and intellectual functioning were assessed in the children along with brain MRI categorization. Very strong relationships were noted among the VSS, CFCS, and SLPG, although these three communication systems provide complementary information, especially for children with mid-range communication impairment. These three communication classification systems were strongly related with the MACS, but moderately related with the GMFCS. Multiple logistic regression analysis indicated that manual ability and intellectual functioning were significantly related with VSS and CFCS function, whereas only intellectual functioning was significantly related with SLPG functioning in children with CP. Communication function in children with a periventricular white matter lesion (PVWL) varied widely. In the cases with a PVWL, poor functioning was more common on the SLPG, compared to the VSS and CFCS. Very strong relationships were noted among three communication classification systems that are closely related with intellectual ability. Compared to gross motor function, manual ability seemed more closely related with communication function in these children. © Copyright: Yonsei University College of Medicine 2018.

On safety classification of instrumentation and control systems and their components

International Nuclear Information System (INIS)

Yastrebenetskij, M.A.; Rozen, Yu.V.

2004-01-01

Safety classification of instrumentation and control systems (I and C) and their components (hardware, software, software-hardware complexes) is described: - evaluation of classification principles and criteria in Ukrainian standards and rules; comparison between Ukrainian and international principles and criteria; possibility and ways of coordination of Ukrainian and international standards related to (I and C) safety classification

Use of The International Classification of Functioning, Disability and Health (ICF as a conceptual framework and common language for disability statistics and health information systems

Directory of Open Access Journals (Sweden)

Kostanjsek Nenad

2011-05-01

Full Text Available Abstract A common framework for describing functional status information is needed in order to make this information comparable and of value. The World Health Organization’s International Classification of Functioning, Disability and Health (ICF, which has been approved by all its member states, provides this common language and framework. The article provides an overview of ICF taxonomy, introduces the conceptual model which underpins ICF and elaborates on how ICF is used at population and clinical level. Furthermore, the article presents key features of the ICF tooling environment and outlines current and future developments of the classification.

BIMLR: a method for constructing rooted phylogenetic networks from rooted phylogenetic trees.

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Wang, Juan; Guo, Maozu; Xing, Linlin; Che, Kai; Liu, Xiaoyan; Wang, Chunyu

2013-09-15

Rooted phylogenetic trees constructed from different datasets (e.g. from different genes) are often conflicting with one another, i.e. they cannot be integrated into a single phylogenetic tree. Phylogenetic networks have become an important tool in molecular evolution, and rooted phylogenetic networks are able to represent conflicting rooted phylogenetic trees. Hence, the development of appropriate methods to compute rooted phylogenetic networks from rooted phylogenetic trees has attracted considerable research interest of late. The CASS algorithm proposed by van Iersel et al. is able to construct much simpler networks than other available methods, but it is extremely slow, and the networks it constructs are dependent on the order of the input data. Here, we introduce an improved CASS algorithm, BIMLR. We show that BIMLR is faster than CASS and less dependent on the input data order. Moreover, BIMLR is able to construct much simpler networks than almost all other methods. BIMLR is available at http://nclab.hit.edu.cn/wangjuan/BIMLR/. © 2013 Elsevier B.V. All rights reserved.

Polytomy identification in microbial phylogenetic reconstruction

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Lin Guan

2011-12-01

Full Text Available Abstract Background A phylogenetic tree, showing ancestral relations among organisms, is commonly represented as a rooted tree with sets of bifurcating branches (dichotomies for simplicity, although polytomies (multifurcating branches may reflect more accurate evolutionary relationships. To represent the true evolutionary relationships, it is important to systematically identify the polytomies from a bifurcating tree and generate a taxonomy-compatible multifurcating tree. For this purpose we propose a novel approach, "PolyPhy", which would classify a set of bifurcating branches of a phylogenetic tree into a set of branches with dichotomies and polytomies by considering genome distances among genomes and tree topological properties. Results PolyPhy employs a machine learning technique, BLR (Bayesian logistic regression classifier, to identify possible bifurcating subtrees as polytomies from the trees resulted from ComPhy. Other than considering genome-scale distances between all pairs of species, PolyPhy also takes into account different properties of tree topology between dichotomy and polytomy, such as long-branch retraction and short-branch contraction, and quantifies these properties into comparable rates among different sub-branches. We extract three tree topological features, 'LR' (Leaf rate, 'IntraR' (Intra-subset branch rate and 'InterR' (Inter-subset branch rate, all of which are calculated from bifurcating tree branch sets for classification. We have achieved F-measure (balanced measure between precision and recall of 81% with about 0.9 area under the curve (AUC of ROC. Conclusions PolyPhy is a fast and robust method to identify polytomies from phylogenetic trees based on genome-wide inference of evolutionary relationships among genomes. The software package and test data can be downloaded from http://digbio.missouri.edu/ComPhy/phyloTreeBiNonBi-1.0.zip.

Phylogenetic study of the arginine-vasotocin/arginine-vasopressin-like immunoreactive system in invertebrates.

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Mizuno, J; Takeda, N

1988-01-01

1. A phylogenetic study of arg-vasotocin (AVT)/arg-vasopressin (AVP)-like immunoreactive cells was performed by the PAP method in the central nervous system of invertebrates. 2. The immunoreactivity was detected in the nerve cells of Hydra magnipapillata of the Coelenterata; Neanthes japonica and Pheretima communissima of the Annelida; Pomacea canaliculata, Aplysia kurodai, Oncidium verrucosum, Bradybaena similaris, Achatina fulica, Limax marginatus and Meretrix lamarckii of the Mollusca; Gnorimosphaeroma rayi, Hemigrapsus sanguineus, Gryllus bimaculatus and Baratha brassicae of the Arthropoda; Asterina pectinifera of the Echinodermata; and Halocynthia roretzi of the Protochordata. 3. No immunoreactivity was detected in Bipalium sp. of the Platyhelminthes, or in Procambarus clarkii and Helice tridens of the Arthropoda. 4. From these results, it appears that AVT/AVP is a phylogenetically ancient peptide which is present in a wide variety of invertebrates. 5. The actions of AVT/AVP and its presence in invertebrates are discussed.

Multi-gene phylogenetic analysis reveals that shochu-fermenting Saccharomyces cerevisiae strains form a distinct sub-clade of the Japanese sake cluster.

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Futagami, Taiki; Kadooka, Chihiro; Ando, Yoshinori; Okutsu, Kayu; Yoshizaki, Yumiko; Setoguchi, Shinji; Takamine, Kazunori; Kawai, Mikihiko; Tamaki, Hisanori

2017-10-01

Shochu is a traditional Japanese distilled spirit. The formation of the distinguishing flavour of shochu produced in individual distilleries is attributed to putative indigenous yeast strains. In this study, we performed the first (to our knowledge) phylogenetic classification of shochu strains based on nucleotide gene sequences. We performed phylogenetic classification of 21 putative indigenous shochu yeast strains isolated from 11 distilleries. All of these strains were shown or confirmed to be Saccharomyces cerevisiae, sharing species identification with 34 known S. cerevisiae strains (including commonly used shochu, sake, ale, whisky, bakery, bioethanol and laboratory yeast strains and clinical isolate) that were tested in parallel. Our analysis used five genes that reflect genome-level phylogeny for the strain-level classification. In a first step, we demonstrated that partial regions of the ZAP1, THI7, PXL1, YRR1 and GLG1 genes were sufficient to reproduce previous sub-species classifications. In a second step, these five analysed regions from each of 25 strains (four commonly used shochu strains and the 21 putative indigenous shochu strains) were concatenated and used to generate a phylogenetic tree. Further analysis revealed that the putative indigenous shochu yeast strains form a monophyletic group that includes both the shochu yeasts and a subset of the sake group strains; this cluster is a sister group to other sake yeast strains, together comprising a sake-shochu group. Differences among shochu strains were small, suggesting that it may be possible to correlate subtle phenotypic differences among shochu flavours with specific differences in genome sequences. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Global Stress Classification System for Materials Used in Solar Energy Applications

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Slamova, Karolina; Schill, Christian; Herrmann, Jan; Datta, Pawan; Chih Wang, Chien

2016-08-01

Depending on the geographical location, the individual or combined impact of environmental stress factors and corresponding performance losses for solar applications varies significantly. Therefore, as a strategy to reduce investment risks and operating and maintenance costs, it is necessary to adapt the materials and components of solar energy systems specifically to regional environmental conditions. The project «GloBe Solar» supports this strategy by focusing on the development of a global stress classification system for materials in solar energy applications. The aim of this classification system is to assist in the identification of the individual stress conditions for every location on the earth's surface. The stress classification system could serve as a decision support tool for the industry (manufacturers, investors, lenders and project developers) and help to improve knowledge and services that can provide higher confidence to solar power systems.

Phylogenetics of the Phlebotomine Sand Fly Group Verrucarum (Diptera: Psychodidae: Lutzomyia)

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Cohnstaedt, Lee W.; Beati, Lorenza; Caceres, Abraham G.; Ferro, Cristina; Munstermann, Leonard E.

2011-01-01

Within the sand fly genus Lutzomyia, the Verrucarum species group contains several of the principal vectors of American cutaneous leishmaniasis and human bartonellosis in the Andean region of South America. The group encompasses 40 species for which the taxonomic status, phylogenetic relationships, and role of each species in disease transmission remain unresolved. Mitochondrial cytochrome c oxidase I (COI) phylogenetic analysis of a 667-bp fragment supported the morphological classification of the Verrucarum group into series. Genetic sequences from seven species were grouped in well-supported monophyletic lineages. Four species, however, clustered in two paraphyletic lineages that indicate conspecificity—the Lutzomyia longiflocosa–Lutzomyia sauroida pair and the Lutzomyia quasitownsendi–Lutzomyia torvida pair. COI sequences were also evaluated as a taxonomic tool based on interspecific genetic variability within the Verrucarum group and the intraspecific variability of one of its members, Lutzomyia verrucarum, across its known distribution. PMID:21633028

Phylogenetics of the phlebotomine sand fly group Verrucarum (Diptera: Psychodidae: Lutzomyia).

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Cohnstaedt, Lee W; Beati, Lorenza; Caceres, Abraham G; Ferro, Cristina; Munstermann, Leonard E

2011-06-01

Within the sand fly genus Lutzomyia, the Verrucarum species group contains several of the principal vectors of American cutaneous leishmaniasis and human bartonellosis in the Andean region of South America. The group encompasses 40 species for which the taxonomic status, phylogenetic relationships, and role of each species in disease transmission remain unresolved. Mitochondrial cytochrome c oxidase I (COI) phylogenetic analysis of a 667-bp fragment supported the morphological classification of the Verrucarum group into series. Genetic sequences from seven species were grouped in well-supported monophyletic lineages. Four species, however, clustered in two paraphyletic lineages that indicate conspecificity--the Lutzomyia longiflocosa-Lutzomyia sauroida pair and the Lutzomyia quasitownsendi-Lutzomyia torvida pair. COI sequences were also evaluated as a taxonomic tool based on interspecific genetic variability within the Verrucarum group and the intraspecific variability of one of its members, Lutzomyia verrucarum, across its known distribution.

Practice, science and governance in interaction: European effort for the system-wide implementation of the International Classification of Functioning, Disability and Health (ICF) in Physical and Rehabilitation Medicine.

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Stucki, Gerold; Zampolini, Mauro; Juocevicius, Alvydas; Negrini, Stefano; Christodoulou, Nicolas

2017-04-01

Since its launch in 2001, relevant international, regional and national PRM bodies have aimed to implement the International Classification of Functioning, Disability and Health (ICF) in Physical and Rehabilitation Medicine (PRM), whereby contributing to the development of suitable practical tools. These tools are available for implementing the ICF in day-to-day clinical practice, standardized reporting of functioning outcomes in quality management and research, and guiding evidence-informed policy. Educational efforts have reinforced PRM physicians' and other rehabilitation professionals' ICF knowledge, and numerous implementation projects have explored how the ICF is applied in clinical practice, research and policy. Largely lacking though is the system-wide implementation of ICF in day-to-day practice across all rehabilitation services of national health systems. In Europe, system-wide implementation of ICF requires the interaction between practice, science and governance. Considering its mandate, the UEMS PRM Section and Board have decided to lead a European effort towards system-wide ICF implementation in PRM, rehabilitation and health care at large, in interaction with governments, non-governmental actors and the private sector, and aligned with ISPRM's collaboration plan with WHO. In this paper we present the current PRM internal and external policy agenda towards system-wide ICF implementation and the corresponding implementation action plan, while highlighting priority action steps - promotion of ICF-based standardized reporting in national quality management and assurance programs, development of unambiguous rehabilitation service descriptions using the International Classification System for Service Organization in Health-related Rehabilitation, development of Clinical Assessment Schedules, qualitative linkage and quantitative mapping of data to the ICF, and the cultural adaptation of the ICF Clinical Data Collection Tool in European languages.

Validation of a new classification system for interprosthetic femoral fractures.

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Pires, Robinson Esteves Santos; Silveira, Marcelo Peixoto Sena; Resende, Alessandra Regina da Silva; Junior, Egidio Oliveira Santana; Campos, Tulio Vinicius Oliveira; Santos, Leandro Emilio Nascimento; Balbachevsky, Daniel; Andrade, Marco Antônio Percope de

2017-07-01

Interprosthetic femoral fracture (IFF) incidence is gradually increasing as the population is progressively ageing. However, treatment remains challenging due to several contributing factors, such as poor bone quality, patient comorbidities, small interprosthetic fragment, and prostheses instability. An effective and specific classification system is essential to optimize treatment management, therefore diminishing complication rates. This study aims to validate a previously described classification system for interprosthetic femoral fractures. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nitrogen addition, not initial phylogenetic diversity, increases litter decomposition by fungal communities

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Anthony Stuart Amend

2015-02-01

Full Text Available Fungi play a critical role in the degradation of organic matter. Because different combinations of fungi result in different rates of decomposition, determining how climate change will affect microbial composition and function is fundamental to predicting future environments. Fungal response to global change is patterned by genetic relatedness, resulting in communities with comparatively low phylogenetic diversity. This may have important implications for the functional capacity of disturbed communities if lineages sensitive to disturbance also contain unique traits important for litter decomposition. Here we tested the relationship between phylogenetic diversity and decomposition rates. Leaf litter fungi were isolated from the field and deployed in microcosms as mock communities along a gradient of initial phylogenetic diversity, while species richness was held constant. Replicate communities were subject to nitrogen fertilization comparable to anthropogenic deposition levels. Carbon mineralization rates were measured over the course of sixty-six days. We found that nitrogen fertilization increased cumulative respiration by 24.8%, and that differences in respiration between fertilized and ambient communities diminished over the course of the experiment. Initial phylogenetic diversity failed to predict respiration rates or their change in response to nitrogen fertilization, and there was no correlation between community similarity and respiration rates. Last, we detected no phylogenetic signal in the contributions of individual isolates to respiration rates. Our results suggest that the degree to which phylogenetic diversity predicts ecosystem function will depend on environmental context.

Descriptor Based Classification of Shapes in Terms of Style and Function

DEFF Research Database (Denmark)

Welnicka, Katarzyna; Bærentzen, Jakob Andreas; Aanæs, Henrik

of a specific human being have some commonality that separate them from those of another person. Thus, one could argue that an individual represents a style. Style in the context of biological variation is something that we explore in the work presented here. Specifically, we investigate whether we can define...... of functions, since, as we discuss below, the function of the object (what it is) clearly also has a profound impact on shape. Thus, our work can be summed up as example based classification of digital 3D shapes in both style and function categories....

Disability and Functional Profiles of Patients with Myasthenia Gravis Measured with ICF Classification

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Leonardi, Matilde; Raggi, Alberto; Antozzi, Carlo; Confalonieri, Paolo; Maggi, Lorenzo; Cornelio, Ferdinando; Mantegazza, Renato

2009-01-01

The objective of this study is to describe functional profiles of patients with myasthenia gravis (MG), and the relationships among symptoms, activities and environmental factors (EF), by using WHO's International Classification of Functioning Disability and Health (ICF). Patients were consecutively enrolled at the Besta Institute of Milan, Italy.…

Examining transgender health through the International Classification of Functioning, Disability, and Health's (ICF) Contextual Factors.

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Jacob, Melissa; Cox, Steven R

2017-12-01

For many transgender individuals, medical intervention is necessary to live as their desired gender. However, little is known about Contextual Factors (i.e., Environmental and Personal) that may act as facilitators and barriers in the health of transgender individuals. Therefore, this paper sought to examine Contextual Factors of the World Health Organization's International Classification of Functioning, Disability, and Health that may facilitate or negatively impact the physical, psychological, and social functioning of transgender individuals. A literature review was conducted to identify Environmental and Personal Factors that may influence transgender individuals' physical, psychological, and social functioning. Seven electronic databases were searched. In total, 154 records were reviewed, and 41 articles and other records met inclusion criteria. Three general themes emerged for Environmental Factors: family and social networks, education, and health care. Three general themes also emerged for Personal Factors: socioeconomic status, race, and age. Transgender individuals benefit from gender-affirming services, improved family and social support systems, and competent provider care. Educational training programs, including medical curricula or workshops, might provide the greatest benefit in improving transgender health by increasing the knowledge and cultural competency of health professionals working with this population. Given the diversity of gender expression, differences in lived experiences, and potential for enduring persistent "double discrimination" due to the intersectional relationships between socioeconomic status, race, and/or age, health professionals must approach transgender health using a holistic lens such as the World Health Organization's International Classification of Functioning, Disability, and Health.

Combining anatomical, diffusion, and resting state functional magnetic resonance imaging for individual classification of mild and moderate Alzheimer's disease

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Tijn M. Schouten

2016-01-01

Full Text Available Magnetic resonance imaging (MRI is sensitive to structural and functional changes in the brain caused by Alzheimer's disease (AD, and can therefore be used to help in diagnosing the disease. Improving classification of AD patients based on MRI scans might help to identify AD earlier in the disease's progress, which may be key in developing treatments for AD. In this study we used an elastic net classifier based on several measures derived from the MRI scans of mild to moderate AD patients (N=77 from the prospective registry on dementia study and controls (N=173 from the Austrian Stroke Prevention Family Study. We based our classification on measures from anatomical MRI, diffusion weighted MRI and resting state functional MRI. Our unimodal classification performance ranged from an area under the curve (AUC of 0.760 (full correlations between functional networks to 0.909 (grey matter density. When combining measures from multiple modalities in a stepwise manner, the classification performance improved to an AUC of 0.952. This optimal combination consisted of grey matter density, white matter density, fractional anisotropy, mean diffusivity, and sparse partial correlations between functional networks. Classification performance for mild AD as well as moderate AD also improved when using this multimodal combination. We conclude that different MRI modalities provide complementary information for classifying AD. Moreover, combining multiple modalities can substantially improve classification performance over unimodal classification.

Development of an intelligent system for ultrasonic flaw classification in weldments

International Nuclear Information System (INIS)

Song, Sung-Jin; Kim, Hak-Joon; Cho, Hyeon

2002-01-01

Even though ultrasonic pattern recognition is considered as the most effective and promising approach to flaw classification in weldments, its application to the realistic field inspection is still very limited due to the crucial barriers in cost, time and reliability. To reduce such barriers, previously we have proposed an intelligent system approach that consisted of the following four ingredients: (1) a PC-based ultrasonic testing (PC-UT) system; (2) an effective invariant ultrasonic flaw classification algorithm; (3) an intelligent flaw classification software; and (4) a database with abundant experimental flaw signals. In the present work, for performing the ultrasonic flaw classification in weldments in a real-time fashion in many real word situations, we develop an intelligent system, which is called the 'Intelligent Ultrasonic Evaluation System (IUES)' by the integration of the above four ingredients into a single, unified system. In addition, for the improvement of classification accuracy of flaws, especially slag inclusions, we expand the feature set by adding new informative features, and demonstrate the enhanced performance of the IUES with flaw signals in the database constructed previously. And then, to take care of the increased redundancy in the feature set due to the addition of features, we also propose two efficient schemes for feature selection: the forward selection with trial and error, and the forward selection with criteria of the error probability and the linear correlation coefficients of individual features